------------------------------------------------------------------------ r873 | gsteph | 2016-03-01 15:54:18 +0000 (Tue, 01 Mar 2016) | 5 lines - NEW: Added support for creation of features from CIGAR S and CIGAR H operators. Closes #512. - CHG: Introduced a new CIGAR class to more cleanly handle representing CIGAR strings in Tablet. - CHG: Split out CIGAR feature parsing from the core parsing for getting bases correct in reads. - CHG: Tweaked various aspects of the handling of CIGAR features throughout the code. - CHG: Updated Tablet to allow use of Java 8 features. ------------------------------------------------------------------------ r872 | imilne | 2015-09-01 14:47:26 +0100 (Tue, 01 Sep 2015) | 1 line - NEW: Tagged copy of 1.15.09.01 (public). ------------------------------------------------------------------------ r871 | imilne | 2015-09-01 14:46:23 +0100 (Tue, 01 Sep 2015) | 1 line - BUG: Reverted the included JRE in the installers due to JDK-8134827 (breaking the scrollbars). Refs #467 ------------------------------------------------------------------------ r870 | imilne | 2015-08-28 15:22:30 +0100 (Fri, 28 Aug 2015) | 1 line - NEW: Tagged copy of 1.15.08.28 (public). ------------------------------------------------------------------------ r869 | imilne | 2015-08-28 14:44:11 +0100 (Fri, 28 Aug 2015) | 1 line - NEW: Updated the installers will the latest JREs. ------------------------------------------------------------------------ r868 | gsteph | 2015-08-28 10:15:14 +0100 (Fri, 28 Aug 2015) | 1 line - NEW: The ReadShadower now also shaddows reads pairs as well as the reads under the mouse. Closes #378. ------------------------------------------------------------------------ r867 | imilne | 2015-04-14 13:49:59 +0100 (Tue, 14 Apr 2015) | 1 line - NEW: Some minor refactoring due to class changes in scri-commons. ------------------------------------------------------------------------ r866 | imilne | 2015-04-14 13:32:26 +0100 (Tue, 14 Apr 2015) | 1 line - CHG: Updated a few classes due to scri.commons package renames. ------------------------------------------------------------------------ r865 | imilne | 2015-04-14 10:20:09 +0100 (Tue, 14 Apr 2015) | 1 line - CHG: All dialog/button handling (eg TabletUtils.getButtonPanel()) is now using code from scri-commons instead. Refs #412. ------------------------------------------------------------------------ r864 | imilne | 2015-04-10 09:28:33 +0100 (Fri, 10 Apr 2015) | 1 line - CHG: Minor update to the installer to correct some out of date copyright information. ------------------------------------------------------------------------ r863 | imilne | 2015-03-19 11:12:34 +0000 (Thu, 19 Mar 2015) | 1 line - CHG: Removed the write-file test when running installers as it's not compatible with UAC situations. Closes #212. ------------------------------------------------------------------------ r862 | imilne | 2015-01-19 12:46:06 +0000 (Mon, 19 Jan 2015) | 1 line - NEW: Updated the licence/copyright information for 2015. ------------------------------------------------------------------------ r861 | imilne | 2015-01-19 12:37:36 +0000 (Mon, 19 Jan 2015) | 1 line - NEW: Added SHIFT+mouse wheel support, that scrolls the canvas horizontally. ------------------------------------------------------------------------ r860 | imilne | 2014-11-07 09:21:01 +0000 (Fri, 07 Nov 2014) | 1 line - NEW: Tagged copy of 1.14.11.07 (public). ------------------------------------------------------------------------ r859 | imilne | 2014-11-07 09:20:23 +0000 (Fri, 07 Nov 2014) | 1 line - BUG: Fixed some sqlite locking issues (that affected OS X only). ------------------------------------------------------------------------ r858 | imilne | 2014-10-20 10:10:41 +0100 (Mon, 20 Oct 2014) | 1 line - NEW: Tagged copy of 1.14.10.20 (public). ------------------------------------------------------------------------ r857 | imilne | 2014-10-20 10:10:11 +0100 (Mon, 20 Oct 2014) | 1 line - NEW: Updated the installer ready for a new release. ------------------------------------------------------------------------ r856 | imilne | 2014-07-21 10:10:14 +0100 (Mon, 21 Jul 2014) | 1 line - BUG: Parsing of BAI files was failing when relative input paths were used. Closes #332. ------------------------------------------------------------------------ r855 | imilne | 2014-07-18 13:23:53 +0100 (Fri, 18 Jul 2014) | 1 line - NEW: Updated the installer for Java 1.8.0_11. ------------------------------------------------------------------------ r854 | imilne | 2014-07-18 11:33:43 +0100 (Fri, 18 Jul 2014) | 1 line - NEW: Updated the licence information for 2014. ------------------------------------------------------------------------ r853 | imilne | 2014-07-18 09:51:19 +0100 (Fri, 18 Jul 2014) | 2 lines - NEW: Updated Picard to the latest version. - NEW: Changed the sqlite libraries so that only a single (all systems) jar is used. ------------------------------------------------------------------------ r852 | gsteph | 2014-07-16 16:07:13 +0100 (Wed, 16 Jul 2014) | 2 lines - BUG: The assembly summary dialog was working with the table data, rather than the model data and as such was showing a summary of the filtered set of contigs rather than the full dataset. - CHG: Tablet now displays the filtered and total values for number of contigs and number of reads in the ContigsPanel. ------------------------------------------------------------------------ r851 | imilne | 2014-07-16 14:06:36 +0100 (Wed, 16 Jul 2014) | 2 lines - NEW: More information is provided during the various stages of loading a contig's data. - NEW: Tablet no longer reloads a contig if simply changing the packing mode. ------------------------------------------------------------------------ r850 | imilne | 2014-07-15 15:45:43 +0100 (Tue, 15 Jul 2014) | 1 line - BUG: Packing (paired-pack) of data on large coverage was extremely slow. Closes #331. ------------------------------------------------------------------------ r849 | imilne | 2014-07-10 11:56:38 +0100 (Thu, 10 Jul 2014) | 1 line - NEW: Minor changes to the Citations popup dialog. ------------------------------------------------------------------------ r848 | imilne | 2014-07-10 09:26:43 +0100 (Thu, 10 Jul 2014) | 1 line - BUG: The read2 forward/reverse colour settings were mixed up for the new concordance scheme. ------------------------------------------------------------------------ r847 | imilne | 2014-07-07 14:21:47 +0100 (Mon, 07 Jul 2014) | 1 line - NEW: Added a new colour scheme that handles read number concordance. Closes #329. ------------------------------------------------------------------------ r846 | gsteph | 2014-07-02 10:08:35 +0100 (Wed, 02 Jul 2014) | 1 line - BUG: History snapshot now respects packing mode changes. Closes #328. ------------------------------------------------------------------------ r845 | gsteph | 2014-06-17 10:25:32 +0100 (Tue, 17 Jun 2014) | 2 lines - BUG: CIGAR X was not being dealt with correctly in cases where read sequence was provided. - CHG: Tidied up some redundant conditional statements in SamFileReader. ------------------------------------------------------------------------ r844 | gsteph | 2014-06-16 13:19:16 +0100 (Mon, 16 Jun 2014) | 1 line - CHG: Tweaks to GTF reading to improve gene id display. ------------------------------------------------------------------------ r843 | gsteph | 2014-06-16 11:39:42 +0100 (Mon, 16 Jun 2014) | 1 line - BUG: Previous commit included a bug which would produce an index out of bounds when trying to read certain filetypes, due to an error with the GTF identification code. ------------------------------------------------------------------------ r842 | gsteph | 2014-06-11 11:42:01 +0100 (Wed, 11 Jun 2014) | 1 line - Added experimental support for annotation in the GTF format. ------------------------------------------------------------------------ r841 | imilne | 2014-04-14 09:59:43 +0100 (Mon, 14 Apr 2014) | 1 line - BUG: The application's title bar didn't reset its text after an open assembly was closed. ------------------------------------------------------------------------ r840 | imilne | 2014-04-11 11:33:53 +0100 (Fri, 11 Apr 2014) | 1 line - BUG: The bundled JRE for 64bit linux was actually the 32bit version. ------------------------------------------------------------------------ r839 | gsteph | 2014-04-10 13:32:43 +0100 (Thu, 10 Apr 2014) | 1 line - NEW: Tagged copy of 1.14.04.10 (public). ------------------------------------------------------------------------ r838 | gsteph | 2014-04-10 13:31:04 +0100 (Thu, 10 Apr 2014) | 1 line - NEW: Updated files for new release. ------------------------------------------------------------------------ r837 | gsteph | 2014-04-09 16:04:47 +0100 (Wed, 09 Apr 2014) | 1 line - CHG: Ensure all forms of "snp" type features are drawn specially by calling toUpperCase() on the feature type in the rendering code. ------------------------------------------------------------------------ r836 | gsteph | 2014-04-08 15:43:07 +0100 (Tue, 08 Apr 2014) | 1 line - NEW: Added a VcfReader which reads VCF formatted annotation files and loads them as features within Tablet. Closes #317. ------------------------------------------------------------------------ r835 | gsteph | 2014-04-07 14:54:39 +0100 (Mon, 07 Apr 2014) | 1 line - BUG: The more statistics dialog now deals with remote files by using AssemblyFile's length() method and if the returned content length is zero displays an appropriate message. Closes #318. ------------------------------------------------------------------------ r834 | imilne | 2014-04-07 14:35:38 +0100 (Mon, 07 Apr 2014) | 1 line - BUG: The list of example projects wasn't presented in a sorted order. Closes #319. ------------------------------------------------------------------------ r833 | imilne | 2014-04-03 14:20:14 +0100 (Thu, 03 Apr 2014) | 1 line - NEW: Added .bed feature file support. Closes #316. ------------------------------------------------------------------------ r832 | imilne | 2014-03-11 14:40:00 +0000 (Tue, 11 Mar 2014) | 1 line - CHG: Modified the help section of the web files to map to the new directory structure on the ICS web server. ------------------------------------------------------------------------ r831 | imilne | 2014-02-04 10:16:25 +0000 (Tue, 04 Feb 2014) | 1 line - NEW: Implemented various changes to maintain compatibility with new security requirements in Web Start with Java 1.7.0_45 and above. Closes #302. ------------------------------------------------------------------------ r830 | gsteph | 2013-12-17 11:09:37 +0000 (Tue, 17 Dec 2013) | 1 line - BUG: Fixed critical issue preventing SAM files from loading. Closes #301. ------------------------------------------------------------------------ r829 | imilne | 2013-12-13 13:02:29 +0000 (Fri, 13 Dec 2013) | 1 line - NEW: Tagged copy of 1.13.12.13 (public). ------------------------------------------------------------------------ r828 | imilne | 2013-12-13 13:01:48 +0000 (Fri, 13 Dec 2013) | 2 lines - NEW: Updated the web files ready for a new release. - CHG: Reverted the ACE file QA tweak commit from #819. It causes problems with QA based read quality trimming. ------------------------------------------------------------------------ r827 | gsteph | 2013-12-13 10:58:16 +0000 (Fri, 13 Dec 2013) | 1 line - BUG: Numbers of features and the features table are now updated on BAM window size alterations and BAM window moves. Closes #14. ------------------------------------------------------------------------ r826 | gsteph | 2013-12-09 15:36:30 +0000 (Mon, 09 Dec 2013) | 1 line - NEW: Added a new Assembly Summary dialog which can be launched from the ContigsPanel. Closes #299. ------------------------------------------------------------------------ r825 | imilne | 2013-12-04 14:57:20 +0000 (Wed, 04 Dec 2013) | 1 line - NEW: Threaded off drag and drop file loading so that Windows Explorer no longer appears to hang after performing the drop. Closes #296. ------------------------------------------------------------------------ r824 | gsteph | 2013-11-22 13:00:54 +0000 (Fri, 22 Nov 2013) | 1 line - NEW: Missed linux64 binary file from previous commit. Refs #293. ------------------------------------------------------------------------ r823 | gsteph | 2013-11-21 16:22:58 +0000 (Thu, 21 Nov 2013) | 1 line - BUG: Our embedded samtools wasn’t running on 64 bit Centos 6 & 6.4. Closes #293. ------------------------------------------------------------------------ r822 | imilne | 2013-08-30 09:45:01 +0100 (Fri, 30 Aug 2013) | 1 line - BUG: JNLP launched Tablet (on OS X) wasn't loading BAM files. Closes #254. ------------------------------------------------------------------------ r821 | imilne | 2013-08-28 16:19:11 +0100 (Wed, 28 Aug 2013) | 1 line - BUG: Streaming BAM files when running under web start was failing. Closes #252. ------------------------------------------------------------------------ r820 | imilne | 2013-08-15 10:47:34 +0100 (Thu, 15 Aug 2013) | 1 line - BUG: The version-check in the new Install4j code from scri-commons wasn’t working correctly. Refs #225. ------------------------------------------------------------------------ r819 | imilne | 2013-08-14 13:12:59 +0100 (Wed, 14 Aug 2013) | 2 lines - NEW: The Install4j code has been removed, with its functionality replaced by code from scri-commons. Closes #225. - NEW: Modified the ACE file reader to fully ignore QA lines. ------------------------------------------------------------------------ r818 | imilne | 2013-08-05 14:25:54 +0100 (Mon, 05 Aug 2013) | 1 line - NEW: Tagged copy of 1.13.08.05 (public). ------------------------------------------------------------------------ r817 | imilne | 2013-08-05 14:25:24 +0100 (Mon, 05 Aug 2013) | 3 lines - BUG: Fixed an issue with copy/paste keyboard shortcuts on OS X. Closes #220. - NEW: Updated the installers to target JRE 1.7.0_25. - NEW: Updated the web files ready for a new release. ------------------------------------------------------------------------ r816 | imilne | 2013-07-31 09:58:14 +0100 (Wed, 31 Jul 2013) | 1 line - NEW: Tagged copy of 1.13.07.31 (public). ------------------------------------------------------------------------ r815 | imilne | 2013-07-31 09:57:39 +0100 (Wed, 31 Jul 2013) | 1 line - NEW: Updated the web files ready for a new release. ------------------------------------------------------------------------ r814 | imilne | 2013-07-30 16:05:44 +0100 (Tue, 30 Jul 2013) | 1 line - BUG: Solved some issues with Tablet misbehaving when the cache folder location changes. Closes #215. ------------------------------------------------------------------------ r813 | imilne | 2013-07-04 13:19:24 +0100 (Thu, 04 Jul 2013) | 1 line - NEW: Tablet no longer tries to update if it can’t write to its installation directory. Closes #212. ------------------------------------------------------------------------ r812 | imilne | 2013-06-11 12:03:54 +0100 (Tue, 11 Jun 2013) | 1 line - NEW: Moved OS X over to the Nimbus look and feel. Closes #31. ------------------------------------------------------------------------ r811 | imilne | 2013-06-11 10:23:22 +0100 (Tue, 11 Jun 2013) | 2 lines - NEW: Small tweak to the installer to reference the new code signing certificate. - NEW: The number of per-read mismatches against the reference is now shown in the tooltip. Closes #207. ------------------------------------------------------------------------ r810 | imilne | 2013-06-04 11:24:15 +0100 (Tue, 04 Jun 2013) | 1 line - NEW: Upgraded the codebase, installers, webstart configuration, etc to support Java 7 as the minimum version. Closes #121. ------------------------------------------------------------------------ r809 | imilne | 2013-06-04 10:22:15 +0100 (Tue, 04 Jun 2013) | 1 line - BUG: Opening a BAM file (with index) from the command line can cause samtools to fail. Closes #206. ------------------------------------------------------------------------ r808 | gsteph | 2013-05-17 13:26:58 +0100 (Fri, 17 May 2013) | 2 lines - NEW: Tagged copy of 1.13.05.17 (public). ------------------------------------------------------------------------ r807 | gsteph | 2013-05-17 12:58:27 +0100 (Fri, 17 May 2013) | 1 line - NEW: Updated the web files ready for a new release. ------------------------------------------------------------------------ r806 | gsteph | 2013-05-17 09:43:38 +0100 (Fri, 17 May 2013) | 2 lines - BUG: Fixed an issue which meant CIGAR features weren't being generated for the last contig in a SAM file. ------------------------------------------------------------------------ r805 | imilne | 2013-05-02 09:05:15 +0100 (Thu, 02 May 2013) | 1 line - NEW: Tagged copy of 1.13.05.02 (public). ------------------------------------------------------------------------ r804 | imilne | 2013-05-02 09:04:44 +0100 (Thu, 02 May 2013) | 1 line - NEW: Updated the web files ready for a new release. ------------------------------------------------------------------------ r803 | imilne | 2013-04-29 15:58:59 +0100 (Mon, 29 Apr 2013) | 1 line - CHG: Minor changes to the citation information. ------------------------------------------------------------------------ r802 | imilne | 2013-04-25 11:53:19 +0100 (Thu, 25 Apr 2013) | 1 line - NEW: Added an option to allow the cached reference data to be deleted when Tablet exits. Refs #200. ------------------------------------------------------------------------ r801 | gsteph | 2013-04-25 11:11:28 +0100 (Thu, 25 Apr 2013) | 1 line - NEW: Added functionality to clear Tablet's cache (except for the cache files for any currently open assembly). Closes #200. ------------------------------------------------------------------------ r800 | imilne | 2013-04-25 09:47:24 +0100 (Thu, 25 Apr 2013) | 1 line - NEW: Modified the previously cached reference code to check if the original reference file has changed (file:// only; won’t work with http://). Refs #200. ------------------------------------------------------------------------ r799 | imilne | 2013-04-24 15:39:11 +0100 (Wed, 24 Apr 2013) | 1 line - NEW: Added functionality that allows Table to reuse previously cached reference files. Refs #200. ------------------------------------------------------------------------ r798 | imilne | 2013-04-22 09:32:26 +0100 (Mon, 22 Apr 2013) | 1 line - NEW: Tagged copy of 1.13.04.22 (public). ------------------------------------------------------------------------ r797 | imilne | 2013-04-22 09:31:44 +0100 (Mon, 22 Apr 2013) | 3 lines - NEW: Updated the web files ready for a new release. - NEW: Updated all the licence information and copyright headers for 2013. ------------------------------------------------------------------------ r796 | imilne | 2013-04-22 09:26:26 +0100 (Mon, 22 Apr 2013) | 2 lines - CHG: Experimental build for Java 7 again. Refs #121. ------------------------------------------------------------------------ r795 | gsteph | 2013-02-14 10:08:35 +0000 (Thu, 14 Feb 2013) | 4 lines - BUG: Jump to mate functionality now highlights reads, as well as moving to the correct location on contig / BAM window changes. Closes #173. - BUG: Mate position as displayed in the visible reads panel was one base less than it should be. - CHG: Duplicate code for jumping to a read's mate and for jumping to a read's start and end has been consolidated into one location. Refs #173. ------------------------------------------------------------------------ r794 | gsteph | 2013-02-11 09:54:48 +0000 (Mon, 11 Feb 2013) | 1 line - BUG: Parsing of cigar features in SAM files was not being carried out correctly since related changes made in r778. Closes #172. ------------------------------------------------------------------------ r793 | gsteph | 2013-02-08 13:39:17 +0000 (Fri, 08 Feb 2013) | 2 lines - BUG: Reads weren't having their pair's contig set correctly in SAM files. Closes #171. ------------------------------------------------------------------------ r792 | gsteph | 2013-02-07 12:54:10 +0000 (Thu, 07 Feb 2013) | 3 lines - BUG: Fixed issues around searching and ignoring gap characters. Closes #51. - CHG: Removed old finder code related to read sequence search results which are no longer needed. ------------------------------------------------------------------------ r791 | gsteph | 2013-02-07 11:04:54 +0000 (Thu, 07 Feb 2013) | 3 lines - BUG: Ampersands (and other reserved characters) in paths no longer cause Tablet to wipe its recent file list when Tablet starts. Closes #170. - CHG: Removed print statement left in in commit 789. ------------------------------------------------------------------------ r790 | gsteph | 2013-02-06 14:31:34 +0000 (Wed, 06 Feb 2013) | 3 lines - BUG: CIGAR Inserts displaying more bases than they should. - BUG: Dummy read features in BAM files were always being parsed out at a length of 1 as opposed to their actual length. ------------------------------------------------------------------------ r789 | gsteph | 2013-02-05 15:03:57 +0000 (Tue, 05 Feb 2013) | 3 lines - BUG: Tablet no longer fails to navigate to features outwith the current BAM window when using the keyboard to navigate the features table. Closes #135. - CHG: Also removes a print statement left in ReadsCanvas in commit 788. ------------------------------------------------------------------------ r788 | gsteph | 2013-02-05 13:43:49 +0000 (Tue, 05 Feb 2013) | 1 line - BUG: Fixed issue where Tablet was failing to display reads due to a scaling error on contig changes. Closes #169. ------------------------------------------------------------------------ r787 | gsteph | 2013-01-31 11:59:43 +0000 (Thu, 31 Jan 2013) | 1 line - BUG: Sorting the contigs table with an opened contig no longer disables the ribbon bar. Closes #3. ------------------------------------------------------------------------ r786 | gsteph | 2013-01-25 11:56:08 +0000 (Fri, 25 Jan 2013) | 1 line - BUG: Fixed table filter related crashes which would cause Tablet to not close properly and not load a new assembly properly when there was a value in the contigs table filter. Closes #168. ------------------------------------------------------------------------ r785 | gsteph | 2013-01-25 11:11:51 +0000 (Fri, 25 Jan 2013) | 1 line - BUG: Fixed issue with paired read placement where duplicate reads were being produced in cases where a paired read’s mate had the same start position in a different contig. Closes #132. ------------------------------------------------------------------------ r784 | gsteph | 2013-01-24 10:57:37 +0000 (Thu, 24 Jan 2013) | 3 lines - BUG: Fixed issue where CIGAR insertions at the end of reads weren't being displayed by the overlayer. Closes #123. - BUG: Fixed issues introduced in revision 756, which menat only one of potentially many different CIGAR-I events taking place at the same location would be displayed. ------------------------------------------------------------------------ r783 | gsteph | 2013-01-21 16:39:24 +0000 (Mon, 21 Jan 2013) | 1 line - BUG: Fixed an issue which meant our dummy MateLink reads were being found by the VisibleReadsGrabberThread and displayed in the Visible reads table. Closes #167. ------------------------------------------------------------------------ r782 | imilne | 2012-12-17 11:41:24 +0000 (Mon, 17 Dec 2012) | 2 lines - BUG: The code for turning off in-memory caching of BAM files had been commented out. - BUG: Fixed an issue related to parsing of quality in AFG files. ------------------------------------------------------------------------ r781 | imilne | 2012-12-05 16:13:54 +0000 (Wed, 05 Dec 2012) | 1 line - NEW: Tagged copy of 1.12.12.05 (public). ------------------------------------------------------------------------ r780 | imilne | 2012-12-05 16:13:20 +0000 (Wed, 05 Dec 2012) | 1 line - NEW: Updated the installer and web files ready for a new release. ------------------------------------------------------------------------ r779 | imilne | 2012-11-15 10:22:49 +0000 (Thu, 15 Nov 2012) | 2 lines - BUG: Fixed a problem with parsing of and elements from .tablet files. Closes #141. ------------------------------------------------------------------------ r778 | gsteph | 2012-11-14 09:43:41 +0000 (Wed, 14 Nov 2012) | 5 lines - NEW: Added support for dummy read based annotation in the SAM/BAM formats. Closes #22. - NEW: Added support for SEQ == * (no SEQ entry) within SAM/BAM formats. Closes #17. - NEW: Added support for SEQ containing '=' within the SAM/BAM formats. - BUG: Fixed typo in previous commit (777). ------------------------------------------------------------------------ r777 | imilne | 2012-11-06 11:46:22 +0000 (Tue, 06 Nov 2012) | 2 lines - NEW: The features table can now be filtered by type, name, or start/end position. Closes #130. - BUG: Deleting 'max' numbers from the filter box of the contigs panel didn't restore the full list. ------------------------------------------------------------------------ r776 | imilne | 2012-09-03 14:49:31 +0100 (Mon, 03 Sep 2012) | 1 line - NEW: Tagged copy of 1.12.09.03 (public). ------------------------------------------------------------------------ r775 | imilne | 2012-09-03 14:48:53 +0100 (Mon, 03 Sep 2012) | 1 line - BUG: Command line parameters were not being passed to Tablet on OS X. Closes #134. ------------------------------------------------------------------------ r774 | imilne | 2012-08-29 14:05:50 +0100 (Wed, 29 Aug 2012) | 1 line - NEW: Tagged copy of 1.12.08.29 (public). ------------------------------------------------------------------------ r773 | imilne | 2012-08-29 14:05:04 +0100 (Wed, 29 Aug 2012) | 1 line - NEW: Updated the installer and web files ready for a new release. ------------------------------------------------------------------------ r772 | imilne | 2012-08-20 15:34:38 +0100 (Mon, 20 Aug 2012) | 4 lines - BUG: Features were not being drawn once you moved away from the initial BAM window position. Refs #93. - NEW: Tablet now warns if a newly selected cache file location is not empty. - CHG: Tweaked the Feature selection colours again to try to limit the number of too-faint colours that might get selected. ------------------------------------------------------------------------ r771 | imilne | 2012-08-14 19:37:34 +0100 (Tue, 14 Aug 2012) | 3 lines - BUG: Packs where the inter-read spacing was greater than 0 (the default) were not showing link lines properly. - CHG: Complete rewrite of the packing code to merge normal and paired packing code. ------------------------------------------------------------------------ r770 | imilne | 2012-08-10 15:49:10 +0100 (Fri, 10 Aug 2012) | 4 lines - BUG: Fixed the remaining issues with the paired-pack mode. Refs #93. - BUG: Fixed link lines not showing up when zoomed out beyond 1:1. Refs #93. - CHG: Removed a lot of the old getLineData code from the packing classes (all the stuff that has been replaced by getPixelData). Refs #93. ------------------------------------------------------------------------ r769 | imilne | 2012-08-10 13:27:39 +0100 (Fri, 10 Aug 2012) | 1 line - BUG: Fixed some of the rendering issues with the paired-pack mode. Refs #93. ------------------------------------------------------------------------ r768 | imilne | 2012-08-09 13:10:56 +0100 (Thu, 09 Aug 2012) | 1 line - NEW: If no Name tag is found in a GFF3 file, Tablet will use the ID tag instead (if it exists). Closes #128. ------------------------------------------------------------------------ r767 | imilne | 2012-08-09 12:05:51 +0100 (Thu, 09 Aug 2012) | 1 line - CHG: Removed some of the lighter colours from the fixed (216 web safe) palette used for selecting track colours. Closes #127. ------------------------------------------------------------------------ r766 | imilne | 2012-08-09 09:24:58 +0100 (Thu, 09 Aug 2012) | 3 lines - CHG: Reinstated the stateChanged method for tracking canvas movement. Refs #93. - CHG: Modified the variable name for the cache directory so that all installs will recreate/recalculate its location. ------------------------------------------------------------------------ r765 | imilne | 2012-08-07 15:42:55 +0100 (Tue, 07 Aug 2012) | 1 line - NEW: Added licence information to the About dialog. Closes #131. ------------------------------------------------------------------------ r764 | imilne | 2012-08-07 14:13:37 +0100 (Tue, 07 Aug 2012) | 1 line - BUG: Hopefully the final attempt at fixing the canvas size/zoom issues. Refs #93. ------------------------------------------------------------------------ r763 | imilne | 2012-07-12 11:14:03 +0100 (Thu, 12 Jul 2012) | 1 line - BUG: Fixed a problem that meant Tablet’s position on screen (after being closed) wasn’t remembered properly for the next start-up. Closes #126. ------------------------------------------------------------------------ r762 | imilne | 2012-07-03 16:15:52 +0100 (Tue, 03 Jul 2012) | 1 line - NEW: Updated the installer (with the addition of code signing for Windows and OS X executables) and the build script for jnlp with the new signing certificate details. ------------------------------------------------------------------------ r761 | imilne | 2012-06-29 15:26:16 +0100 (Fri, 29 Jun 2012) | 1 line - CHG: More attempts at fixing the canvas size/zoom issues. Refs #93. ------------------------------------------------------------------------ r760 | imilne | 2012-06-28 15:36:44 +0100 (Thu, 28 Jun 2012) | 1 line - CHG: Renamed all the underscore (eg _ntW) temp variables from the superzoom codebase. Refs #93. ------------------------------------------------------------------------ r759 | imilne | 2012-06-28 09:24:13 +0100 (Thu, 28 Jun 2012) | 1 line - BUG: Fixed a repaint issue that caused a wrong canvas size when the canvas width was less than the window width. Refs #93. ------------------------------------------------------------------------ r758 | imilne | 2012-06-20 10:03:19 +0100 (Wed, 20 Jun 2012) | 1 line - CHG: Updated generic types (where possible) to use the Java 7 diamond operator shortcut. Refs #121. ------------------------------------------------------------------------ r757 | imilne | 2012-06-19 16:02:34 +0100 (Tue, 19 Jun 2012) | 4 lines - NEW: Updated the installer to target Java 7. Refs #121. - NEW: The install4j bundle for OS X now includes JRE 7. Refs #121. - NEW: Updated the build script to target Java 7 only. Refs #121. - NEW: Updated the jnlp webstart launcher to ensure the minimum JRE allowed is 1.7. Refs #121. ------------------------------------------------------------------------ r756 | gsteph | 2012-06-19 10:19:54 +0100 (Tue, 19 Jun 2012) | 2 lines - NEW: Added support for marking Cigar-D events on a feature track. Closes #100. - NEW: Added support for marking Cigar-N events on a feature track. ------------------------------------------------------------------------ r755 | imilne | 2012-06-18 09:59:41 +0100 (Mon, 18 Jun 2012) | 1 line - CHG: Removed the picard additions that we no longer use. ------------------------------------------------------------------------ r754 | imilne | 2012-06-15 10:47:52 +0100 (Fri, 15 Jun 2012) | 1 line - BUG: Fixed some issues with certain types of search parameters. Closes #16. ------------------------------------------------------------------------ r753 | imilne | 2012-06-15 10:30:29 +0100 (Fri, 15 Jun 2012) | 1 line - NEW: Saving a contig summary now warns that only the currently loaded BAM window is included in the out (and also gives an option to open the file). Closes #34. ------------------------------------------------------------------------ r752 | imilne | 2012-06-14 09:36:19 +0100 (Thu, 14 Jun 2012) | 3 lines - CHG: Complete rewrite of the file tracking code so that all input methods are fully synchronized. Existing MRU lists will be lost though. Closes #5. - NEW: Improved support for .tablet files with multiple gff3 entries, and default contig:position information. Closes #107. ------------------------------------------------------------------------ r751 | gsteph | 2012-06-11 14:06:53 +0100 (Mon, 11 Jun 2012) | 1 line - BUG: PairOutlineOverlayer was still adjusting its stroke size at different zoom levels. It now no longer does so, reflecting the behaviour of OutlinerOverlay. ------------------------------------------------------------------------ r750 | imilne | 