JAL-1369 jalview2xml tests need to be run sequentially
[jalview.git] / src /
2016-05-20 gmungocJAL-2114 accept "<123..178" or "123..>178" format
2016-05-19 gmungocJAL-2114 added single-locus case and more error tests
2016-05-19 gmungocJAL-2114 parser + tests for GenBank location descriptors
2016-05-18 tcofoegbumerge
2016-05-18 tcofoegbuJAL-1563 smarter support for advanced querying of Unipr...
2016-05-18 gmungocJAL-2049 set sequence feature group to "Jalview" for...
2016-05-18 gmungocJAL-2049 use HGVS notation for variant on protein residue
2016-05-17 tcofoegbuJAL-2106 JAL-1926 updated source doc for set/getSourceDBRef
2016-05-17 tcofoegbumerge
2016-05-17 tcofoegbuJAL-1270 Fixed anntatedPDBFileInputTest and updated...
2016-05-13 gmungocJAL-2105 capture Ensembl data version, check REST versi...
2016-05-12 gmungocJAL-2104 format tooltips to wrap correctly
2016-05-09 tcofoegbumerge
2016-05-09 tcofoegbuJAL-2101 JAL-2071 JAL-1563 Added fix to enable searchin...
2016-05-09 tcofoegbuJAL-2102 implemented improvement to round FTS's numberi...
2016-05-09 gmungocJAL-2098 identify feature file with "<" in feature...
2016-05-09 gmungocJAL-2018 export graduated feature colours correctly
2016-05-06 Jim ProcterJAL-192 fix javadoc
2016-05-06 Jim ProcterJAL-192 JAL-2099 unused variables
2016-05-06 Jim ProcterJAL-1551 formatting
2016-05-06 Jim ProcterJAL-192 JAL-2099 reuse refactored scale code for wrappe...
2016-05-06 Jim ProcterJAL-192 JAL-2099 factored out calculation from renderin...
2016-05-06 Jim ProcterJAL-192 JAL-2099 factored out calculation from renderin...
2016-05-06 Jim ProcterJAL-192 JAL-2099 factored out calculation from renderin...
2016-05-06 Jim ProcterJAL-2100 centre triangles on hidden column vertical...
2016-05-06 Jim ProcterJAL-2100 optimisation
2016-05-06 Jim ProcterJAL-2100 triangles shown below in jvdesktop unwrapped...
2016-05-06 Jim ProcterJAL-192 patch off-by-one for pathological gap case
2016-05-05 Jim ProcterJAL-192 patch for off-by one and pathological case...
2016-05-04 gmungocJAL-2092 hide columns with/without feature
2016-05-04 gmungocMerge branch 'groovy/JAL-2074_upgradeto2.4.4' into...
2016-05-04 tcofoegbumerge
2016-05-04 tcofoegbuJAL-1563 JAL-2091 Added total result count to Uniprot...
2016-05-04 gmungocJAL-2090 removed test for Java > 1.1 to enable transparency
2016-05-03 gmungocJAL-2050 hide introns also when fetching Ensembl xrefs...
2016-05-03 tcofoegbuJAL-2091 disable pagination buttons during initialisation
2016-05-03 tcofoegbuJAL-1563 JAL-2091 Added generic pagination for FTS...
2016-05-02 tcofoegbuJAL-1563 Fixed Uniprot FTS result-set count error,...
2016-05-02 gmungocJAL-1812 bind Groovy to Jalview rather than Desktop...
2016-04-29 tcofoegbumerge
2016-04-29 tcofoegbuJAL-1563 house keeping/updated API doc for new method... merge/JAL-1563_uniprot-free-text-search
2016-04-29 tcofoegbuJAL-1563 Further increased swing timer for search textf...
2016-04-29 gmungocJAL-2051 better checking of retrieved / duplicated...
2016-04-29 gmungocMerge branch 'develop' of https://source.jalview.org...
2016-04-29 Jim ProcterJAL-192 need visible and actual sequence limits for...
2016-04-29 Jim ProcterJAL-192 fix bounds when no hidden regions, and when...
2016-04-29 Jim ProcterJAL-192 scale origin relative to start of reference...
2016-04-29 Jim ProcterJAL-966 JAL-1553
 todo: remove UI components from Colum...
2016-04-29 Jim ProcterJAL-1551 formatting

2016-04-29 Jim ProcterJAL-192 ‘efficiently’ locate visible bounds for a seque...
