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JAL-1705 tidy and todo comment, no functional change
[jalview.git]
/
src
/
jalview
/
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
tree
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commitdiff
2016-01-21
gmungoc
JAL-1705 get xrefs only for dna/peptide; code tidy
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
2016-01-12
gmungoc
JAL-1191 cache isA (great-)grandparents as well for...
tree
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commitdiff
2016-01-08
gmungoc
JAL-1705 DbSourceProxy properties converted to methods...
tree
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commitdiff
2016-01-05
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
2015-12-03
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
2015-11-30
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
2015-11-21
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
2015-11-10
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
2015-11-09
gmungoc
JAL-1705 type enum can encapsulate the corresponding...
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
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
2015-10-08
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
2015-10-02
gmungoc
JAL-1815 restore split frame geometry including horizon...
tree
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commitdiff
2015-10-02
Jim Procter
JAL-1900 JAL-1625 disable iconify button for internal...
tree
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commitdiff
2015-10-01
tcofoegbu
JAL-1912 Double.NaN breaks JSON serialization - added...
tree
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commitdiff
2015-10-01
tcofoegbu
JAL-1912 refactor annotation refsequence assignemnt...
tree
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commitdiff
2015-09-30
tcofoegbu
house keeping
tree
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commitdiff
2015-09-30
tcofoegbu
JAL-1860 house keeping
tree
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commitdiff
2015-09-30
tcofoegbu
JAL-1852 made disabling querying of unpublished PDB...
tree
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commitdiff
2015-09-30
tcofoegbu
JAL-1912 added support of tcoffee annotation and other...
tree
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commitdiff
2015-09-30
tcofoegbu
JAL-1852 disable querying of unpublished PDB entries...
tree
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commitdiff
2015-09-29
tcofoegbu
JAL-1896 fixed NPE for RNA Helice without equivalent...
tree
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commitdiff
2015-09-28
tcofoegbu
merge
tree
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commitdiff
2015-09-28
tcofoegbu
JAL-1896 revised implementation to construct a ColourSc...
tree
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commitdiff
2015-09-28
gmungoc
JAL-1909 repaint complementary alignment panel after...
tree
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commitdiff
2015-09-25
gmungoc
JAL-1859 try hoverDelay of 0.1s in Jmol for more respon...
tree
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commitdiff
2015-09-25
tcofoegbu
merge
tree
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commitdiff
2015-09-25
tcofoegbu
JAL-1907 bugfix for NPE while parsing a features file
tree
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commitdiff
2015-09-25
gmungoc
JAL-1815 restore split frame geometry correctly includi...
tree
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commitdiff
2015-09-25
tcofoegbu
merge
tree
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commitdiff
2015-09-25
tcofoegbu
JAL-1860 disabled default enter behaviour on pdb search...
tree
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commitdiff
2015-09-24
gmungoc
JAL-1905 parse url including & correctly
tree
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commitdiff
2015-09-24
gmungoc
JAL-1904 parse feature file colours on to alignment...
tree
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commitdiff
2015-09-24
tcofoegbu
JAL-1860 only allow enter key when valid selection...
tree
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commitdiff
2015-09-24
tcofoegbu
JAL-1860 keyboard operation of pdb sequence fetcher...
tree
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commitdiff
2015-09-24
tcofoegbu
JAL-1896 bugfix to enabled Jalview restore clustal...
tree
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commitdiff
2015-09-22
tcofoegbu
JAL-1774 house keeping
tree
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commitdiff
2015-09-21
tcofoegbu
merge
tree
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commitdiff
2015-09-21
tcofoegbu
JAL-1774 modifed warning dialog to use JVDialog rather...
tree
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commitdiff
2015-09-21
gmungoc
JAL-1799 update height of annotation labels to match...
tree
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commitdiff
2015-09-21
gmungoc
JAL-1152 set initial state of show alignment/sequence...
tree
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commitdiff
2015-09-18
gmungoc
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2015-09-18
Jim Procter
JAL-1889 remove non-UTF8 characters so we can build...
tree
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commitdiff
2015-09-18
tcofoegbu
JAL-1774 JAL-1506 revised implementaion for clear highl...
tree
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commitdiff
2015-09-18
tcofoegbu
JAL-1506 revised implementation to clear only selected...
tree
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commitdiff
2015-09-18
gmungoc
JAL-1859 reinstated full path to file option (for local...
tree
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commitdiff
2015-09-17
tcofoegbu
JAL-1774 bugfix for misleading message after trying...
tree
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commitdiff
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