2012-06-11 11:54:58 +0100 (Mon, 11 Jun 2012) | 3 lines - NEW: Added support for contig and position information to the .tablet file. Refs #107. - BUG: Passing in command-line positions (within a contig) resulted in being out by one base. Closes #120. ------------------------------------------------------------------------ r749 | gsteph | 2012-05-31 09:51:51 +0100 (Thu, 31 May 2012) | 1 line - BUG: Since the implementation of super zoom Tablet has had a bug where the variants slider could cause the canvas to scroll. This has been fixed. ------------------------------------------------------------------------ r748 | imilne | 2012-05-29 13:07:55 +0100 (Tue, 29 May 2012) | 2 lines - NEW: Read group information is now shown in the tooltip. Closes #103. - BUG: Fixed an exception with copying read data to the clipboard if the read’s mate was unmapped. ------------------------------------------------------------------------ r747 | gsteph | 2012-05-08 16:04:23 +0100 (Tue, 08 May 2012) | 1 line - BUG: Fixed rendering issues with CIGAR-I live highlighting. Closes #110. ------------------------------------------------------------------------ r746 | imilne | 2012-05-08 14:19:02 +0100 (Tue, 08 May 2012) | 1 line - BUG: Painting the coverage (tracking) canvas on datasets with negative offsets was throwing ArrayOutOfBounds exceptions. Refs #93. ------------------------------------------------------------------------ r745 | imilne | 2012-05-08 13:51:52 +0100 (Tue, 08 May 2012) | 3 lines - NEW: Added an option to control whether colouring is done at all zoom levels or not. Refs #93. - NEW: Updated Picard to the latest version (1.68). - NEW: Updated the installer so that Java 1.7_04 is used for Windows and Linux. ------------------------------------------------------------------------ r744 | imilne | 2012-05-03 11:24:53 +0100 (Thu, 03 May 2012) | 3 lines - NEW: Renamed the zoom level preferences variable so that it will correctly reset to a suitable default for all users when they get the new super-zoom version. Refs #93. - NEW: Reinstated the option to enable/disable read caching to disk, along with a newer option to not cache data from BAM files unless desired. ------------------------------------------------------------------------ r743 | imilne | 2012-05-02 09:34:45 +0100 (Wed, 02 May 2012) | 1 line - BUG: Fixed a problem with the branch merge that meant paging left was broken again. ------------------------------------------------------------------------ r742 | imilne | 2012-05-01 11:49:59 +0100 (Tue, 01 May 2012) | 1 line - NEW: Merged all the changes (so far) from the super-zoom branch back into the trunk. Refs #93. ------------------------------------------------------------------------ r741 | imilne | 2012-04-30 15:54:36 +0100 (Mon, 30 Apr 2012) | 1 line - NEW: Updated the code (double-click and smooth scroll) to centre-remember its positions while zooming. Refs #93. ------------------------------------------------------------------------ r740 | imilne | 2012-04-30 13:50:37 +0100 (Mon, 30 Apr 2012) | 1 line - NEW: Updated the tracking canvas code to work with the new super-zoom layout space. Refs #93. ------------------------------------------------------------------------ r739 | imilne | 2012-04-20 13:46:23 +0100 (Fri, 20 Apr 2012) | 1 line - NEW: Updated the list of publications and articles citing Tablet. ------------------------------------------------------------------------ r738 | imilne | 2012-04-11 14:49:14 +0100 (Wed, 11 Apr 2012) | 1 line - NEW: Tablet will now check that the specified (via header) contig lengths in a sam file match the actual lengths read from the reference file. Closes #108. ------------------------------------------------------------------------ r737 | imilne | 2012-04-03 14:14:38 +0100 (Tue, 03 Apr 2012) | 1 line - BUG: Mouse navigation via the "green" BAM window arrows was no longer working. Closes #109. ------------------------------------------------------------------------ r736 | imilne | 2012-03-30 12:31:10 +0100 (Fri, 30 Mar 2012) | 1 line - NEW: Added preliminary support for reading assembly information from .tablet files. Refs #107. ------------------------------------------------------------------------ r735 | imilne | 2012-03-27 11:19:51 +0100 (Tue, 27 Mar 2012) | 1 line - BUG: Starting Tablet without an internet connection (and check for updates enabled) was causing a crash. Closes #101. ------------------------------------------------------------------------ r734 | imilne | 2012-03-26 10:03:46 +0100 (Mon, 26 Mar 2012) | 1 line - NEW: Tagged copy of 1.12.03.26 (public). ------------------------------------------------------------------------ r733 | imilne | 2012-03-26 10:00:36 +0100 (Mon, 26 Mar 2012) | 1 line - NEW: Updated the web files ready for a new (bug fix) release. ------------------------------------------------------------------------ r732 | gsteph | 2012-03-09 15:42:32 +0000 (Fri, 09 Mar 2012) | 1 line - NEW: Enabled coverage export for BAM files. ------------------------------------------------------------------------ r731 | gsteph | 2012-03-09 15:34:26 +0000 (Fri, 09 Mar 2012) | 1 line - BUG: An error in the ReadFileCache was causing a crash on some 1000genome project BAM files. Closes #92. ------------------------------------------------------------------------ r730 | gsteph | 2012-02-28 16:13:26 +0000 (Tue, 28 Feb 2012) | 3 lines - NEW: Updated the SnapshotGrabber to work with the new super-zoom code. Refs #93. - NEW: Updated the CigarIHighlighter to work with the new super-zoom code. Refs #93. ------------------------------------------------------------------------ r729 | gsteph | 2012-02-28 13:52:11 +0000 (Tue, 28 Feb 2012) | 1 line - NEW: Updated the PairOutlinerOverlay to work with the new super-zoom code. Refs #93. ------------------------------------------------------------------------ r728 | gsteph | 2012-02-28 11:24:26 +0000 (Tue, 28 Feb 2012) | 2 lines - NEW: Updated both the ReadHighlighter and ConsensusHighlighter to work with the new super-zoom code. Refs #93. - BUG: Replace ntW in if test of NameOverlayer with _ntW. Refs #93. ------------------------------------------------------------------------ r727 | gsteph | 2012-02-28 10:02:56 +0000 (Tue, 28 Feb 2012) | 1 line - NEW: NameOverlayer now works with the super-zoom code. Refs #93. ------------------------------------------------------------------------ r726 | gsteph | 2012-02-27 15:47:20 +0000 (Mon, 27 Feb 2012) | 1 line - NEW: Basic support for super-zoom in the overview canvas. Refs #93. ------------------------------------------------------------------------ r725 | gsteph | 2012-02-27 14:38:47 +0000 (Mon, 27 Feb 2012) | 1 line - NEW: Updates to the FeaturesCanvas and the FeaturesCanvasML so that they work with super-zooming. Refs #93. ------------------------------------------------------------------------ r724 | gsteph | 2012-02-27 10:34:54 +0000 (Mon, 27 Feb 2012) | 3 lines - NEW: CigarOverlayer has been adapted for the new style of zooming code. Refs #93. - BUG: The column highlighting code from commit 723 could be off by a pixel. Refs #93. ------------------------------------------------------------------------ r723 | gsteph | 2012-02-24 11:55:59 +0000 (Fri, 24 Feb 2012) | 1 line - NEW: Column highlighting has been adapted to work with the super-zoom code. Refs #93. ------------------------------------------------------------------------ r722 | gsteph | 2012-02-24 10:01:45 +0000 (Fri, 24 Feb 2012) | 1 line - NEW: Updated the Paired Pack to make it work with the new style of rendering for super-zooming. Refs #93. ------------------------------------------------------------------------ r721 | imilne | 2012-02-21 15:03:40 +0000 (Tue, 21 Feb 2012) | 2 lines - NEW: The read canvas menu popup should now be detecting its base position correctly. Refs #93. - BUG: Outlining columns wasn’t quite correct at zoom levels < 1. Refs #93. ------------------------------------------------------------------------ r720 | gsteph | 2012-02-21 14:59:50 +0000 (Tue, 21 Feb 2012) | 1 line - NEW: Updated the Paired Stack to make it work with the new style of rendering for super-zooming. ------------------------------------------------------------------------ r719 | imilne | 2012-02-21 13:16:51 +0000 (Tue, 21 Feb 2012) | 1 line - CHG: Added some conversion methods (base-pixel and pixel-base) and updated lots of the code to use them instead of their own local conversions. Refs #93. ------------------------------------------------------------------------ r718 | gsteph | 2012-02-21 13:11:45 +0000 (Tue, 21 Feb 2012) | 1 line - NEW: Updated Stack to make it work with the new style of rendering for super-zooming. Refs #93. ------------------------------------------------------------------------ r717 | imilne | 2012-02-21 10:07:33 +0000 (Tue, 21 Feb 2012) | 1 line - NEW: Read shadowing now works with the new zoom levels. Refs #93. ------------------------------------------------------------------------ r716 | gsteph | 2012-02-20 16:05:13 +0000 (Mon, 20 Feb 2012) | 3 lines - BUG: The code for calculating the right hand value for the scale canvas was still incorrect in situations where the BAM window was not at the start of the contig. Refs #93. - NEW: Updated the moveTo, pageLeft and pageRight methods within the CanvasController to work with the new zoom code. ------------------------------------------------------------------------ r715 | imilne | 2012-02-20 14:28:19 +0000 (Mon, 20 Feb 2012) | 2 lines - BUG: The mouse detection code for the tracking canvases (scale, consensus, protein) was still incorrect. Refs #93. - NEW: The protein canvas now disables rendering once the zoom ratio drops below 1. Refs #93. ------------------------------------------------------------------------ r714 | imilne | 2012-02-20 11:59:14 +0000 (Mon, 20 Feb 2012) | 4 lines - NEW: Fixed the outlining (of reads, rows, and columns) with the new zoom levels. Refs #93. - NEW: Added (but disabled) code to *not* detect a read when over the spacer gap between them at zoom levels <= 1. Refs #93. - BUG: Fixed an off-by-one problem with the new offset (blue background) code. ------------------------------------------------------------------------ r713 | gsteph | 2012-02-20 09:25:24 +0000 (Mon, 20 Feb 2012) | 1 line - NEW: Updated the navigation overlay to deal with the new scaling code. Refs #93. ------------------------------------------------------------------------ r712 | imilne | 2012-02-17 14:59:42 +0000 (Fri, 17 Feb 2012) | 1 line - NEW: Correct pixel/base mouse detection is now working for the tooltips. Refs #93. ------------------------------------------------------------------------ r711 | gsteph | 2012-02-17 14:59:05 +0000 (Fri, 17 Feb 2012) | 2 lines - NEW: Updated the scale canvas to deal with the new scaling code for the Tablet super zoom feature. Refs #93. ------------------------------------------------------------------------ r710 | imilne | 2012-02-17 13:47:48 +0000 (Fri, 17 Feb 2012) | 2 lines - NEW: Rendering by colour (rather than bitmap) at the new zoom levels now works with variant highlighting. Refs #93. ------------------------------------------------------------------------ r709 | imilne | 2012-02-17 09:14:56 +0000 (Fri, 17 Feb 2012) | 2 lines - NEW: Rendering now maintains the colour schemes at the 1:1 ratio (still drops to ‘red’ at ratios < 1). Refs #93. ------------------------------------------------------------------------ r708 | imilne | 2012-02-16 15:24:02 +0000 (Thu, 16 Feb 2012) | 3 lines - BUG: Fixed the zoom slider so that it generates correct ratio values < 1 and > 1 (font size fixes). Refs #93. - BUG: Fixed the colour scheme generation code so that it continued to work with ratios less than 1. Refs #93. ------------------------------------------------------------------------ r707 | gsteph | 2012-02-16 14:56:35 +0000 (Thu, 16 Feb 2012) | 3 lines - BUG: Fixed issues with the PackRow getPixelData method which were causing rendering errors. Refs #93. - CHG: Removed a check from the old style drawing of ReadsCanvas which was previously preventing crashes before the bug fix for getPixelData. Refs #93. - BUG: Fixed a bug in the calculation of the blue off-contig rectangle on the right hand side of assemblies. Refs #93. ------------------------------------------------------------------------ r706 | imilne | 2012-02-15 15:02:22 +0000 (Wed, 15 Feb 2012) | 1 line - NEW: Updated the consensus canvas to work with the new zooming. Refs #93. ------------------------------------------------------------------------ r705 | gsteph | 2012-02-15 14:52:56 +0000 (Wed, 15 Feb 2012) | 2 lines - NEW: Updated the ReadsCanvas to take into account offsets. Refs #93. - NEW: Updated the LineData to include references to the relevant read for each pixel of the display. Refs #93. ------------------------------------------------------------------------ r704 | imilne | 2012-02-13 16:01:48 +0000 (Mon, 13 Feb 2012) | 2 lines - NEW: Checked in the experimental code for super-zooming. Refs #93. ------------------------------------------------------------------------ r703 | imilne | 2012-02-13 15:51:29 +0000 (Mon, 13 Feb 2012) | 1 line - NEW: Created a branch to hold the experimental zooming code. ------------------------------------------------------------------------ r702 | imilne | 2012-02-06 14:08:53 +0000 (Mon, 06 Feb 2012) | 1 line - NEW: Tagged copy of 1.12.02.06 (public). ------------------------------------------------------------------------ r701 | imilne | 2012-02-06 14:08:16 +0000 (Mon, 06 Feb 2012) | 2 lines - NEW: Updated the web files ready for a new release. - BUG: Renamed the prefs variable for the search type to cope with the reduction in available options. ------------------------------------------------------------------------ r700 | imilne | 2012-02-01 10:29:32 +0000 (Wed, 01 Feb 2012) | 2 lines - NEW: Updated scri-commons. - BUG: Fixed an issue with the JumpTo dialog being unavailable if the screen resolution had changed since the last time it was visible. Closes #90. ------------------------------------------------------------------------ r699 | gsteph | 2012-01-24 11:25:15 +0000 (Tue, 24 Jan 2012) | 1 line - NEW: Searching for subsequences now also searches the reverse complement of a sequence. Closes #50. ------------------------------------------------------------------------ r698 | gsteph | 2012-01-24 10:29:16 +0000 (Tue, 24 Jan 2012) | 2 lines - BUG: Fixed an issue which was causing the page left / right functionality to behave incorrectly in contigs with negative space. Closes #83. ------------------------------------------------------------------------ r697 | gsteph | 2012-01-23 16:11:57 +0000 (Mon, 23 Jan 2012) | 2 lines - NEW: Added a snapshot history feature which allows the user to browse quickly between points of interest they have previously visited in a contig. Closes #70. ------------------------------------------------------------------------ r696 | imilne | 2012-01-18 14:19:24 +0000 (Wed, 18 Jan 2012) | 3 lines - NEW: All keyboard shortcuts are now handled by a new KeyManager class. - BUG: Fixed the problem with keyboard shortcuts only working if their associated ribbon button was on the active tab. Closes #81. ------------------------------------------------------------------------ r695 | imilne | 2012-01-18 09:41:01 +0000 (Wed, 18 Jan 2012) | 1 line - CHG: Updated the copyright and licence information for 2012. ------------------------------------------------------------------------ r694 | imilne | 2012-01-16 14:54:52 +0000 (Mon, 16 Jan 2012) | 1 line - CHG: Removed the SCRI-is-now-Hutton dialog as it is no longer needed. ------------------------------------------------------------------------ r693 | imilne | 2011-12-22 11:29:09 +0000 (Thu, 22 Dec 2011) | 3 lines - NEW: Added a new dialog for customising visualization colours. Closes #72. - NEW: Changed more of the renderers to request their colours from ColorPrefs. ------------------------------------------------------------------------ r692 | imilne | 2011-12-20 13:48:22 +0000 (Tue, 20 Dec 2011) | 1 line - CHG: Changed the internal mechanism for referencing the colours so that lookups are always via a hashmap. Refs #72. ------------------------------------------------------------------------ r691 | gsteph | 2011-12-15 10:19:45 +0000 (Thu, 15 Dec 2011) | 2 lines - NEW: Implemented an overlay for showing Cigar Insertions. This is added in place of the previous mouse-over highlight code. Closes #82. - BUG: Fixed issue where ctrl + f shortcut would open up the Read Group tab instead of the Find panel. Closes #74. ------------------------------------------------------------------------ r690 | imilne | 2011-12-09 09:21:11 +0000 (Fri, 09 Dec 2011) | 2 lines - NEW: All the colours – for just the colour schemes (for now) – are now saved to tablet-colors.xml and can be edited there by the user. Refs #72. ------------------------------------------------------------------------ r689 | gsteph | 2011-11-23 09:04:33 +0000 (Wed, 23 Nov 2011) | 2 lines - CHG: Refactored enzyme finding functionality out into a subclass of Finder. Closes #64. ------------------------------------------------------------------------ r688 | gsteph | 2011-11-22 14:13:14 +0000 (Tue, 22 Nov 2011) | 4 lines - NEW: It is now possible to copy features to the clipboard from the features track. - CHG: Tidied up cigar highlighting code. Closes #62. - CHG: Refactored out duplication from FeaturesPanel and FeaturesCanvasML into methods in DisplayData for getting the padded and unpadded values for a given base. Closes #63. Closes #45. ------------------------------------------------------------------------ r687 | imilne | 2011-11-01 14:30:28 +0000 (Tue, 01 Nov 2011) | 1 line - NEW: Tagged copy of 1.11.11.01 (public). ------------------------------------------------------------------------ r686 | gsteph | 2011-11-01 14:24:32 +0000 (Tue, 01 Nov 2011) | 4 lines - NEW: Added full restriction enzyme support. Enzymes can be selected, they will then be searched for and added to the FeaturesPanel and plotted on the FeaturesCanvas. Closes #4. - BUG: getTagsAsHTMLString in Feature wasn’t designed to cope with Features without tags. - CHG: Tweaks to features panel and features canvas to remove unused references to consensus data. ------------------------------------------------------------------------ r685 | imilne | 2011-11-01 14:02:40 +0000 (Tue, 01 Nov 2011) | 2 lines - NEW: Updated the web files ready for a new release. - NEW: Included an information file detailing the "licence" for REBASE. ------------------------------------------------------------------------ r684 | imilne | 2011-11-01 09:16:09 +0000 (Tue, 01 Nov 2011) | 1 line - NEW: Finally added a suitable icon for the read length colour scheme. ------------------------------------------------------------------------ r683 | imilne | 2011-10-26 10:03:48 +0100 (Wed, 26 Oct 2011) | 1 line - NEW: Updated the install4j configuration file to use Java 7 (update1) installers for Windows and Linux. ------------------------------------------------------------------------ r682 | imilne | 2011-10-25 14:26:58 +0100 (Tue, 25 Oct 2011) | 1 line - NEW: Individual reads can now be outlined by right clicking on them. Closes #52. ------------------------------------------------------------------------ r681 | imilne | 2011-10-24 14:07:34 +0100 (Mon, 24 Oct 2011) | 1 line - NEW: The read group colouring now uses the same grey colour for all disabled colours. Refs #48. ------------------------------------------------------------------------ r680 | gsteph | 2011-10-24 14:00:50 +0100 (Mon, 24 Oct 2011) | 1 line - BUG: The BAM code wasn't checking if the read was unmapped or not. Closes #36. ------------------------------------------------------------------------ r679 | imilne | 2011-10-20 11:49:52 +0100 (Thu, 20 Oct 2011) | 1 line - NEW: Tooltips for features (on the canvas and in the table) now support all their tags. Refs #37. ------------------------------------------------------------------------ r678 | imilne | 2011-10-19 11:05:58 +0100 (Wed, 19 Oct 2011) | 1 line - NEW: Added right-click Colour-by options to the Reads Group table. Closes #15. ------------------------------------------------------------------------ r677 | imilne | 2011-10-17 13:33:39 +0100 (Mon, 17 Oct 2011) | 3 lines - NEW: Added the ability to copy the ReadsGroup table to the clipboard. Refs #15. - CHG: Updated the source to use a new wrapper (ReadGroup.java) for read group information that encapsulates the data from Picard. ------------------------------------------------------------------------ r676 | imilne | 2011-10-14 11:42:55 +0100 (Fri, 14 Oct 2011) | 1 line - NEW: Updated Picard to version 1.54. ------------------------------------------------------------------------ r675 | imilne | 2011-10-14 11:39:38 +0100 (Fri, 14 Oct 2011) | 2 lines - NEW: The ReadsGroup table now supports tooltips that show every tag/value for each row. Refs #15. - NEW: Updated some web files. ------------------------------------------------------------------------ r674 | imilne | 2011-10-14 09:32:13 +0100 (Fri, 14 Oct 2011) | 3 lines - CHG: Updated the colour code behind all the dialogs so that they look more native on OSX. Refs #31. - CHG: Fixed the layout for some of the dialogs where things weren’t aligning quite right on OSX. Refs #31. ------------------------------------------------------------------------ r673 | imilne | 2011-10-13 15:51:33 +0100 (Thu, 13 Oct 2011) | 1 line - BUG: Fixed a problem with long file paths causing problems with the combo boxes on OS X. Closes #28. ------------------------------------------------------------------------ r672 | gsteph | 2011-10-12 14:44:17 +0100 (Wed, 12 Oct 2011) | 1 line - BUG: The cigar / paired labels were visible on the visible reads panel at Tablet load time. They also didn’t adjust their visibility on selection / de-selection. Both have been rectified. Closes #27. ------------------------------------------------------------------------ r671 | imilne | 2011-10-11 13:35:10 +0100 (Tue, 11 Oct 2011) | 1 line - NEW: The ReadsGroup table now lists all the tags (if they have information) whenever a read group is selected. Note that Picard appears to be missing the PG tag. Refs #15. ------------------------------------------------------------------------ r670 | gsteph | 2011-10-11 10:16:27 +0100 (Tue, 11 Oct 2011) | 1 line - BUG: SamFileReader bug introduced prior to the last release (introduced in svn 628) as part of a refactor while adding preliminary read group functionality. Closes #24. ------------------------------------------------------------------------ r669 | imilne | 2011-10-10 15:32:48 +0100 (Mon, 10 Oct 2011) | 1 line - CHG: The ReadGroup table now displays all read groups (using IDs) along with their platform tag information. Refs #15. ------------------------------------------------------------------------ r668 | gsteph | 2011-10-10 13:54:04 +0100 (Mon, 10 Oct 2011) | 5 lines - NEW: FeatureTrack now utilises the IntervalTree implementation in SCRI-Commons. Closes #13. - NEW: The features on screen are now stored to prevent mouse handling code to have to get the same features out of the tree again. - CHG: Rather than storing a FeatureTrack Contig now stores an ArrayList of Feature objects and creates the FeatureTrack and its associated Interval Tree as required. - BUG: The properties file has been fixed to remove an additional space from the tablet tip for right clicking on pair-link lines. ------------------------------------------------------------------------ r667 | imilne | 2011-10-07 14:47:41 +0100 (Fri, 07 Oct 2011) | 1 line - NEW: Added a simple MD5 calculator method. Refs #8. ------------------------------------------------------------------------ r666 | imilne | 2011-10-06 09:16:18 +0100 (Thu, 06 Oct 2011) | 1 line - NEW: Added the version of samtools used by Tablet to the About Tablet dialog box. ------------------------------------------------------------------------ r665 | gsteph | 2011-10-05 14:34:50 +0100 (Wed, 05 Oct 2011) | 3 lines - NEW: Two new colours were introduced into the Read Type scheme. These represent first in pair (mate in different contig) and second in pair (mate in different contig). - CHG: All booleans in ReadMetaData are now saved as one byte in the ReadFileCache, with the (current) four booleans stored in the lowest four bits of the byte. ------------------------------------------------------------------------ r664 | gsteph | 2011-10-04 11:52:20 +0100 (Tue, 04 Oct 2011) | 1 line - BUG: Reads which had more than one CIGAR insert at the same location lost all but the first insert at that location for the read. This has been rectified. ------------------------------------------------------------------------ r663 | imilne | 2011-10-04 11:47:58 +0100 (Tue, 04 Oct 2011) | 2 lines - NEW: Tablet now outputs its version and prefs file location as part of the log output. ------------------------------------------------------------------------ r662 | gsteph | 2011-09-27 09:26:17 +0100 (Tue, 27 Sep 2011) | 1 line - CHG: Replaced the classic scheme with the variants scheme. The new colour scheme is designed to make it very easy to spot bases which differ from the consensus / reference. ------------------------------------------------------------------------ r661 | gsteph | 2011-09-22 14:39:47 +0100 (Thu, 22 Sep 2011) | 1 line - CHG: BAM files loaded without reference data now display their length in the title label of the ribbon. ------------------------------------------------------------------------ r660 | imilne | 2011-09-22 11:54:19 +0100 (Thu, 22 Sep 2011) | 3 lines - BUG: Modified the read group parsing code to cope with read group headers that lacked the Sample Name (SM) tag. - BUG: Due to a design flaw in Picard, validation stringency wasn’t being set correctly for objects that needed to parse the header. ------------------------------------------------------------------------ r659 | imilne | 2011-09-19 11:15:52 +0100 (Mon, 19 Sep 2011) | 1 line - NEW: Added a missing resource icon. ------------------------------------------------------------------------ r658 | imilne | 2011-09-19 11:07:32 +0100 (Mon, 19 Sep 2011) | 1 line - NEW: Added a new colour scheme that highlights read length. ------------------------------------------------------------------------ r657 | imilne | 2011-09-16 09:04:08 +0100 (Fri, 16 Sep 2011) | 1 line - NEW: The portion of reference sequence mapping to a feature can now be copied to the clipboard. ------------------------------------------------------------------------ r656 | imilne | 2011-09-13 10:07:28 +0100 (Tue, 13 Sep 2011) | 3 lines - NEW: All the tables (in the control panel) can now have their contents copied to the clipboard via right-click menu options. - NEW: Updated Picard to the latest version. - NEW: Updated the installers so that Java 7 is used with Windows builds. ------------------------------------------------------------------------ r655 | imilne | 2011-09-09 09:35:55 +0100 (Fri, 09 Sep 2011) | 1 line - CHG: Made a minor change to the Feature class so that Tablet will use (slightly) less memory when lots of them are loaded. ------------------------------------------------------------------------ r654 | imilne | 2011-09-08 14:39:38 +0100 (Thu, 08 Sep 2011) | 1 line - NEW: The selections for colour schemes have now been moved to their own tab within the ribbon bar. ------------------------------------------------------------------------ r653 | imilne | 2011-08-23 14:43:25 +0100 (Tue, 23 Aug 2011) | 1 line - BUG: If a feature overlapped another (ie, went from 1-500, with another at 50-60), then often the extended feature wouldn’t be drawn. ------------------------------------------------------------------------ r652 | imilne | 2011-08-22 11:35:18 +0100 (Mon, 22 Aug 2011) | 3 lines - BUG: Dragging GFF files into the interface when the “warn if existing file open” option was active was showing the message box when it shouldn’t have. - BUG: Cancelling a BAM-window data load after dragging the BamBar slider resulted in the overlay not being removed from the canvas. ------------------------------------------------------------------------ r651 | imilne | 2011-08-17 08:21:44 +0100 (Wed, 17 Aug 2011) | 3 lines - NEW: Added a new option (in the Options dialog) to allow the user to switch off variant tagging/highlighting for unknown, padded, or N bases. - NEW: Updated the help documentation for the Tablet Options to include details on this new option and also to refresh the screenshots. ------------------------------------------------------------------------ r650 | imilne | 2011-08-16 09:12:20 +0100 (Tue, 16 Aug 2011) | 1 line - NEW: Made some changes to allow us to run Tablet under JRE7 (but maintain compatibility with JRE6). ------------------------------------------------------------------------ r649 | imilne | 2011-08-12 15:49:11 +0100 (Fri, 12 Aug 2011) | 1 line - NEW: Added some better icons for the Read Group colouring stuff. ------------------------------------------------------------------------ r648 | imilne | 2011-08-11 14:34:35 +0100 (Thu, 11 Aug 2011) | 1 line - NEW: Changed the copyright labels to show ICS/JHI information rather than SCRI. ------------------------------------------------------------------------ r647 | imilne | 2011-08-10 13:47:18 +0100 (Wed, 10 Aug 2011) | 1 line - NEW: Tagged copy of 1.11.08.10 (public). ------------------------------------------------------------------------ r646 | imilne | 2011-08-10 13:46:47 +0100 (Wed, 10 Aug 2011) | 1 line - NEW: Updated the web pages ready for a new release. ------------------------------------------------------------------------ r645 | gsteph | 2011-08-10 10:23:53 +0100 (Wed, 10 Aug 2011) | 1 line - NEW: Setup a default colour palette of 20 colours for the read group colour scheme. ------------------------------------------------------------------------ r644 | imilne | 2011-08-10 10:14:47 +0100 (Wed, 10 Aug 2011) | 1 line - NEW: Added a missing icon. ------------------------------------------------------------------------ r643 | imilne | 2011-08-05 11:36:08 +0100 (Fri, 05 Aug 2011) | 1 line - NEW: Updated the control table icons. ------------------------------------------------------------------------ r642 | imilne | 2011-07-25 13:43:38 +0100 (Mon, 25 Jul 2011) | 3 lines - BUG: Reverting back to zip code BAM detection causes issues on some files with no end-of-line characters in the header. - BUG: RegEx characters included in a BAM file’s name (eg ‘[]’) were stopping Tablet from locating the corresponding BAI file. ------------------------------------------------------------------------ r641 | gsteph | 2011-07-13 11:53:08 +0100 (Wed, 13 Jul 2011) | 1 line - NEW: Added a Prefs variable which governs the number of insert events a CIGAR-I feature has to relate to before it is added to a Contig. ------------------------------------------------------------------------ r640 | imilne | 2011-07-08 14:34:29 +0100 (Fri, 08 Jul 2011) | 3 lines - BUG: The overview canvas wasn’t updating when edits to the ReadGroup colour scheme were made. - BUG: Selecting the Color All or Color None options would toggle their states rather than setting them. ------------------------------------------------------------------------ r639 | imilne | 2011-07-08 14:19:36 +0100 (Fri, 08 Jul 2011) | 3 lines - CHG: The ReadGroups panel now uses a JTable instead of a JList. - NEW: Each entry in the list can be "coloured" or not via a tickbox, allowing greyscale colouring for everything not selected. -CHG: Simplified some of the enabled/disabled functionality of the ReadGroups scheme by allowing it to always be active, even when non-readGroup data is loaded. ------------------------------------------------------------------------ r638 | imilne | 2011-07-06 10:24:43 +0100 (Wed, 06 Jul 2011) | 1 line - CHG: The preferences setting for telling Picard to use less-strict BAM validation checks is now on by default. ------------------------------------------------------------------------ r637 | gsteph | 2011-07-06 09:30:22 +0100 (Wed, 06 Jul 2011) | 1 line - NEW: Added CitationDialog to Tablet. This is a dialog designed to gently remind users to cite Tablet where