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JAL-1997 default empty tooltip required for correct behaviour
[jalview.git]
/
src
/
2016-02-01
gmungoc
JAL-1705 further unit tests
tree
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commitdiff
2016-02-01
gmungoc
JAL-1705 set Uniprot xref as 'source dbref' (for SIFTS...
tree
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commitdiff
2016-02-01
gmungoc
JAL-1191 more terms added to SequenceOntologyLite
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commitdiff
2016-02-01
gmungoc
Merge branch 'develop' into features/JAL-653_JAL-1766_h...
tree
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commitdiff
2016-02-01
gmungoc
JAL-1705 JAL-1191 SequenceOntologyLite added as hard...
tree
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commitdiff
2016-01-30
gmungoc
JAL-1705 refactored cross-reference fetching (CCDS...
tree
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commitdiff
2016-01-29
tcofoegbu
merge from develop
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commitdiff
2016-01-29
tcofoegbu
JAL-1979 refactor out duplicated similar block of code...
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commitdiff
2016-01-29
gmungoc
JAL-1705 fetch Uniprot and PDB xrefs for Ensembl protei...
tree
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commitdiff
2016-01-29
gmungoc
JAL-1705 copy feature settings when opening a split...
tree
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commitdiff
2016-01-28
gmungoc
JAL-1705 refine feature copying to including 5' and...
tree
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commitdiff
2016-01-28
gmungoc
JAL-1705 tests added, minor bugfix and refactoring
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commitdiff
2016-01-28
gmungoc
Merge branch 'develop' into JAL-1705_trialMerge
tree
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commitdiff
2016-01-28
gmungoc
JAL-1705 merge contiguous ranges when constructing...
tree
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commitdiff
2016-01-27
gmungoc
JAL-1705 add exon name to features and render on peptid...
tree
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commitdiff
2016-01-27
tcofoegbu
JAL-1479 fixed off-by-one error in SIFTS mapping output...
tree
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commitdiff
2016-01-27
gmungoc
JAL-1705 use GET for single queries; set gene name...
tree
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commitdiff
2016-01-26
gmungoc
JAL-1705 derive transcript sequences from gene sequence...
tree
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commitdiff
2016-01-26
tcofoegbu
develop merge
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commitdiff
2016-01-26
tcofoegbu
JAL-1999 JAL-1479 implemented configurable fail-safe...
tree
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commitdiff
2016-01-25
tcofoegbu
JAL-1998 bugfix for division by zero error for PDB...
tree
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commitdiff
2016-01-25
gmungoc
JAL-1705 EnsemblGene added, and related refactoring
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commitdiff
2016-01-25
gmungoc
JAL-1997 database browser support tooltip if available
tree
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commitdiff
2016-01-23
gmungoc
JAL-1355 get dialog title from message bundle
tree
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commitdiff
2016-01-23
gmungoc
JAL-1705 copy 'show sequence features' setting in ...
tree
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commitdiff
2016-01-23
gmungoc
JAL-1705 todo comment re writing DBRefEntry/SequenceFea...
tree
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commitdiff
2016-01-23
gmungoc
JAL-1705 compute peptide variants from dna; add "conseq...
tree
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commitdiff
2016-01-21
tcofoegbu
JAL-1479 JAL-1979 bugfix to check entire annotation...
tree
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commitdiff
2016-01-21
gmungoc
JAL-1705 transfer features to the dataset sequence...
tree
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commitdiff
2016-01-21
gmungoc
JAL-1705 reworked Ensembl clients now fetching and...
tree
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commitdiff
2016-01-21
gmungoc
JAL-653 refactor / tidy
tree
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commitdiff
2016-01-21
gmungoc
JAL-653 JAL-1705 set strand for GFF sequence feature
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commitdiff
2016-01-21
gmungoc
JAL-653 comments/javadoc tidy only
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commitdiff
2016-01-21
gmungoc
JAL-1796 parse ensembl genomic coordinates to set start...
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commitdiff
2016-01-21
gmungoc
JAL-1705 AlignmentUtils method renamed
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commitdiff
2016-01-21
gmungoc
JAL-1705 ENSEMBL added, unused constants removed
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commitdiff
2016-01-21
gmungoc
JAL-1705 features transferred to CDS sequence; makeExon...
tree
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commitdiff
2016-01-21
gmungoc
JAL-1705 redundant comment removed
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commitdiff
2016-01-21
gmungoc
JAL-1705 suppress jvsuffix (for sequence id matching...
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commitdiff
2016-01-21
gmungoc
JAL-1705 unused import removed
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commitdiff
2016-01-21
gmungoc
JAL-1705 include dummy sequences in returned alignment
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commitdiff
2016-01-21
tcofoegbu
JAL-1479 JAL-1979 updated the modified-aminoacid triple...
tree
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commitdiff
2016-01-21
gmungoc
JAL-1705 added isSequenceVariant(), commonly used SO...
tree
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commitdiff
2016-01-21
gmungoc
JAL-1705 isFromForwardStrand added; toString (for debug...
tree
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commitdiff
2016-01-21
gmungoc
JAL-1705 canonicalise ENSEMBL name; code tidy
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commitdiff
2016-01-21
gmungoc
JAL-1705 get xrefs only for dna/peptide; code tidy
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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
2016-01-12
gmungoc
JAL-1191 cache isA (great-)grandparents as well for...
tree
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commitdiff
2016-01-11
gmungoc
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-01-11
gmungoc
JAL-1989 additional ways to 'mirror' show/hide columns...
tree
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commitdiff
2016-01-11
tcofoegbu
JAL-1990 added a progress indicator for Structure Choos...
