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JAL-2403 improved ScoreModelI hierarchy as per Kira's review suggestions
[jalview.git] / src / jalview / io /
2015-10-05 Jim ProcterMerge branch 'develop' into features/JAL-1912_biojson... tree | commitdiff
2015-10-05 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch tree | commitdiff
2015-10-05 tcofoegbuJAL-1908 bugfix tree | commitdiff
2015-10-05 tcofoegbuJAL-1912 updated AnnotationDisplaySettingPojo tree | commitdiff
2015-10-01 tcofoegbuJAL-1912 Double.NaN breaks JSON serialization - added... tree | commitdiff
2015-10-01 tcofoegbuJAL-1912 refactor annotation refsequence assignemnt... tree | commitdiff
2015-09-30 tcofoegbuJAL-1912 added support of tcoffee annotation and other... tree | commitdiff
2015-09-29 tcofoegbuJAL-1896 fixed NPE for RNA Helice without equivalent... tree | commitdiff
2015-09-28 tcofoegbuJAL-1896 revised implementation to construct a ColourSc... tree | commitdiff
2015-09-25 tcofoegbuJAL-1907 bugfix for NPE while parsing a features file tree | commitdiff
2015-09-24 gmungocJAL-1904 parse feature file colours on to alignment... tree | commitdiff
2015-09-24 tcofoegbuJAL-1896 bugfix to enabled Jalview restore clustal... tree | commitdiff
2015-09-22 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch tree | commitdiff
2015-09-16 tcofoegbuJAL-1486 off-by-one error bugfix tree | commitdiff
2015-09-16 tcofoegbuJAL-1881 Bugfix for annotation import from BioJS tree | commitdiff
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin... tree | commitdiff
2015-09-10 Jim ProcterJAL-1645 licencing for new files in src tree | commitdiff
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports tree | commitdiff
2015-09-07 tcofoegbuJAL-1831 updated BioJSON schema tree | commitdiff
2015-09-05 Jim ProcterMerge branch 'bugfix/JAL-841_JAL-1081' into develop tree | commitdiff
2015-09-04 tcofoegbuJAL-793 added ability to visualise raw BioJSON in the... tree | commitdiff
2015-09-03 Jim ProcterJAL-1863 allow RNA secondary structure rows exported... tree | commitdiff
2015-09-03 tcofoegbumerge tree | commitdiff
2015-09-03 tcofoegbuJAL-793 use default custom export settings for html... tree | commitdiff
2015-09-03 gmungocMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2015-09-02 tcofoegbuJAL-1740 migrated BioJSMSAViewer git repo to https... tree | commitdiff
2015-09-02 gmungocJAL-1544 spelling tree | commitdiff
2015-09-02 gmungocJAL-1355 User error text externalised to message bundle tree | commitdiff
2015-08-26 gmungocJAL-1830 dropped reference counts for mappings, instead... tree | commitdiff
2015-08-24 tcofoegbuJAL-1641 externalised save_as_biojs_html tree | commitdiff
2015-08-21 tcofoegbuJAL-1443 bug fix for loading pasted alignments from... tree | commitdiff
2015-08-21 tcofoegbuJAL-1831 updated json schema doc tree | commitdiff
2015-08-18 tcofoegbuJAL-1861 bugfix to allow parsing of stockholm files... tree | commitdiff
2015-08-18 tcofoegbuJAL-1835 added UI for BioJSON embbeding preference tree | commitdiff
2015-08-18 tcofoegbuJAL-1835 made BioJSON embedding to html exports configu... tree | commitdiff
2015-08-14 tcofoegbuJAL-1831 added changes to allow auto-generation of... tree | commitdiff
2015-08-13 tcofoegbuJAL-1641 added type to BioJSON sequence object and... tree | commitdiff
2015-08-11 tcofoegbumerge tree | commitdiff
2015-08-11 tcofoegbuadd ability to launch jalview from exported html +... tree | commitdiff
2015-08-10 Jim ProcterMerge branch 'release/2_9_documentation' into develop tree | commitdiff
2015-08-10 tcofoegbuJAL-1486 fixed flatfile output of visible region for... tree | commitdiff
2015-08-07 tcofoegbuJAL-1824 updated caching procedure for pdb entries... tree | commitdiff
2015-08-04 tcofoegbuJAL-1816 fixed bug in identify file preventing it from... tree | commitdiff
2015-07-30 tcofoegbuJAL-1443 modified exception notifications tree | commitdiff
2015-07-23 tcofoegbuResolved merge conflict in EdtiCommandTest.java tree | commitdiff
2015-07-23 tcofoegbuJAL-1819 Test cases for Identify file tree | commitdiff
2015-07-23 Jim ProcterMerge branch 'bug/JAL-1819_isNaN' into Release_2_9_Branch tree | commitdiff
2015-07-23 Jim ProcterMerge branch 'bug/JAL-1819_isNaN' into develop tree | commitdiff
2015-07-23 Jim ProcterJAL-1819 commented out debugging message to stderr bug/JAL-1819_isNaN tree | commitdiff
2015-07-23 Jim ProcterJAL-1551 JAL-1819 formatting/imports tree | commitdiff
