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JAL-2102 right justify 'Mass' in uniprot FTS, and 'Max Observed Residue' in PDB FTS...
[jalview.git]
/
src
/
jalview
/
datamodel
/
2016-06-01
Jim Procter
fix build
tree
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commitdiff
2016-05-31
gmungoc
JAL-2023 adjustments to mappings added for split frame...
tree
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commitdiff
2016-05-31
gmungoc
JAL-2110 refactor + tests to allow a dbref version...
tree
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commitdiff
2016-05-31
Jim Procter
Merge branch 'develop' into features/JAL-2113_emblXml1.2
tree
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commitdiff
2016-05-30
gmungoc
JAL-1989 equals method strengthened to fully match...
tree
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commitdiff
2016-05-27
gmungoc
JAL-1989 added hashCode and equals, renamed field to...
tree
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commitdiff
2016-05-26
gmungoc
JAL-2113 additions to embl_mapping.xml / data models...
features/JAL-2113_emblXml1.2
tree
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commitdiff
2016-05-23
gmungoc
JAL-2113 remove spaces in sequence from unmarshalling...
tree
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commitdiff
2016-05-23
gmungoc
JAL-2114 save 'raw' ENA location as a sequence feature...
tree
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commitdiff
2016-05-20
gmungoc
JAL-2113 embl_mapping.xml and code updated for EMBL...
tree
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commitdiff
2016-05-17
tcofoegbu
JAL-2106 JAL-1926 updated source doc for set/getSourceDBRef
tree
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commitdiff
2016-05-13
gmungoc
JAL-2105 capture Ensembl data version, check REST versi...
tree
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commitdiff
2016-05-05
Jim Procter
JAL-192 patch for off-by one and pathological case...
tree
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commitdiff
2016-04-29
Jim Procter
JAL-192 need visible and actual sequence limits for...
tree
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commitdiff
2016-04-29
Jim Procter
JAL-192 fix bounds when no hidden regions, and when...
tree
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commitdiff
2016-04-29
Jim Procter
JAL-966 JAL-1553 todo: remove UI components from Colum...
tree
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commitdiff
2016-04-29
Jim Procter
JAL-1551 formatting
tree
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commitdiff
2016-04-29
Jim Procter
JAL-192 ‘efficiently’ locate visible bounds for a seque...
tree
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commitdiff
2016-04-29
Jim Procter
JAL-1551 formatting
tree
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commitdiff
2016-04-23
Jim Procter
JAL-2075 findPosition for SeqCigar (with test)
tree
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commitdiff
2016-04-23
Jim Procter
JAL-2075 formatting
tree
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commitdiff
2016-04-14
gmungoc
JAL-2041 add ID,clinical_significance to feature attrib...
tree
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commitdiff
2016-04-14
gmungoc
JAL-2049 small refactor of constructors to avoid code...
tree
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commitdiff
2016-04-13
Jim Procter
Merge branch 'bug/JAL-2046_ds_sharing_features_broken...
tree
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commitdiff
2016-04-11
tcofoegbu
JAL-2054 Renamed getStartEnd in AlignFrame to getVisibl...
tree
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commitdiff
2016-04-08
Jim Procter
JAL-2050 JAL-1722 new getSelectedRange() method to...
tree
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commitdiff
2016-04-08
Jim Procter
JAL-2053 JAL-1551 javadoc and simpler code
tree
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commitdiff
2016-04-05
Jim Procter
JAL-2046 add/delete SequenceFeature operate on dataset...
tree
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commitdiff
2016-04-05
Jim Procter
JAL-2046 setSequenceFeature contract implementation...
tree
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commitdiff
2016-04-05
Jim Procter
JAL-2046 explicit contract for get/set SequenceFeatures...
tree
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commitdiff
2016-04-05
Jim Procter
JAL-2046 remove javadoc
tree
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commitdiff
2016-04-05
Jim Procter
JAL-2046 simpler deriveSequence - promote to dataset...
