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JAL-3010 refactoring to support feature type grouping by ontology
[jalview.git]
/
src
/
jalview
/
io
/
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
2016-02-25
tcofoegbu
JAL-1919 initial support for mmCIF using JMol API....
tree
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commitdiff
2016-02-25
gmungoc
JAL-2015 parse/write Jalview feature format pushed...
tree
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commitdiff
2016-02-24
gmungoc
JAL-2015 JAL-1956 rollout of FeatureColourI in place of
JAL-1956_featureStyles
tree
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commitdiff
2016-02-19
gmungoc
JAL-1705 JAL-1191 more terms added to hard-coded version
tree
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commitdiff
2016-02-19
gmungoc
JAL-1706 reverted setting start position as too confusi...
tree
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commitdiff
2016-02-12
gmungoc
JAL-1191 additions to SOLite, tweak to test
tree
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commitdiff
2016-02-12
gmungoc
JAL-1705 take feature ID for description if nothing...
tree
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commitdiff
2016-02-12
gmungoc
Merge branch 'develop' into
tree
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commitdiff
2016-02-09
tcofoegbu
merge develop
tree
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commitdiff
2016-02-09
tcofoegbu
JAL-1976 catch and handle OOM Error
tree
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commitdiff
2016-02-09
tcofoegbu
JAL-1976 Added progress indicators for HTML_SVG and...
tree
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commitdiff
2016-02-01
gmungoc
JAL-1705 further unit tests
tree
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commitdiff
2016-02-01
gmungoc
JAL-1191 more terms added to SequenceOntologyLite
tree
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commitdiff
2016-02-01
gmungoc
JAL-1705 JAL-1191 SequenceOntologyLite added as hard...
tree
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commitdiff
2016-01-28
gmungoc
Merge branch 'develop' into JAL-1705_trialMerge
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
2016-01-26
gmungoc
JAL-1705 derive transcript sequences from gene sequence...
tree
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commitdiff
2016-01-25
gmungoc
JAL-1705 EnsemblGene added, and related refactoring
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
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
tree
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commitdiff
2016-01-21
gmungoc
JAL-653 comments/javadoc tidy only
tree
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commitdiff
2016-01-21
gmungoc
JAL-1796 parse ensembl genomic coordinates to set start...
tree
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commitdiff
2016-01-21
gmungoc
JAL-1705 include dummy sequences in returned alignment
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
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
tcofoegbu
JAL-1991 bug fix for some flat-file printers to check...
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-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-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 hold AlignedCodonFrame collections as list...
tree
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commitdiff
2015-11-30
gmungoc
JAL-652 further refactoring / tests
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
2015-11-11
tcofoegbu
merge
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
2015-10-30
Jim Procter
JAL-1954 rejigged PFAMFile to split on â\tâ if no space...
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
2015-10-22
tcofoegbu
JAL-1479 added basic support for SIFTs mapping - more...
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
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
2015-10-08
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
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
tcofoegbu
JAL-1912 added documentation
features/JAL-1912_biojson-per-sequence-annotation
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
Jim Procter
Merge branch 'develop' into features/JAL-1912_biojson...
tree
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commitdiff
2015-10-05
Jim Procter
Merge branch 'develop' into Release_2_9_0b1_Branch
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
2015-10-01
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
JAL-1912 added support of tcoffee annotation and other...
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
JAL-1896 revised implementation to construct a ColourSc...
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
2015-09-24
gmungoc
JAL-1904 parse feature file colours on to alignment...
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
Jim Procter
Merge branch 'develop' into Release_2_9_0b1_Branch
tree
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commitdiff
2015-09-16
tcofoegbu
JAL-1486 off-by-one error bugfix
tree
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commitdiff
2015-09-16
tcofoegbu
JAL-1881 Bugfix for annotation import from BioJS
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
2015-09-07
tcofoegbu
JAL-1831 updated BioJSON schema
tree
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commitdiff
2015-09-05
Jim Procter
Merge branch 'bugfix/JAL-841_JAL-1081' into develop
tree
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commitdiff
2015-09-04
tcofoegbu
JAL-793 added ability to visualise raw BioJSON in the...
tree
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commitdiff
2015-09-03
Jim Procter
JAL-1863 allow RNA secondary structure rows exported...
tree
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commitdiff
2015-09-03
tcofoegbu
merge
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
2015-09-03
gmungoc
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2015-09-02
tcofoegbu
JAL-1740 migrated BioJSMSAViewer git repo to https...
tree
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commitdiff
2015-09-02
gmungoc
JAL-1544 spelling
tree
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commitdiff
2015-09-02
gmungoc
JAL-1355 User error text externalised to message bundle
tree
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commitdiff
2015-08-26
gmungoc
JAL-1830 dropped reference counts for mappings, instead...
tree
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commitdiff
2015-08-24
tcofoegbu
JAL-1641 externalised save_as_biojs_html
tree
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commitdiff
2015-08-21
tcofoegbu
JAL-1443 bug fix for loading pasted alignments from...
tree
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commitdiff
2015-08-21
tcofoegbu
JAL-1831 updated json schema doc
tree
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commitdiff
2015-08-18
tcofoegbu
JAL-1861 bugfix to allow parsing of stockholm files...
tree
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commitdiff
2015-08-18
tcofoegbu
JAL-1835 added UI for BioJSON embbeding preference
tree
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commitdiff
2015-08-18
tcofoegbu
JAL-1835 made BioJSON embedding to html exports configu...
tree
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commitdiff
2015-08-14
tcofoegbu
JAL-1831 added changes to allow auto-generation of...
tree
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commitdiff
2015-08-13
tcofoegbu
JAL-1641 added type to BioJSON sequence object and...
tree
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commitdiff
2015-08-11
tcofoegbu
merge
tree
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commitdiff
2015-08-11
tcofoegbu
add ability to launch jalview from exported html +...
tree
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commitdiff
2015-08-10
Jim Procter
Merge branch 'release/2_9_documentation' into develop
tree
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commitdiff
2015-08-10
tcofoegbu
JAL-1486 fixed flatfile output of visible region for...
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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