2015-07-23 Jim ProcterJAL-1819 use Float.isNaN() to check for NaNs! tree | commitdiff
2015-07-21 tcofoegbuJAL-1443 bugfix to prevent loading of unidentifiable... tree | commitdiff
2015-07-09 tcofoegbuJAL-1806 bug fix to loop through the entire data file... tree | commitdiff
2015-07-08 gmungocJAL-1759 merge from develop tree | commitdiff
2015-07-02 tcofoegbuJAL-1443 data validation for empty content before loadi... tree | commitdiff
2015-07-01 tcofoegbuhouse keeping tree | commitdiff
2015-06-30 tcofoegbuJAL-1641 round trip test/refactoring tree | commitdiff
2015-06-30 Jim ProcterJAL-1682 JAL-1645 remove references to 2.8.3 tree | commitdiff
2015-06-28 Jim ProcterJAL-1421 todo: remove java.util.Vector from jalview... tree | commitdiff
2015-06-26 Jim ProcterJAL-1705 - allow a FileParse to be constructed directly... tree | commitdiff
2015-06-26 tcofoegbuJAL-1641 fixed broken functionalities after refactor tree | commitdiff
2015-06-25 Jim ProcterMerge branch 'develop' into features/JAL-653_JAL-1766_h... tree | commitdiff
2015-06-25 Jim ProcterJAL-1780 JAL-653 JAL-1892 brackets in wrong place broke... tree | commitdiff
2015-06-25 Jim ProcterMerge branch 'develop' into features/JAL-653_JAL-1766_h... tree | commitdiff
2015-06-24 Jim ProcterJAL-653 JAL-1780 JAL-1892 fix jalviewLite compilation tree | commitdiff
2015-06-23 Jim ProcterMerge branch 'merge/develop_JAL-1780_JAL-653_JAL-1892... tree | commitdiff
2015-06-23 Jim ProcterJAL-1782 JAL-1780 JAL-653 JAL-1892 update patched refac... tree | commitdiff
2015-06-22 Jim ProcterJAL-1780 JAL-653 Format/AppletFormat import and export... tree | commitdiff
2015-06-19 Jim ProcterJAL-653 JAL-1780 refactor getGroups so HTMLfile/JSONfil... tree | commitdiff
2015-06-19 Jim ProcterJAL-1780 JAL-653 organise imports tree | commitdiff
2015-06-19 tcofoegbuJAL-1270 JUnit to TestNG refactoring tree | commitdiff
2015-06-18 Jim ProcterJAL-653 JAL-1780 JAL-1543 javadoc and comment about... tree | commitdiff
2015-06-18 Jim ProcterJAL-1780 JAL-653 moved AlignExportSettings reference... tree | commitdiff
2015-06-17 Jim ProcterJAL-1784 minimise data duplication, and report out... tree | commitdiff
2015-06-17 Jim ProcterJAL-1784 refactor parse method to directly parse FilePa... tree | commitdiff
2015-06-17 Jim ProcterMerge branch 'features/JAL-653_gffalignments' into... tree | commitdiff
2015-06-17 Jim ProcterMerge branch 'features/JAL-653_gffalignments' into... tree | commitdiff
2015-06-17 Jim ProcterMerge branch 'develop' into features/JAL-653_gffalignments features/JAL-653_gffalignments tree | commitdiff
2015-06-17 Jim ProcterMerge branch 'develop' into features/JAL-1780_export... tree | commitdiff
2015-06-17 tcofoegbuJAL-1780 more support for export setting for flatfile... features/JAL-1780_export-settings_flatfile tree | commitdiff
2015-06-15 Jim ProcterJAL-1775 FileLoader javadoc tree | commitdiff
2015-06-15 Jim ProcterJAL-1775 fix regression from commit 70f9c4700f20a8fa57e... tree | commitdiff
2015-06-15 tcofoegbuJAL-1641 clean up tree | commitdiff
2015-06-15 tcofoegbuclean up tree | commitdiff
2015-06-12 tcofoegbuJAL-1641 refactor tree | commitdiff
2015-06-11 Jim ProcterJAL-653 tidy comments tree | commitdiff
2015-06-10 tcofoegbuupdated build.xml tree | commitdiff
2015-06-10 tcofoegbuJAL-1641 updated applet version tree | commitdiff
2015-06-09 tcofoegbuJAL-1488 bug-fix for incorrect start/end position in... tree | commitdiff
2015-06-07 Jim ProcterJAL-429 remove pointless code from phylip parser features/JAL-653_rebased_gffalignments tree | commitdiff
2015-06-07 Jim ProcterJAL-653 GFF recognition for identifyFile and format... tree | commitdiff
2015-06-07 Jim ProcterJAL-653 basic GFF3 alignment import wrapper class tree | commitdiff
2015-06-06 Jim ProcterJAL-653 make sure dummy sequences created during GFF... tree | commitdiff
2015-06-06 Jim ProcterJAL-653 first stab at parsing GFF3 pragmas to support... tree | commitdiff
2015-06-06 Jim ProcterJAL-653 gff version number field tree | commitdiff
2015-06-05 tcofoegbuJAL-1760 JAL-1641 Serialisation of Hidden Seqs and... tree | commitdiff
2015-06-05 Jim ProcterJAL-653 set the warningMessage for the file source... tree | commitdiff
2015-06-05 Jim ProcterJAL-653 GFF attributes parsing mechanism, with first... tree | commitdiff
2015-06-05 Jim ProcterJAL-653 trim initial tab in sequence feature ATTRIBUTES tree | commitdiff
2015-06-05 Jim ProcterJAL-653 allow dummy sequences to be created if a sequen... tree | commitdiff
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