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JAL-1563 smarter support for advanced querying of Uniprot FTS
[jalview.git] / src / jalview / datamodel /
2016-05-17 tcofoegbuJAL-2106 JAL-1926 updated source doc for set/getSourceDBRef tree | commitdiff
2016-05-13 gmungocJAL-2105 capture Ensembl data version, check REST versi... tree | commitdiff
2016-05-05 Jim ProcterJAL-192 patch for off-by one and pathological case... tree | commitdiff
2016-04-29 Jim ProcterJAL-192 need visible and actual sequence limits for... tree | commitdiff
2016-04-29 Jim ProcterJAL-192 fix bounds when no hidden regions, and when... tree | commitdiff
2016-04-29 Jim ProcterJAL-966 JAL-1553
 todo: remove UI components from Colum... tree | commitdiff
2016-04-29 Jim ProcterJAL-1551 formatting
 tree | commitdiff
2016-04-29 Jim ProcterJAL-192 ‘efficiently’ locate visible bounds for a seque... tree | commitdiff
2016-04-29 Jim ProcterJAL-1551 formatting tree | commitdiff
2016-04-23 Jim ProcterJAL-2075 findPosition for SeqCigar (with test) tree | commitdiff
2016-04-23 Jim ProcterJAL-2075 formatting tree | commitdiff
2016-04-14 gmungocJAL-2041 add ID,clinical_significance to feature attrib... tree | commitdiff
2016-04-14 gmungocJAL-2049 small refactor of constructors to avoid code... tree | commitdiff
2016-04-13 Jim ProcterMerge branch 'bug/JAL-2046_ds_sharing_features_broken... tree | commitdiff
2016-04-11 tcofoegbuJAL-2054 Renamed getStartEnd in AlignFrame to getVisibl... tree | commitdiff
2016-04-08 Jim ProcterJAL-2050 JAL-1722 new getSelectedRange() method to... tree | commitdiff
2016-04-08 Jim ProcterJAL-2053 JAL-1551 javadoc and simpler code tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 add/delete SequenceFeature operate on dataset... tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 setSequenceFeature contract implementation... tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 explicit contract for get/set SequenceFeatures... tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 remove javadoc tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 simpler deriveSequence - promote to dataset... tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 clarify contract for copy constructor and... tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 explicitly copy char[] when cloning sequence... tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 safer createDatasetSequence manipulates privat... tree | commitdiff
2016-04-04 Jim ProcterJAL-2001 drop isSelected(int) in favour of original... tree | commitdiff
2016-04-04 Jim ProcterJAL-2001 catch -ve column values tree | commitdiff
2016-04-04 Jim ProcterJAL-2001 faster check for a column being selected tree | commitdiff
2016-04-04 Jim ProcterJAL-2001 javadoc tree | commitdiff
2016-04-04 Jim ProcterJAL-2001 faster getMax/getMin selected column, with... tree | commitdiff
2016-04-04 Jim ProcterJAL-2001 JAL-1722 - store selection as ArrayList and... tree | commitdiff
2016-04-01 gmungocJAL-1705 ensure the right mapping is used to align... tree | commitdiff
2016-04-01 gmungocJAL-1705 reworked AlignmentUtils.makeCdsAlignment and... tree | commitdiff
2016-04-01 gmungocJAL-1705 include stop codon in mapped CDS range so... tree | commitdiff
2016-04-01 gmungocJAL-2037 set DBRefEntry.version to "0" not "" in EMBL... tree | commitdiff
2016-03-28 gmungocJAL-1705 Javadoc / debug output tweaks tree | commitdiff
2016-03-21 gmungocMerge branch 'features/JAL-653_JAL-1766_htslib_refseqsu... tree | commitdiff
2016-03-21 gmungocMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-03-21 gmungocJAL-2029 further fixes to get correct xrefs and xrefs... tree | commitdiff
2016-03-21 gmungocJAL-2029 many-to-many EnsemblCDS-to-Uniprot mappings tree | commitdiff
2016-03-21 tcofoegbudevelop merge tree | commitdiff
2016-03-03 tcofoegbuJAL-1919 fixed bug causing PDBfile test failure tree | commitdiff
2016-03-03 tcofoegbuJAL-1919 PDBfile and JmolParser refactor tree | commitdiff
2016-03-02 gmungocJAL-1705 include any unmapped protein start 'X' when... tree | commitdiff
2016-03-01 gmungocJAL-1705 align CDS and peptide products to transcripts tree | commitdiff
2016-02-19 gmungocJAL-1705 handle case of sequence with no dataset sequence tree | commitdiff
2016-02-12 gmungocJAL-1705 JAL-1686 stronger SequenceFeature.equals(... tree | commitdiff
