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Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
[jalview.git]
/
src
/
jalview
/
ext
/
2020-05-11
gmungoc
JAL-2422 JAL-3551 viewer text/variables generalised...
tree
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commitdiff
2020-05-11
gmungoc
JAL-2422 restore saved ChimeraX session from project
tree
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commitdiff
2020-04-30
gmungoc
JAL-3551 save structure viewer session refactorings...
tree
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commitdiff
2020-04-30
gmungoc
JAL-3551 tidied error handling for HTTP request
tree
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commitdiff
2020-04-25
gmungoc
Merge branch 'develop' into feature/JAL-3551Pymol
tree
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commitdiff
2020-04-21
Jim Procter
JAL-3407 add GPL license to Jalview source files
tree
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commitdiff
2020-03-31
gmungoc
JAL-3210 JAL-3130 merge changes to JSON processing
tree
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commitdiff
2020-03-30
gmungoc
JAL-3210 debug logging commented out
tree
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commitdiff
2020-03-30
gmungoc
Merge branch 'develop' into Jalview-JS/develop
tree
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commitdiff
2020-03-16
gmungoc
JAL-3551 tidying, improved commands, fix Jmol model...
tree
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commitdiff
2020-03-16
gmungoc
JAL-3551 the correct PyMOL colour by chain command
tree
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commitdiff
2020-03-13
gmungoc
JAL-3551 working proof of concept of Jalview driving...
tree
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commitdiff
2020-03-09
gmungoc
Merge branch 'develop' into feature/JAL-2422ChimeraX
tree
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commitdiff
2020-03-03
gmungoc
JAL-3158 superseded superposeStructures methods removed
tree
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commitdiff
2020-03-03
gmungoc
JAL-3518 more pull up / test coverage of structure...
tree
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commitdiff
2020-02-29
gmungoc
JAL-3518 correct override for ChimeraX colour by residues
tree
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commitdiff
2020-02-28
gmungoc
JAL-3518 basic refactoring / pull up of superposeStruct...
tree
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commitdiff
2020-02-21
gmungoc
JAL-3518 more extraction of ChimeraX commands as overrides
tree
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commitdiff
2020-02-21
gmungoc
JAL-2422 tidy of methods and parameters
tree
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commitdiff
2020-02-21
gmungoc
JAL-2422 general pull-up/removal of common or unused...
tree
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commitdiff
2020-02-20
gmungoc
JAL-2422 pull-up refactoring of structure commands...
tree
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commitdiff
2020-02-06
gmungoc
JAL-1842 adjust code to match changed semantics of...
tree
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commitdiff
2020-02-06
gmungoc
JAL-1842 remove redundant call to FeatureRenderer.featu...
tree
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commitdiff
2020-02-06
gmungoc
JAL-3509 better placement of call to notifyFeaturesChan...
tree
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commitdiff
2020-02-06
gmungoc
JAL-3509 coerce RESNUM to hidden (really) after fetchin...
tree
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commitdiff
2020-02-04
gmungoc
JAL-2422 pull up refactoring in preparation for Chimera...
tree
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commitdiff
2020-01-31
gmungoc
JAL-2422 temporary hacks removed; use hex colours for...
tree
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commitdiff
2020-01-30
gmungoc
JAL-2422 save/restore ChimeraX session
tree
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commitdiff
2020-01-28
gmungoc
JAL-2422 ChimeraX added to Preferences
tree
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commitdiff
2020-01-14
gmungoc
JAL-2422 proof of concept adaptations for ChimeraX...
tree
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commitdiff
2019-12-13
gmungoc
JAL-2422 'label' command to highlight ChimeraX residue...
tree
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commitdiff
2019-12-13
gmungoc
JAL-2422 write Jalview features to ChimeraX via command...
tree
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commitdiff
2019-12-13
gmungoc
JAL-2422 basic proof of concept of ChimeraX opened...
tree
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commitdiff
2019-10-08
gmungoc
Merge branch 'develop' into Jalview-JS/develop
tree
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commitdiff
2019-08-22
gmungoc
JAL-3121 round trip GFF attributes including map-valued...
tree
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commitdiff
2019-07-16
gmungoc
JAL-3210 Merge branch 'develop' into trialMerge
tree
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commitdiff
2019-07-05
gmungoc
JAL-3187 initial refactoring towards peptide variant...
tree
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commitdiff
2019-06-18
Jim Procter
Merge branch 'features/JAL-2349_matrixvis' into merge...
tree
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commitdiff
2019-06-14
gmungoc
JAL-3302 transfer visible 'linked' features to Chimera
tree
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commitdiff
2019-06-11
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
tree
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commitdiff
2019-06-11
gmungoc
JAL-3143 also parse "phase" from JSON response if present
tree
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commitdiff
2019-06-07
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
tree
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commitdiff
2019-06-07
gmungoc
JAL-2738 use GeneLocus extends DBRefEntry to hold chrom...
tree
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commitdiff
2019-06-06
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2019-05-31
Ben Soares
JAL-3247 Adjusted Uninstall Old Jalview.app to just...
tree
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commitdiff
2019-05-29
gmungoc
JAL-2738 accept .csi, default to GRCh37:homo_sapiens...
tree
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commitdiff
2019-05-06
gmungoc
JAL-3244 delete obsolete method
tree
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commitdiff
2019-04-26
gmungoc
JAL-2743 class Javadoc
tree
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commitdiff
2019-04-23
Jim Procter
Merge branch 'develop' into bug/JAL-3224_getdown_change...