tree
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commitdiff
2016-04-05
Jim Procter
JAL-2046 clarify contract for copy constructor and...
tree
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commitdiff
2016-04-05
Jim Procter
JAL-2046 explicitly copy char[] when cloning sequence...
tree
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commitdiff
2016-04-05
Jim Procter
JAL-2046 safer createDatasetSequence manipulates privat...
tree
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commitdiff
2016-04-04
Jim Procter
JAL-2001 drop isSelected(int) in favour of original...
tree
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commitdiff
2016-04-04
Jim Procter
JAL-2001 catch -ve column values
tree
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commitdiff
2016-04-04
Jim Procter
JAL-2001 faster check for a column being selected
tree
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commitdiff
2016-04-04
Jim Procter
JAL-2001 javadoc
tree
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commitdiff
2016-04-04
Jim Procter
JAL-2001 faster getMax/getMin selected column, with...
tree
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commitdiff
2016-04-04
Jim Procter
JAL-2001 JAL-1722 - store selection as ArrayList and...
tree
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commitdiff
2016-04-01
gmungoc
JAL-1705 ensure the right mapping is used to align...
tree
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commitdiff
2016-04-01
gmungoc
JAL-1705 reworked AlignmentUtils.makeCdsAlignment and...
tree
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commitdiff
2016-04-01
gmungoc
JAL-1705 include stop codon in mapped CDS range so...
tree
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commitdiff
2016-04-01
gmungoc
JAL-2037 set DBRefEntry.version to "0" not "" in EMBL...
tree
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commitdiff
2016-03-28
gmungoc
JAL-1705 Javadoc / debug output tweaks
tree
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commitdiff
2016-03-21
gmungoc
Merge branch 'features/JAL-653_JAL-1766_htslib_refseqsu...
tree
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commitdiff
2016-03-21
gmungoc
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-03-21
gmungoc
JAL-2029 further fixes to get correct xrefs and xrefs...
tree
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commitdiff
2016-03-21
gmungoc
JAL-2029 many-to-many EnsemblCDS-to-Uniprot mappings
tree
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commitdiff
2016-03-21
tcofoegbu
develop merge
tree
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commitdiff
2016-03-03
tcofoegbu
JAL-1919 fixed bug causing PDBfile test failure
tree
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commitdiff
2016-03-03
tcofoegbu
JAL-1919 PDBfile and JmolParser refactor
tree
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commitdiff
2016-03-02
gmungoc
JAL-1705 include any unmapped protein start 'X' when...
tree
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commitdiff
2016-03-01
gmungoc
JAL-1705 align CDS and peptide products to transcripts
tree
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commitdiff
2016-02-19
gmungoc
JAL-1705 handle case of sequence with no dataset sequence
tree
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commitdiff
2016-02-12
gmungoc
JAL-1705 JAL-1686 stronger SequenceFeature.equals(...
tree
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commitdiff
2016-01-28
gmungoc
Merge branch 'develop' into JAL-1705_trialMerge
tree
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commitdiff
2016-01-26
gmungoc
JAL-1705 derive transcript sequences from gene sequence...
tree
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commitdiff
2016-01-23
gmungoc
JAL-1705 todo comment re writing DBRefEntry/SequenceFea...
tree
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commitdiff
2016-01-21
gmungoc
JAL-1705 ENSEMBL added, unused constants removed
tree
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commitdiff
2016-01-21
gmungoc
JAL-1705 suppress jvsuffix (for sequence id matching...
tree
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commitdiff
2016-01-21
gmungoc
JAL-1705 toString() added (for debugging)
tree
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commitdiff
2016-01-21
gmungoc
JAL-1705 isEmpty() and (debug) toString() methods added
tree
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commitdiff
2016-01-21
tcofoegbu
JAL-1919 basic support for importing and viewing mmCIF...
tree
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commitdiff
2016-01-11
gmungoc
JAL-1989 more unit tests and encapsulation for ColumnSe...
