Merge branch 'JAL-3878_ws-overhaul-3' into with_ws_overhaul-3
[jalview.git] / src / jalview / datamodel / SequenceI.java
2022-12-14 Jim ProcterMerge branch 'develop' into update_212_Dec_merge_with_2...
2022-11-21 Jim ProcterMerge commit 'alpha/update_2_12_for_2_11_2_series_merge...
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0
2021-09-17 Jim ProcterJAL-2226 new method to search for annotation matching...
2020-05-18 Jim ProcterMerge branch 'alpha/JAL-3362_Jalview_212_alpha' into...
2019-09-26 Jim ProcterJAL-3070 allow SequenceI.findPositions(0,column+1)...
2019-06-04 Jim ProcterMerge branch 'develop' into developtomchmmer
2019-03-13 gmungocMerge branch 'develop' into trialMerge
2019-03-05 gmungocMerge remote-tracking branch 'origin/bug/JAL-2839findWi...
2019-03-01 gmungocMerge branch 'feature/intervalStoreJ' into merge/JAL...
2019-02-28 gmungocJAL-3140 confine intervalstore imports to jalview.datam...
2019-02-04 hansonrrefactoring for DBMODList
2019-01-26 hansonrJalview.isJS() --> Platform.isJS(), DBRefEntry[] -...
2018-12-17 Jim ProcterMerge branch 'develop' into bug/JAL-2541cutRelocateFeatures
2018-11-29 gmungocJAL-3140 NCList now via IntervalStore library
2018-04-16 gmungocJAL-2629 JAL-2937 remove redundant is/setHMMConsensusSe...
2018-03-30 gmungocJAL-2941 'map hmm to RF' removed pending clarifications
2018-03-16 gmungocMerge branch 'develop' into trialMerge
2018-03-09 gmungocJAL-2839 Finder refactoring prior to fixing the defect
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
2018-02-28 gmungocJAL-2629 some tidying of Hmmer commands (wip)
2018-02-22 gmungocJAL-2629 tidy tests, refactor hmmer node mapping slightly
2018-02-20 gmungocJAL-2629 removed SequenceI.get/setLastPosition and...
2018-02-20 gmungocMerge branch 'develop' into features/mchmmer
2018-01-22 kiramtJAL-2579 Moved locateVisibleStartOfSequence to Sequence...
2018-01-19 kiramtJAL-2759 Changes to getVisibleSequenceStrings after...
2017-11-22 gmungocJAL-2069 spike updated with latest (FeatureTypeSettings)
2017-11-22 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-11-21 kiramtMerge branch 'develop' into feature/JAL-2759
2017-11-16 Jim ProcterMerge branch 'develop' into bug/JAL-2541cutRelocateFeatures
2017-11-16 Jim ProcterMerge branch 'bug/JAL-2829deleteCharsWithGaps' into...
2017-11-15 gmungocJAL-2835 spike updated with latest
2017-11-13 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-11-13 gmungocJAL-2176 removed unused Sequence.index
2017-11-13 gmungocMerge branch 'bug/JAL-2829deleteCharsWithGaps' into
2017-11-10 gmungocJAL-2562 updated findPosition javadoc to match behaviour
2017-11-07 Jim ProcterJAL-2822 JAL-2684 clarified javadoc
2017-10-20 gmungocPush 1793 latest to spike branch
2017-10-19 gmungocJAL-2755 add missing Javadoc
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-09-28 gmungocJAL-1796 GeneLociI as distinguished DBRefEntry
2017-09-26 gmungocJAL-2738 promote setGeneLoci to SequenceI!
2017-09-25 gmungocJAL-2738 getGeneLoci promoted to SequenceI
2017-09-21 kiramtJAL-2674 Rewrote propagateInsertions
2017-09-14 gmungocJAL-2541 working Cut/Undo with feature relocation
2017-09-14 gmungocJAL-2541 revised cut with features (work in progress)
2017-08-29 osboxesJAL-2629 HMMs dropped on the alignment now map to the...
2017-08-18 TZVanaaltenMerge branch 'develop' into features/hmmer
2017-08-11 TZVanaaltenJAL-2629 add ability to build a HMM from a group
2017-08-04 TZVanaaltenJAL-2629 multiple HMMs can now be dropped onto an alignment
2017-07-27 TZVanaaltenJAL-2629 moved HMM storage location to placeholder...
2017-06-22 gmungocJAL-2481 JAL-2593 JAL-2526 further optimisation of...
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the...
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-06-09 gmungocJAL-2480 tidy javadoc
2017-06-05 gmungocMerge branch 'features/JAL-2526sequenceCursor' into
2017-06-05 gmungocMerge branch 'features/JAL-2446NCList' into
2017-06-05 gmungocMerge branch 'features/JAL-2446NCList' into features/JAL-2526sequenceCursor
2017-06-05 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-06-04 Jim ProcterJAL-2291 SequenceI.getInsertionsAsBits for convenient...
2017-06-01 gmungocJAL-2526 zapCursor() renamed sequenceChanged()
2017-06-01 gmungocJAL-2754 Sequence.findFeatures(fromCol, toCol) features/JAL-2754findFeaturesByColumn
2017-05-30 gmungocJAL-2526 first draft of findIndex/findPosition with...
2017-05-29 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-05-29 gmungocJAL-2526 Sequence.findPositions to get residue position...
2017-05-27 Jim ProcterJAL-2562 javadoc TODO
2017-05-25 gmungocJAL-2557 removal of Sequence.sequenceFeatures
2017-04-27 gmungocJAL-2480 don't allow null type in SequenceFeature
2017-04-26 gmungocJAL-2490 findFeaturesAtRes with performant feature...
2017-04-18 gmungocJAL-2480 SequenceFeaturesI encapsulates features api
2017-03-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-653_JAL-1766_htslib_refseqsupport
2017-03-20 gmungocJAL-2446 FeatureStore with NCList - work in progress
2016-11-14 gmungocJAL-2296 report whether SequenceFeature actually added...
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch...
2016-10-05 Jim ProcterJAL-2189 source formatting
2016-10-03 gmungocJAL-2110 additional tests for setDatasetSequence, javad...
2016-09-28 Jim ProcterJAL-2210 instrument setDBRefs to call ensurePrimaries
2016-09-16 gmungocJAL-2157 JAL-1803 refactored Sequence.updatePDBIds...
2016-09-07 Jim ProcterJAL-1803 first pass at updatePDBEntry
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
2016-07-12 Jim ProcterJAL-2110 javadoc
2016-06-23 Jim ProcterJAL-2110 SequenceI.isProtein method
2016-05-17 tcofoegbuJAL-2106 JAL-1926 updated source doc for set/getSourceDBRef
2016-04-05 Jim ProcterJAL-2046 explicit contract for get/set SequenceFeatures...
2015-11-05 tcofoegbuJAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc...
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2
2015-10-15 tcofoegbuJAL-1479 refactored SequenceI interface - changed getDB...
2015-10-14 tcofoegbuJAL-1926 added supporting model changes to enable savin...
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports
2015-08-07 tcofoegbuJAL-1824 updated caching procedure for pdb entries...
2015-06-12 tcofoegbuJAL-1641 refactor
2015-06-05 tcofoegbuJAL-1760 JAL-1641 Serialisation of Hidden Seqs and...
2015-06-05 Jim ProcterJAL-653 refactor sequence interface to separate concret...
2015-05-12 gmungocJAL-1712 fixes/tests for Castor binding and 'show flank...
2015-04-13 gmungocJAL-1693 make exon alignment for get-xref splitframe...
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in...
next