appropriate. ------------------------------------------------------------------------ r636 | imilne | 2011-07-05 09:29:16 +0100 (Tue, 05 Jul 2011) | 1 line - CHG: Updated the installers to include Java 1.6.0_26 as the bundled JRE version. ------------------------------------------------------------------------ r635 | imilne | 2011-07-05 09:18:49 +0100 (Tue, 05 Jul 2011) | 3 lines - BUG: The recent-file tooltips on Linux and OS X weren’t working with paths beginning with “/”. - BUG: Restored the pre Java 1.6_23 BAM detection speed. ------------------------------------------------------------------------ r634 | imilne | 2011-07-04 14:34:30 +0100 (Mon, 04 Jul 2011) | 1 line - BUG: Some of the progress tracking code for the Finder was broken due to the RegEx improvements. ------------------------------------------------------------------------ r633 | imilne | 2011-07-04 14:15:01 +0100 (Mon, 04 Jul 2011) | 3 lines - BUG: The cached consensus code was causing problems with the finder (and coverage/snp exporters) due to them loading other consensuses from the cache. - CHG: All searches are now case insensitive. ------------------------------------------------------------------------ r632 | imilne | 2011-07-04 11:31:41 +0100 (Mon, 04 Jul 2011) | 1 line - CHG: String values in read tooltips longer than 75 characters will now be truncated. ------------------------------------------------------------------------ r631 | gsteph | 2011-07-04 10:21:04 +0100 (Mon, 04 Jul 2011) | 5 lines - BUG: The Finder could crash when searching in the consensus sequence over all contigs due to a change in the way Consnensus sequences are stored (they are now cached to disk). - CHG: Swapped out custom searching code for a regular expressions based technique when searching for subsequences within reads and the consensus. - NEW: Added code to handle searching for restriction enzyme sites for forthcoming restriction enzyme features. - BUG: Removed un-wanted print out statements from FindTableModel. ------------------------------------------------------------------------ r630 | imilne | 2011-06-27 09:24:25 +0100 (Mon, 27 Jun 2011) | 1 line - NEW: Added drag and drop support for GFF3 files. ------------------------------------------------------------------------ r629 | imilne | 2011-06-14 09:26:56 +0100 (Tue, 14 Jun 2011) | 1 line - NEW: Added lots of articles citing Tablet to the papers.shtml file on the web. ------------------------------------------------------------------------ r628 | gsteph | 2011-06-03 16:00:37 +0100 (Fri, 03 Jun 2011) | 4 lines - NEW: ReadGroup colour scheme added. Colours reads based on their ReadGroup from a SAM/BAM file. - NEW: New Read Group panel in the tab panel. It provides a listing of read groups and allows selection of custom colours for them. - NEW: Custom colors are persisted to a tablet-colours.xml file. ------------------------------------------------------------------------ r627 | imilne | 2011-05-23 14:03:06 +0100 (Mon, 23 May 2011) | 1 line - NEW: Added a new class to store color preferences that can be used by the color schemes (specifically the new ReadGroup one). ------------------------------------------------------------------------ r626 | gsteph | 2011-05-09 16:24:32 +0100 (Mon, 09 May 2011) | 1 line - BUG: Toggling Show Bases wasn't causing the screen to refresh. ------------------------------------------------------------------------ r625 | imilne | 2011-05-03 09:53:08 +0100 (Tue, 03 May 2011) | 1 line - NEW: Tagged copy of 1.11.05.03 (public). ------------------------------------------------------------------------ r624 | imilne | 2011-05-03 09:52:27 +0100 (Tue, 03 May 2011) | 1 line - NEW: Updated the web pages for a new release. ------------------------------------------------------------------------ r623 | imilne | 2011-04-27 16:03:42 +0100 (Wed, 27 Apr 2011) | 1 line - NEW: Improved the performance of the new contig-caching code by getting the output writer to flush its output before reading. ------------------------------------------------------------------------ r622 | gsteph | 2011-04-26 14:04:09 +0100 (Tue, 26 Apr 2011) | 1 line - NEW: Added basic SNP finding functionality for Micha. Only works with BAM and is restricted to SCRI users. ------------------------------------------------------------------------ r621 | imilne | 2011-04-26 11:44:12 +0100 (Tue, 26 Apr 2011) | 1 line - NEW: Changed the way some of the primary tables work, so that they now remember their column position and sort selection (for the current session). This code was added to the Find table as well, but it can't remember its state because the table physically changes based on the search type. ------------------------------------------------------------------------ r620 | gsteph | 2011-04-26 11:21:19 +0100 (Tue, 26 Apr 2011) | 1 line - CHG: Altered TaskDialog.showFileOpen calls to use the new tidier style call and replaced with TaskDialog.showOpenLog where appropriate. ------------------------------------------------------------------------ r619 | gsteph | 2011-04-25 11:22:05 +0100 (Mon, 25 Apr 2011) | 1 line - BUG: FindPanel did not allow re-selection of search results. ------------------------------------------------------------------------ r618 | imilne | 2011-04-21 12:01:40 +0100 (Thu, 21 Apr 2011) | 1 line - BUG: "Success" messages for some of the export routines were still being displayed even if the user cancelled the job. ------------------------------------------------------------------------ r617 | imilne | 2011-04-20 15:33:28 +0100 (Wed, 20 Apr 2011) | 1 line - NEW: More changes to give Tablet (and its web files) the JHI look and feel. ------------------------------------------------------------------------ r616 | imilne | 2011-04-20 14:58:04 +0100 (Wed, 20 Apr 2011) | 1 line - NEW: More changes to give Tablet (and its web files) the JHI look and feel. ------------------------------------------------------------------------ r615 | imilne | 2011-04-20 14:44:17 +0100 (Wed, 20 Apr 2011) | 1 line - BUG: The ReadIDs weren't being incremented properly during searching (with the new code), meaning the results could be wrong. ------------------------------------------------------------------------ r614 | imilne | 2011-04-15 13:23:54 +0100 (Fri, 15 Apr 2011) | 1 line - NEW: Merged the refactor branch back into the trunk. ------------------------------------------------------------------------ r613 | imilne | 2011-04-15 13:20:03 +0100 (Fri, 15 Apr 2011) | 1 line - CHG: (Temporary) rename of some files to allow the refactor branch to merge back with the main trunk. ------------------------------------------------------------------------ r612 | imilne | 2011-04-14 13:33:48 +0100 (Thu, 14 Apr 2011) | 1 line - NEW: Some more tweaks to try to reduce memory consumption with very large numbers of contigs (eg, 200,000+). ------------------------------------------------------------------------ r611 | imilne | 2011-04-14 11:51:04 +0100 (Thu, 14 Apr 2011) | 1 line - NEW: Consensus data is now cached to disk. ------------------------------------------------------------------------ r610 | gsteph | 2011-04-12 15:49:51 +0100 (Tue, 12 Apr 2011) | 3 lines - BUG: Fixed the enabled states of some elements in the ReadsPanel so that components are disabled where appropriate. - BUG: Fixed the copyDataToClipboard method of ReadsPanel so it outputs the same format of data as the ReadsCanvasInfoPane copyDataToClipboard. - BUG: Fixed positioning of results table in FindPanel. It hadn't been moved following the move of the helpLabel to the top of the panel. ------------------------------------------------------------------------ r609 | gsteph | 2011-04-07 13:10:28 +0100 (Thu, 07 Apr 2011) | 1 line - BUG: ConsensusSubsequenceDialog would crash when no reference data was loaded (plus AssemblyPanel step wasn't needed). ------------------------------------------------------------------------ r608 | gsteph | 2011-04-07 09:32:30 +0100 (Thu, 07 Apr 2011) | 2 lines - CHG: Removed NumberInPair from ReadNameData and ReadSQLCache as the only place it was being used we could also get it from ReadMetaData and tweaked associated classes. - CHG: Removed useless database cache hit from ReadCanvasMenu. ------------------------------------------------------------------------ r607 | gsteph | 2011-04-07 09:20:28 +0100 (Thu, 07 Apr 2011) | 2 lines - CHG: Refactored PairedPackRow to remove messy line drawing code and replace it with cleaner code similar to that of PairedStackRow. - BUG: PairedStackCreator wasn't cancelling jobs correctly due to a missing okToRun check. ------------------------------------------------------------------------ r606 | imilne | 2011-04-07 09:16:22 +0100 (Thu, 07 Apr 2011) | 1 line - BUG: The ResultSet returned from the new database searches wasn't been closed after each call. ------------------------------------------------------------------------ r605 | imilne | 2011-04-06 15:04:14 +0100 (Wed, 06 Apr 2011) | 1 line - CHG: Edited the build script so that .txt files (in the lib directory) are ignored during unit tests. ------------------------------------------------------------------------ r604 | imilne | 2011-04-06 14:24:42 +0100 (Wed, 06 Apr 2011) | 1 line - BUG: The initial (temp) cache created by the AFG file reader was passing null contigs into the database creation code. ------------------------------------------------------------------------ r603 | gsteph | 2011-04-06 11:19:54 +0100 (Wed, 06 Apr 2011) | 3 lines - CHG: Improved the mechanism used to search for read names across non-BAM datasets (should be significantly faster). - NEW: Contigs now have an id and it is stored alongside every read (in that contig) in the SQL database. - CHG: Simplified the FindPanel's gui so that all the search options are check boxes and the type of search is the only remaining combo box. ------------------------------------------------------------------------ r602 | gsteph | 2011-04-06 11:15:02 +0100 (Wed, 06 Apr 2011) | 1 line - BUG: Read names with :1 /1 etc postfixes were being truncated by one character prior to the postfix. ------------------------------------------------------------------------ r601 | imilne | 2011-04-04 13:41:30 +0100 (Mon, 04 Apr 2011) | 1 line - NEW: Some more changes related to the new Controller class (mainly zooming related). ------------------------------------------------------------------------ r600 | gsteph | 2011-04-01 08:39:21 +0100 (Fri, 01 Apr 2011) | 1 line - BUG: Fixed off by one bug in the pos attribute of the read printer output. ------------------------------------------------------------------------ r599 | imilne | 2011-03-29 11:48:28 +0100 (Tue, 29 Mar 2011) | 1 line - NEW: Moved all of the "tricky" control code out of AssemblyPanel and into a new class (CanvasController) that now handles resizes, movement, zooming, etc. ------------------------------------------------------------------------ r598 | imilne | 2011-03-25 14:11:38 +0000 (Fri, 25 Mar 2011) | 1 line - BUG: The total read count shown in the contigs panel was suffering from integer overflow when the count was very high. ------------------------------------------------------------------------ r597 | imilne | 2011-03-25 14:02:42 +0000 (Fri, 25 Mar 2011) | 4 lines - NEW: Huge refactor of the info pane (tooltip) classes. There is now a single ReadsCanvasInfoPane class that is responsible for gathering the data, and a ReadsCanvasInfoPaneRenderer to do the actual drawing. - NEW: Removed all the code from the layout managers that is responsible for finding a pair of reads given a line and nucleotide position. It simply isn't needed any more. - NEW: Added code to the layout managers to find a pair of reads given a point *between* two reads (ie, on the link line). - CHG: Renamed the getPair() method of MatedRead to be getMate(). ------------------------------------------------------------------------ r596 | imilne | 2011-03-25 13:53:13 +0000 (Fri, 25 Mar 2011) | 1 line - BUG: Tooltips over the features panel were broken after the recent changes to the table models. ------------------------------------------------------------------------ r595 | gsteph | 2011-03-24 13:38:43 +0000 (Thu, 24 Mar 2011) | 1 line - NEW: Bug fix - ConsensusSubsequenceDialog did not handle setting up its model correctly. Now properly handles situations where contig.getVisualStart() is less than 1. ------------------------------------------------------------------------ r594 | imilne | 2011-03-18 09:10:47 +0000 (Fri, 18 Mar 2011) | 1 line - NEW: Started work on updating the client to include JHI colour schemes and logos. ------------------------------------------------------------------------ r593 | imilne | 2011-03-17 13:16:50 +0000 (Thu, 17 Mar 2011) | 1 line - NEW: Added a missing resource icon. ------------------------------------------------------------------------ r592 | imilne | 2011-03-16 14:46:21 +0000 (Wed, 16 Mar 2011) | 2 lines - NEW: Improved the way table renderers are handled, so that they are now always static inner classes of their associated table model. They also now make "proper" calls back to the model to retrieve additional data they may need, rather than fudging it via the getValueAt(row, col) method. - NEW: Removed or edited some renderers that were duplicating code already available in scri-commons' NumberFormatCellRenderer. ------------------------------------------------------------------------ r591 | imilne | 2011-03-16 09:31:43 +0000 (Wed, 16 Mar 2011) | 1 line - CHG: Renamed all the Matisse generated classes for better readability. ------------------------------------------------------------------------ r590 | gsteph | 2011-03-15 14:21:49 +0000 (Tue, 15 Mar 2011) | 3 lines - NEW: A new inheritance structure for the Pack layout styles with PairedPack extending from Pack and PairedPackRow extending from PackRow. - CHG: Rename PackSetCreator and PairedPackSetCreator to PackCreator and PairedPackCreator in line with previous renaming of classes. - CHG: A small tidy up of PairOutlinerOverlay to remove duplicate code. ------------------------------------------------------------------------ r589 | gsteph | 2011-03-15 09:54:06 +0000 (Tue, 15 Mar 2011) | 1 line - BUG: The previous (refactor) commit didn't compile due to this missing edit. ------------------------------------------------------------------------ r588 | imilne | 2011-03-15 09:31:06 +0000 (Tue, 15 Mar 2011) | 1 line - CHG: One of the links from the help's contents page was broken. ------------------------------------------------------------------------ r587 | imilne | 2011-03-14 14:51:50 +0000 (Mon, 14 Mar 2011) | 1 line - NEW: Tagged copy of 1.11.03.14 (public). ------------------------------------------------------------------------ r586 | imilne | 2011-03-14 14:50:34 +0000 (Mon, 14 Mar 2011) | 2 lines - BUG: Made a small modification to the file detection code to cope with the broken gzip routines in the latest version of Java. - CHG: Updated the web pages for a new (OS X only) release because the other versions can stay with pre 1.6.0_23 JREs. ------------------------------------------------------------------------ r585 | gsteph | 2011-03-07 16:45:11 +0000 (Mon, 07 Mar 2011) | 1 line - CHG: Renamed StackSet, PackSet, Pack and ReadPair to Stack, Pack, PackRow and PairedStackRow. Also tidied up variable names associated to these classes throughout the project. ------------------------------------------------------------------------ r584 | gsteph | 2011-03-07 13:42:27 +0000 (Mon, 07 Mar 2011) | 1 line - CHG: Cleaned up the getLineData() code in ReadPair for readability. ------------------------------------------------------------------------ r583 | imilne | 2011-03-04 15:53:11 +0000 (Fri, 04 Mar 2011) | 1 line - CHG: Cleaned up the getLineData() method within Pack.java for readability. ------------------------------------------------------------------------ r582 | gsteph | 2011-03-04 15:05:58 +0000 (Fri, 04 Mar 2011) | 2 lines - CHG: Renamed the tablet.gui.viewer.color classes for better clarification. ------------------------------------------------------------------------ r581 | imilne | 2011-03-04 14:30:47 +0000 (Fri, 04 Mar 2011) | 5 lines - CHG: Changed the tablet.data IReadManager implementations so that they no longer need to know about the colour scheme in use when presenting their "line" data back to the canvas. - NEW: Added a new LineData class to hold both per-base information as returned by an IReadManager. Each base holds a reference to the ReadMetaData at that position, and the index within the read (offset from the read's start). - CHG: Refactored the structure of tablet.gui.viewer.colors. ColorScheme has been deleted. Two new top level classes now exist: ReadColorScheme and ProteinColorScheme. - CHG: Simplified (and tidied up) the code within each colour scheme implementation. - CHG: The color schemes are now responsible for determing what image to paint based on not only the raw data (A,C,G,T, etc) but also the read's type/direction/etc. ------------------------------------------------------------------------ r580 | imilne | 2011-03-03 09:33:38 +0000 (Thu, 03 Mar 2011) | 1 line - NEW: Created a new branch ready for March 2011's refactoring. ------------------------------------------------------------------------ r579 | gsteph | 2011-03-03 09:17:56 +0000 (Thu, 03 Mar 2011) | 1 line - CHG: Moved Rate tablet code from FilePanel to HelpPanel. ------------------------------------------------------------------------ r578 | imilne | 2011-02-18 10:57:32 +0000 (Fri, 18 Feb 2011) | 1 line - NEW: Tagged copy of 1.11.02.18 (public). ------------------------------------------------------------------------ r577 | imilne | 2011-02-18 10:56:58 +0000 (Fri, 18 Feb 2011) | 1 line - NEW: Added some final edits to some of web pages before a new release. ------------------------------------------------------------------------ r576 | imilne | 2011-02-18 09:55:28 +0000 (Fri, 18 Feb 2011) | 1 line - CHG: Updated the Jump To Base dialog to include an extra label describing its new contig:pos jump-to functionality. ------------------------------------------------------------------------ r575 | gsteph | 2011-02-18 09:36:46 +0000 (Fri, 18 Feb 2011) | 1 line - CHG: Enabled ratings stars. ------------------------------------------------------------------------ r574 | gsteph | 2011-02-17 15:36:04 +0000 (Thu, 17 Feb 2011) | 6 lines - NEW: The JumpToDialog now supports navigating to positions in contigs outwith the current contig. - NEW: The search code can now ignore pads and ns when looking for matches. - NEW: Tooltips are displayed when the user mouses over features in the features track. - NEW: CopySubsequenceDialog allows the user to copy subsequences of the consensus / reference in fasta format. - BUG: Progress bar now switches to indeterminate mode when indexing the paired reads cache. - NEW: Added new and updated old help topics. ------------------------------------------------------------------------ r573 | gsteph | 2011-02-07 11:20:32 +0000 (Mon, 07 Feb 2011) | 1 line - NEW: Tablet now accepts contig and position arguments in the form of view:contigName:position when loading with a file from the command line. ------------------------------------------------------------------------ r572 | imilne | 2011-02-07 09:34:47 +0000 (Mon, 07 Feb 2011) | 1 line - NEW: The table headers are now included in the output from the contig table's copy-to-clipboard right-click option. ------------------------------------------------------------------------ r571 | imilne | 2011-02-04 14:15:18 +0000 (Fri, 04 Feb 2011) | 1 line - NEW: Made some minor changes to how Tablet handles its cache files to try and improve clean-up after exit. ------------------------------------------------------------------------ r570 | imilne | 2011-02-04 11:36:31 +0000 (Fri, 04 Feb 2011) | 1 line - CHG: Renamed sam.jar to picard.jar to avoid confusion with the file containing samtools. ------------------------------------------------------------------------ r569 | imilne | 2011-02-04 11:33:38 +0000 (Fri, 04 Feb 2011) | 1 line - NEW: Updated the web start launcher to include the extra jar file needed for running samtools. ------------------------------------------------------------------------ r568 | imilne | 2011-02-04 11:20:30 +0000 (Fri, 04 Feb 2011) | 4 lines - NEW: Reimplemented read-counts for BAM files by natively wrapping and running samtools. - NEW: Added an option to the Options dialog to provide an alternative path to samtools if Tablet's bundled copies for Windows, OS X and Linux won't run. - NEW: Included copies of the binaries for samtools. - CHG: Modified the help pages to reflect this new feature. ------------------------------------------------------------------------ r567 | gsteph | 2011-01-31 14:29:20 +0000 (Mon, 31 Jan 2011) | 1 line - BUG: Wrong name was being displayed for out of contig mates. The position of mates was also out by one relative to their actual position in the contig. ------------------------------------------------------------------------ r566 | gsteph | 2011-01-31 13:18:55 +0000 (Mon, 31 Jan 2011) | 1 line - BUG: Unclipped start position for read instead of alignment start was being shown in the BAM search results. ------------------------------------------------------------------------ r565 | imilne | 2011-01-31 11:29:19 +0000 (Mon, 31 Jan 2011) | 1 line - BUG: Detection of unsorted SAM files still wasn't correct (fasta files pre-fill the hashtable making it a useless aid in detection). ------------------------------------------------------------------------ r564 | imilne | 2011-01-31 09:10:33 +0000 (Mon, 31 Jan 2011) | 2 lines - BUG: Fixed array-out-of-bounds exceptions with SAM files containing paired-data (due to contig offsets for accessing the cache data). - NEW: The above fix requires SAM files (with paired-end data) to be sorted. Tablet now warns if a file is loaded that doesn't meet this condition. ------------------------------------------------------------------------ r563 | imilne | 2011-01-25 14:39:49 +0000 (Tue, 25 Jan 2011) | 1 line - NEW: Updated source code licence information for 2011. ------------------------------------------------------------------------ r562 | imilne | 2011-01-25 11:29:53 +0000 (Tue, 25 Jan 2011) | 1 line - NEW: Tagged copy of 1.11.01.25 (public). ------------------------------------------------------------------------ r561 | imilne | 2011-01-25 11:29:08 +0000 (Tue, 25 Jan 2011) | 1 line - NEW: Checked in various documentation changes ready for a new release. ------------------------------------------------------------------------ r560 | imilne | 2011-01-25 09:48:41 +0000 (Tue, 25 Jan 2011) | 2 lines - NEW: Reverted (some) of the changes related to BAM index reading because it's just too slow for us to use until Picard can perform at the same (instant) speed as samtools. - NEW: Updated Picard to version 1.38. ------------------------------------------------------------------------ r559 | imilne | 2011-01-25 09:28:01 +0000 (Tue, 25 Jan 2011) | 1 line - NEW: Misc changes related to the BAM index issue. ------------------------------------------------------------------------ r558 | imilne | 2011-01-25 08:52:50 +0000 (Tue, 25 Jan 2011) | 1 line - NEW: Checked in the Pre-Christmas Breakout code (still partially unfinished). ------------------------------------------------------------------------ r557 | imilne | 2010-12-14 09:43:46 +0000 (Tue, 14 Dec 2010) | 1 line - BUG: The canvas wasn't resizing itself properly when changing between contigs that both had less than a screen width's amount of data. ------------------------------------------------------------------------ r556 | imilne | 2010-12-07 10:13:08 +0000 (Tue, 07 Dec 2010) | 1 line - NEW: Updated the OS X sqlite library to be from www.zentus.com/sqlitejdbc because it's a better universal binary. ------------------------------------------------------------------------ r555 | imilne | 2010-12-07 10:12:09 +0000 (Tue, 07 Dec 2010) | 1 line - NEW: Added CTRL+mousewheel zooming to the main canvas. ------------------------------------------------------------------------ r554 | gsteph | 2010-11-24 10:13:09 +0000 (Wed, 24 Nov 2010) | 6 lines - NEW: The table in ReadsPanel can now export the screen data. Additionally the table now has a right click context menu for jumping to reads' starts, ends and pairs and also for copying data to the clipboard. - CHG: Fixed alignment of the table in FeaturesPanel. - CHG: Stopped ReadPrinter from outputting new lines between fasta sequences. - BUG: Reverted to old PairSearching code for post load pair operations as once the reads have been sorted we cannot use the database index. - BUG: Fixed potential rendering bugs in Pack and ReadPair concerning unmapped reads and pair link line drawing. ------------------------------------------------------------------------ r553 | imilne | 2010-11-23 09:36:15 +0000 (Tue, 23 Nov 2010) | 2 lines - NEW: Changed the "open log" messages and updated some of the other error messages to ensure they give the option too. - CHG: Updated the installer for the latest version of install4j (that contains the fixes for non-launching on Ubuntu 10.10 and the log file not being generated on Linux). ------------------------------------------------------------------------ r552 | gsteph | 2010-11-18 09:53:37 +0000 (Thu, 18 Nov 2010) | 8 lines - CHG: Code tidy-ups / minor changes in DisplayDataCalculator, Contig, StackSet and FindPanel. - CHG: Performance improvements in Pack and ReadPair. These improve the performance of drawing pair link lines. - NEW: You can now export all the reads in a contig from the ReadsCanvasMenu, the changes are mainly in ReadPrinter and Commands. - CHG: ReadsCanvasMenu has be re-arranged to include Export to file and Jump to sub-menus. - CHG: ReadsCanvasInfoPane rendering has been altered so that the pair rendering is separated into a sub-class and a new ReadsCanvasInfoPaneRenderer now governs positioning and rendering of both info panes. This necessitated some changes to NavigationOverlay, OutlinerOverlay and PairOutlinerOverlay. - NEW: A new Visible Reads tab has been added to the tabs at the left hand side. This displays the reads visible on screen in a table. The reads are passed to the table from the new VisibleReadsGrabberThread. - CHG: Fixed a typo in the faq. - CHG: Changed the images used on the tabs for Contigs and Features to better fit with the new Visible Reads image. ------------------------------------------------------------------------ r551 | imilne | 2010-11-17 14:50:20 +0000 (Wed, 17 Nov 2010) | 2 lines - NEW: BAM assemblies will now show the correct read counts for all contigs, so long as the index file was generated with samtools 0.1.8 or higher. - NEW: Updated Picard to 1.35, and included our TabletStats access class in the jar too. ------------------------------------------------------------------------ r550 | imilne | 2010-11-15 14:05:06 +0000 (Mon, 15 Nov 2010) | 1 line - CHG: Removed the last of the linear search code used while searching for a read's mate. All the code now uses DB lookups instead. ------------------------------------------------------------------------ r549 | imilne | 2010-11-15 13:54:12 +0000 (Mon, 15 Nov 2010) | 1 line - NEW: Updated the (new) pair searching code so that it copes with read names that end in :1 or /1 (when marking pairs). ------------------------------------------------------------------------ r548 | imilne | 2010-10-25 13:59:06 +0100 (Mon, 25 Oct 2010) | 1 line - CHG: Updated the help text to better describe the SOAP formats that Tablet accepts. ------------------------------------------------------------------------ r547 | gsteph | 2010-10-22 13:47:39 +0100 (Fri, 22 Oct 2010) | 1 line - CHG: Missed commit for previous check-in of changes to improve speed of pair searching. ------------------------------------------------------------------------ r546 | gsteph | 2010-10-22 13:40:37 +0100 (Fri, 22 Oct 2010) | 1 line - CHG: Improvements made to pair searching code. Now use an index on the name column in the database and a lookup on this column. ------------------------------------------------------------------------ r545 | gsteph | 2010-10-15 10:27:01 +0100 (Fri, 15 Oct 2010) | 5 lines - NEW: Extracted ProgressDialog, ITrackableJob and SimpleJob into SCRI-Commons, made changes to accommodate using the SCRI-Commons versions of these classes. - NEW: Utilising the new TaskDialog in SCRI-Commons to present error messages which allow you to open up the log file. - CHG: Altered SamFileReader to better handle files which have been produced by tools which haven't adhered to the SAM specification. - BUG: Introduced progress bar for pairing reads step in DisplayDataCalculator. - CHG: Modified PairSearcher to get a speed boost on pairing of reads. ------------------------------------------------------------------------ r544 | imilne | 2010-09-29 13:59:47 +0100 (Wed, 29 Sep 2010) | 1 line - NEW: The log file is now written to ~/.scri-bioinf/tablet.log rather than to the install directory. ------------------------------------------------------------------------ r543 | gsteph | 2010-09-22 15:43:12 +0100 (Wed, 22 Sep 2010) | 1 line - NEW: Tagged copy of 1.10.09.22.1 (public). ------------------------------------------------------------------------ r542 | gsteph | 2010-09-22 14:38:35 +0100 (Wed, 22 Sep 2010) | 1 line - NEW: Tagged copy of 1.10.09.22 (public). ------------------------------------------------------------------------ r541 | imilne | 2010-09-20 12:30:35 +0100 (Mon, 20 Sep 2010) | 1 line - BUG: Fixed a problem with the build script for web start files still pointing to the wrong directory on the web server. ------------------------------------------------------------------------ r540 | gsteph | 2010-09-20 12:27:13 +0100 (Mon, 20 Sep 2010) | 1 line - NEW: Tagged copy of 1.10.09.20 (public). ------------------------------------------------------------------------ r539 | gsteph | 2010-09-20 12:19:54 +0100 (Mon, 20 Sep 2010) | 4 lines - NEW: Added searching for sequences within the consensus / reference. - BUG: Fixed class cast error affecting reads canvas info panes in rare cases. - BUG: Fixed issue where CIGAR-I features weren't being refreshed along with the data. - NEW: Updated the usual web pages ready for a new release. ------------------------------------------------------------------------ r538 | imilne | 2010-09-20 10:03:41 +0100 (Mon, 20 Sep 2010) | 1 line - NEW: Added the coveragestats.py script from Aaron Liston, and updated the download www page to point to it. ------------------------------------------------------------------------ r537 | gsteph | 2010-09-16 16:08:24 +0100 (Thu, 16 Sep 2010) | 1 line - BUG: Fix for issue causing InfoPane to not display when under a column containing a feature that isn't a cigar feature. ------------------------------------------------------------------------ r536 | gsteph | 2010-09-16 11:43:27 +0100 (Thu, 16 Sep 2010) | 1 line - BUG: Missed file for last commit. ------------------------------------------------------------------------ r535 | gsteph | 2010-09-16 10:29:17 +0100 (Thu, 16 Sep 2010) | 2 lines - BUG: Fixes for issues where SAM files weren't being paired properly. - BUG: Fix for issue with read names which have pair information in them breaking pairing code. ------------------------------------------------------------------------ r534 | imilne | 2010-09-10 11:46:28 +0100 (Fri, 10 Sep 2010) | 1 line - NEW: Tagged copy of 1.10.09.10 (public). ------------------------------------------------------------------------ r533 | imilne | 2010-09-10 11:44:54 +0100 (Fri, 10 Sep 2010) | 1 line - NEW: Updated the usual files for a new release. ------------------------------------------------------------------------ r532 | gsteph | 2010-09-10 11:34:58 +0100 (Fri, 10 Sep 2010) | 3 lines - BUG: Fixes to increase speed of PairedPackSetCreator, particularly when dealing with deep stacks of unpaired reads with the same start position. - BUG: Tidied up display of the pair outliner, including making it behave more like the read outliner at different zoom levels. - NEW: Updated various help topics and introduced some new