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JAL 1960 added code to restrict structure chooser to discover only PDB and Uniprot...
[jalview.git] / src / jalview / analysis /
2015-10-28 tcofoegbuJAL-1952 bugfix tree | commitdiff
2015-10-22 tcofoegbuJAL-1479 added basic support for SIFTs mapping - more... tree | commitdiff
2015-10-15 tcofoegbuJAL-1479 refactored SequenceI interface - changed getDB... tree | commitdiff
2015-10-14 tcofoegbuJAL-1926 added supporting model changes to enable savin... tree | commitdiff
2015-10-07 Jim ProcterJAL-1894 source formatting tree | commitdiff
2015-09-14 gmungocJAL-1880 handle sequence offsets properly when mapping... 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
2015-09-09 gmungocJAL-1619 'align protein as cDNA' now leaves unmapped... tree | commitdiff
2015-09-07 gmungocJAL-1636 translate stop codon as '*', mouseover * as... tree | commitdiff
2015-09-07 gmungocJAL-1152 check 'autocalculated' not 'null sequenceRef... tree | commitdiff
2015-08-17 gmungocJAL-1800 separated SearchResults.getCharacters() from... tree | commitdiff
2015-08-10 Jim ProcterJAL-736 relocate group associated conservation symbols... tree | commitdiff
2015-08-10 Jim ProcterJAL-736 source formatting tree | commitdiff
2015-08-07 tcofoegbuJAL-1824 updated caching procedure for pdb entries... tree | commitdiff
2015-07-23 Jim ProcterJAL-1819 use Float.isNaN() to check for NaNs! tree | commitdiff
2015-07-08 gmungocJAL-1759 merge from develop tree | commitdiff
2015-07-01 gmungocJAL-1681 more condensed tooltip where codons share... tree | commitdiff
2015-06-05 Jim ProcterMerge branch 'develop' into features/JAL-653_gffalignments tree | commitdiff
2015-06-05 Jim ProcterJAL-1115 JAL-653 partial introduction of List interface... tree | commitdiff
2015-06-04 gmungocJAL-1750 small tidy of AlignSeq.printMapping (+Junit) tree | commitdiff
2015-06-04 gmungocJAL-1544 spelling in javadoc only tree | commitdiff
2015-05-29 Jim ProcterMerge branch 'JAL-1755_npe_groupconsensus' into develop tree | commitdiff
2015-05-29 Jim ProcterJAL-1755 fix for NPE when setting up temporary variables tree | commitdiff
2015-05-15 gmungocJAL-1737 ignore non-positional annotations for display tree | commitdiff
2015-05-15 gmungocJAL-1270 added test for regex actually used; include... tree | commitdiff
2015-05-15 gmungocJAL-1270 main methods converted to JUnit tree | commitdiff
2015-05-12 gmungocJAL-1712 fixes/tests for Castor binding and 'show flank... tree | commitdiff
2015-04-21 gmungocJAL-1693 mappings added back to the original alignment tree | commitdiff
2015-04-14 gmungocJAL-1693 generate multiple exon sequences for 1-many... tree | commitdiff
2015-04-13 gmungocJAL-1693 make exon alignment for get-xref splitframe... tree | commitdiff
2015-03-30 gmungocJAL-1264 remove broken applet build dependencies tree | commitdiff
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch tree | commitdiff
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in... tree | commitdiff
2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e... tree | commitdiff
2015-02-19 gmungocJAL-1665 refactored Sequence.getSequenceFeatures features/sequenceFeatureRefactor tree | commitdiff
2015-02-12 Jim ProcterJAL-1350 cloned method and tested equivalence for using... tree | commitdiff
2015-02-12 Jim ProcterJAL-1115 switch to lists in SequenceGroup tree | commitdiff
2015-02-02 Charles OfoegbuMerge branch 'bug/JAL-1644_Finder-logic-improvement... tree | commitdiff
2015-02-02 Charles OfoegbuJAL-1644 added null check for sequence description... tree | commitdiff
2015-02-02 Charles OfoegbuMerge commit tree | commitdiff
2015-02-02 Charles OfoegbuJAL-1644 revised Finder's implementation to use a flag... tree | commitdiff
2015-02-02 Charles OfoegbuMerge branch 'bug/JAL-1644_Finder-logic-improvement... tree | commitdiff
2015-02-02 Charles OfoegbuJAL-1644 improvment of finder logic to include the... tree | commitdiff
2015-01-28 Jim Procter JAL-674 patch to make Mapping.compareTransferredToR... tree | commitdiff
2015-01-07 Jim ProcterJAL-1483 patches to make test case pass: hamming distan... tree | commitdiff
2015-01-07 Jim ProcterJAL-1483 source formatting tree | commitdiff
2015-01-07 Jim ProcterJAL-1483 refactor NJTree constructor to allow preconfig... tree | commitdiff
2015-01-07 Jim ProcterJAL-1483 organise imports tree | commitdiff
2014-12-22 Jim ProcterMerge: 497958b 68dcaa7 tree | commitdiff
2014-12-15 Jim ProcterJAL-1620 version bump and release notes tree | commitdiff
