JAL-966 SearchResultsI now on viewmodels.AlignmentViewport rather than on SeqCanvas
[jalview.git] / src / jalview / datamodel /
2016-06-20 Jim ProcterJAL-2110 copy alcodonframes only if copy constructor...
2016-06-19 Jim ProcterJAL-2110 JAL-2131 JAL-1765 remove reference to jalview...
2016-06-16 Jim ProcterJAL-2110 todo - select mappings involving sequences...
2016-06-16 Jim ProcterJAL-2110 equals and hashcode should check fromSeq
2016-06-16 Jim ProcterJAL-2110 typo caused infinite loop
2016-06-16 gmungocJAL-2112 optimisation of EMBL CDS parsing
2016-06-15 Jim ProcterMerge branch 'develop' into features/JAL-2110_crossRefD...
2016-06-14 gmungocJAL-2114 more helpful reporting of parse failures
2016-06-14 gmungocJAL-2110 ensure "UniProtKB/Swiss-Prot" dbrefs canonical...
2016-06-14 gmungocJAL-1686 JAL-2110 equals and/or hashCode method added
2016-06-09 gmungocJAL-2110 work in progress
2016-06-01 Jim Procterfix build
2016-05-31 gmungocJAL-2023 adjustments to mappings added for split frame...
2016-05-31 gmungocJAL-2110 refactor + tests to allow a dbref version...
2016-05-31 Jim ProcterMerge branch 'develop' into features/JAL-2113_emblXml1.2
2016-05-30 gmungocJAL-1989 equals method strengthened to fully match...
2016-05-30 Jim ProcterMerge branch 'develop' into efficiency/JAL-2034_JAL...
2016-05-27 gmungocJAL-1989 added hashCode and equals, renamed field to...
2016-05-26 gmungocJAL-2113 additions to embl_mapping.xml / data models... features/JAL-2113_emblXml1.2
2016-05-23 gmungocJAL-2113 remove spaces in sequence from unmarshalling...
2016-05-23 gmungocJAL-2114 save 'raw' ENA location as a sequence feature...
2016-05-20 gmungocJAL-2113 embl_mapping.xml and code updated for EMBL...
2016-05-17 tcofoegbuJAL-2106 JAL-1926 updated source doc for set/getSourceDBRef
2016-05-13 gmungocJAL-2105 capture Ensembl data version, check REST versi...
2016-05-05 Jim ProcterJAL-192 patch for off-by one and pathological case...
2016-04-29 Jim ProcterJAL-192 need visible and actual sequence limits for...
2016-04-29 Jim ProcterJAL-192 fix bounds when no hidden regions, and when...
2016-04-29 Jim ProcterJAL-966 JAL-1553
 todo: remove UI components from Colum...
2016-04-29 Jim ProcterJAL-1551 formatting

2016-04-29 Jim ProcterJAL-192 ‘efficiently’ locate visible bounds for a seque...
2016-04-29 Jim ProcterJAL-1551 formatting
2016-04-23 Jim ProcterJAL-2075 findPosition for SeqCigar (with test)
2016-04-23 Jim ProcterJAL-2075 formatting
2016-04-14 gmungocJAL-2041 add ID,clinical_significance to feature attrib...
2016-04-14 gmungocJAL-2049 small refactor of constructors to avoid code...
2016-04-13 Jim ProcterMerge branch 'bug/JAL-2046_ds_sharing_features_broken...
2016-04-11 tcofoegbuJAL-2054 Renamed getStartEnd in AlignFrame to getVisibl...
2016-04-11 Jim ProcterMerge branch 'develop' into efficiency/JAL-2034_JAL...
2016-04-08 Jim ProcterJAL-2050 JAL-1722 new getSelectedRange() method to...
2016-04-08 Jim ProcterJAL-2053 JAL-1551 javadoc and simpler code
2016-04-05 Jim ProcterJAL-2046 add/delete SequenceFeature operate on dataset...
2016-04-05 Jim ProcterJAL-2046 setSequenceFeature contract implementation...
2016-04-05 Jim ProcterJAL-2046 explicit contract for get/set SequenceFeatures...
2016-04-05 Jim ProcterJAL-2046 remove javadoc
2016-04-05 Jim ProcterJAL-2046 simpler deriveSequence - promote to dataset...
2016-04-05 Jim ProcterJAL-2046 clarify contract for copy constructor and...
2016-04-05 Jim ProcterJAL-2046 explicitly copy char[] when cloning sequence...