tree
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commitdiff
2016-01-08
gmungoc
JAL-1705 DbSourceProxy properties converted to methods...
tree
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commitdiff
2015-12-22
gmungoc
JAL-653 encapsulate Strand, Attributes, Status of Seque...
tree
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commitdiff
2015-12-22
gmungoc
JAL-653 realise virtual mappings and align when adding...
tree
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commitdiff
2015-12-22
gmungoc
JAL-653 GFF new/refactored helper classes
tree
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commitdiff
2015-12-22
gmungoc
JAL-653 AlignedCodonFrame internal refactor, merge...
tree
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commitdiff
2015-12-03
gmungoc
JAL-653 handle reverse strand mapping in SearchResults...
tree
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commitdiff
2015-12-03
gmungoc
JAL-653 mappings always reside on the dataset alignment...
tree
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commitdiff
2015-11-30
gmungoc
JAL-653 (experimental) methods to resolve dummy to...
tree
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commitdiff
2015-11-30
gmungoc
JAL-653 getStrand javadoc/refactor/test
tree
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commitdiff
2015-11-30
gmungoc
JAL-1421 use generics JAL-1551 @Override annotations...
tree
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commitdiff
2015-11-21
gmungoc
JAL-653 JAL-1968 FeaturesFile now handles Jalview or...
tree
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commitdiff
2015-11-16
tcofoegbu
JAL-1967 JAL-1479 refactored sequence<->structure mappi...
tree
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commitdiff
2015-11-05
tcofoegbu
JAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc...
tree
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commitdiff
2015-10-29
tcofoegbu
JAL-1926 JAL-1479 updated PDBfile fetcher to add source...
tree
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commitdiff
2015-10-28
tcofoegbu
JAL-1479 added support for SIFTs mapping output viewing...
tree
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commitdiff
2015-10-15
tcofoegbu
JAL-1479 refactored SequenceI interface - changed getDB...
tree
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commitdiff
2015-10-14
tcofoegbu
JAL-1926 added supporting model changes to enable savin...
tree
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commitdiff
2015-10-08
tcofoegbu
merge
tree
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commitdiff
2015-10-07
Jim Procter
JAL-1894 source formatting
tree
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commitdiff
2015-10-07
Jim Procter
JAL-1912 formatting
tree
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commitdiff
2015-10-07
Jim Procter
JAL-1912 javadoc for adjustForAlignment stating current...
tree
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commitdiff
2015-10-07
Jim Procter
JAL-1912 efficiency: look up sequenceMapping once per...
tree
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commitdiff
2015-10-05
tcofoegbu
JAL-1912 added null check for SequenceMapping variable...
tree
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commitdiff
2015-10-01
tcofoegbu
JAL-1912 Double.NaN breaks JSON serialization - added...
tree
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commitdiff
2015-09-14
gmungoc
JAL-1880 handle sequence offsets properly when mapping...
tree
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commitdiff
2015-09-10
Jim Procter
JAL-1645 licencing for new files in src
tree
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commitdiff
2015-09-10
Jim Procter
JAL-1645 source formatting and organise imports
tree
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commitdiff
2015-09-03
tcofoegbu
JAL-793 use default custom export settings for html...
tree
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commitdiff
2015-09-01
Jim Procter
JAL-1853 make getVisibleSeqs more memory efficient...
tree
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commitdiff
2015-09-01
Jim Procter
JAL-1853 refactor clip routine from getSequenceStrings
tree
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commitdiff
2015-09-01
Jim Procter
patch for JAL-1853 - use given gap character to reconst...
tree
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commitdiff
2015-08-17
gmungoc
JAL-1800 separated SearchResults.getCharacters() from...
tree
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commitdiff
2015-08-17
gmungoc
JAL-1800 SearchResults.equals() to allow smarter mouseo...
tree
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commitdiff
2015-08-07
tcofoegbu
JAL-1824 updated caching procedure for pdb entries...
tree
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commitdiff
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