ones. ------------------------------------------------------------------------ r531 | gsteph | 2010-09-08 09:45:26 +0100 (Wed, 08 Sep 2010) | 2 lines - NEW: It is now possible to export all of the reads on screen to a file. - BUG: Fixes for a bug where the second read in a pair could not be highlighted from the find panel. ------------------------------------------------------------------------ r530 | gsteph | 2010-09-03 09:18:12 +0100 (Fri, 03 Sep 2010) | 2 lines - NEW: Exporting of the reads in a column from the right click menu on the reads canvas. - NEW: Clicking on a Cigar-I feature allows you to toggle the CigarIHighlighter on and off for that feature. ------------------------------------------------------------------------ r529 | gsteph | 2010-09-01 09:42:36 +0100 (Wed, 01 Sep 2010) | 2 lines - NEW: A first attempt at the CigarI highlighting based on FeaturesCanvas mouse input. - BUG: PairOutlinerOverlay could draw links between paired reads in the normal packed mode. ------------------------------------------------------------------------ r528 | imilne | 2010-08-30 10:52:53 +0100 (Mon, 30 Aug 2010) | 1 line - NEW: The start of basic mouse detection over the features canvas. ------------------------------------------------------------------------ r527 | gsteph | 2010-08-25 13:44:45 +0100 (Wed, 25 Aug 2010) | 5 lines - NEW: CigarIHighlighter is a new overlay which allows for cigar feature highlighting. - CHG: Changes to cigar parsing to allow for the new cigar feature highlighting. - CHG: An extra colour has been added to the ReadTypeColorScheme, this allows differentiation between orphaned reads and single end reads. - BUG: Fixed a bug which prevented SAM files from loading. ------------------------------------------------------------------------ r526 | imilne | 2010-08-20 15:20:38 +0100 (Fri, 20 Aug 2010) | 2 lines - NEW: Added code to ensure CIGAR_I features are always added and visible (by default) on the features track. - NEW: Added custom rendering ("I" bar style) for CIGAR_I features. ------------------------------------------------------------------------ r525 | imilne | 2010-08-19 09:24:49 +0100 (Thu, 19 Aug 2010) | 4 lines - NEW: Features now render in a unique colour per type. - NEW: Added a few short paragraphs of help text for visualizing features. - NEW: Added a right-click "Select tracks" menu option to the features canvas. - BUG: The features weren't rendering when no reference file was provided. ------------------------------------------------------------------------ r524 | gsteph | 2010-08-11 14:10:49 +0100 (Wed, 11 Aug 2010) | 2 lines - CHG: BandStyles uses a JPopupMenu to handle changing the current pack style. - CHG: ReadsCanvasInfoPane has been updated to use internationalised strings for its new UI elements. ------------------------------------------------------------------------ r523 | gsteph | 2010-08-11 14:06:11 +0100 (Wed, 11 Aug 2010) | 3 lines - BUG: An error in the ReadPair class was causing pair link lines to disappear when zoomed out and both reads fully on-screen. - BUG: Errors in the pack code meant rendering of pair link lines wasn't correct at window edges. - BUG: An error condition was not handled in PairSearcher which could leave the ReadsCanvas in an unusable state after jumping around the bam file using the BamBam bar. ------------------------------------------------------------------------ r522 | gsteph | 2010-08-11 14:02:09 +0100 (Wed, 11 Aug 2010) | 2 lines - BUG: SAM/BAM readers now deal with unpaired data correctly by marking Assembly.isPaired as false. - BUG: The ReadSQLCache is now suitably reset if the connection to the database was interrupted through error conditions. ------------------------------------------------------------------------ r521 | imilne | 2010-08-09 15:29:46 +0100 (Mon, 09 Aug 2010) | 6 lines - NEW: Moved the Select Tracks link to a better place within the NBFeaturesPanelControls class. - NEW: Added mouse drag navigation to all TrackingCanvas classes. - NEW: The first three feature types found during import are now auto-added to the display. - NEW: Added a mouse tracking class to the Features canvas (scale positions only for now). - CHG: Disabled the "Browser" file scanner for now. - BUG: Weirdly, outline paints on the features using alpha transparencies do not work. They must be solid. ------------------------------------------------------------------------ r520 | imilne | 2010-08-06 14:07:09 +0100 (Fri, 06 Aug 2010) | 4 lines - CHG: Removed the concept of "data only" from the read cache, as it only stores data we want now - all supplementary stuff is in sqlite. - NEW: Added a new colour scheme - Read Type - that paints reads based on type: unpaired, 1st in pair, or 2nd in pair. - NEW: Simplified (for now) the methods used to determine offsets to colour schemes when requesting the raw data (byte[]) from the read cache objects. - CHG: 1st/2nd in pair data is now stored in the read cache in addition to the sqlite cache. ------------------------------------------------------------------------ r519 | gsteph | 2010-08-04 09:28:26 +0100 (Wed, 04 Aug 2010) | 1 line - BUG: Fixed issue where a pair of reads could be added twice if the furthest left read in the pair straddles the bam window. ------------------------------------------------------------------------ r518 | imilne | 2010-08-04 09:19:09 +0100 (Wed, 04 Aug 2010) | 1 line - NEW: Updated the GFF reader to cope with files containing ##FASTA directives. ------------------------------------------------------------------------ r517 | gsteph | 2010-08-03 08:54:25 +0100 (Tue, 03 Aug 2010) | 2 lines - BUG: Fix for issue where ReadInfoPanes could display incorrect information on grab scrolling. - CHG: Removal of output line which should have been removed before previous check-in in PairOutlinerOverlay ------------------------------------------------------------------------ r516 | gsteph | 2010-07-30 11:19:17 +0100 (Fri, 30 Jul 2010) | 2 lines - NEW: Pack Style Changer button in BandStyles. - CHG: Errors in previous checkins for PairOutlinerOverlay and ReadsCanvasML have been corrected. ------------------------------------------------------------------------ r515 | gsteph | 2010-07-30 10:12:21 +0100 (Fri, 30 Jul 2010) | 2 lines - NEW: A visPaired Prefs variable for when paired data is being viewed. - BUG: FindPanel wouldn't scroll to the selected contig in the contigs list when highlighting it. ------------------------------------------------------------------------ r514 | gsteph | 2010-07-30 10:09:42 +0100 (Fri, 30 Jul 2010) | 3 lines - NEW: ReadsCanvas includes new logic to get the correct ReadManager. - NEW: ReadsCanvasInfoPane has been updated to display pair information, included drawing a secondary InfoPane with information about a read's pair. - NEW: ReadsCanvasMenu now contains option to jump to a read's pair and options to jump to either side of a line connecting a pair. ------------------------------------------------------------------------ r513 | gsteph | 2010-07-30 10:06:08 +0100 (Fri, 30 Jul 2010) | 1 line - NEW: Creation of the PairOutlinerOverlay which highlights both members of a pair and draws a solid line between them. ------------------------------------------------------------------------ r512 | gsteph | 2010-07-30 10:03:58 +0100 (Fri, 30 Jul 2010) | 2 lines - NEW: Ace, AFG, Maq and SOAP readers have been updated to set Assembly.isPaired to false; - NEW: BAM and SAM readers have been altered so that they create MatedReads where appropriate. ------------------------------------------------------------------------ r511 | gsteph | 2010-07-30 10:01:17 +0100 (Fri, 30 Jul 2010) | 1 line - NEW: Changes to the colour schemes to accomodate the new PairLinkColorState which has been included to draw the links between members of a pair. ------------------------------------------------------------------------ r510 | gsteph | 2010-07-30 09:56:45 +0100 (Fri, 30 Jul 2010) | 4 lines - NEW: DisplayDataCalculator contains new logic to select which of the packing / stacking schemes to utilise. - NEW: PairedPackSetCreator behaves like the normal PackSetCreator, but places members of pairs on the same row (where possible) and prevents any read from being packed in between them. - NEW: PairedStackCreator behaves like the normal StackCreator, but places members of a piar on the same row if possible. - NEW: PairSearch is a utility class which searches for a read's pair given either a MatedRead, or a name and a position. ------------------------------------------------------------------------ r509 | gsteph | 2010-07-30 09:51:46 +0100 (Fri, 30 Jul 2010) | 5 lines - NEW: Changes to the core data api to account for the new pack and stack types. - NEW: Pack can now be used as the basis of both the normal PackSet and the new PairedPackSet. - NEW: Pack now draws dotted lines between members of a pair where appropriate. - NEW: ReadPair introduced as the basis of the PairedStack.java. - NEW: PairedStack is a new stack which keeps both members of a pair on the same row of the display if possible. ------------------------------------------------------------------------ r508 | gsteph | 2010-07-30 09:31:15 +0100 (Fri, 30 Jul 2010) | 6 lines - NEW: Creation of MatedRead class which extends Read and is used in cases where paired reads are found in the data. Currently this will only be with SAM/BAM data. - NEW: ReadNameData now includes information on paired-end reads. This includes the insert size, whether or not the pair is a proper pair and the number in the pair this read is. - NEW: Addes the insert size, proper pair and number in pair information to the ReadSQL cache. - BUG: Added a resetCache option in ReadSQLCache overcoming a bug which resulted in the ReadSQLCache not being cleared out on changes of contig. - CHG: Removed misleading comment from ReadFileCache which misrepresented the data being stored. ------------------------------------------------------------------------ r507 | imilne | 2010-07-27 13:23:20 +0100 (Tue, 27 Jul 2010) | 1 line - BUG: Feature types (SNP, INDEL, etc) were still being added even if the feature they belonged to was rejected during the import. ------------------------------------------------------------------------ r506 | imilne | 2010-07-27 11:27:23 +0100 (Tue, 27 Jul 2010) | 1 line - NEW: Added a dialog for editing which feature tracks are active and for adjusting their order. ------------------------------------------------------------------------ r505 | gsteph | 2010-07-13 10:21:02 +0100 (Tue, 13 Jul 2010) | 1 line - BUG: Fix which prevents the red box representing the window clipping on the edge of the overview canvas when it hasn't been sub-setted. ------------------------------------------------------------------------ r504 | imilne | 2010-07-06 15:56:46 +0100 (Tue, 06 Jul 2010) | 4 lines - NEW: Added a licence file for the sqlite stuff. - CHG: Modified the webstart code/build scripts to cope with sqlite. - NEW: Re-added the original all-versions sqlite jar file for exclusive webstart use (the installers will continue to use platform specific jars). - CHG: Updated the scripts for logging and webstart to run from their folders (.htaccess etc). ------------------------------------------------------------------------ r503 | imilne | 2010-07-06 11:50:54 +0100 (Tue, 06 Jul 2010) | 2 lines - NEW: Major changes to the installer to cope with install4j 5. - CHG: Changed the sqlite jars to custom edits from www.xerial.org for each platform. Still need to work out licensing. ------------------------------------------------------------------------ r502 | gsteph | 2010-06-24 12:14:15 +0100 (Thu, 24 Jun 2010) | 3 lines - NEW: Added jar files for SQLite and native libraries for each platform. - NEW: Created a new SQL cache which stores the read name, unpadded length, cigar and mateContig in an sqlite database file. - NEW: Updated Tablet code to use this new SQL cache where appropriate. ------------------------------------------------------------------------ r501 | imilne | 2010-06-21 15:28:38 +0100 (Mon, 21 Jun 2010) | 1 line - NEW: Moved the default location for saving prefs information from ~/.tablet.xml to ~/.scri-bioinf/tablet.xml (with old files being automatically moved over if found). ------------------------------------------------------------------------ r500 | imilne | 2010-06-18 13:14:38 +0100 (Fri, 18 Jun 2010) | 2 lines - NEW: File scanning will now list whether files are compressed or not. - NEW: File scanning for BAM can now count the contigs/ref seqs used at the time of assembly creation. ------------------------------------------------------------------------ r499 | imilne | 2010-06-18 12:35:41 +0100 (Fri, 18 Jun 2010) | 1 line - NEW: Table now warns if the reference length expected by a BAM file differs from that of the actual reference imported by the user. ------------------------------------------------------------------------ r498 | imilne | 2010-06-18 09:52:09 +0100 (Fri, 18 Jun 2010) | 1 line - BUG: BAM assemblies still showed ? for the read count when in a window where the genuine number of reads was zero. ------------------------------------------------------------------------ r497 | gsteph | 2010-06-18 09:23:45 +0100 (Fri, 18 Jun 2010) | 1 line - BUG: Fixed unformatted large numbers in OverviewCanvas. ------------------------------------------------------------------------ r496 | imilne | 2010-06-17 14:17:05 +0100 (Thu, 17 Jun 2010) | 1 line - CHG: More changes and tweaks to colours and highlighting. ------------------------------------------------------------------------ r495 | imilne | 2010-06-17 11:20:52 +0100 (Thu, 17 Jun 2010) | 1 line - NEW: Selecting a read from the Find Reads table will now also highlight it on the overview. ------------------------------------------------------------------------ r494 | imilne | 2010-06-17 10:00:13 +0100 (Thu, 17 Jun 2010) | 2 lines - BUG: Fixed the problem with the contigs table still showing BAM read counts etc even after a contig load failure or cancellation. - CHG: Changed the highlight colours used by the overview window to try and make them work a bit better with all the colour schemes. ------------------------------------------------------------------------ r493 | imilne | 2010-06-17 09:10:20 +0100 (Thu, 17 Jun 2010) | 2 lines - BUG: Fixed problems with the coverage array being null while the scale canvas was still drawing. - BUG: The consensus length information was wrong for non-BAM assemblies after all the recent changes. ------------------------------------------------------------------------ r492 | imilne | 2010-06-16 15:42:14 +0100 (Wed, 16 Jun 2010) | 1 line - NEW: Updated the Import Assembly dialog to cope with no longer requiring reference files for BAM. ------------------------------------------------------------------------ r491 | imilne | 2010-06-16 14:38:55 +0100 (Wed, 16 Jun 2010) | 1 line - NEW: Fixed the final remaining problems with loading BAM files without a reference file. ------------------------------------------------------------------------ r490 | imilne | 2010-06-16 11:44:02 +0100 (Wed, 16 Jun 2010) | 1 line - NEW: Enabled proper number format cell rendering on the Features and Find tables too. ------------------------------------------------------------------------ r489 | imilne | 2010-06-16 11:35:16 +0100 (Wed, 16 Jun 2010) | 3 lines - NEW: Started working on allowing BAM files to be loaded without reference data (still to be completed). - NEW: The Contigs Table now contains custom rendering based on what data is available. - CHG: Moved some of the Contig class's variables into an inner class to tidy it up a bit (mainly stuff related to display). ------------------------------------------------------------------------ r488 | imilne | 2010-06-16 09:12:56 +0100 (Wed, 16 Jun 2010) | 1 line - CHG: Minor change to the build file to cope with Ant 1.8 ------------------------------------------------------------------------ r487 | imilne | 2010-06-14 13:55:42 +0100 (Mon, 14 Jun 2010) | 4 lines - NEW: Lots of new additions to the assembly browser scanner. - CHG: Major changes to the way files are handled, detected and loaded. - CHG: Only one open/close operation is needed per file now to detect its type (rather than one open/close per possible type) - all types are distinguishable form a single one line read (including BAM). - CHG: The file readers have been simplified by ensuring they are only called once the file types are known. They no longer have to determine if they *can* read a file or not; they just do. ------------------------------------------------------------------------ r486 | imilne | 2010-06-11 11:26:21 +0100 (Fri, 11 Jun 2010) | 2 lines - NEW: Added new classes to tablet.io that can perform file scanning (of assembly files). - NEW: Added a new frame - ScannerFrame - that contains the results of these scans. Still a lot of work to be done to it. ------------------------------------------------------------------------ r485 | imilne | 2010-06-08 10:04:24 +0100 (Tue, 08 Jun 2010) | 1 line - NEW: Added a few more entries to the FAQ. ------------------------------------------------------------------------ r484 | imilne | 2010-06-04 11:01:02 +0100 (Fri, 04 Jun 2010) | 1 line - NEW: Made the (current) 500 results limit on searches into a user-configurable amount (guiSearchLimit). No UI for changing it yet though. ------------------------------------------------------------------------ r483 | imilne | 2010-06-02 11:02:49 +0100 (Wed, 02 Jun 2010) | 1 line - NEW: Minor changes to the way images are returned from the colour schemes (doesn't affect anything, but makes HWA tests easier). ------------------------------------------------------------------------ r482 | imilne | 2010-05-31 14:23:32 +0100 (Mon, 31 May 2010) | 2 lines - CHG: Modified the installer so that we no longer need the separate tablet and tablet64 launchers. - NEW: Added installer file type association for ace, afg, sam, and bam (for OS X only). ------------------------------------------------------------------------ r481 | imilne | 2010-05-28 11:37:07 +0100 (Fri, 28 May 2010) | 1 line - NEW: Updated source code licence information for 2010 (finally!). ------------------------------------------------------------------------ r480 | imilne | 2010-05-28 10:08:15 +0100 (Fri, 28 May 2010) | 1 line - NEW: Some code clean-up after running PMD. ------------------------------------------------------------------------ r479 | imilne | 2010-05-28 09:32:54 +0100 (Fri, 28 May 2010) | 1 line - NEW: Tweaked the Feature class to not point directly at settings from Prefs. ------------------------------------------------------------------------ r478 | imilne | 2010-05-28 09:12:29 +0100 (Fri, 28 May 2010) | 3 lines - NEW: Experimented with custom rendering of SNPs. - NEW: Updated the Feature class to support padded and unpadded values, determined at runtime. - NEW: The binary search code for displaying features can now deal with the padded/unpadded state; toggling it causes the features to jump position on the display (as they should). ------------------------------------------------------------------------ r477 | imilne | 2010-05-27 14:56:26 +0100 (Thu, 27 May 2010) | 1 line - CHG: Updated to the latest version of Picard. ------------------------------------------------------------------------ r476 | imilne | 2010-05-27 09:16:23 +0100 (Thu, 27 May 2010) | 1 line - NEW: Missed file from the previous commit. ------------------------------------------------------------------------ r475 | imilne | 2010-05-26 14:08:55 +0100 (Wed, 26 May 2010) | 1 line - NEW: Added a summary message describing the result of importing features from a GFF3 file. ------------------------------------------------------------------------ r474 | imilne | 2010-05-26 10:08:41 +0100 (Wed, 26 May 2010) | 2 lines - NEW: Added basic rendering of the features, with the standard binary search (window based) method of locating what to draw. - NEW: Feature (the class) now tracks a list of all "types" for the current project. This list is used to determine what tracks to draw. ------------------------------------------------------------------------ r473 | imilne | 2010-05-24 16:05:57 +0100 (Mon, 24 May 2010) | 4 lines - NEW: First commit for new graphical features support. - NEW: Added changes to the data API to support visual features, merging the old FeaturesList with a new FeatureTrack class to represent a "track" of features (on screen). - NEW: Added a (non functional) canvas class ready to draw the features. - NEW: Added a class - FeatureTrackCreator - to handle dynamically building feature track objects as contigs are selected. ------------------------------------------------------------------------ r472 | imilne | 2010-05-21 16:17:36 +0100 (Fri, 21 May 2010) | 1 line - NEW: Tagged copy of 1.10.05.21 (public). ------------------------------------------------------------------------ r471 | imilne | 2010-05-21 16:17:05 +0100 (Fri, 21 May 2010) | 2 lines - BUG: Fixed a critical bug that was resulting in some contigs hiding reads when in packed mode. - CHG: Updated the web pages for a new release. ------------------------------------------------------------------------ r470 | imilne | 2010-05-18 13:40:12 +0100 (Tue, 18 May 2010) | 1 line - NEW: Tagged copy of 1.10.05.18 (public). ------------------------------------------------------------------------ r469 | imilne | 2010-05-18 13:39:35 +0100 (Tue, 18 May 2010) | 2 lines - NEW: Various changes to the web pages ready for a new release. - NEW: Updated the help to cover some of the new Options Dialog settings. ------------------------------------------------------------------------ r468 | imilne | 2010-05-14 15:22:23 +0100 (Fri, 14 May 2010) | 2 lines - NEW: Added an option to the Options Dialog for switching ambiguity translation on or off. - CHG: Changed some of the prefs options so that certain classes that shouldn't really have access to them no longer do. They now use their own public copies that can be set externally. ------------------------------------------------------------------------ r467 | gsteph | 2010-05-14 14:44:11 +0100 (Fri, 14 May 2010) | 2 lines - NEW: Added option to set Picard SAMFileReader's validation stringency to lenient to surpress SamValidation errors. - BUG: Fixed issue where Tablet didn't re-initialise the bamReader object leaving Tablet unusable until the data was loaded again after a SamValidation error. ------------------------------------------------------------------------ r466 | imilne | 2010-05-14 14:37:53 +0100 (Fri, 14 May 2010) | 3 lines - NEW: Added a (not yet settable) option to Sequence to force DNA ambiguity codes to be read as N. - NEW: Updated the protein translator to treat any base with an N as ok (codon will translate to X) rather than having it skip the base. - BUG: Fixed a problem copying any of the reverse strand protein translations to the clipboard. ------------------------------------------------------------------------ r465 | imilne | 2010-05-13 14:08:38 +0100 (Thu, 13 May 2010) | 1 line - NEW: Added links to Twitter. ------------------------------------------------------------------------ r464 | imilne | 2010-05-12 15:49:55 +0100 (Wed, 12 May 2010) | 2 lines - NEW: Implemented a new method of determining the version number using the manifest file from the jar. - CHG: Updated the web start code to rely on this too, rather than using argument parsing. ------------------------------------------------------------------------ r463 | imilne | 2010-05-07 14:23:49 +0100 (Fri, 07 May 2010) | 1 line - CHG: Minor change to the webstart files to make their naming a bit clearer. ------------------------------------------------------------------------ r462 | imilne | 2010-05-06 13:16:05 +0100 (Thu, 06 May 2010) | 1 line - NEW: Tagged copy of 1.10.05.06 (public). ------------------------------------------------------------------------ r461 | imilne | 2010-05-06 13:10:22 +0100 (Thu, 06 May 2010) | 1 line - NEW: Added a shortcut to the Subset option on the Overview canvas's right click menu. ------------------------------------------------------------------------ r460 | gsteph | 2010-05-06 13:01:28 +0100 (Thu, 06 May 2010) | 2 lines - NEW: Overview subsetting has been implemented, allowing users to focus in on smaller sections of the overview. - NEW: An Overview section has been added to the advanced tab of the ribbon. ------------------------------------------------------------------------ r459 | imilne | 2010-05-06 13:01:15 +0100 (Thu, 06 May 2010) | 1 line - NEW: Various changes to the web pages ready for a new release (including updating screenshots). ------------------------------------------------------------------------ r458 | imilne | 2010-05-06 09:24:38 +0100 (Thu, 06 May 2010) | 1 line - NEW: Tweaks and modifications (and i18n text) for the Open Example Assembly dialog. ------------------------------------------------------------------------ r457 | imilne | 2010-05-06 08:33:46 +0100 (Thu, 06 May 2010) | 1 line - NEW: Added a warning message about using samtools to generate index files for BAM files (if the .bai index is missing). ------------------------------------------------------------------------ r456 | imilne | 2010-05-05 14:42:55 +0100 (Wed, 05 May 2010) | 1 line - NEW: Added and updated help for the Preferences dialog. ------------------------------------------------------------------------ r455 | imilne | 2010-05-05 14:38:18 +0100 (Wed, 05 May 2010) | 1 line - BUG: The previous commit (for BAM dialog changes) didn't compile. ------------------------------------------------------------------------ r454 | gsteph | 2010-05-05 11:56:44 +0100 (Wed, 05 May 2010) | 3 lines - BUG: Fixed the finder so that it displays the correct messages when doing both a search for reads and a search for subsequences and one where the results label wasn't being updated properly. - BUG: Fixed a bug that meant subsequence searching was case-sensitive. ------------------------------------------------------------------------ r453 | imilne | 2010-05-05 11:51:13 +0100 (Wed, 05 May 2010) | 2 lines - NEW: Made some visual modifications to the Adjust BAM Window Size dialog. - NEW: Added the www help content for the dialog too. ------------------------------------------------------------------------ r452 | gsteph | 2010-05-05 09:52:00 +0100 (Wed, 05 May 2010) | 1 line - BUG: Fixed a bug where the bamFinder would search on an empty string. ------------------------------------------------------------------------ r451 | gsteph | 2010-05-04 15:01:19 +0100 (Tue, 04 May 2010) | 1 line - BUG: Fixed a number of bugs with the finder, particularly the subsequence finder. ------------------------------------------------------------------------ r450 | gsteph | 2010-05-04 14:41:15 +0100 (Tue, 04 May 2010) | 1 line - CHG: The SamFileReader now checks for all possible header fields to decide if this is a SAM file or not. ------------------------------------------------------------------------ r449 | imilne | 2010-05-03 14:12:28 +0100 (Mon, 03 May 2010) | 2 lines - NEW: Added ribbon and menu options for the read shadowing. - CHG: Modified the RibbonController to maintain static references to each of its bands (for access to event handling by other classes). ------------------------------------------------------------------------ r448 | gsteph | 2010-04-30 09:15:08 +0100 (Fri, 30 Apr 2010) | 2 lines - CHG: Updated the SAM jar we're using to version 1.18. - NEW: Added the sam-version.txt file which is a place to quickly check which version of the sam jar file we are currently using. ------------------------------------------------------------------------ r447 | imilne | 2010-04-28 15:55:20 +0100 (Wed, 28 Apr 2010) | 2 lines - NEW: Added a new tab to the preferences option to contain assembly import settings. - NEW: Added a checkbox for setting the state of the ace QA read trimming option on or off. ------------------------------------------------------------------------ r446 | imilne | 2010-04-28 11:37:59 +0100 (Wed, 28 Apr 2010) | 1 line - CHG: Minor edit to lighten the intensity of the read shadower. ------------------------------------------------------------------------ r445 | imilne | 2010-04-28 11:37:24 +0100 (Wed, 28 Apr 2010) | 1 line - NEW: First attempt at parsing QA tags in ace files and either keeping/ignoring the poor regions of a read. ------------------------------------------------------------------------ r444 | imilne | 2010-04-28 09:19:27 +0100 (Wed, 28 Apr 2010) | 1 line - NEW: Added the Overlay Read Names option to the new ribbon controls. ------------------------------------------------------------------------ r443 | imilne | 2010-04-27 09:23:03 +0100 (Tue, 27 Apr 2010) | 1 line - NEW: Checked in a missing file. ------------------------------------------------------------------------ r442 | imilne | 2010-04-23 11:33:41 +0100 (Fri, 23 Apr 2010) | 1 line - NEW: Added another new ribbon band - BandOverlays - with two options so far: enable read info tips on/off and show base text on/off. ------------------------------------------------------------------------ r441 | imilne | 2010-04-22 11:36:55 +0100 (Thu, 22 Apr 2010) | 2 lines - NEW: Added a (Preferences) option to force Tablet to separate reads in the packed layout by at least the specified number of bases. - CHG: Changes to the help and screenshots for the above. ------------------------------------------------------------------------ r440 | imilne | 2010-04-21 14:49:22 +0100 (Wed, 21 Apr 2010) | 1 line - BUG: Fixed the "jiggle" problem where the canvas moves by a few pixels when switching between contigs. ------------------------------------------------------------------------ r439 | imilne | 2010-04-21 09:24:46 +0100 (Wed, 21 Apr 2010) | 2 lines - NEW: Created a new band for the BAM options. - CHG: Removed the BAM settings from the Tablet Options dialog. ------------------------------------------------------------------------ r438 | imilne | 2010-04-19 11:19:07 +0100 (Mon, 19 Apr 2010) | 3 lines - NEW: Created an Advanced ribbon bar. - NEW: Created a new band just for the protein options (and added it to the Advanced bar). - CHG: Removed the proteins button from the current Options band. ------------------------------------------------------------------------ r437 | gsteph | 2010-04-15 15:25:34 +0100 (Thu, 15 Apr 2010) | 1 line - CHG: Altered the example dataset dialog so that it could load files from other servers. ------------------------------------------------------------------------ r436 | imilne | 2010-04-15 11:21:27 +0100 (Thu, 15 Apr 2010) | 1 line - NEW: Refactored/renamed the classes related to the ribbon, ready for redesigning it. ------------------------------------------------------------------------ r435 | imilne | 2010-04-15 09:13:48 +0100 (Thu, 15 Apr 2010) | 1 line - NEW: Updates to a couple of the web pages. ------------------------------------------------------------------------ r434 | gsteph | 2010-04-14 15:34:00 +0100 (Wed, 14 Apr 2010) | 1 line - NEW: A new dialog has been added for opening example datasets. This queries a properties file on our server to populate the dialog with our current set of example datasets. ------------------------------------------------------------------------ r433 | imilne | 2010-04-14 14:27:31 +0100 (Wed, 14 Apr 2010) | 1 line - NEW: Added some changes to the Open Assembly dialog to support example files. ------------------------------------------------------------------------ r432 | imilne | 2010-04-02 10:55:19 +0100 (Fri, 02 Apr 2010) | 1 line - NEW: Changed the layout of the search tab's controls. ------------------------------------------------------------------------ r431 | gsteph | 2010-03-30 15:31:05 +0100 (Tue, 30 Mar 2010) | 2 lines - NEW: Read shadowing implemented. Shadows the reads which intersect with a line which is either in the centre of the ReadsCanvas, or under the mouseBase. This can also be locked in position when in the mode that follows the mouse. - NEW: Added ability to turn off fonts on bases in the enhanced display mode. ------------------------------------------------------------------------ r430 | gsteph | 2010-03-23 11:31:22 +0000 (Tue, 23 Mar 2010) | 1 line - NEW: A new search