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2016-05-13 Jim ProcterJAL-2103 propagate inserts only used for reconstructing... features/JAL-2103 commit | commitdiff | tree | snapshot
2016-05-13 Jim ProcterJAL-2103 always remove gaps from input sequence, then... commit | commitdiff | tree | snapshot
2016-05-12 Jim ProcterJAL-2103 patch routine for inserting gaps for hidden... commit | commitdiff | tree | snapshot
2016-05-12 Jim ProcterJAL-2103 typo and more explicit javadoc commit | commitdiff | tree | snapshot
2016-05-12 Jim ProcterJAL-2103 fix test commit | commitdiff | tree | snapshot
2016-05-12 Jim ProcterJAL-2103 fallback to returning trimmed profile if full... commit | commitdiff | tree | snapshot
2016-05-12 Jim ProcterJAL-2103 - refactored msa transformation routines and... commit | commitdiff | tree | snapshot
2016-05-10 Jim ProcterJAL-2103 don’t get full-width alignment if MSA based... commit | commitdiff | tree | snapshot
2016-05-10 Jim ProcterJAL-2103 extracted result processing code to allow... commit | commitdiff | tree | snapshot
2016-05-10 Jim ProcterJAL-2103 reinstate legacy behaviour (when full_MSA... commit | commitdiff | tree | snapshot
2016-05-10 Jim ProcterJAL-2103 proof of concept - patch to retrieve full... commit | commitdiff | tree | snapshot
2016-05-10 Jim ProcterJAL-1551 formatting commit | commitdiff | tree | snapshot
2016-05-09 gmungocJAL-2098 identify feature file with "<" in feature... commit | commitdiff | tree | snapshot
2016-05-09 gmungocJAL-2018 export graduated feature colours correctly commit | commitdiff | tree | snapshot
2016-05-06 Jim ProcterMerge branch 'features/JAL-192_scalerelativetoseq'... commit | commitdiff | tree | snapshot
2016-05-06 Jim ProcterJAL-192 fix javadoc commit | commitdiff | tree | snapshot
2016-05-06 Jim ProcterJAL-192 JAL-2099 unused variables commit | commitdiff | tree | snapshot
2016-05-06 Jim ProcterJAL-1551 formatting commit | commitdiff | tree | snapshot
2016-05-06 Jim ProcterJAL-192 JAL-2099 reuse refactored scale code for wrappe... commit | commitdiff | tree | snapshot
2016-05-06 Jim ProcterJAL-192 JAL-2099 factored out calculation from renderin... commit | commitdiff | tree | snapshot
2016-05-06 Jim ProcterJAL-192 JAL-2099 factored out calculation from renderin... commit | commitdiff | tree | snapshot
2016-05-06 Jim ProcterJAL-192 JAL-2099 factored out calculation from renderin... commit | commitdiff | tree | snapshot
2016-05-06 Jim ProcterJAL-2100 centre triangles on hidden column vertical... commit | commitdiff | tree | snapshot
2016-05-06 Jim ProcterJAL-2100 optimisation commit | commitdiff | tree | snapshot
2016-05-06 Jim ProcterJAL-2100 triangles shown below in jvdesktop unwrapped... commit | commitdiff | tree | snapshot
2016-05-06 Jim ProcterJAL-192 patch off-by-one for pathological gap case commit | commitdiff | tree | snapshot
2016-05-05 gmungocJAL-2068 better documentation in example script commit | commitdiff | tree | snapshot
2016-05-05 Jim ProcterJAL-192 patch for off-by one and pathological case... commit | commitdiff | tree | snapshot
2016-05-04 gmungocMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-05-04 gmungocJAL-2074 reinstated xerces-impl.jar commit | commitdiff | tree | snapshot
2016-05-04 Jim ProcterRevert "JAL-2074 removed xerces to explore wierdness" commit | commitdiff | tree | snapshot
2016-05-04 gmungocJAL-2092 hide columns with/without feature commit | commitdiff | tree | snapshot
2016-05-04 gmungocJAL-2074 corrected classpathentry for Groovy 2.4.6 commit | commitdiff | tree | snapshot