2016-04-29 Jim ProcterJAL-1551 formatting
2016-04-29 gmungocMerge branch 'develop' of https://source.jalview.org...
2016-04-28 tcofoegbuJAL-1563 increased swing timer for search action from...
2016-04-28 gmungocJAL-2083 removed use of reflection for Groovy
2016-04-28 tcofoegbuJAL-1563 Implemented hack to make table both scrollable...
2016-04-27 tcofoegbuJAL-1563 Added Id (Uniprot Id) to the dynamic column...
2016-04-27 Jim ProcterJAL-192 fix off-by-one for alignment ruler with no...
2016-04-27 Jim ProcterJAL-192 show reference sequence position and residue...
2016-04-27 tcofoegbuJAL-1563 Added fix to prevent swing timer from reinitia...
2016-04-27 Jim ProcterJAL-1366 JAL-2086 reinstate bolding of reference sequence
2016-04-27 Jim ProcterJAL-2085 JAL-2086 fix hiddenRepSequence and new referen...
2016-04-27 tcofoegbuJAL-1563 Modified Uniprot data column configurations...
2016-04-27 tcofoegbure-enabled new uniprot sequence fetcher on spike branch
2016-04-26 Jim ProcterJAL-2079 fix broken cherry-pick conflict merge
2016-04-26 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie...
2016-04-26 Jim ProcterJAL-2079 use new service to retrieve Rfam Seed alignment
2016-04-26 Jim ProcterJAL-2079 disable RFAM(Full) source until we can retriev...
2016-04-26 Jim ProcterJAL-2079 update URL for RFAM and PFAM sources
2016-04-26 tcofoegbumerge
2016-04-26 Jim ProcterJAL-2079 allow prefix+<XFAMID>+suffix type URL signature
2016-04-26 tcofoegbuJAL-1563 reverted to old uniprot fetcher to enable...
2016-04-26 Jim ProcterJAL-2077 reinstate JAL-1554 fix for left-then-right...
2016-04-26 Jim ProcterJAL-2077 reinstate annotation label popup by handling...
2016-04-26 gmungocJAL-1981 catch any exception when setting QuaQua look...
2016-04-26 Jim ProcterMerge branch 'develop' into groovy/JAL-2074_upgradeto2.4.4 groovy/JAL-2074_upgradeto2.4.4
2016-04-26 tcofoegbumerge
2016-04-26 tcofoegbuJAL-2071 improvement to get column data files as InputS...
2016-04-26 gmungocMerge branch 'develop' of https://source.jalview.org...
2016-04-26 tcofoegbuJAL-2071 changed extension for data column config files
2016-04-26 gmungocMerge branch 'develop' of https://source.jalview.org...
2016-04-26 tcofoegbuJAL-2071 resolved fts data column config file path...
2016-04-26 tcofoegbuJAL-2071 House keeping
2016-04-26 tcofoegbuJAL-2071 improvement to reduce webservice requests...
2016-04-25 Jim ProcterJAL-2074 disable security manager at start up re: lopic...
2016-04-25 tcofoegbudevelop merge
2016-04-25 tcofoegbudevelop merge
2016-04-25 tcofoegbuJAL-2071 added unit tests for FTSRestClient features/JAL-1563_uniprot-free-text-search
2016-04-25 gmungocJAL-1812 JAL-2068 only allow one Groovy console open...
2016-04-24 Jim ProcterJAL-1551 JAL-2077 formatting
2016-04-24 Jim ProcterJAL-2077 - reinstate popups on osx
2016-04-24 Jim ProcterMerge branch 'JAL-2075_features_hiddeng' into develop
2016-04-24 Jim ProcterJAL-2075 make GroovyConsole a singleton so tests requir...
2016-04-23 Jim ProcterJAL-2075 fix: use AlignmentView.getVisibleContigs and...
2016-04-23 Jim ProcterJAL-2075 findPosition for SeqCigar (with test)
2016-04-23 Jim ProcterJAL-2075 formatting
2016-04-22 tcofoegbuJAL-1563 JAL-2071 Update and completed implementation...
2016-04-22 tcofoegbuJAL-2071 further refactoring, optimisation, and house...
2016-04-22 gmungocJAL-1812 JAL-2068 add Run Groovy Script to AlignFrame...
2016-04-22 gmungocJAL-2068 code and test for case of minValue == maxValue
2016-04-22 gmungocJAL-2068 framework and example scripts for pluggable...
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