for read subsequence feature has been added. ------------------------------------------------------------------------ r429 | imilne | 2010-03-16 09:09:04 +0000 (Tue, 16 Mar 2010) | 1 line - NEW: Updated the web site with changes to the maps. ------------------------------------------------------------------------ r428 | imilne | 2010-03-15 15:43:50 +0000 (Mon, 15 Mar 2010) | 2 lines - CHG: Modified the ACE parser (yet again) to completely ignore base quality information. - NEW: Added a new button ("Tag Variants") that can turn on/off the red highlighting of variants in the overview displays (main and popup). ------------------------------------------------------------------------ r427 | imilne | 2010-03-12 16:16:37 +0000 (Fri, 12 Mar 2010) | 3 lines - NEW: Added a new colouring scheme based on read direction. - CHG: Modified the "data only" access methods to the read cache to pull back raw data plus orientation. - CHG: All colour schemes can now do (in red) tagging of variants on the overviews. ------------------------------------------------------------------------ r426 | gsteph | 2010-03-05 11:47:01 +0000 (Fri, 05 Mar 2010) | 1 line - NEW: Code changes to pre-empt work on resizable overview canvases. ------------------------------------------------------------------------ r425 | imilne | 2010-03-04 16:16:31 +0000 (Thu, 04 Mar 2010) | 1 line - NEW: Tagged copy of 1.10.03.04 (public). ------------------------------------------------------------------------ r424 | imilne | 2010-03-04 16:15:41 +0000 (Thu, 04 Mar 2010) | 2 lines - NEW: Changes and updates to some of the help. - NEW: Changes to the web files ready for a new release. ------------------------------------------------------------------------ r423 | imilne | 2010-03-04 15:44:14 +0000 (Thu, 04 Mar 2010) | 1 line - BUG: Fixed multiple issues in the AFG parser related to clr and gap information. ------------------------------------------------------------------------ r422 | imilne | 2010-03-04 12:14:26 +0000 (Thu, 04 Mar 2010) | 1 line - BUG: The unpadded length of a read wasn't being shown. ------------------------------------------------------------------------ r421 | imilne | 2010-03-04 11:41:26 +0000 (Thu, 04 Mar 2010) | 1 line - CHG: Fixing PNG/png filename issues in svn for the help. ------------------------------------------------------------------------ r420 | imilne | 2010-03-04 11:40:28 +0000 (Thu, 04 Mar 2010) | 1 line - CHG: Fixing PNG/png filename issues in svn for the help. ------------------------------------------------------------------------ r419 | imilne | 2010-03-03 11:00:18 +0000 (Wed, 03 Mar 2010) | 2 lines - NEW: Added some additional file extensions to the Open dialogs to catch variations of fasta and gff. - NEW: The BamFileReader class now properly extends TrackableReader, allowing it to use transfer rates and the normal reference reader rather than its own implementation. This also allows for gziped fasta files with BAM. ------------------------------------------------------------------------ r418 | gsteph | 2010-03-03 10:04:19 +0000 (Wed, 03 Mar 2010) | 1 line - NEW: FeaturesList code now uses a binary search to search for duplicate features before adding a new feature. This required a change to the compareTo method in Feature to make its comparison work on all parts of a feature. ------------------------------------------------------------------------ r417 | imilne | 2010-03-02 15:34:35 +0000 (Tue, 02 Mar 2010) | 2 lines - NEW: Updated the protein translation code to run in the new background task implementation. - CHG: Modified the Executor service used to one that can track the active tasks internally, rather than relying on atomic integers. ------------------------------------------------------------------------ r416 | gsteph | 2010-03-02 13:05:27 +0000 (Tue, 02 Mar 2010) | 1 line - NEW: A new method of calculating and storing the paddedToUnpadded and unpaddedToPadded mappings has been implemented. ------------------------------------------------------------------------ r415 | imilne | 2010-02-26 14:12:12 +0000 (Fri, 26 Feb 2010) | 2 lines - NEW: Updated the install4j project with the latest JREs. - CHG: More refactoring of the background task implementation, making a new package for it, and getting it to work properly with Java's concurrency classes. Event handling is now used to notify listeners that a job is finished, so they can then ask that job for its data. ------------------------------------------------------------------------ r414 | gsteph | 2010-02-25 16:22:52 +0000 (Thu, 25 Feb 2010) | 4 lines - NEW: Tablet now displays coordinates of the current data window and the bases currently on screen on the overview canvas. - BUG: Fixed bug which caused information not to show on reads canvas when moving the BAMBAM bar. - NEW: Added some initial help for BAM visualization. ------------------------------------------------------------------------ r413 | imilne | 2010-02-25 15:14:20 +0000 (Thu, 25 Feb 2010) | 1 line - CHG: Modified the Sequence.setData() method to take a StringBuilder instead of a String. This means no conversion (or allocation) has to be done between StringBuilder and String, which saves memory when reading data at load time. ------------------------------------------------------------------------ r412 | imilne | 2010-02-25 14:24:42 +0000 (Thu, 25 Feb 2010) | 1 line - CHG: Memory for consensus/reference base qualities isn't allocated now if the file they came from doesn't support qualities. The quality information is obviously no longer rendered either. (This saves a byte per base x the length of the consensus). ------------------------------------------------------------------------ r411 | imilne | 2010-02-25 13:45:26 +0000 (Thu, 25 Feb 2010) | 1 line - BUG: Clicking "Browse" in the Open Assembly dialog with an existing http url in the text box will now open the browser at the last visited folder, rather than resetting to the default because the url doesn't equal a valid file. ------------------------------------------------------------------------ r410 | imilne | 2010-02-25 12:52:46 +0000 (Thu, 25 Feb 2010) | 6 lines - BUG: Cancelling loading (of BAM) didn't finish as quickly as it should. - NEW: Implemented a new way of running background tasks (such as padded->unpadded mappings) that can now happen post contig-viewing. Added new classes BackgroundJob and TaskManager for handling this. - CHG: Modified the BaseMappingCalculator to be a BackgroundJob instead of a SimpleJob. - CHG: The Jump To dialog and clicking on features operations now warn if they can't run due to the padded/unpadded mappings not being available (ie, they're still being calculated). - CHG: The Scale Bar will ignore showing unpadded bases if the calculations aren't ready. - NEW: Added a background tasks "tracker" to the status bar. ------------------------------------------------------------------------ r409 | gsteph | 2010-02-24 14:50:13 +0000 (Wed, 24 Feb 2010) | 1 line - BUG: Fixed bug which caused Tablet to not exit correctly when a filter had been applied in the ContigsPanel. ------------------------------------------------------------------------ r408 | imilne | 2010-02-24 14:19:47 +0000 (Wed, 24 Feb 2010) | 1 line - BUG: Mismatch values (per contig) were still being calculated wrong. Now they are simply the number of mismatched bases (across all reads) divided by the total number of bases (ignoring overhanging regions). ------------------------------------------------------------------------ r407 | imilne | 2010-02-24 09:17:15 +0000 (Wed, 24 Feb 2010) | 1 line - CHG: Updated the detection code for GFF3 files to deal with malformed ##gff-version headers. ------------------------------------------------------------------------ r406 | imilne | 2010-02-23 15:27:41 +0000 (Tue, 23 Feb 2010) | 2 lines - BUG: The mismatch percentage calculations could go wrong with either no reference to check against, or (probably) more than 20 million reads. - NEW: The Contigs Table will now clear previous values (for read count and mismatch %) when a new BAM contig (or bambam bar block) is loaded. ------------------------------------------------------------------------ r405 | imilne | 2010-02-23 13:44:56 +0000 (Tue, 23 Feb 2010) | 2 lines - NEW: Loading of BAM data blocks can now be cancelled. - BUG: It wasn't possible to cancel the calculations for padding/unpadded mappings. ------------------------------------------------------------------------ r404 | imilne | 2010-02-23 13:33:41 +0000 (Tue, 23 Feb 2010) | 2 lines - NEW: Added a tooltip to the bambam bar. - NEW: Stopped reloading of BAM data (via the bar) if the start and end points hadn't actually changed after a user-drag. ------------------------------------------------------------------------ r403 | imilne | 2010-02-23 13:23:30 +0000 (Tue, 23 Feb 2010) | 2 lines - NEW: Added options to the Preferences Dialog to deal with caching and BAM window sizes. - NEW: Added a right-click menu to the bambam bar for skipping back to the previous ghost, and adjusting the window size. ------------------------------------------------------------------------ r402 | gsteph | 2010-02-23 11:47:58 +0000 (Tue, 23 Feb 2010) | 2 lines - NEW: Searching by read name has been enabled for indexed BAM reading. - NEW: A FeaturesList class has been introduced to centralise the checking for duplicate features in one place and ensuring it only happens when features are being added. ------------------------------------------------------------------------ r401 | imilne | 2010-02-22 15:00:09 +0000 (Mon, 22 Feb 2010) | 3 lines - NEW: Added the "BamBam Bar" for quick navigation around bam assemblies. - BUG: Fixed a rare (but critical) bug in the Progress Dialog that attempted to check the state of the job when it was null. - BUG: The Jump To Dialog was out by 1bp when checking valid padded positions. ------------------------------------------------------------------------ r400 | imilne | 2010-02-20 14:56:15 +0000 (Sat, 20 Feb 2010) | 1 line - NEW: Dramatically improved the speed of assembly detection by making a precursor guess of which reader to try an assembly with based on its file extension. If that fails, the others are then tried in order just as they currently are. ------------------------------------------------------------------------ r399 | imilne | 2010-02-19 15:16:11 +0000 (Fri, 19 Feb 2010) | 1 line - NEW: Added more information to the DisplayDataCalculator progress dialog (specifically for loading BAM). ------------------------------------------------------------------------ r398 | imilne | 2010-02-19 14:37:06 +0000 (Fri, 19 Feb 2010) | 2 lines - NEW: Added exception handling for when accessing BAM files goes wrong. - CHG: Modified all of the error messages to point the user at the output.log file for further details. ------------------------------------------------------------------------ r397 | imilne | 2010-02-19 11:45:59 +0000 (Fri, 19 Feb 2010) | 1 line - NEW: Added the license information for samtools. ------------------------------------------------------------------------ r396 | imilne | 2010-02-19 11:38:01 +0000 (Fri, 19 Feb 2010) | 2 lines - CHG: Modified the find read start/end code to work with BAM assemblies. - CHG: Modified the Features Panel to work with BAM assemblies. ------------------------------------------------------------------------ r395 | imilne | 2010-02-19 10:56:18 +0000 (Fri, 19 Feb 2010) | 2 lines - NEW: Page left/right functionality is now working properly with BAM. - CHG: Modified the moveTo code to load BAM blocks so that we always have an overlapping region of 1/5 of the data (either to the left or to the right, depending on the direction of the move). ------------------------------------------------------------------------ r394 | imilne | 2010-02-19 09:30:21 +0000 (Fri, 19 Feb 2010) | 2 lines - NEW: The JumpTo dialog (and column highlighting) is now working properly with the new visual block code and all assembly types. - BUG: BAM assemblies didn't have their file name in the title bar. ------------------------------------------------------------------------ r393 | imilne | 2010-02-18 15:35:06 +0000 (Thu, 18 Feb 2010) | 1 line - BUG: Threaded off the calls to determine assembly type in the Open Assembly dialog to avoid the interface hanging while slow calls to remote http addresses are parsed. ------------------------------------------------------------------------ r392 | imilne | 2010-02-18 14:03:17 +0000 (Thu, 18 Feb 2010) | 1 line - NEW: The canvas-area navigation buttons will now turn green when the edge of the visual region has been reached, but more data is still available if the view was jumped right or left (for BAM). ------------------------------------------------------------------------ r391 | imilne | 2010-02-18 12:14:27 +0000 (Thu, 18 Feb 2010) | 1 line - NEW: BAM assemblies now have the data block cached to disk rather than held in memory. ------------------------------------------------------------------------ r390 | imilne | 2010-02-16 16:03:07 +0000 (Tue, 16 Feb 2010) | 3 lines - NEW: BAM detection for indexed files is now working in the Open dialog. - NEW: Skipping the reference file is not allowed for BAM files (popup error in Open dialog, or Exception with drag n drop). - CHG: Various bits of tidying up to the BAM reading code. ------------------------------------------------------------------------ r389 | gsteph | 2010-02-16 14:56:44 +0000 (Tue, 16 Feb 2010) | 1 line - CHG: Fixes for the coverage printer required by code changes for indexed BAM support. Note: coverage printer is not available for indexed BAM assemblies and displays an error message to the user. ------------------------------------------------------------------------ r388 | imilne | 2010-02-16 12:05:55 +0000 (Tue, 16 Feb 2010) | 3 lines - CHG: Moved all the BAIFileReader code into BamFileReader. It is now the only BAM file reader, and will only read from indexed BAM files. - CHG: Tidied up some of the Assembly class's methods (no more isBam(), etc). - BUG: Added some additional checks to the ACE reading code to throw errors when the expected number of base quality scores does not match the consensus sequence's length. ------------------------------------------------------------------------ r387 | imilne | 2010-02-16 11:41:19 +0000 (Tue, 16 Feb 2010) | 1 line - NEW: The scale values for all canvases should now be working. ------------------------------------------------------------------------ r386 | gsteph | 2010-02-16 09:42:06 +0000 (Tue, 16 Feb 2010) | 1 line - CHG: Mismatch percentage only counts read bases under the consensus. ------------------------------------------------------------------------ r385 | gsteph | 2010-02-16 09:41:39 +0000 (Tue, 16 Feb 2010) | 1 line - CHG: Mismatch percentage only counts read bases under the consensus. ------------------------------------------------------------------------ r384 | imilne | 2010-02-15 16:13:37 +0000 (Mon, 15 Feb 2010) | 2 lines - CHG: Lots of changes to offset code to swap positive/negative values, due to having contig return +ve getVisualStart() (which simply makes the code easier to work with in the long run). - NEW: Hopefully got coverage calculations working for all cases (normal and BAM). ------------------------------------------------------------------------ r383 | imilne | 2010-02-15 14:53:06 +0000 (Mon, 15 Feb 2010) | 1 line - CHG: Contig has now changed to contain the concept of visual start/end which is different from data start/end (when using BAM). ------------------------------------------------------------------------ r382 | gsteph | 2010-02-12 16:11:06 +0000 (Fri, 12 Feb 2010) | 1 line - NEW: Friday night commit for sake of backup. ------------------------------------------------------------------------ r381 | gsteph | 2010-02-12 13:36:50 +0000 (Fri, 12 Feb 2010) | 1 line - NEW: More work on BAM handling. ------------------------------------------------------------------------ r380 | imilne | 2010-02-11 14:52:10 +0000 (Thu, 11 Feb 2010) | 3 lines - NEW: Updated sam.jar to 1.13 - NEW: The Bam Reader now contains some preliminary code for loading data blocks. - NEW: The setContig method for data display will attempt to query-retrieve the appropriate bam data. ------------------------------------------------------------------------ r379 | imilne | 2010-02-10 09:17:39 +0000 (Wed, 10 Feb 2010) | 1 line - NEW: Refactored the code to remove the need for the IAssemblyReader interface. BAIFileReader now just extends from TrackableReader, even though it doesn't do file tracking. ------------------------------------------------------------------------ r378 | gsteph | 2010-02-10 09:07:17 +0000 (Wed, 10 Feb 2010) | 1 line - NEW: Started work on opening a BAM file. ------------------------------------------------------------------------ r377 | imilne | 2010-02-09 15:52:37 +0000 (Tue, 09 Feb 2010) | 2 lines - NEW: Deleted the FAI reader (all its code is now just part of the BAIReader). - NEW: BaiFileReader now tracks its fasta/bai download progress. ------------------------------------------------------------------------ r376 | gsteph | 2010-02-09 15:16:47 +0000 (Tue, 09 Feb 2010) | 1 line - NEW: Added method to download a BAI file if required for streaming a bam file over a url connection. ------------------------------------------------------------------------ r375 | imilne | 2010-02-09 14:15:43 +0000 (Tue, 09 Feb 2010) | 1 line - NEW: Started working on indexed BAM support. ------------------------------------------------------------------------ r374 | gsteph | 2010-02-08 15:27:47 +0000 (Mon, 08 Feb 2010) | 1 line - BUG: Command line argument parsing was wrong due to the new jnlp version parsing. ------------------------------------------------------------------------ r373 | imilne | 2010-02-08 14:09:48 +0000 (Mon, 08 Feb 2010) | 1 line - NEW: The page left/right arrows are no longer painted on the display if the left/right edges have been reached. ------------------------------------------------------------------------ r372 | imilne | 2010-02-08 10:02:33 +0000 (Mon, 08 Feb 2010) | 1 line - NEW: Tagged copy of 1.10.02.08 (public). ------------------------------------------------------------------------ r371 | imilne | 2010-02-08 10:02:05 +0000 (Mon, 08 Feb 2010) | 2 lines - NEW: Updated the web pages for a new release. - BUG: Fixed a build.xml file that was stopping Tablet from running with java -jar (and also broke the installers). ------------------------------------------------------------------------ r370 | gsteph | 2010-02-05 16:04:46 +0000 (Fri, 05 Feb 2010) | 2 lines - NEW: Mismatch Percentages are now calculated for contigs and displayed in the contigs browser. They also appear in tooltips and are filterable. - NEW: CIGAR information is now included when a read is copied to the clipboard. ------------------------------------------------------------------------ r369 | imilne | 2010-02-05 15:58:00 +0000 (Fri, 05 Feb 2010) | 1 line - CHG: Changed the code to use Assembly.hasCigar() for determining CIGAR status. Assembly.isBam() still exists (and is no longer set by the sam reader) but isn't used - yet. ------------------------------------------------------------------------ r368 | imilne | 2010-02-05 15:43:27 +0000 (Fri, 05 Feb 2010) | 2 lines - CHG: Removed the name option for sam/bam CIGAR insertion features. - NEW: The list of CIGAR features is now sorted by base position. ------------------------------------------------------------------------ r367 | imilne | 2010-02-05 15:20:42 +0000 (Fri, 05 Feb 2010) | 2 lines - NEW: Swapped the order in which data is written to the reads cache, so that the raw DNA data comes first (and can be read out quickly if only the DNA is needed, eg for display). - CHG: Updated the help files to cover sam/bam support. ------------------------------------------------------------------------ r366 | imilne | 2010-02-05 12:04:09 +0000 (Fri, 05 Feb 2010) | 2 lines - NEW: The Open Assembly dialog now supports detection of BAM files. - NEW: Updated the Browse dialogs for opening files to list sam and bam extensions too. ------------------------------------------------------------------------ r365 | imilne | 2010-02-05 11:40:26 +0000 (Fri, 05 Feb 2010) | 1 line - NEW: The memory used up by PackSet and StackSet objects after a contig is removed from display is now cleared (ie, no more than 1 PackSet/StackSet instance will exist at any time). ------------------------------------------------------------------------ r364 | imilne | 2010-02-05 09:59:43 +0000 (Fri, 05 Feb 2010) | 1 line - NEW: The Padded->Unpadded mappings array is now cached. ------------------------------------------------------------------------ r363 | imilne | 2010-02-05 09:19:05 +0000 (Fri, 05 Feb 2010) | 1 line - BUG: Fixed a problem with non-BAM assembly data failing to load because it doesn't have CIGAR entries. ------------------------------------------------------------------------ r362 | imilne | 2010-02-05 09:01:40 +0000 (Fri, 05 Feb 2010) | 1 line - CHG: Renamed the ReadFileCacheIndex class to ArrayLongFileCache and made it behave the same as the other int[] caches, but for long[] obviously. ------------------------------------------------------------------------ r361 | gsteph | 2010-02-05 09:00:07 +0000 (Fri, 05 Feb 2010) | 1 line - NEW: Inclusion of CigarFeature for processing Cigar insertions. ------------------------------------------------------------------------ r360 | gsteph | 2010-02-04 16:53:08 +0000 (Thu, 04 Feb 2010) | 3 lines - NEW: Features are created out of Cigar Insertion operations. - NEW: Insertion counts are displayed in the tooltip for feautres in the features panel. - NEW: Cigar strings are shown in read tooltips for both SAM and BAM files. ------------------------------------------------------------------------ r359 | imilne | 2010-02-04 16:07:33 +0000 (Thu, 04 Feb 2010) | 3 lines - NEW: Unpadded->Padded mapping arrays are now cached (if the consensus length is greater than 1Mbases). - NEW: Added a new set of interfaces and classes for dealing with cached int[] arrays. - CHG: Updated the DisplayData code to use the new cache rather than an actual int[] array. ------------------------------------------------------------------------ r358 | imilne | 2010-02-04 09:21:35 +0000 (Thu, 04 Feb 2010) | 2 lines - NEW: Added a memory-based implementation of the reads cache (enabled via the xml preferences for now). - BUG: Changed the file-deletion handling of the cache directory so that it will only delete files created by Tablet (in case someone pointed their cache at c:\). ------------------------------------------------------------------------ r357 | imilne | 2010-02-03 16:06:38 +0000 (Wed, 03 Feb 2010) | 4 lines - NEW: Added a new super-class (TabletCache.java) that provides basic cache functionality. - CHG: FileCache (and its index) are now called ReadFileCache and extend from TabletCache. - CHG: Updated scri-commons.jar with the new version that correctly handles EOF in rnd file reads (and longs). - NEW: Updated the build, jnlp, and batch files to contain links to the samtools jar file. ------------------------------------------------------------------------ r356 | gsteph | 2010-02-03 16:05:00 +0000 (Wed, 03 Feb 2010) | 1 line - NEW: Fixed bugs in CigarParserTest and CigarParser. ------------------------------------------------------------------------ r355 | gsteph | 2010-02-03 13:55:14 +0000 (Wed, 03 Feb 2010) | 2 lines - NEW: Cigar parsing now deletes inserts from the reads. ------------------------------------------------------------------------ r354 | imilne | 2010-02-01 08:33:20 +0000 (Mon, 01 Feb 2010) | 1 line - NEW: Added support for Java Web Start launches of Tablet. ------------------------------------------------------------------------ r353 | imilne | 2010-01-28 14:30:51 +0000 (Thu, 28 Jan 2010) | 1 line - NEW: Tagged copy of 1.10.01.28 (public). ------------------------------------------------------------------------ r352 | imilne | 2010-01-28 14:30:11 +0000 (Thu, 28 Jan 2010) | 1 line - NEW: Updated the web files for a new release. ------------------------------------------------------------------------ r351 | imilne | 2010-01-28 13:44:18 +0000 (Thu, 28 Jan 2010) | 1 line - CHG: Tidied up and reformatted the right-click menu options for the Contigs Table. ------------------------------------------------------------------------ r350 | imilne | 2010-01-28 13:33:13 +0000 (Thu, 28 Jan 2010) | 1 line - NEW: Added an option to toggle on or off the use of regular expressions in searches. ------------------------------------------------------------------------ r349 | imilne | 2010-01-28 11:12:35 +0000 (Thu, 28 Jan 2010) | 1 line - NEW: The names of features (if available) are now parsed in GFF3 files. ------------------------------------------------------------------------ r348 | imilne | 2010-01-28 10:13:21 +0000 (Thu, 28 Jan 2010) | 4 lines - NEW: Features are merged on subsequent loads of GFF files (ie, no duplicates will be read). - NEW: The tooltip for features now displays their name. - BUG: The unpadded length of the consensus sequence wasn't being stored. - NEW: Features outside the acceptable bounds (padded or unpadded) for the current contig are now highlighted in red in the table. ------------------------------------------------------------------------ r347 | imilne | 2010-01-26 13:16:04 +0000 (Tue, 26 Jan 2010) | 1 line - NEW: Updated (and tidied) the Feature class so that it can support the GFF3 name tag (which isn't parsed yet). ------------------------------------------------------------------------ r346 | gsteph | 2010-01-26 11:49:30 +0000 (Tue, 26 Jan 2010) | 1 line - NEW: Features out of the scope of the sequence are highlighted in red. ------------------------------------------------------------------------ r345 | imilne | 2010-01-26 10:18:35 +0000 (Tue, 26 Jan 2010) | 1 line - CHG: Removed support for parsing consensus/read tags in ACE files. GFF3 files will now be on the only supported way of importing feature details into Tablet. ------------------------------------------------------------------------ r344 | imilne | 2010-01-19 11:08:57 +0000 (Tue, 19 Jan 2010) | 1 line - NEW: Added MB/s (or KB/s) transfer rate tracking to the assembly importing code. ------------------------------------------------------------------------ r343 | imilne | 2010-01-18 15:13:22 +0000 (Mon, 18 Jan 2010) | 2 lines - BUG: Any http:// links were being wrongly parsed on the front page. - BUG: ReferenceFileReader.java didn't like the gzip stream code (zip parsing was reading too many bytes from the stream, even when it wasn't a gzip file). ------------------------------------------------------------------------ r342 | imilne | 2010-01-18 13:22:31 +0000 (Mon, 18 Jan 2010) | 2 lines - NEW: Updated the license/help files for 2010. - NEW: Tablet now supports reading from gzip compressed streams (single file only). ------------------------------------------------------------------------ r341 | imilne | 2010-01-18 11:27:14 +0000 (Mon, 18 Jan 2010) | 1 line - NEW: Tablet can now read from http input streams in addition to file streams. ------------------------------------------------------------------------ r340 | imilne | 2010-01-15 13:03:39 +0000 (Fri, 15 Jan 2010) | 1 line - NEW: Added a right-click "save reads summary" option to the contigs table. ------------------------------------------------------------------------ r339 | gsteph | 2009-12-16 11:34:16 +0000 (Wed, 16 Dec 2009) | 3 lines - NEW: Creation of the Ruler Bar for aiding with subsetting. - NEW: Ctrl click subset selection from overview included. - BUG: Fixed issue with packset and stackset for large datasets in the subset version of Tablet. ------------------------------------------------------------------------ r338 | imilne | 2009-12-16 11:17:53 +0000 (Wed, 16 Dec 2009) | 3 lines - NEW: Added a (.xml preferences file only) option to get the CoveragePrinter to only print coverage values for bases that ARE NOT a pad. - BUG: The CoveragePrinter could crash if bad swing timing resulted in a getMessage() call before the contig reference had been initialized. - CHG: Updated all references to the email address to point to tablet@ rather than bioinf@. ------------------------------------------------------------------------ r337 | imilne | 2009-12-15 09:38:38 +0000 (Tue, 15 Dec 2009) | 1 line - NEW: Added in a missing icon needed by the previous commit. ------------------------------------------------------------------------ r336 | imilne | 2009-12-14 16:39:46 +0000 (Mon, 14 Dec 2009) | 1 line - NEW: Added an option to copy the contigs table's data to the clipboard. ------------------------------------------------------------------------ r335 | imilne | 2009-12-14 15:27:46 +0000 (Mon, 14 Dec 2009) | 1 line - NEW: Tagged copy of 1.09.12.14 (public). ------------------------------------------------------------------------ r334 | imilne | 2009-12-14 15:27:22 +0000 (Mon, 14 Dec 2009) | 1 line - NEW: Updated the usual web pages ready for a new release. ------------------------------------------------------------------------ r333 | gsteph | 2009-12-14 15:11:15 +0000 (Mon, 14 Dec 2009) | 1 line - CHG: Changes to the error handling of the file parsing code, including the removal of the ImportHandler class. ------------------------------------------------------------------------ r332 | imilne | 2009-12-14 11:51:28 +0000 (Mon, 14 Dec 2009) | 2 lines - NEW: The Export Image option on the Application Menu is now part of a sub menu within the original button (now renamed just "Export"). - NEW: Added the Export Coverage feature as a proper feature, accessible from the Application Menu. ------------------------------------------------------------------------ r331 | gsteph | 2009-12-14 11:29:53 +0000 (Mon, 14 Dec 2009) | 1 line - BUG: Fixed issue where the warning about closing the application could show twice when the ApplicationMenu's Exit Tablet button was used. ------------------------------------------------------------------------ r330 | gsteph | 2009-12-14 10:18:59 +0000 (Mon, 14 Dec 2009) | 1 line - BUG: Fixed overlays not being removed properly. ------------------------------------------------------------------------ r329 | imilne | 2009-12-11 16:07:15 +0000 (Fri, 11 Dec 2009) | 1 line - NEW: Added a cancel button to the progress dialog (that animates its appearance on Windows and Linux). On OS X it is simply always-on because the animation flickers due to OS X's rubbish Java support. ------------------------------------------------------------------------ r328 | gsteph | 2009-12-11 14:28:44 +0000 (Fri, 11 Dec 2009) | 1 line - BUG: Fixed issed with name overlayer not taking into account the consensus offset. ------------------------------------------------------------------------ r327 | imilne | 2009-12-11 14:18:38 +0000 (Fri, 11 Dec 2009) | 1 line - NEW: Added a (hidden) feature to export coverage information across all contigs (for just the contig itself, not any offset regions). ------------------------------------------------------------------------ r326 | gsteph | 2009-12-11 12:02:47 +0000 (Fri, 11 Dec 2009) | 1 line - CHG: Removed println. ------------------------------------------------------------------------ r325 | gsteph | 2009-12-11 12:00:57 +0000 (Fri, 11 Dec 2009) | 1 line - BUG: Fixed issue with contig being reset when the ContigsPanel is sorted. ------------------------------------------------------------------------ r324 | imilne | 2009-12-11 09:53:58 +0000 (Fri, 11 Dec 2009) | 1 line - BUG: Fixed an ACE parsing bug that was tripping up Tablet when badly formatted CT (contig) tags were encountered. ------------------------------------------------------------------------ r323 | imilne | 2009-12-08 10:25:19 +0000 (Tue, 08 Dec 2009) | 1 line - NEW: Tagged copy of 1.09.12.08 (public). ------------------------------------------------------------------------ r322 | imilne | 2009-12-08 10:24:37 +0000 (Tue, 08 Dec 2009) | 2 lines - NEW: Updated the usual web pages ready for a new release. ------------------------------------------------------------------------ r321 | imilne | 2009-12-08 10:13:41 +0000 (Tue, 08 Dec 2009) | 2 lines - CHG: Upped the default timeout for all tooltips to 8 seconds. - NEW: Added some additional coverage statistics, that are displayed are tooltips over the coverage and overview (coverage only) panels. ------------------------------------------------------------------------ r320 | gsteph | 2009-12-07 16:47:55 +0000 (Mon, 07 Dec 2009) | 3 lines - NEW: Changes to allow for subset coverage overviews. - NEW: ReadHighlighting updated to deal with subsets. - BUG: A few fixes to the ScaleCanvas code. ------------------------------------------------------------------------ r319 | gsteph | 2009-12-07 11:55:19 +0000 (Mon, 07 Dec 2009) | 2 lines - CHG: Changed the way NameOverlayer behaves so it is no longer looping waiting to be faded out while it is displaying. - NEW: Added shortcut information to the tooltip for the overlay names button. ------------------------------------------------------------------------ r318 | imilne | 2009-12-07 10:38:33 +0000 (Mon, 07 Dec 2009) | 2 lines - BUG: The cache folder location could still be inaccessible for some users on a multi-user system if a previous user had locked down the root scri-tablet folder. - NEW: Tablet now performs a check of the cache folder location on every startup (or after modification), and warns the user if it can't be written to. ------------------------------------------------------------------------ r317 | gsteph | 2009-12-07 10:26:35 +0000 (Mon, 07 Dec 2009) | 1 line - NEW: Inclusion of NameOverlayer.java for the overlaying of names on the display. ------------------------------------------------------------------------ r316 | gsteph | 2009-12-07 10:16:38 +0000 (Mon, 07 Dec 2009) | 1 line - NEW: Added the ability to overlay the names of reads on the display. ------------------------------------------------------------------------ r315 | imilne | 2009-12-07 09:42:41 +0000 (Mon, 07 Dec 2009) | 1 line - NEW: Split the About Tablet dialog into two tabs - the main one, plus one for the group's avatar images. ------------------------------------------------------------------------ r314 | imilne | 2009-12-04 15:26:53 +0000 (Fri, 04 Dec 2009) | 1 line - CHG: Updated some of the help files. ------------------------------------------------------------------------ r313 | imilne | 2009-12-04 14:16:17 +0000 (Fri, 04 Dec 2009) | 4 lines - NEW: Added a link to Java regex help from the Find Reads panel. - BUG: Fixed a bug that was causing maq files (with contigs named numerically) to be detected as sam files. - NEW: Added a panel to the front page to link out to publication/citation information. - NEW: Added some new files to the web site for holding publication information. ------------------------------------------------------------------------ r312 | imilne | 2009-12-03 09:59:51 +0000 (Thu, 03 Dec 2009) | 7 lines - CHG: i18n text wasn't available for the control panel tabs' tooltips. - BUG: Selecting features still set the title text on the features tab. - CHG: Updated all the code to use a single shared NumberFormat object (in TabletUtils). - NEW: Tooltips are now displayed when hovering the mouse over the tables. - NEW: Unpadded->Padded and Padded->Unpadded data is shown (as a tooltip) for the features. - NEW: The Find Read results table is now sortable by its column headers. - BUG: The jump to position movement from the Find Reads results was out by 1 base (although the highlight itself was correct). ------------------------------------------------------------------------ r311 | gsteph | 2009-12-02 15:18:45 +0000 (Wed, 02 Dec 2009) | 1 line - NEW: Updated to port subview changes to the Coverage class. ------------------------------------------------------------------------ r310 | gsteph | 2009-12-02 14:25:20 +0000 (Wed, 02 Dec 2009) | 1 line - NEW: New packing code gives real performance increase to creating packsets. ------------------------------------------------------------------------ r309 | gsteph | 2009-12-02 12:17:25 +0000 (Wed, 02 Dec 2009) | 1 line - NEW: Changes made to ensure the ScaleCanvas, ProteinCanvas, ConsensusCanvas to allow subviewing. These changes mostly pertain to correct display of the scale bar. ------------------------------------------------------------------------ r308 | imilne | 2009-12-01 08:59:24 +0000 (Tue, 01 Dec 2009) | 1 line - BUG: The features tab still had its text set when a new contig was selected. ------------------------------------------------------------------------ r307 | gsteph | 2009-11-27 15:50:52 +0000 (Fri, 27 Nov 2009) | 1 line - NEW: Tablet's ReadCanvas can now display a subset of the data. ------------------------------------------------------------------------ r306 | imilne | 2009-11-27 13:34:36 +0000 (Fri, 27 Nov 2009) | 1 line - NEW: Created a new branch to hold code while experimenting with sub-setting the data shown in the views. ------------------------------------------------------------------------ r305 | gsteph | 2009-11-27 13:28:39 +0000 (Fri, 27 Nov 2009) | 1 line - CHG: Removed the NOTUSED byte from Sequence and changed a number of other classes to deal with this. ------------------------------------------------------------------------ r304 | imilne | 2009-11-27 13:26:56 +0000 (Fri, 27 Nov 2009) | 1 line - NEW: Tagged copy of 0.09.11.25 (public). ------------------------------------------------------------------------ r303 | imilne | 2009-11-25 09:42:22 +0000 (Wed, 25 Nov 2009) | 2 lines - NEW: Updated the find code to always select the chosen contig, even if the main list had been filtered so that it was hidden. - NEW: Various updates to the web page for a new release. ------------------------------------------------------------------------ r302 | gsteph | 2009-11-23 16:34:43 +0000 (Mon, 23 Nov 2009) | 3 lines - CHG: Altered the display of search table when no data is available. - CHG: Tweaked the disabling of the FeaturesPanel. - NEW: Updated the help to include images which display the nextFeature, prevFeature buttons. ------------------------------------------------------------------------ r301 | gsteph | 2009-11-23 14:22:05 +0000 (Mon, 23 Nov 2009) | 2 lines - NEW: Search for read feature added. - CHG: Revamp of the Contig/Features browser, this is now icon based and includes the search tab as well. ------------------------------------------------------------------------ r300 | imilne | 2009-11-09 13:10:35 +0000 (Mon, 09 Nov 2009) | 3 lines - NEW: Enhanced the progress dialog with the ability to display custom messages as the sub task(s) run. - NEW: Added progress messages (contig and read count) to all file readers. - NEW: Added progress messages to the tasks run during contig display (DisplayDataCalculator and PackSetCreator). ------------------------------------------------------------------------ r299 | imilne | 2009-11-06 20:18:17 +0000 (Fri, 06 Nov 2009) | 1 line - NEW: Tagged copy of 0.09.11.06 (public). ------------------------------------------------------------------------ r298 | imilne | 2009-11-06 14:57:19 +0000 (Fri, 06 Nov 2009) | 3 lines - NEW: Added experimental support for reading from SAM files. - NEW: Added a new section to the website containing a guide to converting between assembly formats. - NEW: Updates to the usual web pages ready for a new release. ------------------------------------------------------------------------ r297 | gsteph | 2009-11-06 13:59:20 +0000 (Fri, 06 Nov 2009) | 1 line - BUG: Fixed issue where read data was not being copied to the clipboard due to changes in the way Tablet stores read data. ------------------------------------------------------------------------ r296 | gsteph | 2009-11-06 13:51:48 +0000 (Fri, 06 Nov 2009) | 1 line - NEW: Parser for Cigar Strings used as part of the SAM format. ------------------------------------------------------------------------ r295 | gsteph | 2009-11-05 10:26:14 +0000 (Thu, 05 Nov 2009) | 1 line - CHG: MaqToAce converter now produces Ace files which Consed can consume. ------------------------------------------------------------------------ r294 | imilne | 2009-11-04 09:39:30 +0000 (Wed, 04 Nov 2009) | 1 line - NEW: Tagged copy of 0.09.11.04 (public). ------------------------------------------------------------------------ r293 | imilne | 2009-11-04 09:35:42 +0000 (Wed, 04 Nov 2009) | 1 line - NEW: Updated the usual web pages ready for a new release. ------------------------------------------------------------------------ r292 | imilne | 2009-11-04 09:31:31 +0000 (Wed, 04 Nov 2009) | 2 lines - NEW: Extended the list of recently access documents on the front page to ten elements. - NEW: Added tooltips to the recently accessed list in the Application Menu (but they don't work very well due to the RichToolTip API enforcing a fixed width). ------------------------------------------------------------------------ r291 | imilne | 2009-11-04 08:42:23 +0000 (Wed, 04 Nov 2009) | 2 lines - NEW: The list of recently accessed files (on the front page) now contains tooltips showing the full path, and icons for single/multiple documents. - BUG: The version of Tablet showed up as x.xx.xx.xx if started from a directory other than its installed directory. ------------------------------------------------------------------------ r290 | imilne | 2009-11-04 08:40:07 +0000 (Wed, 04 Nov 2009) | 1 line - NEW: Tagged copy of 0.09.10.30 (public). ------------------------------------------------------------------------ r289 | imilne | 2009-11-02 12:11:35 +0000 (Mon, 02 Nov 2009) | 1 line - BUG: Fixed some GUI alignment layout issues when running on Linux. ------------------------------------------------------------------------ r288 | imilne | 2009-10-30 15:07:07 +0000 (Fri, 30 Oct 2009) | 2 lines - CHG: Disabled the keyboard shortcuts for the next/prev feature buttons until we can sort out the lag problems with holding the keys down. - CHG: Updated the web files ready for a new release. ------------------------------------------------------------------------ r287 | gsteph | 2009-10-30 14:56:27 +0000 (Fri, 30 Oct 2009) | 3 lines - BUG: Fixed issue with moving to previous and next features when the bases are unpadded. - CHG: The Features tab now displays itself when prevFeature or nextFeature are pressed. - NEW: The Features tab now autoscrolls when the prevFeature and nextFeautre buttons are being used. ------------------------------------------------------------------------ r286 | imilne | 2009-10-30 10:10:37 +0000 (Fri, 30 Oct 2009) | 1 line - NEW: Merged in the changes from the cache branch. ------------------------------------------------------------------------ r285 | gsteph | 2009-10-30 09:56:11 +0000 (Fri, 30 Oct 2009) | 1 line - CHG: General code tidy up in various classes. ------------------------------------------------------------------------ r284 | imilne | 2009-10-30 09:54:32 +0000 (Fri, 30 Oct 2009) | 1 line - CHG: General code tidy-up and removal of redundant classes. ------------------------------------------------------------------------ r283 | imilne | 2009-10-30 09:24:57 +0000 (Fri, 30 Oct 2009) | 3 lines - NEW: Added a hack to improve rendering performance while the overview is still generating, as the render code and the overview code will be fighting for cache access. The render code now gets priority (the overview code pauses if its detects the main canvas rendering). - NEW: Added an option to the Preferences dialog to allow the user to change the location of the cache folder. - NEW: Updated the help to include a topic for the above. ------------------------------------------------------------------------ r282 | imilne | 2009-10-29 15:27:19 +0000 (Thu, 29 Oct 2009) | 3 lines - NEW: Added more information on importing assemblies to the help documentation. - NEW: Added information on the new warnings tab in the Preferences dialog. - CHG: Fixed various spelling errors throughout the help. ------------------------------------------------------------------------ r281 | imilne | 2009-10-29 13:09:51 +0000 (Thu, 29 Oct 2009) | 1 line - NEW: Added a new panel to the preferences dialog to toggle the on/off of the various popup warnings that Tablet can generate (and the user can disable). ------------------------------------------------------------------------ r280 | imilne | 2009-10-29 11:45:56 +0000 (Thu, 29 Oct 2009) | 2 lines - NEW: Fixed the HistoryComboBox resize problems with the import dialog (setPrototypeDisplayValue()). - CHG: Changed the dialog to separate the notes from the main input controls. ------------------------------------------------------------------------ r279 | imilne | 2009-10-29 09:58:23 +0000 (Thu, 29 Oct 2009) | 2 lines - BUG: SOAP/MAQ imports weren't setting the project name correctly if the reference file was excluded. - NEW: Tablet now (optionally) warns about not including a reference file. ------------------------------------------------------------------------ r278 | imilne | 2009-10-29 09:18:46 +0000 (Thu, 29 Oct 2009) | 3 lines - CHG: The import assembly dialog has been completely redesigned, and now just asks for the primary assembly file and an accompanying reference file (if needed). - NEW: File type detection happens as soon as a file is selected in the import dialog. - NEW: Tablet no longer *needs* to be provided with reference/consensus data for SOAP and MAQ. If the files are skipped, the reads can still be loaded and viewed, but obviously there will be no consensus visualization. ------------------------------------------------------------------------ r277 | gsteph | 2009-10-28 09:35:39 +0000 (Wed, 28 Oct 2009) | 1 line - NEW: PrevFeature and NextFeature buttons added to iterate over features. ------------------------------------------------------------------------ r276 | gsteph | 2009-10-27 16:20:02 +0000 (Tue, 27 Oct 2009) | 2 lines - CHG: Updated the AFG reader to support the new disk cache. ------------------------------------------------------------------------ r275 | mbayer | 2009-10-27 11:55:46 +0000 (Tue, 27 Oct 2009) | 1 line - NEW: Have added information on loading MAQ and SOAP output into the help text. ------------------------------------------------------------------------ r274 | imilne | 2009-10-27 11:15:18 +0000 (Tue, 27 Oct 2009) | 3 lines - NEW: Reference/consensus information for MAQ and SOAP can now be provided by either FASTA or FASTQ files, depending on what the user has available. - NEW: Added a new class (ReferenceFileReader.java) to handle fasta/fastq file reading that is independent of the main assembly readers. - CHG: Removed the checks for ASCII (Tablet will now always assume it is). ------------------------------------------------------------------------ r273 | imilne | 2009-10-25 16:18:25 +0000 (Sun, 25 Oct 2009) | 1 line - CHG: Removed the "current directory" flag set by the installer, so that "tablet " launches will find the file if run from the file's directory (and Tablet is on the path). ------------------------------------------------------------------------ r272 | imilne | 2009-10-22 15:36:47 +0100 (Thu, 22 Oct 2009) | 1 line - NEW: Random-access reading from the file cache is now buffered. ------------------------------------------------------------------------ r271 | imilne | 2009-10-22 08:56:15 +0100 (Thu, 22 Oct 2009) | 1 line - NEW: Removed the JRE 1.5 target requirement from the build file. ------------------------------------------------------------------------ r270 | imilne | 2009-10-21 15:35:36 +0100 (Wed, 21 Oct 2009) | 2 lines - NEW: Access to the disk cache is now synchronised. - CHG: Reverted ReadsCanvas back to its previous (non data-sync aware state), as with the cache itself synchronised, performance is better with the original code. ------------------------------------------------------------------------ r269 | imilne | 2009-10-20 15:14:20 +0100 (Tue, 20 Oct 2009) | 2 lines - NEW: SOAP and MAQ import are working again after being converted to use the enhanced disk cache (AFG still to be done). - CHG: Base position comparisons are now done per read as and when they are found during load (it has to happen before save-to-cache). Loading is now a single operation, with a single progress bar track. ------------------------------------------------------------------------ r268 | imilne | 2009-10-20 15:02:37 +0100 (Tue, 20 Oct 2009) | 1 line - BUG: The multi-threaded rendering code was painting the wrong lines due to incorrect starting positions being passed to each sub thread. ------------------------------------------------------------------------ r267 | imilne | 2009-10-20 14:19:42 +0100 (Tue, 20 Oct 2009) | 1 line - CHG: Included the (missing) link to the sample data page on the web site. ------------------------------------------------------------------------ r266 | imilne | 2009-10-20 11:57:44 +0100 (Tue, 20 Oct 2009) | 1 line - NEW: The main rendering code is now multi-core capable again. The data is fetched in a single thread, before rendering itself is split over the cores. ------------------------------------------------------------------------ r265 | imilne | 2009-10-20 09:12:50 +0100 (Tue, 20 Oct 2009) | 3 lines - NEW: DNA base information (for all reads) is now kept in the disk cache. - CHG: All file parsers (apart from ACE) have been disabled. - NEW: Render code is single threaded again, to avoid disk access clashes. ------------------------------------------------------------------------ r264 | imilne | 2009-10-19 14:51:54 +0100 (Mon, 19 Oct 2009) | 1 line - CHG: Fixed a typo on the screenshots web page. ------------------------------------------------------------------------ r263 | imilne | 2009-10-19 10:11:04 +0100 (Mon, 19 Oct 2009) | 1 line - CHG: Set the splitter border to empty (which looks nicer). ------------------------------------------------------------------------ r262 | gsteph | 2009-10-02 16:52:32 +0100 (Fri, 02 Oct 2009) | 1 line - BUG: Fixed issue with maqtoace converter. ------------------------------------------------------------------------ r261 | imilne | 2009-10-02 15:44:50 +0100 (Fri, 02 Oct 2009) | 3 lines - NEW: Added some help for padded/unpadded features. - NEW: The installer now creates a subdir called utils and generates a MaqToAce executable there. - BUG: Fixed an installer bug with the link to Tablet Help (on Windows start menu). ------------------------------------------------------------------------ r260 | gsteph | 2009-10-02 14:26:19 +0100 (Fri, 02 Oct 2009) | 1 line - NEW: Added the MaqToAce conversion files and the new tablet.io.utils package. ------------------------------------------------------------------------ r259 | imilne | 2009-10-02 14:10:15 +0100 (Fri, 02 Oct 2009) | 1 line - NEW: Feature positions can now be tagged as either padded or unpadded. ------------------------------------------------------------------------ r258 | imilne | 2009-10-02 12:00:26 +0100 (Fri, 02 Oct 2009) | 1 line - CHG: Updated the installer to display a white background behind the SCRI image regardless of the window size. ------------------------------------------------------------------------ r257 | imilne | 2009-10-02 10:12:02 +0100 (Fri, 02 Oct 2009) | 1 line - CHG: Updated scri-commons.jar to the version with (spaces-in-labels) fix for HyperLinkLabel code. ------------------------------------------------------------------------ r256 | imilne | 2009-10-02 09:31:47 +0100 (Fri, 02 Oct 2009) | 1 line - NEW: Tagged copy of 0.09.10.02 (public). ------------------------------------------------------------------------ r255 | imilne | 2009-10-02 09:28:40 +0100 (Fri, 02 Oct 2009) | 1 line - BUG: Fixed a parsing error with fasta/fastq files. ------------------------------------------------------------------------ r254 | imilne | 2009-10-01 15:59:41 +0100 (Thu, 01 Oct 2009) | 1 line - NEW: Added an FAQ to the website (and linked to it from within Tablet itself). ------------------------------------------------------------------------ r253 | imilne | 2009-10-01 14:40:08 +0100 (Thu, 01 Oct 2009) | 1 line - NEW: Tagged copy of 0.09.10.01 (public). ------------------------------------------------------------------------ r252 | imilne | 2009-10-01 14:39:31 +0100 (Thu, 01 Oct 2009) | 5 lines - NEW: Made various improvements to the installer to try to fix issues with Linux compatibility. - CHG: Added a proper version of the SCRI logo to the installer. - NEW: Updated various web site files ready for releasing a new version. - NEW: Tablet no longer pushes the user to the "what's new" on first run after an update, as this functionality is now in the updater itself (user initiated too). - CHG: Disabled the previous change to override the Preferences API as it turned out install4j was using it. ------------------------------------------------------------------------ r251 | imilne | 2009-09-29 15:55:55 +0100 (Tue, 29 Sep 2009) | 1 line - NEW: Made the filtering of features by type case insensitive. ------------------------------------------------------------------------ r250 | gsteph | 2009-09-29 11:42:10 +0100 (Tue, 29 Sep 2009) | 1 line - NEW: Added ability to filter features by type. ------------------------------------------------------------------------ r249 | imilne | 2009-09-29 10:13:55 +0100 (Tue, 29 Sep 2009) | 1 line - NEW: Added prompts for confirming assembly close if the relevant option is selected or app-exit occurs. ------------------------------------------------------------------------ r248 | imilne | 2009-09-29 09:17:24 +0100 (Tue, 29 Sep 2009) | 1 line - NEW: Added a disabled implementation of java.util.prefs (via scri-commons) to clear up the various error messages that occur on Linux when the user doesn't have writeable access to the JRE directory (for .systemprefs access). ------------------------------------------------------------------------ r247 | imilne | 2009-09-20 14:38:36 +0100 (Sun, 20 Sep 2009) | 1 line - BUG: Fixed the problem with keyboard shortcuts not working for zooming in/out/resetting if using the numpad. ------------------------------------------------------------------------ r246 | imilne | 2009-09-20 14:16:17 +0100 (Sun, 20 Sep 2009) | 1 line - NEW: Server logging now includes detection of 32 or 64bit JRE. ------------------------------------------------------------------------ r245 | imilne | 2009-09-11 14:40:56 +0100 (Fri, 11 Sep 2009) | 1 line - NEW: Tagged copy of 0.09.09.11 (public). ------------------------------------------------------------------------ r244 | imilne | 2009-09-11 14:39:12 +0100 (Fri, 11 Sep 2009) | 1 line - NEW: Final changes to some web site files before releasing a new update (plus a new page for hosting sample data). ------------------------------------------------------------------------ r243 | imilne | 2009-09-11 14:14:52 +0100 (Fri, 11 Sep 2009) | 2 lines - NEW: Separate tablet.vmoptions files are now created for 32 and 64 bit versions. This required splitting the installer so that it uses two launchers, but only the relevant one is included in the final 32 or 64 .exe/.sh file. - NEW: Tablet now redirects to whats-new.shtml after a new version is installed (used to point to the svn log). ------------------------------------------------------------------------ r242 | imilne | 2009-09-10 14:46:40 +0100 (Thu, 10 Sep 2009) | 3 lines - NEW: Added in the files from the web site. - CHG: Updated some of the front-page help links. - NEW: The rating value (although not used yet) is sent as part of the server ping. ------------------------------------------------------------------------ r241 | gsteph | 2009-09-10 11:08:43 +0100 (Thu, 10 Sep 2009) | 1 line - CHG: Altered Pack and PackSetCreator to improve load times for large contigs. ------------------------------------------------------------------------ r240 | imilne | 2009-09-10 08:57:43 +0100 (Thu, 10 Sep 2009) | 1 line - NEW: Updated the protein translator to cope with sequences that start with runs of NNNN etc. ------------------------------------------------------------------------ r239 | imilne | 2009-09-09 15:57:19 +0100 (Wed, 09 Sep 2009) | 1 line - BUG: Read orientation was the wrong way around when copying data to the clipboard. ------------------------------------------------------------------------ r238 | gsteph | 2009-09-07 15:06:00 +0100 (Mon, 07 Sep 2009) | 1 line - NEW: Help Links have now been activated on the splash screen. ------------------------------------------------------------------------ r237 | imilne | 2009-09-07 15:03:43 +0100 (Mon, 07 Sep 2009) | 1 line - NEW: Enabled the Send Feedback link on the front page. ------------------------------------------------------------------------ r236 | imilne | 2009-09-07 14:39:00 +0100 (Mon, 07 Sep 2009) | 1 line - NEW: Enabled the functionality of the help buttons for the various dialog boxes (and the ribbon). ------------------------------------------------------------------------ r235 | imilne | 2009-09-07 14:27:29 +0100 (Mon, 07 Sep 2009) | 1 line - NEW: Added the link-to-help code in TabletUtils. ------------------------------------------------------------------------ r234 | gsteph | 2009-09-07 14:21:19 +0100 (Mon, 07 Sep 2009) | 1 line - BUG: Fixed soap file being loaded when Maq file was specified. ------------------------------------------------------------------------ r233 | imilne | 2009-09-07 14:08:28 +0100 (Mon, 07 Sep 2009) | 1 line - NEW: Added exception checking to (hopefully) catch OutOfMemory errors and direct the user to the help topic on tablet.vmoptions. ------------------------------------------------------------------------ r232 | imilne | 2009-09-07 13:19:25 +0100 (Mon, 07 Sep 2009) | 2 lines - NEW: Updated the filters information (MAQ now lists .maq and .txt) and added multiple filter options for all file types (all, assembly, txt). ------------------------------------------------------------------------ r231 | gsteph | 2009-09-07 12:18:41 +0100 (Mon, 07 Sep 2009) | 2 lines - CHG: Reinstated ratings panel and set it and its label to be invisible. - BUG: Fixed incorrectly ordered panels in Open Assembly Dialog. ------------------------------------------------------------------------ r230 | gsteph | 2009-09-07 12:03:08 +0100 (Mon, 07 Sep 2009) | 1 line - CHG: Added files missing from last commit. ------------------------------------------------------------------------ r229 | gsteph | 2009-09-07 11:57:19 +0100 (Mon, 07 Sep 2009) | 2 lines - NEW: Added support for Maq assembly file type. - BUG: Fixed bug with read metadata not being set up correctly for SOAP files. ------------------------------------------------------------------------ r228 | imilne | 2009-09-07 11:47:33 +0100 (Mon, 07 Sep 2009) | 1 line - BUG: Added a check for base quality scores with values higher than 100 in the ACE file parser. ------------------------------------------------------------------------ r227 | imilne | 2009-09-07 10:28:34 +0100 (Mon, 07 Sep 2009) | 2 lines - NEW: The Hide Contigs List button is now functional. - NEW: Added a different panel to the main display for showing when a contig isn't selected. ------------------------------------------------------------------------ r226 | imilne | 2009-09-04 15:37:47 +0100 (Fri, 04 Sep 2009) | 2 lines - CHG: Various fixes to the icons (especially under OS X). - CHG: The web link in the About Dialog is now a HyperTextLabel. ------------------------------------------------------------------------ r225 | imilne | 2009-09-04 14:26:16 +0100 (Fri, 04 Sep 2009) | 3 lines - NEW: The installer will now build 64bit versions for both Windows and Linux. - CHG: Modified the colours in the contig panel. - CHG: Disabled the Nimbus font size overrides - they're just not working in anything post JRE 1.6.0_13 ------------------------------------------------------------------------ r224 | imilne | 2009-09-03 14:05:26 +0100 (Thu, 03 Sep 2009) | 1 line - NEW: Added the licence header to all the current source code files. ------------------------------------------------------------------------ r223 | imilne | 2009-09-03 13:58:19 +0100 (Thu, 03 Sep 2009) | 2 lines - NEW: Added file filters to all the open/save dialogs. - NEW: Added a new application-menu option to export the current view (of the reads) as a PNG image. ------------------------------------------------------------------------ r222 | imilne | 2009-09-02 15:59:14 +0100 (Wed, 02 Sep 2009) | 1 line - NEW: Added licence information. ------------------------------------------------------------------------ r221 | imilne | 2009-09-02 15:34:55 +0100 (Wed, 02 Sep 2009) | 1 line - CHG: Support for GFF3 features is now more generic, so any (column 3 from the file) feature should import that has a start and end position. ------------------------------------------------------------------------ r220 | imilne | 2009-08-27 13:27:28 +0100 (Thu, 27 Aug 2009) | 2 lines - NEW: Added various icons that were missing from previous commits. - CHG: Updated some of the front page text. ------------------------------------------------------------------------ r219 | gsteph | 2009-08-27 10:31:31 +0100 (Thu, 27 Aug 2009) | 1 line - BUG: Fixed issue with html formatting causing links with spaces in them to jump in length. ------------------------------------------------------------------------ r218 | gsteph | 2009-08-27 09:15:45 +0100 (Thu, 27 Aug 2009) | 1 line - NEW: Added the NavPanel class for the display when the user starts the program. ------------------------------------------------------------------------ r217 | gsteph | 2009-08-26 16:58:19 +0100 (Wed, 26 Aug 2009) | 1 line - NEW: NavigationPanel has been introduced, this is presented to the user when the program starts. ------------------------------------------------------------------------ r216 | imilne | 2009-08-18 14:06:23 +0100 (Tue, 18 Aug 2009) | 1 line - NEW: Commands.java now uses the static TabletUtils method for file browsing. ------------------------------------------------------------------------ r215 | imilne | 2009-08-18 13:27:39 +0100 (Tue, 18 Aug 2009) | 1 line - NEW: The Open Assembly dialog now remembers that last file type selected. ------------------------------------------------------------------------ r214 | imilne | 2009-08-18 13:10:45 +0100 (Tue, 18 Aug 2009) | 4 lines - BUG: Fixed some of the Netbeans layout issues with the new Open Assembly dialog. - CHG: Changed the recent file lists (for each supported file type) to be tab-delimited strings rather than arrays. - CHG: Tweaks and modifications to the on-screen text for the Open Assembly dialog. - NEW: The combo boxes of the dialog now update as selections are made upon them. ------------------------------------------------------------------------ r213 | gsteph | 2009-08-18 11:04:08 +0100 (Tue, 18 Aug 2009) | 1 line -NEW: Run task in build.xml. ------------------------------------------------------------------------ r212 | gsteph | 2009-08-17 15:28:15 +0100 (Mon, 17 Aug 2009) | 1 line - NEW: Includes some new text for ImportAssemblyDialog ------------------------------------------------------------------------ r211 | gsteph | 2009-08-17 15:27:10 +0100 (Mon, 17 Aug 2009) | 1 line - CHG: Updated to utilise new file loading dialog ImportAssemblyDialog ------------------------------------------------------------------------ r210 | gsteph | 2009-08-17 15:26:09 +0100 (Mon, 17 Aug 2009) | 1 line - NEW: New dialog for loading files. ------------------------------------------------------------------------ r209 | gsteph | 2009-08-17 15:25:08 +0100 (Mon, 17 Aug 2009) | 1 line - NEW: Method to get the filename of a file given a filepath / browse for a new file. ------------------------------------------------------------------------ r208 | gsteph | 2009-08-17 15:24:17 +0100 (Mon, 17 Aug 2009) | 1 line - NEW: Now includes recent file lists for ACE, AFG and SOAP files ------------------------------------------------------------------------ r207 | imilne | 2009-08-14 14:52:42 +0100 (Fri, 14 Aug 2009) | 1 line - NEW: The list of recently accessed documents now supports file arrays. ------------------------------------------------------------------------ r206 | imilne | 2009-08-14 14:03:40 +0100 (Fri, 14 Aug 2009) | 1 line - BUG: Multiple file inputs on the command line all used args[0] instead of the array index (args[i]). ------------------------------------------------------------------------ r205 | imilne | 2009-08-14 13:46:54 +0100 (Fri, 14 Aug 2009) | 2 lines - NEW: The assembly name is now correctly named from the file it came from (and always from the SOAP rather than the FASTA file in SOAP's case). - NEW: Modified the start-up routines (on OS X too) to support command line arguments that provide Tablet with more than one file. ------------------------------------------------------------------------ r204 | imilne | 2009-08-14 12:55:41 +0100 (Fri, 14 Aug 2009) | 3 lines - NEW: TrackableReader.java can now track multiple files, and provides a single global indicator of progress (across the combination of files it is reading from). - NEW: Added a parser for handling the SOAP assembly format. This expects two files - SOAP and FASTA. - NEW: The import handling code will now supports file[] array inputs, and will attempt to parse inputs as either ACE or AFG (for a single file) or SOAP for two files. ------------------------------------------------------------------------ r203 | imilne | 2009-08-13 15:44:17 +0100 (Thu, 13 Aug 2009) | 1 line - NEW: Started working on modifying the io code to support multi-file assembly inputs, by allowing the classes to work from arrays of File objects, rather than a single instance. ------------------------------------------------------------------------ r202 | gsteph | 2009-08-13 13:55:57 +0100 (Thu, 13 Aug 2009) | 1 line - CHG: Updated to reflect change in accesibility of BufferedRandomAccessFile ------------------------------------------------------------------------ r201 | gsteph | 2009-08-13 13:50:33 +0100 (Thu, 13 Aug 2009) | 1 line - NEW: Updated scri-commons.jar with BufferedRandomAccessFile ------------------------------------------------------------------------ r200 | gsteph | 2009-08-13 13:38:53 +0100 (Thu, 13 Aug 2009) | 1 line - NEW: Now uses BufferedRandomAccessFile from scri.commons.file ------------------------------------------------------------------------ r199 | imilne | 2009-08-12 15:16:43 +0100 (Wed, 12 Aug 2009) | 1 line - NEW: Modified the installer to now include a .vmoptions file as part of the install. This can be modified by the end user to tweak JVM settings. ------------------------------------------------------------------------ r198 | imilne | 2009-08-12 13:48:06 +0100 (Wed, 12 Aug 2009) | 1 line - BUG: Fixed some errors that can occur when attempting to update the main canvas when it doesn't actually have any data to draw. ------------------------------------------------------------------------ r197 | imilne | 2009-08-12 09:59:17 +0100 (Wed, 12 Aug 2009) | 2 lines - NEW: Updated scri-commons.jar which now has support for storing String[] arrays. - CHG: Modified the code to use a String array for holding the list of recently accessed documents. ------------------------------------------------------------------------ r196 | imilne | 2009-08-11 10:04:13 +0100 (Tue, 11 Aug 2009) | 1 line - BUG: Mouse over events on the standard/text live preview buttons were still running (and generating exceptions) even when the buttons were disabled. ------------------------------------------------------------------------ r195 | imilne | 2009-08-11 09:58:07 +0100 (Tue, 11 Aug 2009) | 4 lines - NEW: All pre-display calculations for showing a contig are now performed in a new class; DisplayDataCalculator.java - NEW: The progress tracking dialog now returns whether the job result was ok, failed or cancelled. - NEW: Selecting a contig will now run the calculations for it as a trackable job, that *can* be cancelled (resulting in the contig not being displayed). - CHG: DisplayData.java is now just a bean-class, containing no analysis methods of its own. ------------------------------------------------------------------------ r194 | imilne | 2009-08-10 15:19:57 +0100 (Mon, 10 Aug 2009) | 1 line - CHG: Modified the progress tracking dialog so that it starts the job before it even attempts to build itself, and then only makes itself visible if the job is still running by the time it is ready to appear. ------------------------------------------------------------------------ r193 | imilne | 2009-08-07 15:15:07 +0100 (Fri, 07 Aug 2009) | 1 line - CHG: Removed packset creation from the import process and changed it so that it only runs (per contig) at the time the contig is selected for display. ------------------------------------------------------------------------ r192 | imilne | 2009-08-07 14:20:16 +0100 (Fri, 07 Aug 2009) | 1 line - BUG: Fixed the broken unit test for the AFG names cache due to reducing the maximum length per name that could be stored. ------------------------------------------------------------------------ r191 | imilne | 2009-08-07 14:17:54 +0100 (Fri, 07 Aug 2009) | 2 lines - NEW: The AfgFileReader will now use a disk-based cache of names during reading to reduce memory usage. - CHG: Made various modifications to the AFG parser in an attempt to make it run faster (to offset the overhead of using a non-buffered RandomAccessFile for the cache). ------------------------------------------------------------------------ r190 | imilne | 2009-08-07 09:25:51 +0100 (Fri, 07 Aug 2009) | 1 line - NEW: The classic colour scheme now renders onto off-white squares, which helps to distinguish them from the background in addition to making the colour scheme usable at low zoom levels. ------------------------------------------------------------------------ r189 | mbayer | 2009-08-06 16:22:37 +0100 (Thu, 06 Aug 2009) | 1 line - NEW: Added a file parser for the AFG format used by the AMOS project and Velvet, plus the necessary hooks into the system. Made some minor changes to Read.java and Sequence.java in the process. The parser is still slow and wasteful on memory and needs further optimization. ------------------------------------------------------------------------ r188 | imilne | 2009-08-06 15:27:22 +0100 (Thu, 06 Aug 2009) | 1 line - CHG: Modified the build routine so that Test classes will not be included in the final distribution. ------------------------------------------------------------------------ r187 | imilne | 2009-08-06 13:30:35 +0100 (Thu, 06 Aug 2009) | 1 line - NEW: Added a new class that supplies temporary disk-based storage for read names as they are parsed from a file. ------------------------------------------------------------------------ r186 | imilne | 2009-08-06 11:20:15 +0100 (Thu, 06 Aug 2009) | 1 line - BUG: Fixed a layout bug that caused selecting contigs with less data than could fill the current screen size to not display properly (because it's the scrollbars changing that causes a compute-resize event). ------------------------------------------------------------------------ r185 | imilne | 2009-08-05 14:38:46 +0100 (Wed, 05 Aug 2009) | 2 lines - NEW: Added mouse tracking to the coverage canvas. - NEW: Added a ribbon control for showing or hiding the coverage canvas. ------------------------------------------------------------------------ r184 | imilne | 2009-08-05 11:50:15 +0100 (Wed, 05 Aug 2009) | 1 line - NEW: Added another tracking canvas that provides a histogram of coverage per base (unlike the coverage overview that uses averages). A dotted line does provide a reference for the overall average though. ------------------------------------------------------------------------ r183 | imilne | 2009-08-05 09:18:34 +0100 (Wed, 05 Aug 2009) | 1 line - CHG: Created a new base class (TrackingCanvas.java) for all the canvases that track the ReadsCanvas. ------------------------------------------------------------------------ r182 | imilne | 2009-08-04 13:50:10 +0100 (Tue, 04 Aug 2009) | 1 line - NEW: Fixed and tidied up some of the unit tests due to the refactored code. ------------------------------------------------------------------------ r181 | imilne | 2009-08-04 13:26:17 +0100 (Tue, 04 Aug 2009) | 1 line - BUG: Fixed a (rare) bug that could occur during loading if the tracking timer attempted to determine load progress before the file handle had been created. ------------------------------------------------------------------------ r180 | imilne | 2009-08-04 11:58:28 +0100 (Tue, 04 Aug 2009) | 1 line - CHG: Updated all the Matisse code to use Java 1.6 library calls so that swing-layout.jar can be removed as it isn't needed. ------------------------------------------------------------------------ r179 | imilne | 2009-08-04 11:34:12 +0100 (Tue, 04 Aug 2009) | 4 lines - CHG: Stage 2 of refactoring the code to cope with moving display-only variables into a new class (DisplayData). - NEW: Calculation of position mapping data now happens in its own class. - NEW: Coverage values per base (under the mouse) are shown on the scale canvas. - CHG: "Position (unpadded position)" strings are now [pos] U[upos] CV[cvg] for position, unpadded position, and coverage value. ------------------------------------------------------------------------ r178 | imilne | 2009-08-04 09:00:46 +0100 (Tue, 04 Aug 2009) | 1 line - CHG: Stage 1 of refactoring the code to cope with moving display-only variables into a new class (DisplayData). This information needs to be calculated when a contig is selected. ------------------------------------------------------------------------ r177 | imilne | 2009-07-31 14:05:43 +0100 (Fri, 31 Jul 2009) | 1 line - NEW: Added a fade-in animation effect for the overview graphics. ------------------------------------------------------------------------ r176 | imilne | 2009-07-31 12:08:57 +0100 (Fri, 31 Jul 2009) | 3 lines - CHG: Changed the hide overview button to open up a drop down menu with options for showing/hiding the overview AND for selecting which overview graphic type to display. - NEW: Added a new breakaway overview class that is responsible purely for mouse interaction. - NEW: Right clicking on the overview now opens its options menu. ------------------------------------------------------------------------ r175 | imilne | 2009-07-31 09:40:36 +0100 (Fri, 31 Jul 2009) | 3 lines - NEW: Split the overview canvas into a base panel capable of calling upon other classes to generate the actual image. - NEW: The original data overview generation now happens in a new class; ScaledOverviewFactory.java - NEW: Added a new class for generating a coverage overview; CoverageOverviewFactory.java ------------------------------------------------------------------------ r174 | imilne | 2009-07-29 15:18:58 +0100 (Wed, 29 Jul 2009) | 1 line - NEW: First commit of a class that can handle calculating coverage statistics. ------------------------------------------------------------------------ r173 | imilne | 2009-07-29 12:04:43 +0100 (Wed, 29 Jul 2009) | 1 line - NEW: Added an about dialog. ------------------------------------------------------------------------ r172 | imilne | 2009-07-29 10:02:21 +0100 (Wed, 29 Jul 2009) | 1 line - BUG: The native file open dialog on OS X didn't display properly if opened via the ribbon's application menu (it was hidden behind it). ------------------------------------------------------------------------ r171 | imilne | 2009-07-29 09:36:20 +0100 (Wed, 29 Jul 2009) | 1 line - NEW: Added a second tab of options to the preferences dialog that contains the controls for choosing which characters to use for DNA/Protein gap/stop display. ------------------------------------------------------------------------ r170 | imilne | 2009-07-28 14:57:00 +0100 (Tue, 28 Jul 2009) | 1 line - Committed in what is pretty much a copy of the main tab from Flapjack's preferences dialog. This handles language and update options so far. ------------------------------------------------------------------------ r169 | imilne | 2009-07-28 11:17:54 +0100 (Tue, 28 Jul 2009) | 1 line - NEW: Added support for changing the rendered character used for DNA gaps ("*" or "-") and protein stop codons ("." or "*"). ------------------------------------------------------------------------ r168 | imilne | 2009-07-28 09:41:58 +0100 (Tue, 28 Jul 2009) | 1 line - CHG: The unpadded/padded mapping information for each consensus is no longer stored in memory at all times. If a consensus is to be displayed, the mappings are calculated, and then removed from memory when not being displayed. This significantly reduces memory usage on assemblies with a large number of contigs as only one contig at a time will hold this data. ------------------------------------------------------------------------ r167 | imilne | 2009-07-27 08:28:32 +0100 (Mon, 27 Jul 2009) | 1 line - CHG: Instances of StringBuffer changed to the unsynchronized StringBuilder class. ------------------------------------------------------------------------ r166 | imilne | 2009-07-22 19:27:31 +0100 (Wed, 22 Jul 2009) | 1 line - NEW: Added scri-commons (finally). ------------------------------------------------------------------------ r165 | imilne | 2009-07-22 15:44:06 +0100 (Wed, 22 Jul 2009) | 1 line - NEW: Implemented a method for multi-core rendering of the main display, with each core handling the drawing of its own independent set of lines (eg, core-0 would draw lines 0, 2, 4, etc, while core-1 was drawing lines 1, 3, 5, etc). ------------------------------------------------------------------------ r164 | imilne | 2009-07-22 14:21:04 +0100 (Wed, 22 Jul 2009) | 1 line - NEW: Some changes made for (very) minor tweaks for performance. ------------------------------------------------------------------------ r163 | imilne | 2009-07-22 11:22:19 +0100 (Wed, 22 Jul 2009) | 2 lines - CHG: Updated some of the thread setName() calls again. - NEW: Added a debug count of non-daemon threads to the status bar. ------------------------------------------------------------------------ r162 | imilne | 2009-07-22 10:18:48 +0100 (Wed, 22 Jul 2009) | 3 lines - NEW: The multi-core code in PackSetCreator now uses the JDK 1.5 Executor interfaces. - NEW: The BasePositionComparator code now runs in a multi threaded manner too, splitting tasks on a per read basis. - CHG: Changed the hash tables in some of the file parsing code to be hash maps. ------------------------------------------------------------------------ r161 | imilne | 2009-07-21 15:26:34 +0100 (Tue, 21 Jul 2009) | 1 line - CHG: Changed from Vector to ArrayList for most of the rest of the code. ------------------------------------------------------------------------ r160 | imilne | 2009-07-21 14:49:00 +0100 (Tue, 21 Jul 2009) | 2 lines - NEW: Various performance improvements due to switching from synchronized Vectors to unsynchronized ArrayLists. Any synchronization (not that any is needed yet) can be done externally by Tablet code rather than the Java API. - NEW: Added Thread.setName() calls to some classes to help with profiling. ------------------------------------------------------------------------ r159 | imilne | 2009-07-21 09:36:34 +0100 (Tue, 21 Jul 2009) | 1 line - BUG: One of the ribbon's new keyboard shortcuts clashed with an existing one. ------------------------------------------------------------------------ r158 | imilne | 2009-07-20 14:17:07 +0100 (Mon, 20 Jul 2009) | 1 line - NEW: The packset creation code is now multi-core aware, and (on my development PC) will now run almost twice as fast using 2 cores instead of 1. ------------------------------------------------------------------------ r157 | imilne | 2009-07-17 15:08:27 +0100 (Fri, 17 Jul 2009) | 1 line - NEW: If a .ace file has a .gff file in the same directory as it, then Tablet will now auto-import it at the same time as loading the assembly. ------------------------------------------------------------------------ r156 | imilne | 2009-07-17 15:05:26 +0100 (Fri, 17 Jul 2009) | 1 line - BUG: U and C may have been mixed up during rendering of the arrows. ------------------------------------------------------------------------ r155 | imilne | 2009-07-17 14:28:48 +0100 (Fri, 17 Jul 2009) | 1 line - NEW: GFF3 features can now be imported and attached to an existing assembly. ------------------------------------------------------------------------ r154 | imilne | 2009-07-17 12:28:50 +0100 (Fri, 17 Jul 2009) | 1 line - NEW: Added the button/icon option for importing features to the ribbon (event handling still to be done). ------------------------------------------------------------------------ r153 | imilne | 2009-07-17 11:51:25 +0100 (Fri, 17 Jul 2009) | 1 line - NEW: Implemented a new method of letting each file parser check to see if it can parse a file before the main read method is called. ------------------------------------------------------------------------ r152 | imilne | 2009-07-17 10:30:53 +0100 (Fri, 17 Jul 2009) | 3 lines - NEW: Added a class for GFF3 file parsing. - NEW: The main import handler is now much simpler, calling a new class AssemblyFileHandler as part 1 of its 3 tasks. This is the class now responsible for determining which file parser to use on any given input file. - CHG: The old AssemblyReader class is now renamed TrackableReader and contains the common code for line counting and ProgressInputStream/BufferedReader objects. All file parsers, including the GFF3Reader now inherit from it. ------------------------------------------------------------------------ r151 | imilne | 2009-07-15 14:10:25 +0100 (Wed, 15 Jul 2009) | 1 line - BUG: The progress dialog's assembly reference was only cleared on a clean run - cancelled or failed runs would still maintain it. ------------------------------------------------------------------------ r150 | imilne | 2009-07-15 09:02:22 +0100 (Wed, 15 Jul 2009) | 1 line - NEW: Removed some of the contig==null checks that the drawing code makes that aren't needed now that the display areas are invisible when the current contig *is* null. ------------------------------------------------------------------------ r149 | imilne | 2009-07-14 15:19:17 +0100 (Tue, 14 Jul 2009) | 3 lines - BUG: (Potentially memory leak related) - References through to any of the tablet.data objects from the rendering code are now removed whenever the display components are switched off. - CHG: Tidied up the colour scheme code that still had contig references within it from the (failed) attempt at having it cache the schemes. This is no longer needed. ------------------------------------------------------------------------ r148 | imilne | 2009-07-14 14:28:19 +0100 (Tue, 14 Jul 2009) | 2 lines - BUG: (Potentially memory leak related) - References through to the assembly held by the loading progress dialog are now properly removed after use. ------------------------------------------------------------------------ r147 | imilne | 2009-07-14 12:45:04 +0100 (Tue, 14 Jul 2009) | 1 line - CHG: Recoded the progress dialog to use Swing timers instead of a custom thread. ------------------------------------------------------------------------ r146 | imilne | 2009-07-14 11:27:13 +0100 (Tue, 14 Jul 2009) | 1 line - BUG: (Potentially memory leak related) - References to the assembly held by the contig and features panel are now properly cleared after the assembly is closed. ------------------------------------------------------------------------ r145 | imilne | 2009-07-13 10:05:17 +0100 (Mon, 13 Jul 2009) | 3 lines - NEW: Added new options for highlighting/outlining a selected row or column of the display (up to a maximum of five per contig). - NEW: Added icons for more of the right-click menu options. - CHG: The move-over highlighting code now forms part of the new OutlinerOverlay class. ------------------------------------------------------------------------ r144 | imilne | 2009-07-10 14:44:16 +0100 (Fri, 10 Jul 2009) | 1 line - NEW: Created a new data sub package for auxiliary data, and moved the Feature class into it too. ------------------------------------------------------------------------ r143 | imilne | 2009-07-10 14:31:23 +0100 (Fri, 10 Jul 2009) | 1 line - CHG: Renamed the NavigationHighlighter class to NavigationOverlay. ------------------------------------------------------------------------ r142 | imilne | 2009-07-10 14:17:46 +0100 (Fri, 10 Jul 2009) | 1 line - NEW: The read under the mouse is now tracked by the overview canvas (in blue) in addition to the main canvas (in red). ------------------------------------------------------------------------ r141 | imilne | 2009-07-10 12:45:24 +0100 (Fri, 10 Jul 2009) | 1 line - NEW: Added a right-click menu option to locate, jump to, and highlight the start or the end of a selected read. ------------------------------------------------------------------------ r140 | imilne | 2009-07-10 11:28:21 +0100 (Fri, 10 Jul 2009) | 1 line - NEW: Added a status bar to the bottom of the screen to show random help messages/tips. ------------------------------------------------------------------------ r139 | imilne | 2009-07-10 08:45:38 +0100 (Fri, 10 Jul 2009) | 2 lines - NEW: Copy to clipboard is now a right-click menu option for the consensus sequence. - BUG: Some of the displays for numerical values were still showing raw numbers rather than formatted versions (eg 1000 instead of 1,000). ------------------------------------------------------------------------ r138 | imilne | 2009-07-09 14:21:15 +0100 (Thu, 09 Jul 2009) | 2 lines - NEW: Standard slider (or keyboard) zooms should now maintain focus on whatever was in the centre of the screen. - NEW: Mouse zooming is now possible by double-clicking a point of interest on the main canvas. ------------------------------------------------------------------------ r137 | imilne | 2009-07-08 11:39:36 +0100 (Wed, 08 Jul 2009) | 1 line - BUG: The scale bar position information was wrong when the mouse was actually over the scale bar (as opposed to any of the other canvases). ------------------------------------------------------------------------ r136 | imilne | 2009-07-08 11:32:05 +0100 (Wed, 08 Jul 2009) | 2 lines - NEW: Proteins are now drawn in a single block per codon. We now store 3 sets of 21 states, for the left block, centre block and right block. The three blocks combined render as one because their gradients match. - CHG: More changes to the visual look of stop codons, including red text for the classic scheme. ------------------------------------------------------------------------ r135 | imilne | 2009-07-08 09:56:09 +0100 (Wed, 08 Jul 2009) | 1 line - BUG: The text-based protein scheme did not have the new stop codon font applied to it. ------------------------------------------------------------------------ r134 | imilne | 2009-07-08 09:41:52 +0100 (Wed, 08 Jul 2009) | 1 line - NEW: Reverted the open file dialog on OS X back to its AWT (rather than Swing) implementation for better native compatibility. It provides very limited program-level control but we're not (yet) doing anything advanced with it. ------------------------------------------------------------------------ r133 | imilne | 2009-07-08 09:20:16 +0100 (Wed, 08 Jul 2009) | 1 line - NEW: The unpadded/ungapped length of the consensus is now shown as part of the contig summary label. ------------------------------------------------------------------------ r132 | imilne | 2009-07-08 09:12:04 +0100 (Wed, 08 Jul 2009) | 1 line - CHG: Changed the colour for a stop codon to dark grey and gave it a better unicode-based character. ------------------------------------------------------------------------ r131 | imilne | 2009-07-07 10:07:42 +0100 (Tue, 07 Jul 2009) | 1 line - CHG: Modified the default window width and height to be a little wider and taller. ------------------------------------------------------------------------ r130 | imilne | 2009-07-07 09:36:39 +0100 (Tue, 07 Jul 2009) | 1 line - NEW: Reinstated the clean-up code to remove cache files once Tablet is closed. ------------------------------------------------------------------------ r129 | imilne | 2009-07-06 15:22:55 +0100 (Mon, 06 Jul 2009) | 2 lines - NEW: The unpadded length of a read is calculated at parse-time and stored as part of its meta data cache. - NEW: The ace file parser now writes cache information at the point of read-data parsing (RD) rather than name parsing (AF). U/C info is held locally in memory until it can be saved. The name is now parsed from the RD rather than the AF tag. ------------------------------------------------------------------------ r128 | imilne | 2009-07-06 13:39:34 +0100 (Mon, 06 Jul 2009) | 1 line - BUG: The file cache wasn't writing int values correctly (bytes as ints, so fine for values up to 255). This would have affected very long read names. ------------------------------------------------------------------------ r127 | imilne | 2009-07-04 09:24:57 +0100 (Sat, 04 Jul 2009) | 1 line - NEW: The vector of contigs now has the correct initial size pre-set for it during ACE file parsing. ------------------------------------------------------------------------ r126 | imilne | 2009-07-03 14:23:34 +0100 (Fri, 03 Jul 2009) | 1 line - NEW: Tweaked the pixel borders between some of the components to maintain a constant 5px gap between whichever panels are visible. ------------------------------------------------------------------------ r125 | imilne | 2009-07-03 13:13:01 +0100 (Fri, 03 Jul 2009) | 1 line - BUG: Opening files on OS X (via the Dock or Finder) should now work properly. ------------------------------------------------------------------------ r124 | imilne | 2009-07-03 09:32:32 +0100 (Fri, 03 Jul 2009) | 2 lines - NEW: SCRI branding added to the installer. - NEW: Tablet will now do a check-for-version-diff and display the svn log file if a new version is run. ------------------------------------------------------------------------ r123 | imilne | 2009-07-03 08:44:31 +0100 (Fri, 03 Jul 2009) | 4 lines - CHG: The code for processing base qualities has been moved into AceFileReader.java from Consensus.java where it makes more sense. - NEW: Added various error handling catches to the ace file parser and i18n strings for displaying them. - NEW: The ace file parser now tracks the current line number at all times. - NEW: System.gc() is run before a new import in an attempt to free up memory first. ------------------------------------------------------------------------ r122 | imilne | 2009-07-02 15:06:14 +0100 (Thu, 02 Jul 2009) | 1 line - BUG: File sizes for certain (very) large files were being reported incorrectly, which resulted in the import progress bar displaying the wrong percentage value. ------------------------------------------------------------------------ r121 | imilne | 2009-07-02 14:14:57 +0100 (Thu, 02 Jul 2009) | 1 line - NEW: Added some additional job cancelled detection code to the import handler so it will exit (more gracefully than it did) from a cancelled import operation. ------------------------------------------------------------------------ r120 | imilne | 2009-07-02 11:25:20 +0100 (Thu, 02 Jul 2009) | 1 line - NEW: Added some memory monitoring displays. ------------------------------------------------------------------------ r119 | imilne | 2009-07-02 09:35:15 +0100 (Thu, 02 Jul 2009) | 1 line - BUG: Removed the caching of colour schemes - it had broken the intensity slider (because it needs to recreate each scheme's alpha value on the fly). ------------------------------------------------------------------------ r118 | imilne | 2009-07-02 09:29:24 +0100 (Thu, 02 Jul 2009) | 2 lines - NEW: Copy to clipboard for protein translations has been implemented. - NEW: The code for formatting sequences into FASTA has been moved into TabletUtils. ------------------------------------------------------------------------ r117 | imilne | 2009-07-01 14:56:37 +0100 (Wed, 01 Jul 2009) | 1 line - NEW: Added a mouse listener for movement over the protein canvas that will track position and display the full name of each protein. ------------------------------------------------------------------------ r116 | imilne | 2009-07-01 14:11:13 +0100 (Wed, 01 Jul 2009) | 1 line - NEW: Right-clicking on the protein canvas will open the options menu for it. ------------------------------------------------------------------------ r115 | imilne | 2009-07-01 13:55:15 +0100 (Wed, 01 Jul 2009) | 2 lines - NEW: Added an popup menu option button to the ribbon for choosing which protein tracks should be visible. - NEW: Added on/off trackers to the preferences for the protein tracks and mapped them to the menu. ------------------------------------------------------------------------ r114 | imilne | 2009-07-01 09:34:37 +0100 (Wed, 01 Jul 2009) | 1 line - NEW: The colour schemes are now cached so each one (scheme and resolution) only needs to be created once. It doesn't seem to use too much memory: ~4MB if every scheme and size is held. ------------------------------------------------------------------------ r113 | imilne | 2009-06-30 16:06:02 +0100 (Tue, 30 Jun 2009) | 1 line - NEW: The protein canvas now creates all six reading frames in a background thread before displaying them, updating its local cache whenever the selected consensus sequence changes. ------------------------------------------------------------------------ r112 | imilne | 2009-06-30 14:19:42 +0100 (Tue, 30 Jun 2009) | 3 lines - NEW: The protein translation (forward, reading frame 1 only) is now shown graphically. - NEW: Added new colour schemes to handle the protein stuff. - NEW: Added another scrollable canvas for the protein translation. ------------------------------------------------------------------------ r111 | imilne | 2009-06-30 11:09:47 +0100 (Tue, 30 Jun 2009) | 1 line - NEW: Updated the protein translator to handle translating in reverse. ------------------------------------------------------------------------ r110 | imilne | 2009-06-30 09:22:41 +0100 (Tue, 30 Jun 2009) | 1 line - NEW: Added a new class (and unit test) to handle protein translations of DNA sequences. Translations are made into Tablet's internal symbol table format. ------------------------------------------------------------------------ r109 | imilne | 2009-06-29 14:55:01 +0100 (Mon, 29 Jun 2009) | 2 lines - NEW: Updates to the data API to cope with future protein translation code. - CHG: Changes to the colour scheme renderers due to changing the data API. ------------------------------------------------------------------------ r108 | imilne | 2009-06-29 13:37:29 +0100 (Mon, 29 Jun 2009) | 1 line - CHG: Source code changes to remove unused imports. ------------------------------------------------------------------------ r107 | imilne | 2009-06-29 13:25:34 +0100 (Mon, 29 Jun 2009) | 2 lines - CHG: Minor change to the text displayed on the Jump To Base dialog. - CHG: Column highlighting now dims the entire view area, not just the area that could contain data. ------------------------------------------------------------------------ r106 | imilne | 2009-06-29 12:25:39 +0100 (Mon, 29 Jun 2009) | 2 lines - NEW: Implemented the jump to an unpadded base functionality of the jump dialog. - CHG: Changed the consensus sequence to maintain mappings between both padded->unpadded and unpadded->padded. ------------------------------------------------------------------------ r105 | imilne | 2009-06-29 10:13:19 +0100 (Mon, 29 Jun 2009) | 2 lines - NEW: Position information for the Jump To Base dialog is now tracked. - NEW: The Jump To Base dialog is now initialized properly and will disappear if a contig is not currently selected. Its control states will update on focus gain. ------------------------------------------------------------------------ r104 | imilne | 2009-06-29 09:41:08 +0100 (Mon, 29 Jun 2009) | 2 lines - NEW: Added the GUI for the Jump to Base dialog. - NEW: Added functionality for jumping to a padded base. Unpadded base jumps are still not working correctly. ------------------------------------------------------------------------ r103 | imilne | 2009-06-26 12:10:38 +0100 (Fri, 26 Jun 2009) | 1 line - NEW: Built the ribbon controls for jumping to a base. The function itself will be added as a separate dialog in a later commit. ------------------------------------------------------------------------ r102 | imilne | 2009-06-26 11:34:55 +0100 (Fri, 26 Jun 2009) | 1 line - NEW: Started working on the navigation ribbon task, adding buttons for the page left/right options. ------------------------------------------------------------------------ r101 | imilne | 2009-06-25 15:43:43 +0100 (Thu, 25 Jun 2009) | 1 line - CHG: Minor edit to