JAL-3676 Documentation in Help for Java Console, Logging and Reporting Bugs
[jalview.git] / src / jalview / ext /
2020-07-31 Ben SoaresMerge branch 'releases/Release_2_11_1_Branch' into...
2020-04-21 Jim ProcterJAL-3407 add GPL license to Jalview source files
2020-02-06 gmungocJAL-1842 adjust code to match changed semantics of...
2020-02-06 gmungocJAL-1842 remove redundant call to FeatureRenderer.featu...
2020-02-06 gmungocJAL-3509 better placement of call to notifyFeaturesChan...
2020-02-06 gmungocJAL-3509 coerce RESNUM to hidden (really) after fetchin...
2019-08-22 gmungocJAL-3121 round trip GFF attributes including map-valued...
2019-07-05 gmungocJAL-3187 initial refactoring towards peptide variant...
2019-06-14 gmungocJAL-3302 transfer visible 'linked' features to Chimera
2019-06-11 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures
2019-06-11 gmungocJAL-3143 also parse "phase" from JSON response if present
2019-06-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures
2019-06-07 gmungocJAL-2738 use GeneLocus extends DBRefEntry to hold chrom...
2019-06-06 gmungocMerge branch 'develop' into trialMerge
2019-05-31 Ben SoaresJAL-3247 Adjusted Uninstall Old Jalview.app to just...
2019-05-29 gmungocJAL-2738 accept .csi, default to GRCh37:homo_sapiens...
2019-05-06 gmungocJAL-3244 delete obsolete method
2019-04-26 gmungocJAL-2743 class Javadoc
2019-04-23 Jim ProcterMerge branch 'develop' into bug/JAL-3224_getdown_change...
2019-04-18 gmungocJAL-3193 dbSource always "ENSEMBL"
2019-04-11 Jim ProcterMerge branch 'develop' into task/JAL-3130_Java_11_inves...
2019-04-10 gmungocJAL-3193 rest.ensemblgenomes.org merged to rest.ensembl.org
2019-04-10 gmungocJAL-3018 REST version updated to 10.0
2019-04-04 Ben SoaresJAL-3130 trying to be Java 1.8 source compatible -...
2019-03-21 Ben SoaresJAL-3130 Replaced deprecated Class.newInstance() with...
2019-03-20 Ben SoaresJAL-3130 Lots of deprecation fixes. See utils/deprecat...
2019-03-08 gmungocJAL-3193 defensive trim of URL read from properties...
2019-02-28 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into merge...
2019-02-20 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into feature...
2019-02-19 gmungocJAL-3187 hacks to get peptide variant in to Jmol hover...
2019-01-29 gmungocJAL-3143 format alleles array for feature description
2019-01-25 gmungocJAL-3187 don't compute variant features on peptide...
2019-01-24 gmungocJAL-3018 Ensembl version updated to 9.0
2019-01-18 gmungocJAL-3143 'id' not 'ID' attribute drives generation...
2018-12-06 gmungocJAL-1854 fix Checkstyle import violations
2018-10-25 gmungocJAL-3143 comma-delimited feature attributes for alleles,
2018-10-25 gmungocJAL-3143 fetch Ensembl(Genomes) features as JSON not GFF
2018-09-03 gmungocJAL-3076 fetch Ensembl sequence as JSON instead of...
2018-09-03 Jim ProcterJAL-3076 clarify javadoc handling single sequence respo... bug/JAL-3076ensemblGeneId
2018-08-10 gmungocJAL-3018 updated to Ensembl REST 7.0
2018-08-10 gmungocJAL-3076 refactor for more efficient scan of 'gene...
2018-08-10 gmungocJAL-3076 fetch Ensembl sequence as JSON instead of...
2018-06-07 gmungocJAL-2755 correct Javadoc and error handling
2018-06-04 gmungocJAL-3018 updated REST versions to 6.3
2018-05-28 gmungocMerge remote-tracking branch 'origin/releases/Release_2...
2018-05-07 Jim ProcterJAL-2321 use StructureImportSettings singleton settings...
2018-05-07 Jim ProcterJAL-2321 allow JmolParser to be configured before parsi...
2018-05-07 gmungocMerge branch 'releases/Release_2_10_4_Branch' into...