tree
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commitdiff
2019-04-18
gmungoc
Merge branch 'develop' into Jalview-JS/develop
tree
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commitdiff
2019-04-18
gmungoc
JAL-3193 dbSource always "ENSEMBL"
tree
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commitdiff
2019-04-16
hansonr
localizes Thread colourby so that it does not cause...
tree
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commitdiff
2019-04-15
gmungoc
Merge branch 'develop' into Jalview-JS/develop
tree
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commitdiff
2019-04-11
Jim Procter
Merge branch 'develop' into task/JAL-3130_Java_11_inves...
tree
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commitdiff
2019-04-10
gmungoc
JAL-3193 rest.ensemblgenomes.org merged to rest.ensembl.org
tree
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commitdiff
2019-04-10
gmungoc
JAL-3018 REST version updated to 10.0
tree
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commitdiff
2019-04-04
Ben Soares
JAL-3130 trying to be Java 1.8 source compatible -...
tree
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commitdiff
2019-04-03
hansonr
replacing @j2sNative with @j2sIgnore where appropriate...
tree
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commitdiff
2019-04-01
gmungoc
JAL-3032 use small example Ensembl gene for JalviewJS
tree
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commitdiff
2019-04-01
hansonr
JSON refactoring of a few methods; fixing JavaScript...
tree
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commitdiff
2019-03-21
Ben Soares
JAL-3130 Replaced deprecated Class.newInstance() with...
tree
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commitdiff
2019-03-20
Ben Soares
JAL-3130 Lots of deprecation fixes. See utils/deprecat...
tree
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commitdiff
2019-03-19
gmungoc
JAL-3210 code formatting only
tree
|
commitdiff
2019-03-13
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2019-03-08
gmungoc
JAL-3193 defensive trim of URL read from properties...
tree
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commitdiff
2019-02-28
gmungoc
Merge branch 'feature/JAL-3143ensemblJSON' into merge...
tree
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commitdiff
2019-02-20
gmungoc
Merge branch 'feature/JAL-3143ensemblJSON' into feature...
tree
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commitdiff
2019-02-19
gmungoc
JAL-3187 hacks to get peptide variant in to Jmol hover...
tree
|
commitdiff
2019-01-29
gmungoc
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of...
tree
|
commitdiff
2019-01-29
gmungoc
Merge branch 'feature/JAL-3143ensemblJSON' into trialMerge
tree
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commitdiff
2019-01-29
gmungoc
JAL-3143 format alleles array for feature description
tree
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commitdiff
2019-01-29
hansonr
time check, iterators
tree
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commitdiff
2019-01-29
hansonr
more iterators out; some time checks
tree
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commitdiff
2019-01-26
hansonr
Platform.timecheck calls removed or commented out.
tree
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commitdiff
2019-01-26
hansonr
Jalview.isJS() --> Platform.isJS(), DBRefEntry[] -...
tree
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commitdiff
2019-01-25
hansonr
JSON refactoring
tree
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commitdiff
2019-01-25
gmungoc
JAL-3187 don't compute variant features on peptide...
tree
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commitdiff
2019-01-24
gmungoc
JAL-3018 Ensembl version updated to 9.0
tree
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commitdiff
2019-01-18
gmungoc
JAL-3143 'id' not 'ID' attribute drives generation...
tree
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commitdiff
2018-12-25
hansonr
better Jmol help link
tree
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commitdiff
2018-12-06
gmungoc
Merge branch 'develop' into Jalview-BH/JAL-3026-JAL...
tree
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commitdiff
2018-12-06
gmungoc
JAL-1854 fix Checkstyle import violations
tree
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commitdiff
2018-11-19
gmungoc
JAL-3032 reinstate methods now available in SwingJS
tree
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commitdiff
2018-11-14
gmungoc
JAL-3032 don't throw Exception to signal chain not...
tree
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commitdiff
2018-11-14
gmungoc
JAL-3152 holding patch for colour Jmol by sequence
tree
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commitdiff
2018-11-12
gmungoc
JAL-3076 JalviewJS requires lower case content-type...
tree
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commitdiff
2018-11-11
hansonr
adds explicit AJAX-allowed
tree
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commitdiff
2018-11-01
gmungoc
Merge branch 'feature/JAL-3143ensemblJSON' into
tree
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commitdiff
2018-11-01
gmungoc
Merge branch 'Jalview-BH/JAL-3026' into
tree
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commitdiff
2018-10-31
gmungoc
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' into...
feature/JAL-3144noJTree
tree
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commitdiff
2018-10-31
gmungoc
JAL-3026 skip unsupported HttpURLConnection methods...
tree
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commitdiff
2018-10-25
gmungoc
JAL-3143 comma-delimited feature attributes for alleles,
tree
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commitdiff
2018-10-25
gmungoc
JAL-3143 fetch Ensembl(Genomes) features as JSON not GFF
tree
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commitdiff
2018-10-17
Jim Procter
Merge branch 'feature/JAL-3063JAXB' into Jalview-BH...
tree
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commitdiff
2018-09-03
gmungoc
JAL-3076 fetch Ensembl sequence as JSON instead of...
tree
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commitdiff
2018-09-03
Jim Procter
JAL-3076 clarify javadoc handling single sequence respo...
bug/JAL-3076ensemblGeneId
tree
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commitdiff
2018-08-27
hansonr
JAL-3026 Jmol functioning; some issues
tree
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commitdiff
2018-08-24
hansonr
JAL-3026 GD#107,128,130,139 build-site.xml
tree
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commitdiff
2018-08-21
hansonr
mc_view references were MCview
tree
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commitdiff
2018-08-10
gmungoc
JAL-3018 updated to Ensembl REST 7.0
tree
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commitdiff
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