remove the beginGroup separator before the packed/stacked ribbon buttons. ------------------------------------------------------------------------ r100 | imilne | 2009-06-25 15:11:56 +0100 (Thu, 25 Jun 2009) | 2 lines - NEW: Added options and icons for hiding various components of the interface. Not all functionality is programmed and not all icons are final. - CHG: Swapped the positions of the Adjust and Display Style tasks. ------------------------------------------------------------------------ r99 | imilne | 2009-06-25 13:49:33 +0100 (Thu, 25 Jun 2009) | 1 line - BUG: Implemented a work-around for the Ribbon API allowing a toggle button that is part of a group to be unselected. ------------------------------------------------------------------------ r98 | imilne | 2009-06-25 12:02:14 +0100 (Thu, 25 Jun 2009) | 2 lines - NEW: Added the options for toggling between packed and stacked display to the ribbon. - NEW: Added a disabled, dummy placeholder icon for possible future "Sort Reads" functionality. ------------------------------------------------------------------------ r97 | imilne | 2009-06-25 09:44:43 +0100 (Thu, 25 Jun 2009) | 2 lines - NEW: Added a colour scheme that just renders plain text, EagleView style. - NEW: Added a live preview gallery to the ribbon for toggling between the colour schemes. ------------------------------------------------------------------------ r96 | imilne | 2009-06-24 14:33:39 +0100 (Wed, 24 Jun 2009) | 1 line - BUG: Fixed the canvas alignments for Windows (OS X will probably be different). ------------------------------------------------------------------------ r95 | imilne | 2009-06-24 14:14:12 +0100 (Wed, 24 Jun 2009) | 1 line - NEW: Added more i18n text, shortcuts, etc to the ribbon. ------------------------------------------------------------------------ r94 | imilne | 2009-06-24 10:22:32 +0100 (Wed, 24 Jun 2009) | 2 lines - NEW: Added another ribbon task for some of the options we now have (infoPane on/off and unpadded scores on/off). - NEW: Added rich tooltips and keyboard shortcuts for more of the ribbon. ------------------------------------------------------------------------ r93 | imilne | 2009-06-23 10:23:56 +0100 (Tue, 23 Jun 2009) | 2 lines - NEW: Enabled the functionality of the close application menu button. - NEW: Control states can now be in one of three modes: assembly closed, assembly opened (but no contig selected) and opened/selected. ------------------------------------------------------------------------ r92 | imilne | 2009-06-23 08:59:26 +0100 (Tue, 23 Jun 2009) | 3 lines - NEW: The number of contigs listed in the tab now updates as the filter runs. - NEW: The last selected filter is stored in the session preferences. - NEW: If a dataset isn't loaded, then the filter controls are disabled. ------------------------------------------------------------------------ r91 | imilne | 2009-06-22 15:45:20 +0100 (Mon, 22 Jun 2009) | 3 lines - NEW: The list of contigs is now filterable by name, contig length, read length, or feature count. - NEW: Added a NetBeans GUI class for providing the filter controls. - CHG: Changed the property keys for a few i18n text entries. ------------------------------------------------------------------------ r90 | imilne | 2009-06-22 13:58:17 +0100 (Mon, 22 Jun 2009) | 1 line - BUG: The last commit messed up the rendering code for the right hand side navigation button. ------------------------------------------------------------------------ r89 | imilne | 2009-06-22 10:04:41 +0100 (Mon, 22 Jun 2009) | 3 lines - NEW: Added keyboard shortcuts for paging left ([) and right (]). - NEW: The number of bases to jump by while paging is now displayed as a tooltip when the mouse is over either of the controls. - NEW: Set the OS X shortcut key detection to a single global location. ------------------------------------------------------------------------ r88 | imilne | 2009-06-19 15:33:05 +0100 (Fri, 19 Jun 2009) | 1 line - NEW: Clicking on the canvas navigation buttons now pages left and right through the data. ------------------------------------------------------------------------ r87 | imilne | 2009-06-19 14:30:44 +0100 (Fri, 19 Jun 2009) | 1 line - NEW: Added graphical navigation controls to the main canvas for paging left and right through the data. Only the graphics for this commit...no paging works yet. ------------------------------------------------------------------------ r86 | imilne | 2009-06-18 16:03:18 +0100 (Thu, 18 Jun 2009) | 2 lines - NEW: Added a right-click popup menu for the main canvas. - NEW: Added options to the popup menu for copying the read name and/or the full read summary (including the sequence data) to the clipboard. ------------------------------------------------------------------------ r85 | imilne | 2009-06-18 15:01:41 +0100 (Thu, 18 Jun 2009) | 2 lines - NEW: Updates to the installer to deal with the recent 1.6.0_13 Apple release. - NEW: Tablet now maintains a user-specific /tmp folder for its cache files and attempts to clean it up on exit too. ------------------------------------------------------------------------ r84 | imilne | 2009-06-18 11:59:08 +0100 (Thu, 18 Jun 2009) | 1 line - BUG: Column highlighting (on features) drew an overlay over the info pane tip too. ------------------------------------------------------------------------ r83 | imilne | 2009-06-18 11:55:58 +0100 (Thu, 18 Jun 2009) | 2 lines - NEW: Added a recent list of opened documents to the application menu. - NEW: Started added keyboard shortcuts for some of the ribbon buttons (eg, CTRL+O). ------------------------------------------------------------------------ r82 | imilne | 2009-06-18 09:26:10 +0100 (Thu, 18 Jun 2009) | 2 lines - NEW: Tidied up some of the loading/selecting code so that the GUI behaves properly when assemblies are loaded or contigs are selected. - CHG: Renamed the visualization band on the home task to be "reads". ------------------------------------------------------------------------ r81 | imilne | 2009-06-17 15:36:51 +0100 (Wed, 17 Jun 2009) | 1 line - NEW: The reads canvas info pane now shows a lot more information and contains graphics too. ------------------------------------------------------------------------ r80 | imilne | 2009-06-17 11:42:58 +0100 (Wed, 17 Jun 2009) | 2 lines - NEW: Removed the entire information panel from the bottom of the screen. - NEW: Read information is now displayed as a graphic overlay on the canvas. ------------------------------------------------------------------------ r79 | imilne | 2009-06-16 09:05:59 +0100 (Tue, 16 Jun 2009) | 3 lines - NEW: The slider controls for zooming and variant highlighting are now part of the ribbon. - CHG: Deleted the old slider controls from the lower control panel. - NEW: Added additional icons for these controls. ------------------------------------------------------------------------ r78 | imilne | 2009-06-15 14:55:22 +0100 (Mon, 15 Jun 2009) | 1 line - NEW: Selecting any of the open options from the ribbon now prompts for the filename before running the open code. ------------------------------------------------------------------------ r77 | imilne | 2009-06-15 14:42:42 +0100 (Mon, 15 Jun 2009) | 4 lines - NEW: Started working with the Flamingo API for providing a ribbon component. - NEW: Created a new sub-package for the ribbon and added classes for handling the main UI, the bands, and the application menu. Not much is functional yet. - NEW: Added lots of new icons needed by the ribbon. - CHG: User logging will now log a previously known SCRI user regardless of their IP address location. ------------------------------------------------------------------------ r76 | imilne | 2009-06-10 11:52:47 +0100 (Wed, 10 Jun 2009) | 1 line - NEW: Mouse overs on the canvas now show unpadded in addition to padded base positions. Positions off the consensus will only show the padded values. ------------------------------------------------------------------------ r75 | imilne | 2009-06-10 09:26:53 +0100 (Wed, 10 Jun 2009) | 3 lines - NEW: Nimbus will now be the default LaF for all non-Apple systems. - NEW: Added a class for handling Nimbus functionality (as it's probably going to be a pain). - CHG: Removed the jar file for the Office LaF. ------------------------------------------------------------------------ r74 | imilne | 2009-06-09 14:38:40 +0100 (Tue, 09 Jun 2009) | 1 line - NEW: Added some of the methods required for better native support on OS X. ------------------------------------------------------------------------ r73 | imilne | 2009-06-09 13:37:09 +0100 (Tue, 09 Jun 2009) | 1 line - NEW: Added OS X and Linux installers to the install4j project. ------------------------------------------------------------------------ r72 | imilne | 2009-05-22 15:29:27 +0100 (Fri, 22 May 2009) | 2 lines - NEW: Added lots of javadoc comments to the data API. - NEW: The ant file can now build javadoc. ------------------------------------------------------------------------ r71 | imilne | 2009-05-22 11:52:51 +0100 (Fri, 22 May 2009) | 3 lines - NEW: The features tab enables or disabled based on whether the selected contig has any features or not. - NEW: The number of features shown in the features tab is also listed in the title for the tab. - NEW: The overview canvas is now drawn with an outline box. ------------------------------------------------------------------------ r70 | imilne | 2009-05-22 11:35:57 +0100 (Fri, 22 May 2009) | 1 line - NEW: Clicking on a feature now highlights it on the main canvas. ------------------------------------------------------------------------ r69 | imilne | 2009-05-22 10:27:37 +0100 (Fri, 22 May 2009) | 1 line - NEW: Added a simple summary label to the top of the display area. ------------------------------------------------------------------------ r68 | imilne | 2009-05-21 15:35:37 +0100 (Thu, 21 May 2009) | 3 lines - NEW: Added (temp) support to the ace file reader to read another type of CT SNP tag (different from before). - BUG: Fixed a problem with certain base quality formatting in ace files. - NEW: The number of features per contig is now listed in the contigs table. ------------------------------------------------------------------------ r67 | imilne | 2009-05-21 15:01:09 +0100 (Thu, 21 May 2009) | 4 lines - NEW: SNP features are now parsed during ACE file reading. - NEW: Imported SNPs are displayed on the features panel. - NEW: Clicking on a feature moves the main canvas to that feature's position. - CHG: Renamed the contig related panels. ------------------------------------------------------------------------ r66 | imilne | 2009-05-21 12:29:01 +0100 (Thu, 21 May 2009) | 6 lines - CHG: Several changes to the data API to better encapsulate certain objects that shouldn't be visible. - BUG: Improved the string parsing of the ACE file reader to better deal with spaces. - NEW: Added in a new data class - Feature - to hold SNPs, etc. - NEW: The Contig class now maintains a list of these features. - NEW: When sorting reads, the length of reads with the same start position is used to sort within them. - NEW: Reading and tracking of files is now done with the new ProgressInputStream class from scri-commons. ------------------------------------------------------------------------ r65 | imilne | 2009-05-20 16:00:57 +0100 (Wed, 20 May 2009) | 2 lines - NEW: Starting preparing the main interface to support features. - BUG: The installer file still contained some unneeded testing variables. ------------------------------------------------------------------------ r64 | imilne | 2009-05-20 15:42:38 +0100 (Wed, 20 May 2009) | 1 line - NEW: Added Install4j.java that was missing from the repository. ------------------------------------------------------------------------ r63 | imilne | 2009-05-20 15:18:11 +0100 (Wed, 20 May 2009) | 1 line - BUG: Another (argh) attempt at getting the overview canvas outline correct. This one is probably wrong too... ------------------------------------------------------------------------ r62 | imilne | 2009-05-20 09:27:54 +0100 (Wed, 20 May 2009) | 1 line - NEW: The installer and the application now support auto-updating from the web. ------------------------------------------------------------------------ r61 | imilne | 2009-05-19 16:01:00 +0100 (Tue, 19 May 2009) | 4 lines - BUG: Progress bar tracking for some jobs (based on SimpleJob) had the incorrect maximum value. - BUG: The progress bar wasn't painting 0% correctly in some cases due to a division by zero error. - NEW: Added a noJRE installer for easier testing (it's much quicker). - CHG: Removed some of the debug messages from AceFileReader.java to clear up the output a little. ------------------------------------------------------------------------ r60 | imilne | 2009-05-19 14:51:57 +0100 (Tue, 19 May 2009) | 6 lines - NEW: Loading the data is now tracked by a progress bar. - NEW: Added in Flapjack's ProgressDialog, and added support for running multiple jobs with multiple labels. - NEW: The ITrackableJob interface now supports multiple sub-jobs as part of the main job. - NEW: Moved the creation of pack sets out of the data API (exposing Pack and PackSet unfortunately), into a new analysis class (PackSetCreator) that performs the same task but is trackable. - CHG: Deleted PostImportOperations.java as other classes now run its tasks. - NEW: Improvements to the ImportHandler to act as the main trackable job during loading. ------------------------------------------------------------------------ r59 | imilne | 2009-05-18 15:18:24 +0100 (Mon, 18 May 2009) | 1 line - BUG: The latest bug fix for the the overview canvas was still wrong. ------------------------------------------------------------------------ r58 | imilne | 2009-05-18 14:35:13 +0100 (Mon, 18 May 2009) | 2 lines - BUG: The right-hand edge of the main canvas was off by 1 pixel in rendering (which affected the scale bar too). - BUG: The scaling factors for the overview canvas were slightly wrong, meaning the red highlighter could move off the canvas at its extremes. ------------------------------------------------------------------------ r57 | imilne | 2009-05-18 10:37:49 +0100 (Mon, 18 May 2009) | 4 lines - BUG: The base comparator method was incorrectly marking reads at positions -1 and length() (against the consensus) as not different when they have to be different because the consensus doesn't exist at those positions. - BUG: The colour scheme was drawing bases with the value of N incorrectly. - CHG: Modifications to the installer. - NEW: The build file will now properly clean and build the two jars (resources and main). ------------------------------------------------------------------------ r56 | imilne | 2009-05-15 15:11:07 +0100 (Fri, 15 May 2009) | 1 line - CHG: Modified the method used for separating the consensus canvas's colour scheme from the reads canvas, so both can now share the same scheme. ------------------------------------------------------------------------ r55 | imilne | 2009-05-15 14:56:03 +0100 (Fri, 15 May 2009) | 1 line - BUG: The consensus canvas was showing intensity highlighting when it really shouldn't have. Fixed by using a separate colour scheme for it (so there's now two schemes in use together). ------------------------------------------------------------------------ r54 | imilne | 2009-05-15 14:43:33 +0100 (Fri, 15 May 2009) | 2 lines - NEW: The code now uses the RB resource bundle handler from scri-commons and most text should now be i18n compatible. - NEW: Added an icon for the main frame (just a temp choice for now). ------------------------------------------------------------------------ r53 | imilne | 2009-05-15 10:01:39 +0100 (Fri, 15 May 2009) | 3 lines - NEW: Added variant highlighting to enhance the intensity of regions that differ from the consensus. - NEW: The number of contigs in an assembly is now displayed after loading. - NEW: The filename of the imported assembly is displayed in the title bar after loading. ------------------------------------------------------------------------ r52 | imilne | 2009-05-15 08:45:39 +0100 (Fri, 15 May 2009) | 1 line - NEW: The scroll bars on the reads canvas now move at more sensible rates (1 click = 1 ntW box size). ------------------------------------------------------------------------ r51 | imilne | 2009-05-14 14:33:32 +0100 (Thu, 14 May 2009) | 2 lines - CHG: The contig panel's list of contigs is now handled by a JTable with multiple columns. - NEW: Added a separate class for handling the table model for contigs. ------------------------------------------------------------------------ r50 | imilne | 2009-05-14 10:28:03 +0100 (Thu, 14 May 2009) | 3 lines - NEW: Added in the jar for the office look and feel. - NEW: Starting adding application icons. - CHG: Removed the ContigPanel from the viewer package and made it part of the main gui package instead. ------------------------------------------------------------------------ r49 | imilne | 2009-05-14 09:39:09 +0100 (Thu, 14 May 2009) | 1 line - NEW: The main image canvas is now back-buffered and will show basic tooltips on mouse overs. ------------------------------------------------------------------------ r48 | imilne | 2009-05-14 08:30:48 +0100 (Thu, 14 May 2009) | 2 lines - NEW: Modified the project to load data either from the command line or via drag and drop. This is still work-in-progress. - NEW: Added a new class to handle the eventual "menu" commands. ------------------------------------------------------------------------ r47 | imilne | 2009-05-12 10:26:25 +0100 (Tue, 12 May 2009) | 3 lines - NEW: Refactored most of the import assembly code to support multiple readers (one per supported file type). - NEW: Added new classes for read exceptions and reading as part of a "trackable job" (similar to Flapjack's thread handling clases). - NEW: Added an abstract base class for all readers (AssemblyReader.java) that holds common variables and handles most of the ITrackableJob implementation for the readers too. ------------------------------------------------------------------------ r46 | imilne | 2009-05-08 15:42:31 +0100 (Fri, 08 May 2009) | 1 line -CHG: Renamed CacheIndex.java to FileCacheIndex.java ------------------------------------------------------------------------ r45 | imilne | 2009-05-08 15:36:17 +0100 (Fri, 08 May 2009) | 3 lines - NEW: The read cache now stores and retrieves objects of type ReadMetaData. - NEW: The read cache now holds the U or C (complemented) value for a Read. - NEW: Mouse overs on a read now show additional information (U/C, length, etc). ------------------------------------------------------------------------ r44 | imilne | 2009-05-08 13:33:06 +0100 (Fri, 08 May 2009) | 3 lines - NEW: Updated the disk cache (for reads) to store the name using only the required number of bytes, along with an index file to assist access into the cache (because each read is no longer a known offset into it). - NEW: Added a new class for handling the indexing. - NEW: Added a unit test for testing the cache and indexing of reads. ------------------------------------------------------------------------ r43 | imilne | 2009-05-07 11:59:30 +0100 (Thu, 07 May 2009) | 2 lines - NEW: The consensus and scale canvases now fit the same dimensions as the reads canvas (with or without the vertical scrollbar). - NEW: Double clicking on the overview canvas now toggles between the two overview graphical styles. ------------------------------------------------------------------------ r42 | imilne | 2009-05-07 11:16:07 +0100 (Thu, 07 May 2009) | 1 line - NEW: Added a mouse tracker to the scale canvas to update its nucleotide position information. ------------------------------------------------------------------------ r41 | imilne | 2009-05-07 11:07:01 +0100 (Thu, 07 May 2009) | 1 line - NEW: Added a mouse tracker to the consensus canvas that updates the scale canvas's nucleotide position information. ------------------------------------------------------------------------ r40 | imilne | 2009-05-07 09:51:10 +0100 (Thu, 07 May 2009) | 3 lines - BUG: The RHS scale-bar value was incorrect. - NEW: The scale canvas's tracking information now overwrites the LHS/RHS values when it gets close to them. - CHG: Updated the code that determines the pX2 RHS canvas position to calculate short canvas sizes as it is calculated. ------------------------------------------------------------------------ r39 | imilne | 2009-05-07 08:22:39 +0100 (Thu, 07 May 2009) | 3 lines - CHG: The build file now produces debug compatible classes (for line numbering). - NEW: Added mouse tracking to the scale bar for the base position under the mouse. - CHG: Tidied up the way the AssemblyPanel class instantiates its child panels. ------------------------------------------------------------------------ r38 | imilne | 2009-05-06 14:03:32 +0100 (Wed, 06 May 2009) | 1 line - NEW: Started working on a scale bar for showing nucleotide base positions. ------------------------------------------------------------------------ r37 | imilne | 2009-05-06 09:29:06 +0100 (Wed, 06 May 2009) | 1 line - NEW: Renaming the project to "Tablet". ------------------------------------------------------------------------ r36 | imilne | 2009-05-06 09:09:28 +0100 (Wed, 06 May 2009) | 1 line - NEW: Renaming the project to "Tablet". ------------------------------------------------------------------------ r35 | imilne | 2009-05-06 09:06:07 +0100 (Wed, 06 May 2009) | 1 line - NEW: Renaming the project to "Tablet". ------------------------------------------------------------------------ r34 | imilne | 2009-05-06 09:02:23 +0100 (Wed, 06 May 2009) | 1 line - NEW: Renaming the project to "Tablet" (may take several commits). ------------------------------------------------------------------------ r33 | imilne | 2009-05-04 15:32:23 +0100 (Mon, 04 May 2009) | 2 lines - NEW: Added rendering of the base quality scores for the consensus sequence, coloured red (low) to green (high). - BUG: Resizing of the consensus canvas/panel now works correctly when the zoom level is changed. ------------------------------------------------------------------------ r32 | imilne | 2009-05-04 11:46:44 +0100 (Mon, 04 May 2009) | 1 line - NEW: Reads offset from the consensus are now highlighted by drawing the background of the canvas under them in a different colour from the main area. ------------------------------------------------------------------------ r31 | imilne | 2009-05-01 14:48:39 +0100 (Fri, 01 May 2009) | 1 line - NEW: Implemented an additional method for generating overviews that displays pixels based on the percentage coverage of data (against no data) for the region represented by any given overview pixel. ------------------------------------------------------------------------ r30 | imilne | 2009-05-01 11:25:33 +0100 (Fri, 01 May 2009) | 2 lines - NEW: Added mouse dragging navigation to the overview canvas. - BUG: Fixed a bug in the overview creation due to not taking consensus offsets into account. ------------------------------------------------------------------------ r29 | imilne | 2009-05-01 10:12:04 +0100 (Fri, 01 May 2009) | 2 lines - NEW: The overview canvas is now created in a buffer first, then painted to screen. - NEW: The tracking co-ordinates of the main canvas are fed to the overview for highlighting. ------------------------------------------------------------------------ r28 | imilne | 2009-04-30 15:45:53 +0100 (Thu, 30 Apr 2009) | 1 line - NEW: Added the first (messy) attempt at an overview canvas. It will only refresh on a mouse over (the main canvas). ------------------------------------------------------------------------ r27 | imilne | 2009-04-30 10:20:05 +0100 (Thu, 30 Apr 2009) | 1 line - BUG: String splitting on multiple spaces was failing for certain ACE file inputs. ------------------------------------------------------------------------ r26 | imilne | 2009-04-29 13:51:51 +0100 (Wed, 29 Apr 2009) | 3 lines - NEW: Improved the highlighting of regions where a read differs from the consensus. - NEW: Added mouse drag navigation to the main canvas. - NEW: Added (temporary) double-click event handling to the canvas that toggles between packed and stacked view formats. ------------------------------------------------------------------------ r25 | imilne | 2009-04-29 11:33:32 +0100 (Wed, 29 Apr 2009) | 1 line - NEW: Added a list panel down the LHS of the screen to display (and allow selection of) the contigs within the current assembly. ------------------------------------------------------------------------ r24 | imilne | 2009-04-29 10:07:11 +0100 (Wed, 29 Apr 2009) | 3 lines - NEW: Added a status panel for output labels and zoom controls. - NEW: Added the swing-layout.jar file for Netbeans GUI layout. - NEW: The mouse tracking code now searches for the read name from the disk cache. ------------------------------------------------------------------------ r23 | imilne | 2009-04-28 19:40:02 +0100 (Tue, 28 Apr 2009) | 1 line - NEW: Implemented the search code to allow a PackSet to locate a given nucleotide position within any of its reads (using binary search). ------------------------------------------------------------------------ r22 | imilne | 2009-04-28 16:07:27 +0100 (Tue, 28 Apr 2009) | 3 lines - NEW: Added a mouse listener for the reads canvas. - NEW: Added tracking code to highlight (and draw) the read currently under the mouse. This is implemented for the StackSet only (PackSet still to be done). - NEW: Implemented the Flapjack method of main canvas post-rendering via overlays. ------------------------------------------------------------------------ r21 | imilne | 2009-04-28 14:08:24 +0100 (Tue, 28 Apr 2009) | 1 line - NEW: The canvas will now draw the consensus and the reads while taking into account any read offsets that position those reads beyond the bounds of the consensus (either LHS or RHS). In these cases it means the consensus may not start at position 0 of the canvas, nor end at the width of the canvas. ------------------------------------------------------------------------ r20 | imilne | 2009-04-28 11:31:36 +0100 (Tue, 28 Apr 2009) | 2 lines - NEW: Added a simple install4j installer (zip file only). - NEW: The build file will now jar all the files needed for distribution. ------------------------------------------------------------------------ r19 | imilne | 2009-04-28 10:24:26 +0100 (Tue, 28 Apr 2009) | 1 line - NEW: Added colour schemes to do Flapjack-style image rendering. ------------------------------------------------------------------------ r18 | imilne | 2009-04-28 09:02:05 +0100 (Tue, 28 Apr 2009) | 2 lines - NEW: The consensus sequence is now displayed alongside the main set of reads. - NEW: Added basic red colour-coding for likely SNP locations. ------------------------------------------------------------------------ r17 | imilne | 2009-04-27 12:00:12 +0100 (Mon, 27 Apr 2009) | 1 line - NEW: Searching for on-screen reads when using the PackSet layout now uses a binary search. ------------------------------------------------------------------------ r16 | imilne | 2009-04-27 08:46:04 +0100 (Mon, 27 Apr 2009) | 2 lines - NEW: Added the StackSet class for holding and accessing the reads in a stacked (one read per line) format. - NEW: The graphical output now contains a quick display of the actual nucleotide at each position. ------------------------------------------------------------------------ r15 | imilne | 2009-04-24 15:04:13 +0100 (Fri, 24 Apr 2009) | 1 line - BUG: Fixed a problem with setting new values in a sequence (byte/nibble access problems). ------------------------------------------------------------------------ r14 | imilne | 2009-04-24 13:29:47 +0100 (Fri, 24 Apr 2009) | 1 line - NEW: First attempt at extracting and displaying basic data (probably not working). ------------------------------------------------------------------------ r13 | imilne | 2009-04-24 12:09:34 +0100 (Fri, 24 Apr 2009) | 3 lines - NEW: Added a new interface for accessing data from outside of the data package. - NEW: Added packset code for extracting a "window's" worth of data. - NEW: Continuing work on the canvas drawing code (nothing working yet). ------------------------------------------------------------------------ r12 | imilne | 2009-04-22 16:00:38 +0100 (Wed, 22 Apr 2009) | 2 lines - NEW: Added two classes for the storage of reads in a "packed" (tiled) format. Each pack line will hold multiple non-overlapping reads. The PackSet holds all the lines. - NEW: Added code to create the pack set. ------------------------------------------------------------------------ r11 | imilne | 2009-04-22 09:43:16 +0100 (Wed, 22 Apr 2009) | 2 lines - NEW: Implemented setting of base quality scores using the new data storage methods. - NEW: Implemented the post-processing A->dA etc comparisons using the new data storage methods. ------------------------------------------------------------------------ r10 | imilne | 2009-04-21 14:46:49 +0100 (Tue, 21 Apr 2009) | 4 lines - NEW: Major changes to the storage of nucleotide data within the Sequence class and its subclasses, with the information now stored using two nucleotides per byte of data. - CHG: Commented out some of the sections of code that aren't yet compatible with this new method of data storage. - NEW: Added the libraries for unit testing and a simple test case for the Sequence class. - NEW: Started adding classes that will be used for the GUI (Flapjack code). ------------------------------------------------------------------------ r9 | imilne | 2008-11-14 14:15:18 +0000 (Fri, 14 Nov 2008) | 1 line - NEW: Added a basic Ant build file. ------------------------------------------------------------------------ r8 | imilne | 2008-11-13 10:15:20 +0000 (Thu, 13 Nov 2008) | 1 line - NEW: Added the basic classes required to get the start of a GUI up and running. ------------------------------------------------------------------------ r7 | imilne | 2008-11-13 08:59:58 +0000 (Thu, 13 Nov 2008) | 3 lines - CHG: Renamed the IDataCache interface to IReadCache as that more accurately reflects its purpose (for now anyway). - NEW: Added a class to handle post import processing. - NEW: Added a class responsible for comparing every read's base with the corresponding base in that contig's consensus sequence, and encoding any differences back into the read's data. ------------------------------------------------------------------------ r6 | imilne | 2008-11-12 13:41:09 +0000 (Wed, 12 Nov 2008) | 3 lines - NEW: Added methods to the assembly data classes to print out their contents (for debugging). - BUG: The contig reading code was assigning the data for EVERY read to the FIRST read in its set each time, meaning that the other reads never actually stored anything. - CHG: Tidied up some of the parsing code. ------------------------------------------------------------------------ r5 | imilne | 2008-11-12 10:26:22 +0000 (Wed, 12 Nov 2008) | 1 line - CHG: Updated the DNA table to recognise N (unknown) codes, and to make the "not the same" (different from consensus) codes a bit clearer. ------------------------------------------------------------------------ r4 | imilne | 2008-11-11 15:02:58 +0000 (Tue, 11 Nov 2008) | 2 lines - NEW: Added an interface for "caching" data we don't want in memory, and a disk cache implementation of it. - NEW: Added an Assembly class as a main wrapper for all the data that is loaded. ------------------------------------------------------------------------ r3 | imilne | 2008-11-11 08:42:08 +0000 (Tue, 11 Nov 2008) | 2 lines - NEW: Added the source code developed so far (early experimental ACE file reading code). - NEW: Added the usual batch files for testing from the command line. ------------------------------------------------------------------------ r2 | imilne | 2008-11-11 08:33:20 +0000 (Tue, 11 Nov 2008) | 1 line - NEW: Added the usual folders for basic project structure (src, classes, lib, etc). ------------------------------------------------------------------------ r1 | imilne | 2008-11-11 08:30:59 +0000 (Tue, 11 Nov 2008) | 1 line - NEW: Initial folder import. ------------------------------------------------------------------------