2016-05-04 gmungocMerge branch 'groovy/JAL-2074_upgradeto2.4.4' into... commit | commitdiff | tree | snapshot
2016-05-04 tcofoegbumerge commit | commitdiff | tree | snapshot
2016-05-04 tcofoegbuJAL-1563 JAL-2091 Added total result count to Uniprot... commit | commitdiff | tree | snapshot
2016-05-04 gmungocJAL-2090 removed test for Java > 1.1 to enable transparency commit | commitdiff | tree | snapshot
2016-05-03 gmungocJAL-2050 hide introns also when fetching Ensembl xrefs... commit | commitdiff | tree | snapshot
2016-05-03 Jim ProcterMerge branch 'r291_docs' into develop commit | commitdiff | tree | snapshot
2016-05-03 tcofoegbuJAL-2091 disable pagination buttons during initialisation commit | commitdiff | tree | snapshot
2016-05-03 tcofoegbuJAL-1563 JAL-2091 Added generic pagination for FTS... commit | commitdiff | tree | snapshot
2016-05-02 tcofoegbuJAL-1563 Fixed Uniprot FTS result-set count error,... commit | commitdiff | tree | snapshot
2016-05-02 Jim ProcterJAL-1270 move some Network tests to External (require... commit | commitdiff | tree | snapshot
2016-05-02 Jim ProcterJAL-1270 capitalise test groups commit | commitdiff | tree | snapshot
2016-05-02 Jim ProcterJAL-2089 JAL-1551 formatting commit | commitdiff | tree | snapshot
2016-05-02 Jim ProcterJAL-2089 release 2.9.1 entry in release notes commit | commitdiff | tree | snapshot
2016-04-29 tcofoegbumerge commit | commitdiff | tree | snapshot
2016-04-29 tcofoegbuJAL-1563 house keeping/updated API doc for new method... merge/JAL-1563_uniprot-free-text-search commit | commitdiff | tree | snapshot
2016-04-29 tcofoegbuJAL-1563 Further increased swing timer for search textf... commit | commitdiff | tree | snapshot
2016-04-29 gmungocJAL-2051 better checking of retrieved / duplicated... commit | commitdiff | tree | snapshot
2016-04-29 gmungocMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-04-29 Jim ProcterMerge branch 'features/JAL-192_scalerelativetoseq'... commit | commitdiff | tree | snapshot
2016-04-29 Jim ProcterJAL-192 need visible and actual sequence limits for... commit | commitdiff | tree | snapshot
2016-04-29 Jim ProcterJAL-192 fix bounds when no hidden regions, and when... commit | commitdiff | tree | snapshot
2016-04-29 Jim ProcterJAL-192 scale origin relative to start of reference... commit | commitdiff | tree | snapshot
2016-04-29 Jim ProcterJAL-966 JAL-1553
 todo: remove UI components from Colum... commit | commitdiff | tree | snapshot
2016-04-29 Jim ProcterJAL-1551 formatting
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2016-04-29 Jim ProcterJAL-192 ‘efficiently’ locate visible bounds for a seque... commit | commitdiff | tree | snapshot
2016-04-29 Jim ProcterJAL-1551 formatting commit | commitdiff | tree | snapshot
2016-04-29 gmungocMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-04-28 tcofoegbuJAL-1563 increased swing timer for search action from... commit | commitdiff | tree | snapshot
2016-04-28 gmungocJAL-2083 removed use of reflection for Groovy commit | commitdiff | tree | snapshot
2016-04-28 tcofoegbuJAL-1563 fixed failing tests for FTS Rest Client core commit | commitdiff | tree | snapshot
2016-04-28 tcofoegbuJAL-1563 Increased default response size to 500, and... commit | commitdiff | tree | snapshot
2016-04-28 tcofoegbuJAL-1563 Implemented hack to make table both scrollable... commit | commitdiff | tree | snapshot
2016-04-27 tcofoegbuJAL-1563 Added Id (Uniprot Id) to the dynamic column... commit | commitdiff | tree | snapshot
2016-04-27 Jim ProcterMerge branch 'features/JAL-192_scalerelativetoseq'... commit | commitdiff | tree | snapshot
