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