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JAL-2090 removed test for Java > 1.1 to enable transparency
[jalview.git]
/
src
/
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...
tree
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commitdiff
2016-01-11
tcofoegbu
merge
tree
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commitdiff
2016-01-11
tcofoegbu
JAL-1991 bug fix for some flat-file printers to check...
tree
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commitdiff
2016-01-11
gmungoc
JAL-1989 map hidden column ranges
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
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
tree
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commitdiff
2016-01-05
gmungoc
JAL-1191 check for obsolete term when descriptions...
tree
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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 :-)
tree
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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
tree
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commitdiff
2015-12-22
gmungoc
JAL-1421 parameterised map constructor used
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-391 new Calculate options to Reverse, Reverse Compl...
tree
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commitdiff
2015-12-22
gmungoc
JAL-653 AlignedCodonFrame collections changed from...
tree
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commitdiff
2015-12-22
gmungoc
JAL-653 set showSequenceFeatures=true on loading a...
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
2015-12-22
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...
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
2015-12-03
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
tree
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commitdiff
2015-12-02
gmungoc
JAL-1827 refactored to handle missing residues better
tree
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commitdiff
2015-12-02
gmungoc
JAL-1827 added overloaded method for convenience
tree
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commitdiff
2015-11-30
gmungoc
JAL-1421 generics loop syntax; 'bug?' comment added
tree
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commitdiff
2015-11-30
gmungoc
JAL-653 small comment change only
tree
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commitdiff
2015-11-30
gmungoc
JAL-652 refactored to remove one method
tree
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commitdiff
2015-11-30
gmungoc
JAL-653 (experimental) 'realise' dummy sequences in...
tree
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commitdiff
2015-11-30
gmungoc
JAL-1980 check for null alignment; JAL-1551 @Override...
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
2015-11-30
gmungoc
JAL-652 further refactoring / tests
tree
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commitdiff
2015-11-30
gmungoc
JAL-653 MapList constructor merges any contiguous ranges
tree
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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
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
2015-11-17
tcofoegbu
JAL-1479 Refactored Sifts configuration preference...
tree
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commitdiff
2015-11-16
tcofoegbu
JAL-1967 JAL-1479 refactored sequence<->structure mappi...
tree
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commitdiff
2015-11-13
tcofoegbu
JAL-1479 added transfer of residue annotation for SIFTS...
tree
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commitdiff
2015-11-11
tcofoegbu
JAL-1479 JAL-1957 Added code to enable simultaneous...
tree
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commitdiff
2015-11-11
tcofoegbu
merge
tree
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commitdiff
2015-11-11
tcofoegbu
JAL-1957 JAL-1479 Further optimisation of SIFTs Client...
features/JAL-1479_SIFTS-mapping
tree
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commitdiff
2015-11-10
Jim Procter
JAL-653 added missing pragma string to processing filter
tree
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commitdiff
2015-11-10
Jim Procter
Merge branch 'features/JAL-1705_ensembl' of source...
features/JAL-1705_ensembl
tree
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commitdiff
2015-11-10
tcofoegbu
JAL 1960 added code to restrict structure chooser to...
tree
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commitdiff
2015-11-09
gmungoc
JAL-1705 type enum can encapsulate the corresponding...
tree
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commitdiff
2015-11-05
tcofoegbu
JAL-1479 SiftClient house keeping
tree
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commitdiff
2015-11-05
tcofoegbu
JAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc...
tree
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commitdiff
2015-11-02
tcofoegbu
JAL-1955 Uniprot sequence fetcher refactor
tree
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commitdiff
2015-10-30
Jim Procter
JAL-1954 rejigged PFAMFile to split on ‘\t’ if no space...
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
2015-10-28
tcofoegbu
JAL-1952 bugfix
tree
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commitdiff
2015-10-28
tcofoegbu
JAL-1887 JAL-1479 bugfix for incorrect start/end for...
tree
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commitdiff
2015-10-23
gmungoc
JAL-1943 don't try to unmarshal non-xml files in V1...
tree
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commitdiff
2015-10-22
tcofoegbu
JAL-1479 added basic support for SIFTs mapping - more...
tree
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commitdiff
2015-10-22
tcofoegbu
JAL-1479 implemented preferences for SIFTs / Needleman...
tree
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commitdiff
2015-10-22
tcofoegbu
JAL-1942 JAL-1479 DBRefFetcher refactor
tree
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commitdiff
2015-10-22
gmungoc
JAL-1932 TrimRegionCommand bug fix, tests and purge...
tree
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commitdiff
2015-10-15
Jim Procter
Merge branch 'develop' into features/JAL-653_JAL-1766_h...
tree
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commitdiff
2015-10-15
Jim Procter
Merge branch 'develop' into features/JAL-1705_ensembl
tree
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commitdiff
2015-10-15
tcofoegbu
JAL-1479 refactored SequenceI interface - changed getDB...
tree
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commitdiff
2015-10-15
Jim Procter
JAL-1923 formatting
tree
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commitdiff
2015-10-15
Jim Procter
JAL-1923 add groups to codon-complement and notify...
tree
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commitdiff
2015-10-15
Jim Procter
JAL-1923 fix: don’t add group twice
tree
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commitdiff
2015-10-14
tcofoegbu
JAL-1926 created interface for DBRefEntry
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
2015-10-13
tcofoegbu
JAL-1479 added SIFTS XSD and generated JAXB bindings...
tree
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commitdiff
2015-10-08
Jim Procter
JAL-1894 add licensing
tree
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commitdiff
2015-10-08
Jim Procter
JAL-1894 organise imports
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-1894 organise imports
tree
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commitdiff
2015-10-07
tcofoegbu
JAL-1912 added documentation
features/JAL-1912_biojson-per-sequence-annotation
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
2015-10-07
Jim Procter
Merge branch 'features/JAL-1912_biojson-per-sequence...
tree
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commitdiff
2015-10-05
tcofoegbu
JAL-1912 house keeping
tree
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commitdiff
2015-10-05
tcofoegbu
JAL-1912 added null check for SequenceMapping variable...
tree
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commitdiff
2015-10-05
gmungoc
JAL-1812 set/return currentAlFrame for Groovy in headle...
tree
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commitdiff
2015-10-05
Jim Procter
Merge branch 'develop' into features/JAL-1912_biojson...
tree
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commitdiff
2015-10-05
gmungoc
JAL-1684 JAL-1452 new applet parameters defaultColourNuc
tree
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commitdiff
2015-10-05
tcofoegbu
JAL-1908 bugfix
tree
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commitdiff
2015-10-05
tcofoegbu
JAL-1912 updated AnnotationDisplaySettingPojo
tree
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commitdiff
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