2014-11-27 Jim ProcterJAL-674 add sequence associated annotation rows to... tree | commitdiff
2014-11-23 Jim ProcterMerge branch 'JAL-1569_wuss_vienna_broke' into develop tree | commitdiff
2014-11-23 Jim ProcterMerge branch 'JAL-1569_wuss_vienna_broke' into Release_... tree | commitdiff
2014-11-23 Jim ProcterJAL-1152 avoid NPE on null alignment annotation vector tree | commitdiff
2014-11-20 Jim ProcterJAL-1569 remove log output during RNA secondary structu... tree | commitdiff
2014-11-18 Jim ProcterJAL-674 make temperature factor, local secondary struct... tree | commitdiff
2014-11-14 Jim ProcterMerge branch 'develop' into JAL-1483_featureBasedTreeCalc tree | commitdiff
2014-11-12 Jim ProcterJAL-674 patch broken getMapping function tree | commitdiff
2014-11-04 gmungocJAL-1152 annotation sort algorithm optimisation tree | commitdiff
2014-11-03 gmungocMerge branch 'features/JAL-1152annotationSorting' of... tree | commitdiff
2014-11-03 gmungocJAL-1152 annotation sorting preferences and help docume... tree | commitdiff
2014-11-03 Jim ProcterMerge branch 'develop' into features/JAL-1152annotation... tree | commitdiff
2014-10-31 gmungocJAL-1152 bug fix for 'no sort' case + tests for autocal... tree | commitdiff
2014-10-31 gmungocJAL-1152 menu tweaks plus new option to put Autocalc... tree | commitdiff
2014-10-30 gmungocJAL-1152 with sticky annotation sort order that updates... tree | commitdiff
2014-10-30 Jim ProcterJAL-674 return original and replacement sequences and... tree | commitdiff
2014-10-30 gmungocJAL-1152 prototype of new Annotations menu with sort... tree | commitdiff
2014-10-23 gmungocJAL-1264 further refactoring and tests tree | commitdiff
2014-10-21 Jim ProcterJAL-674 JAL-1551 imports dropped during merge tree | commitdiff
2014-10-21 Jim ProcterJAL-674 patch for duplicate row bug tree | commitdiff
2014-10-21 Jim ProcterJAL-674 patch to ensure existing annotation is properly... tree | commitdiff
2014-10-21 Jim ProcterJAL-674 JAL-207 getTers for aligned sequences in datase... tree | commitdiff
2014-10-21 Jim ProcterJAL-674 refactor method to match and transfer annotatio... tree | commitdiff
2014-09-23 darolmarJAL-1355 tree | commitdiff
2014-08-08 j.procter@dundee... JAL-1483 reformatting and use new feature renderer... tree | commitdiff
2014-06-13 Jim ProcterMerge branch 'Release_2_8_2_Branch' into JAL-1483_featu... tree | commitdiff
2014-06-06 Jim ProcterJAL-1517 source formatting tree | commitdiff
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2 tree | commitdiff
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2 tree | commitdiff
2014-06-05 Jim ProcterMerge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch tree | commitdiff
2014-05-22 Jim ProcterJAL-1503 update version in GPL header tree | commitdiff
2014-05-02 Jim ProcterMerge branch 'JAL-1397' into develop tree | commitdiff
2014-05-01 Jim Proctermake sure valid value for non-gapped calculation with... tree | commitdiff
2014-04-21 Jim ProcterMerge branch 'jims_marckhacks' into develop tree | commitdiff
2014-04-21 Jim ProcterJAL-1466 don't include empty columns if no upstream... tree | commitdiff
2014-04-21 Jim ProcterJAL-1483 cut and paste from SW score model to allow... tree | commitdiff
2014-04-21 Jim ProcterJAL-736 hack to show the conserved property values... tree | commitdiff
2014-04-21 Jim ProcterJAL-1427 make sure we are working with dataset sequence... tree | commitdiff
2014-04-21 Jim ProcterJAL-1481 relevant todo re warning user for broken regex tree | commitdiff
2014-04-21 Jim ProcterJAL-1466 improved test and patched off by one that... tree | commitdiff
2014-04-21 Jim ProcterJAL-1466 new calculation menu option to recover the... tree | commitdiff
2014-04-21 Jim ProcterJAL-1473 refactor score matrices and tree score calcula... tree | commitdiff
2014-02-25 Jim ProcterMerge branch 'JAL-1454_patch' into develop tree | commitdiff
2014-02-25 Jim ProcterJAL-1454 catch exceptions during calculation and report... tree | commitdiff
2014-02-18 Jim ProcterMerge branch 'JAL-1445' into develop tree | commitdiff
2014-02-03 Jim ProcterMerge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge tree | commitdiff
2014-01-29 Jim ProcterJAL-1432 updated copyright notices tree | commitdiff
2013-10-16 Jim ProcterMerge branch 'JAL-1395' into develop tree | commitdiff
2013-10-16 Jim ProcterJAL-1395 do not calculate non-gap consensus when no... tree | commitdiff
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