2016-04-05 Jim ProcterJAL-2046 safer createDatasetSequence manipulates privat...
2016-04-04 Jim ProcterJAL-2001 drop isSelected(int) in favour of original...
2016-04-04 Jim ProcterJAL-2001 catch -ve column values
2016-04-04 Jim ProcterJAL-2001 faster check for a column being selected
2016-04-04 Jim ProcterJAL-2001 javadoc
2016-04-04 Jim ProcterJAL-2001 faster getMax/getMin selected column, with...
2016-04-04 Jim ProcterJAL-2001 JAL-1722 - store selection as ArrayList and...
2016-04-01 gmungocJAL-1705 ensure the right mapping is used to align...
2016-04-01 gmungocJAL-1705 reworked AlignmentUtils.makeCdsAlignment and...
2016-04-01 gmungocJAL-1705 include stop codon in mapped CDS range so...
2016-04-01 gmungocJAL-2037 set DBRefEntry.version to "0" not "" in EMBL...
2016-03-28 gmungocJAL-1705 Javadoc / debug output tweaks
2016-03-25 Jim ProcterJAL-2034 JAL-1421 use ArrayLists, and make ‘selection...
2016-03-25 Jim ProcterJAL-2034 make colour scheme update optional when group...
2016-03-25 Jim ProcterJAL-1551
2016-03-21 gmungocMerge branch 'features/JAL-653_JAL-1766_htslib_refseqsu...
2016-03-21 gmungocMerge branch 'develop' of https://source.jalview.org...
2016-03-21 gmungocJAL-2029 further fixes to get correct xrefs and xrefs...
2016-03-21 gmungocJAL-2029 many-to-many EnsemblCDS-to-Uniprot mappings
2016-03-21 tcofoegbudevelop merge
2016-03-03 tcofoegbuJAL-1919 fixed bug causing PDBfile test failure
2016-03-03 tcofoegbuJAL-1919 PDBfile and JmolParser refactor
2016-03-02 gmungocJAL-1705 include any unmapped protein start 'X' when...
2016-03-01 gmungocJAL-1705 align CDS and peptide products to transcripts
2016-02-19 gmungocJAL-1705 handle case of sequence with no dataset sequence
2016-02-12 gmungocJAL-1705 JAL-1686 stronger SequenceFeature.equals(...
2016-01-28 gmungocMerge branch 'develop' into JAL-1705_trialMerge
2016-01-26 gmungocJAL-1705 derive transcript sequences from gene sequence...
2016-01-23 gmungocJAL-1705 todo comment re writing DBRefEntry/SequenceFea...
2016-01-21 gmungocJAL-1705 ENSEMBL added, unused constants removed
2016-01-21 gmungocJAL-1705 suppress jvsuffix (for sequence id matching...
2016-01-21 gmungocJAL-1705 toString() added (for debugging)
2016-01-21 gmungocJAL-1705 isEmpty() and (debug) toString() methods added
2016-01-21 tcofoegbuJAL-1919 basic support for importing and viewing mmCIF...
2016-01-11 gmungocJAL-1989 more unit tests and encapsulation for ColumnSe...
2016-01-08 gmungocJAL-1705 DbSourceProxy properties converted to methods...
2015-12-22 gmungocJAL-653 encapsulate Strand, Attributes, Status of Seque...
2015-12-22 gmungocJAL-653 realise virtual mappings and align when adding...
2015-12-22 gmungocJAL-653 GFF new/refactored helper classes
2015-12-22 gmungocJAL-653 AlignedCodonFrame internal refactor, merge...
2015-12-03 gmungocJAL-653 handle reverse strand mapping in SearchResults...
2015-12-03 gmungocJAL-653 mappings always reside on the dataset alignment...
2015-11-30 gmungocJAL-653 (experimental) methods to resolve dummy to...
2015-11-30 gmungocJAL-653 getStrand javadoc/refactor/test
2015-11-30 gmungocJAL-1421 use generics JAL-1551 @Override annotations...
2015-11-21 gmungocJAL-653 JAL-1968 FeaturesFile now handles Jalview or...
2015-11-16 tcofoegbuJAL-1967 JAL-1479 refactored sequence<->structure mappi...
2015-11-05 tcofoegbuJAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc...
2015-10-29 tcofoegbuJAL-1926 JAL-1479 updated PDBfile fetcher to add source...
2015-10-28 tcofoegbuJAL-1479 added support for SIFTs mapping output viewing...
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...
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