2018-05-04 Jim ProcterMerge branch 'bug/JAL-2899' into releases/Release_2_10_...
2018-05-01 Jim ProcterJAL-2899 colouring moved from SwingWorker to a backgrou...
2018-04-30 Jim ProcterMerge branch 'bug/JAL-2899' into releases/Release_2_10_...
2018-04-05 Jim ProcterJAL-2945 resolve model as PDB file. Need to verify...
2018-03-16 gmungocJAL-2679 getGeneId() now uses the same pattern as getGe...
2018-03-16 gmungocMerge remote-tracking branch 'origin/releases/Release_2...
2018-03-15 gmungocJAL-2893 enabling Get Crossreferences to ENSEMBLGENOMES
2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge
2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
2018-02-23 Jim ProcterMerge branch 'features/JAL-2885UniprotHttps' into relea...
2018-02-23 Jim ProcterJAL-2885 Ensembl* -> https
2018-02-23 Jim ProcterJAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL
2018-02-20 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
2018-02-12 Jim ProcterJAL-2780 JAL-2781 ahem - add a semicolon if there isn...
2018-02-07 Jim ProcterJAL-2780 JAL-2781 don’t assume contiguous mapping to...
2018-02-02 gmungocJAL-2899 asynchronous Jmol colour updates bug/JAL-2899
2018-01-30 gmungocJAL-1793 update spike build to latest incl stop and...
2018-01-29 gmungocJAL-2743 recoded EnsemblLookup without lambda expressio...
2018-01-26 gmungocMerge branch 'develop' into features/JAL-1793VCF
2018-01-18 gmungocJAL-2679 update query id to actual case of retrieved...
2018-01-17 gmungocJAL-2679 case-insensitive comparison of query and retri...
2018-01-16 gmungocJAL-2679 use object_type=Transcript for lookup of Paren...
2018-01-16 gmungocJAL-2885 uniprot now https, uniprot/ensembl/pfam/xfam...
2017-12-04 gmungocJAL-2850 JAL-1766 option to load contig sequence refere...
2017-12-01 gmungocJAL-2835 spike updated to latest (use specific SO term...
2017-11-30 gmungocJAL-1766 additional tests for stub htsjdk wrapper
2017-11-15 gmungocJAL-2835 spike updated with latest
2017-11-13 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-11-13 gmungocJAL-2679 example accession changed to CAD01290
2017-10-27 gmungocJAL-1793 spike branch updated to latest
2017-10-26 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-10-25 gmungocJAL-2743 fall back to parsing description if chromosome...
2017-10-25 Jim ProcterMerge branch 'bug/JAL-2392_deadlockonpdbdisplay' into...
2017-10-24 gmungocJAL-2738 tidy Javadoc, remove debug logging
2017-10-24 gmungocJAL-2743 look up species and gene loci for Ensembl...
2017-10-24 gmungocJAL-1739 Javadoc updated for Lambda expression parser...
2017-10-24 gmungocJAL-2738 update spike branch with latest
2017-10-24 gmungocMerge branch 'develop' into features/JAL-1793VCF; lambd...
2017-10-23 Jim ProcterMerge branch 'bug/JAL-2253' into develop
2017-10-23 gmungocJAL-1854 keep fallthrough but with comment to suppress...
2017-10-23 gmungocJAL-1854 remove fallthrough of switch case (Checkstyle...
2017-10-20 gmungocPush 1793 latest to spike branch
2017-10-20 gmungocJAL-2253 pull up constant, additional unit test bug/JAL-2253
2017-10-19 gmungocJAL-2755 add lookup of cds/cdna gene loci
2017-10-19 gmungocJAL-2755 add species lookup
2017-10-19 gmungocJAL-2755 rename EnsemblInfo as EnsemblData, add 'true...
2017-10-17 Jim ProcterJAL-2777 patch for whitespace chain bugs/JAL-2777_whitespaceChain
2017-10-10 Jim ProcterMerge branch 'codereviews/JAL-1990_IProgressIndicator_j...
2017-10-09 gmungocJAL-2523 basic sleep and retry (3 times) on 429 respons... features/JAL-2523httpRetries
2017-10-09 gmungocJAL-2523 convenience method to get model organisms
2017-10-04 gmungocJAL-2523 start of refactoring...
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