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Merge branch 'features/JAL-2446NCList' into spikes/mungo
[jalview.git] / src /
2017-05-27 Jim ProcterJAL-2562 javadoc TODO tree | commitdiff
2017-05-26 kiramtJAL-2491 Missed port to applet from JAL-1691 bug/JAL-2491 tree | commitdiff
2017-05-26 tcofoegbuJAL-2465 Improvement to re-instate storing recently... tree | commitdiff
2017-05-26 tcofoegbuJAL-2465 fix to prevent files loaded from the system... tree | commitdiff
2017-05-26 tcofoegbuMerge branch 'features/JAL-1648_cache_user_inputs'... tree | commitdiff
2017-05-26 tcofoegbuJAL-1648 fix to transfer focus back to alignment frame... tree | commitdiff
2017-05-26 gmungocJAL-2290 no update if no change of residue JAL-2547... tree | commitdiff
2017-05-26 gmungocJAL-2480 move ContiguousI and Range to jalview.datamodel tree | commitdiff
2017-05-25 gmungocJAL-2557 removal of Sequence.sequenceFeatures tree | commitdiff
2017-05-25 Jim ProcterMerge branch 'develop' into features/JAL-1648_cache_use... tree | commitdiff
2017-05-25 kiramtJAl-2034 Ported to applet bug/JAL-2034contextchange tree | commitdiff
2017-05-25 kiramtJAL-2034 don't update overview after click without... tree | commitdiff
2017-05-25 gmungocJAL-2050 make SequenceFeature.score final, adjust const... tree | commitdiff
2017-05-25 gmungocJAL-2505 simplifying number of SequenceFeature construc... tree | commitdiff
2017-05-25 gmungocJAL-2490 test coverage of empty and null feature group... tree | commitdiff
2017-05-25 kiramtMerge branch 'bug/JAL-2551' into bug/JAL-2034contextchange tree | commitdiff
2017-05-24 gmungocJAL-2505 make SequenceFeature type, begin, end, feature... tree | commitdiff
2017-05-24 gmungocJAL-2506 relocate Uniprot binding classes, bind to... tree | commitdiff
2017-05-24 gmungocJAL-2505 remove setters for SequenceFeature.begin,end... tree | commitdiff
2017-05-24 gmungocJAL-2529 add object_type=cdna to EnsemblCdna parameters tree | commitdiff
2017-05-24 gmungocMerge branch 'bug/JAL-2541cutWithFeatures' into feature... tree | commitdiff
2017-05-24 gmungocJAL-2505 JAL-2542 SequenceFeatures.shift() to shift... tree | commitdiff
2017-05-24 kiramtJAL-2551 Fix to group colouring when group extent is... bug/JAL-2551 tree | commitdiff
2017-05-24 gmungocJAL-2542 correct adjustment of sequence features for... tree | commitdiff
2017-05-24 kiramtJAL-2034 Added isDefined flag to SequenceGroup tree | commitdiff
2017-05-24 gmungocJAL-2505 delete and readd modified feature after Cut... tree | commitdiff
2017-05-23 Jim ProcterJAL-2549 replace JABAWS 2.1 with 2.2 client and remove... tree | commitdiff
2017-05-23 gmungocJAL-2490 find features for export as GFF, JAL-2548... tree | commitdiff
2017-05-23 gmungocJAL-2547 don't show features in tooltip over a gap bug/JAL-2547tooltipOnGap tree | commitdiff
2017-05-23 gmungocJAL-2490 tidy code and tests for feature export in... tree | commitdiff
2017-05-23 gmungocJAL-2490 improved lookup of features for Export Feature... tree | commitdiff
2017-05-23 gmungocJAL-2480 methods to get features for group tree | commitdiff
2017-05-22 gmungocJAL-2505 use setter not direct access to sf.description tree | commitdiff
2017-05-22 gmungocJAL-2505 updates after conflicting merge of JAL-2504 tree | commitdiff
2017-05-22 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-05-22 gmungocJAL-2504 update the right feature colour when creating... bug/JAL-2510amendFeatures tree | commitdiff
2017-05-22 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-05-22 gmungocJAL-2544 check feature overlaps selection region tree | commitdiff
2017-05-22 gmungocJAL-2543 identify as JSON before HTML tree | commitdiff
2017-05-22 gmungocJAL-2546 JAL-2490 efficient lookup of features, correct... tree | commitdiff
2017-05-22 gmungocJAL-2480 always include all non-positional features... tree | commitdiff
2017-05-22 kiramtMerge remote-tracking branch 'origin/bug/JAL-2256'... tree | commitdiff
2017-05-22 Jim ProcterJAL-2418 patch build - broken htsjdk import tree | commitdiff
2017-05-19 gmungocJAL-2526 removed redundant call to Sequence.findPosition() tree | commitdiff
2017-05-19 gmungocJAL-2490 refactored test for 'hasFeatures' tree | commitdiff
2017-05-19 gmungocJAL-2544 only include features in selected columns... tree | commitdiff
2017-05-19 gmungocJAL-2490 performant lookup of features for sorting tree | commitdiff
2017-05-19 gmungocJAL-2490 only count sequences where feature overlap... tree | commitdiff