2016-01-28 gmungocMerge branch 'develop' into JAL-1705_trialMerge tree | commitdiff
2016-01-26 gmungocJAL-1705 derive transcript sequences from gene sequence... tree | commitdiff
2016-01-23 gmungocJAL-1705 todo comment re writing DBRefEntry/SequenceFea... tree | commitdiff
2016-01-21 gmungocJAL-1705 ENSEMBL added, unused constants removed tree | commitdiff
2016-01-21 gmungocJAL-1705 suppress jvsuffix (for sequence id matching... tree | commitdiff
2016-01-21 gmungocJAL-1705 toString() added (for debugging) tree | commitdiff
2016-01-21 gmungocJAL-1705 isEmpty() and (debug) toString() methods added tree | commitdiff
2016-01-21 tcofoegbuJAL-1919 basic support for importing and viewing mmCIF... tree | commitdiff
2016-01-11 gmungocJAL-1989 more unit tests and encapsulation for ColumnSe... tree | commitdiff
2016-01-08 gmungocJAL-1705 DbSourceProxy properties converted to methods... tree | commitdiff
2015-12-22 gmungocJAL-653 encapsulate Strand, Attributes, Status of Seque... tree | commitdiff
2015-12-22 gmungocJAL-653 realise virtual mappings and align when adding... tree | commitdiff
2015-12-22 gmungocJAL-653 GFF new/refactored helper classes tree | commitdiff
2015-12-22 gmungocJAL-653 AlignedCodonFrame internal refactor, merge... tree | commitdiff
2015-12-03 gmungocJAL-653 handle reverse strand mapping in SearchResults... tree | commitdiff
2015-12-03 gmungocJAL-653 mappings always reside on the dataset alignment... tree | commitdiff
2015-11-30 gmungocJAL-653 (experimental) methods to resolve dummy to... tree | commitdiff
2015-11-30 gmungocJAL-653 getStrand javadoc/refactor/test tree | commitdiff
2015-11-30 gmungocJAL-1421 use generics JAL-1551 @Override annotations... tree | commitdiff
2015-11-21 gmungocJAL-653 JAL-1968 FeaturesFile now handles Jalview or... tree | commitdiff
2015-11-16 tcofoegbuJAL-1967 JAL-1479 refactored sequence<->structure mappi... tree | commitdiff
2015-11-05 tcofoegbuJAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc... tree | commitdiff
2015-10-29 tcofoegbuJAL-1926 JAL-1479 updated PDBfile fetcher to add source... tree | commitdiff
2015-10-28 tcofoegbuJAL-1479 added support for SIFTs mapping output viewing... 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
2015-10-08 tcofoegbumerge tree | commitdiff
2015-10-07 Jim ProcterJAL-1894 source formatting tree | commitdiff
2015-10-07 Jim ProcterJAL-1912 formatting tree | commitdiff
2015-10-07 Jim ProcterJAL-1912 javadoc for adjustForAlignment stating current... tree | commitdiff
2015-10-07 Jim ProcterJAL-1912 efficiency: look up sequenceMapping once per... tree | commitdiff
2015-10-05 tcofoegbuJAL-1912 added null check for SequenceMapping variable... tree | commitdiff
2015-10-01 tcofoegbuJAL-1912 Double.NaN breaks JSON serialization - added... 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
2015-09-03 tcofoegbuJAL-793 use default custom export settings for html... tree | commitdiff
2015-09-01 Jim ProcterJAL-1853 make getVisibleSeqs more memory efficient... tree | commitdiff
2015-09-01 Jim ProcterJAL-1853 refactor clip routine from getSequenceStrings tree | commitdiff
2015-09-01 Jim Procterpatch for JAL-1853 - use given gap character to reconst... tree | commitdiff
2015-08-17 gmungocJAL-1800 separated SearchResults.getCharacters() from... tree | commitdiff
2015-08-17 gmungocJAL-1800 SearchResults.equals() to allow smarter mouseo... tree | commitdiff
2015-08-07 tcofoegbuJAL-1824 updated caching procedure for pdb entries... tree | commitdiff
2015-08-04 tcofoegbuJAL-1821 updated the reference sequence column of struc... tree | commitdiff
2015-07-30 tcofoegbuJAL-1443 modified exception notifications tree | commitdiff
2015-07-23 Jim ProcterMerge branch 'bug/JAL-1819_isNaN' into develop tree | commitdiff
2015-07-23 Jim ProcterJAL-1551 JAL-1819 formatting/imports tree | commitdiff
2015-07-23 Jim ProcterJAL-1819 use Float.isNaN() to check for NaNs! tree | commitdiff
2015-07-21 tcofoegbuJAL-1443 bugfix to prevent loading of unidentifiable... tree | commitdiff
2015-07-08 gmungocJAL-1759 merge from develop tree | commitdiff
2015-07-06 gmungocJAL-1421 generics used for leaner safer code tree | commitdiff
2015-07-03 gmungocMerge branch 'develop' into features/JAL-892varnaToProject tree | commitdiff
2015-07-01 gmungocJAL-1802 handle slide sequences edits in split frame... tree | commitdiff
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