2016-04-27 Jim ProcterJAL-192 fix off-by-one for alignment ruler with no... commit | commitdiff | tree | snapshot
2016-04-27 Jim ProcterMerge branch 'features/JAL-192_scalerelativetoseq'... commit | commitdiff | tree | snapshot
2016-04-27 Jim ProcterJAL-192 show reference sequence position and residue... commit | commitdiff | tree | snapshot
2016-04-27 tcofoegbuJAL-1563 Added fix to prevent swing timer from reinitia... commit | commitdiff | tree | snapshot
2016-04-27 Jim ProcterJAL-1366 JAL-2086 reinstate bolding of reference sequence commit | commitdiff | tree | snapshot
2016-04-27 Jim ProcterJAL-2085 JAL-2086 fix hiddenRepSequence and new referen... commit | commitdiff | tree | snapshot
2016-04-27 tcofoegbuJAL-1563 further modificaiton of the uniprot data colum... commit | commitdiff | tree | snapshot
2016-04-27 tcofoegbuJAL-1563 Modified Uniprot data column configurations... commit | commitdiff | tree | snapshot
2016-04-27 tcofoegbure-enabled new uniprot sequence fetcher on spike branch commit | commitdiff | tree | snapshot
2016-04-26 Jim ProcterJAL-2079 fix broken cherry-pick conflict merge commit | commitdiff | tree | snapshot
2016-04-26 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie... commit | commitdiff | tree | snapshot
2016-04-26 Jim ProcterJAL-2079 update GPL header for new Xfam tests commit | commitdiff | tree | snapshot
2016-04-26 Jim ProcterJAL-2079 use new service to retrieve Rfam Seed alignment commit | commitdiff | tree | snapshot
2016-04-26 Jim ProcterJAL-2084 JAL-2079 removed RFAM(Full) from Xfam Network... commit | commitdiff | tree | snapshot
2016-04-26 Jim ProcterJAL-2079 disable RFAM(Full) source until we can retriev... commit | commitdiff | tree | snapshot
2016-04-26 Jim ProcterJAL-2079 update URL for RFAM and PFAM sources commit | commitdiff | tree | snapshot
2016-04-26 tcofoegbumerge commit | commitdiff | tree | snapshot
2016-04-26 Jim ProcterJAL-2079 allow prefix+<XFAMID>+suffix type URL signature commit | commitdiff | tree | snapshot
2016-04-26 tcofoegbuJAL-1563 reverted to old uniprot fetcher to enable... commit | commitdiff | tree | snapshot
2016-04-26 Jim ProcterJAL-2077 reinstate JAL-1554 fix for left-then-right... commit | commitdiff | tree | snapshot
2016-04-26 Jim ProcterJAL-2077 reinstate annotation label popup by handling... commit | commitdiff | tree | snapshot
2016-04-26 gmungocJAL-1981 catch any exception when setting QuaQua look... commit | commitdiff | tree | snapshot
2016-04-26 Jim ProcterMerge branch 'develop' into groovy/JAL-2074_upgradeto2.4.4 groovy/JAL-2074_upgradeto2.4.4 commit | commitdiff | tree | snapshot
2016-04-26 Jim ProcterMerge branch 'bug/JAL-2080_javaws_slow_291' into develop commit | commitdiff | tree | snapshot
2016-04-26 Jim ProcterJAL-2080 removed all 'Class-Path' references in libs commit | commitdiff | tree | snapshot
2016-04-26 Jim ProcterJAL-2080 removed classpath references to Xerces and... commit | commitdiff | tree | snapshot
2016-04-26 Jim ProcterJAL-2080 mark jalview.jar as main jar resource commit | commitdiff | tree | snapshot
2016-04-26 tcofoegbumerge commit | commitdiff | tree | snapshot
2016-04-26 tcofoegbuJAL-2071 improvement to get column data files as InputS... commit | commitdiff | tree | snapshot
2016-04-26 gmungocMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-04-26 tcofoegbuJAL-2071 changed extension for data column config files commit | commitdiff | tree | snapshot
2016-04-26 gmungocMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-04-26 tcofoegbuJAL-2071 resolved fts data column config file path... commit | commitdiff | tree | snapshot
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