2017-05-19 gmungocJAL-2505 unit test for sort by feature density, Javadoc tree | commitdiff
2017-05-18 gmungocJAL-2490 initial unit tests prior to refactoring tree | commitdiff
2017-05-18 Jim ProcterJAL-2388 return empty hidden columns for fully visible... tree | commitdiff
2017-05-18 gmungocJAL-2490 lookup sequence features for "labelClass" tree | commitdiff
2017-05-18 gmungocJAL-2490 lookup features at each column position tree | commitdiff
2017-05-18 gmungocJAL-2543 html-encode quote characters in feature descri... tree | commitdiff
2017-05-18 gmungocJAL-2490 retrieve visible features only tree | commitdiff
2017-05-18 gmungocJAL-2541 fix to initSeqFrom (and minor code tidy);... tree | commitdiff
2017-05-18 kiramtJAL-2256 Corrected AllCols/Rows iterator behaviour... bug/JAL-2256 tree | commitdiff
2017-05-17 Jim ProcterMerge branch 'bug/JAL-2510amendFeatures' into develop tree | commitdiff
2017-05-17 Jim ProcterMerge branch 'features/JAL-2447experimentalFlag' into... tree | commitdiff
2017-05-17 gmungocJAL-2504 use (and update) defaults for new feature... tree | commitdiff
2017-05-17 gmungocMerge branch 'develop' into bug/JAL-2510amendFeatures tree | commitdiff
2017-05-16 gmungocJAL-2505 unreachable code (for many years) removed tree | commitdiff
2017-05-16 kiramtJAL-2536 Overview window sizing not subject to min... bug/JAL-2536 tree | commitdiff
2017-05-16 gmungocJAL-2505 refactored method removed tree | commitdiff
2017-05-16 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-05-16 gmungocJAL-2505 set helix number as feature group in SequenceF... tree | commitdiff
2017-05-16 gmungocJAL-2517 restore complex colour scheme on Cancel in... bug/JAL-2517cancelAppletColour tree | commitdiff
2017-05-16 gmungocJAL-2403 simplify instantiation / configuration of... tree | commitdiff
2017-05-16 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-05-16 kiramtJAL-2522 Missed fix to applet tree | commitdiff
2017-05-16 gmungocJAL-2505 refactor to set type and group in SequenceFeat... tree | commitdiff
2017-05-16 gmungocJAL-2525 put in missing "transcript" feature type tree | commitdiff
2017-05-16 kiramtJAL-2388 Rationalised hashCode method in HiddenColumns tree | commitdiff
2017-05-16 kiramtMerge branch 'develop' into bug/JAL-2491 tree | commitdiff
2017-05-16 kiramtJAL-2491 Better merge tree | commitdiff
2017-05-16 gmungocJAL-2505 set SequenceFeature group in constructor tree | commitdiff
2017-05-15 Jim ProcterMerge branch 'bug/JAL-2507_rnasecstrstockholm' into... tree | commitdiff
2017-05-15 Jim ProcterJAL-2507 capitalisation for annotation lines generated... tree | commitdiff
2017-05-15 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-05-15 Jim ProcterJAL-2507 case insensitive recognition of annotation... tree | commitdiff
2017-05-15 gmungocJAL-2532 new feature types and colour changes from... tree | commitdiff
2017-05-15 Jim ProcterJAL-2535 quick hack to implement posterior probabilitie... tree | commitdiff
2017-05-15 tcofoegbuJAL-2520 improvement to use URL leaf name for creating... tree | commitdiff
2017-05-15 tcofoegbuJAL-2533 improvement to prune off file extension when... tree | commitdiff
2017-05-15 kiramtMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2017-05-15 kiramtJAL-2388 Add missed optimisation tree | commitdiff
2017-05-15 kiramtJAL-2491 Better merge but not quite right yet tree | commitdiff
2017-05-15 Jim ProcterMerge branch 'features/JAL-2376_add-horizontal-bar... tree | commitdiff
2017-05-15 Jim ProcterJAL-2371 create a default ResidueShader when constructi... tree | commitdiff
2017-05-15 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-05-15 kiramtMerge remote-tracking branch 'origin/develop' into... tree | commitdiff
2017-05-15 gmungocJAL-2490 use findFeatures() for efficient feature overl... tree | commitdiff
2017-05-15 kiramtJAL-2491 Tidies tree | commitdiff
2017-05-15 gmungocJAL-2480 redundant code (from merge?) removed tree | commitdiff
2017-05-15 gmungocJAL-2480 redundant code removed tree | commitdiff
2017-05-12 kiramtJAL-2491 Tidy tree | commitdiff
2017-05-12 kiramtJAL-2491 Tidies to Overview panel calls in light of... tree | commitdiff
2017-05-12 gmungocJAL-2490 performant findFeaturesAtRes tree | commitdiff
2017-05-12 gmungocJAL-2483 efficient lookup of feature types and groups... tree | commitdiff
2017-05-12 gmungocJAL-2525 get sequence features for Ontology term(s... tree | commitdiff
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