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JAL-2629 remove annotation when exporting for hmmbuild
[jalview.git]
/
src
/
jalview
/
datamodel
/
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
2016-03-25
Jim Procter
JAL-2034 JAL-1421 use ArrayLists, and make ‘selection...
tree
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commitdiff
2016-03-25
Jim Procter
JAL-2034 make colour scheme update optional when group...
tree
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commitdiff
2016-03-25
Jim Procter
JAL-1551
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
2015-10-16
Jim Procter
JAL-1925 update source version in license
Release_2_9_0b2
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
Jim Procter
JAL-1894 update year/version in copyright
tree
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commitdiff
2015-10-08
Jim Procter
Merge branch 'develop' into Release_2_9_0b1_Branch
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
2015-09-22
Jim Procter
Merge branch 'develop' into Release_2_9_0b1_Branch
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 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
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
2015-08-04
tcofoegbu
JAL-1821 updated the reference sequence column of struc...
tree
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commitdiff
2015-07-30
tcofoegbu
JAL-1443 modified exception notifications
tree
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commitdiff
2015-07-23
Jim Procter
Merge branch 'bug/JAL-1819_isNaN' into Release_2_9_Branch
tree
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commitdiff
2015-07-23
Jim Procter
Merge branch 'bug/JAL-1819_isNaN' into develop
tree
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commitdiff
2015-07-23
Jim Procter
JAL-1551 JAL-1819 formatting/imports
tree
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commitdiff
2015-07-23
Jim Procter
JAL-1819 use Float.isNaN() to check for NaNs!
tree
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commitdiff
2015-07-21
tcofoegbu
JAL-1443 bugfix to prevent loading of unidentifiable...
tree
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commitdiff
2015-07-08
gmungoc
JAL-1759 merge from develop
tree
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commitdiff
2015-07-06
gmungoc
JAL-1421 generics used for leaner safer code
tree
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commitdiff
2015-07-03
gmungoc
Merge branch 'develop' into features/JAL-892varnaToProject
tree
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commitdiff
2015-07-01
gmungoc
JAL-1802 handle slide sequences edits in split frame...
tree
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commitdiff
2015-07-01
gmungoc
Merge branch 'develop' into features/JAL-1759jmolUpdate
tree
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commitdiff
2015-06-26
tcofoegbu
JAL-1641 fixed broken functionalities after refactor
tree
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commitdiff
2015-06-26
gmungoc
Merge branch 'develop' into features/JAL-892varnaToProject
tree
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commitdiff
2015-06-26
gmungoc
Merge branch 'develop' into features/JAL-1759jmolUpdate
tree
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commitdiff
2015-06-22
Jim Procter
JAL-1780 JAL-653 Format/AppletFormat import and export...
tree
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commitdiff
2015-06-18
gmungoc
JAL-892 JAL-1779 save/restore Varna viewer to/from...
tree
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commitdiff
2015-06-18
gmungoc
JAL-1781 annotation.sequenceRef now sequence id not...
features/JAL-1781annotationXmlIds
tree
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commitdiff
2015-06-17
Jim Procter
Merge branch 'develop' into features/JAL-653_gffalignments
features/JAL-653_gffalignments
tree
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commitdiff
2015-06-15
Jim Procter
JAL-1775 patch for regression from Anne Menard’s pseudo...
tree
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commitdiff
2015-06-15
Jim Procter
JAL-1775 patch for regression from Anne Menard’s pseudo...
tree
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commitdiff
2015-06-15
Jim Procter
JAL-1775 patch regression bug when displayChar is null...
tree
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commitdiff
2015-06-15
Jim Procter
fix for JAL-1775 (and reorganise imports)
tree
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commitdiff
2015-06-15
Jim Procter
JAL-1775 patch regression bug when displayChar is null...
tree
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commitdiff
2015-06-15
Jim Procter
fix for JAL-1775 (and reorganise imports)
tree
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commitdiff
2015-06-12
tcofoegbu
JAL-1641 refactor
tree
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commitdiff
2015-06-10
gmungoc
Merge remote-tracking branch
tree
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commitdiff
2015-06-10
gmungoc
JAL-1764 save Chimera/Jmol state as separate entries...
tree
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commitdiff
2015-06-06
Jim Procter
JAL-653 allow a dummy sequence to take on attributes...
tree
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commitdiff
2015-06-05
tcofoegbu
JAL-1760 JAL-1641 Serialisation of Hidden Seqs and...
tree
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commitdiff
2015-06-05
Jim Procter
JAL-653 abstract sequence model to support file backed...
tree
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commitdiff
2015-06-05
Jim Procter
JAL-653 refactor sequence interface to separate concret...
tree
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commitdiff
2015-06-05
Jim Procter
JAL-845 jim @mungo: should this be in a package local...
tree
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commitdiff
2015-06-05
Jim Procter
JAL-1551 formatting
tree
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commitdiff
2015-06-05
Jim Procter
JAL-653 allow dummy sequences to be created if a sequen...
tree
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commitdiff
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