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commitdiff
2016-01-11
tcofoegbu
merge
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commitdiff
2016-01-11
tcofoegbu
JAL-1991 bug fix for some flat-file printers to check...
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commitdiff
2016-01-11
gmungoc
JAL-1989 map hidden column ranges
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commitdiff
2016-01-11
gmungoc
JAL-1989 more unit tests and encapsulation for ColumnSe...
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commitdiff
2016-01-08
gmungoc
JAL-1705 DbSourceProxy properties converted to methods...
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commitdiff
2016-01-07
tcofoegbu
merge
tree
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commitdiff
2016-01-07
tcofoegbu
JAL-1479 implemented timestamp based caching of SIFTS...
tree
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commitdiff
2016-01-05
gmungoc
Merge remote-tracking branch 'origin/features/JAL-1705_...
tree
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commitdiff
2016-01-05
gmungoc
JAL-653 typed map for feature colours in method signature
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commitdiff
2016-01-05
gmungoc
JAL-1191 check for obsolete term when descriptions...
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commitdiff
2015-12-23
gmungoc
JAL-1191 zipped SO OBO file added to /resources, more...
tree
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commitdiff
2015-12-22
gmungoc
JAL-1191 and provide the SO OBO file in /resources :-)
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commitdiff
2015-12-22
gmungoc
JAL-1191 SequenceOntology wrapping/caching SO.OBO via...
tree
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commitdiff
2015-12-22
gmungoc
JAL-1191 stub class for a SequenceOntology wrapper
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commitdiff
2015-12-22
gmungoc
JAL-1421 parameterised map constructor used
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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-391 new Calculate options to Reverse, Reverse Compl...
tree
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commitdiff
2015-12-22
gmungoc
JAL-653 AlignedCodonFrame collections changed from...
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commitdiff
2015-12-22
gmungoc
JAL-653 set showSequenceFeatures=true on loading a...
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commitdiff
2015-12-22
gmungoc
JAL-653 GFF new/refactored helper classes
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commitdiff
2015-12-22
gmungoc
JAL-653 AlignedCodonFrame internal refactor, merge...
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commitdiff
2015-12-22
gmungoc
JAL-653 hold AlignedCodonFrame collections as list...
tree
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commitdiff
2015-12-09
Jim Procter
JAL-1982 hotfix to prevent NPE with applet launch on...
tree
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commitdiff
2015-12-03
gmungoc
JAL-653 code tidy / tests for 'realise gff mappings'
tree
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commitdiff
2015-12-03
gmungoc
JAL-653 handle reverse strand mapping in SearchResults...
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commitdiff
2015-12-03
gmungoc
JAL-653 mappings always reside on the dataset alignment...
tree
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commitdiff
2015-12-03
gmungoc
JAL-653 handle reverse strand mappings also
tree
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commitdiff
2015-12-03
gmungoc
JAL-1827 code and comment tidy up
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commitdiff
2015-12-02
gmungoc
JAL-1827 refactored to handle missing residues better
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commitdiff
2015-12-02
gmungoc
JAL-1827 added overloaded method for convenience
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commitdiff
2015-11-30
gmungoc
JAL-1421 generics loop syntax; 'bug?' comment added
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commitdiff
2015-11-30
gmungoc
JAL-653 small comment change only
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commitdiff
2015-11-30
gmungoc
JAL-652 refactored to remove one method
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commitdiff
2015-11-30
gmungoc
JAL-653 (experimental) 'realise' dummy sequences in...
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commitdiff
2015-11-30
gmungoc
JAL-1980 check for null alignment; JAL-1551 @Override...
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commitdiff
2015-11-30
gmungoc
JAL-653 (experimental) methods to resolve dummy to...
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commitdiff
2015-11-30
gmungoc
JAL-653 getStrand javadoc/refactor/test
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commitdiff
2015-11-30
gmungoc
JAL-1421 use generics JAL-1551 @Override annotations...
tree
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commitdiff
2015-11-30
gmungoc
JAL-652 further refactoring / tests
tree
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commitdiff
2015-11-30
gmungoc
JAL-653 MapList constructor merges any contiguous ranges
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commitdiff
2015-11-25
tcofoegbu
JAL-1479 refactored DBRef fetching code to StructureCho...
tree
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commitdiff
2015-11-25
tcofoegbu
JAL-1479 applet build debug
tree
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commitdiff
2015-11-25
tcofoegbu
JAL-1479 bugfix after decoupling SIFTS preference settings
tree
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commitdiff
2015-11-23
tcofoegbu
JAL-1479 commented out DBRef fetching code from SIFTS...
tree
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commitdiff
2015-11-21
gmungoc
JAL-1968 remove feature links
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commitdiff
2015-11-21
gmungoc
JAL-653 JAL-1968 FeaturesFile now handles Jalview or...
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commitdiff
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