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JAL-629 Test tidyup
[jalview.git] / src / jalview / ext /
2020-02-21 gmungocJAL-3518 more extraction of ChimeraX commands as overrides tree | commitdiff
2020-02-21 gmungocJAL-2422 tidy of methods and parameters tree | commitdiff
2020-02-21 gmungocJAL-2422 general pull-up/removal of common or unused... tree | commitdiff
2020-02-20 gmungocJAL-2422 pull-up refactoring of structure commands... tree | commitdiff
2020-02-06 gmungocJAL-1842 adjust code to match changed semantics of... tree | commitdiff
2020-02-06 gmungocJAL-1842 remove redundant call to FeatureRenderer.featu... tree | commitdiff
2020-02-06 gmungocJAL-3509 better placement of call to notifyFeaturesChan... tree | commitdiff
2020-02-06 gmungocJAL-3509 coerce RESNUM to hidden (really) after fetchin... tree | commitdiff
2020-02-04 gmungocJAL-2422 pull up refactoring in preparation for Chimera... tree | commitdiff
2020-01-31 gmungocJAL-2422 temporary hacks removed; use hex colours for... tree | commitdiff
2020-01-30 gmungocJAL-2422 save/restore ChimeraX session tree | commitdiff
2020-01-28 gmungocJAL-2422 ChimeraX added to Preferences tree | commitdiff
2020-01-14 gmungocJAL-2422 proof of concept adaptations for ChimeraX... tree | commitdiff
2019-12-13 gmungocJAL-2422 'label' command to highlight ChimeraX residue... tree | commitdiff
2019-12-13 gmungocJAL-2422 write Jalview features to ChimeraX via command... tree | commitdiff
2019-12-13 gmungocJAL-2422 basic proof of concept of ChimeraX opened... tree | commitdiff
2019-10-08 gmungocMerge branch 'develop' into Jalview-JS/develop tree | commitdiff
2019-08-22 gmungocJAL-3121 round trip GFF attributes including map-valued... tree | commitdiff
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge tree | commitdiff
2019-07-05 gmungocJAL-3187 initial refactoring towards peptide variant... tree | commitdiff
2019-06-18 Jim ProcterMerge branch 'features/JAL-2349_matrixvis' into merge... tree | commitdiff
2019-06-14 gmungocJAL-3302 transfer visible 'linked' features to Chimera tree | commitdiff
2019-06-11 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures tree | commitdiff
2019-06-11 gmungocJAL-3143 also parse "phase" from JSON response if present tree | commitdiff
2019-06-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures tree | commitdiff
2019-06-07 gmungocJAL-2738 use GeneLocus extends DBRefEntry to hold chrom... tree | commitdiff
2019-06-06 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2019-05-31 Ben SoaresJAL-3247 Adjusted Uninstall Old Jalview.app to just... tree | commitdiff
2019-05-29 gmungocJAL-2738 accept .csi, default to GRCh37:homo_sapiens... tree | commitdiff
2019-05-06 gmungocJAL-3244 delete obsolete method tree | commitdiff
2019-04-26 gmungocJAL-2743 class Javadoc tree | commitdiff
2019-04-23 Jim ProcterMerge branch 'develop' into bug/JAL-3224_getdown_change... tree | commitdiff
2019-04-18 gmungocMerge branch 'develop' into Jalview-JS/develop tree | commitdiff
2019-04-18 gmungocJAL-3193 dbSource always "ENSEMBL" tree | commitdiff
2019-04-16 hansonrlocalizes Thread colourby so that it does not cause... tree | commitdiff
2019-04-15 gmungocMerge branch 'develop' into Jalview-JS/develop tree | commitdiff
2019-04-11 Jim ProcterMerge branch 'develop' into task/JAL-3130_Java_11_inves... tree | commitdiff
2019-04-10 gmungocJAL-3193 rest.ensemblgenomes.org merged to rest.ensembl.org tree | commitdiff
2019-04-10 gmungocJAL-3018 REST version updated to 10.0 tree | commitdiff
2019-04-04 Ben SoaresJAL-3130 trying to be Java 1.8 source compatible -... tree | commitdiff
2019-04-03 hansonrreplacing @j2sNative with @j2sIgnore where appropriate... tree | commitdiff
2019-04-01 gmungocJAL-3032 use small example Ensembl gene for JalviewJS tree | commitdiff
2019-04-01 hansonrJSON refactoring of a few methods; fixing JavaScript... tree | commitdiff
2019-03-21 Ben SoaresJAL-3130 Replaced deprecated Class.newInstance() with... tree | commitdiff
2019-03-20 Ben SoaresJAL-3130 Lots of deprecation fixes. See utils/deprecat... tree | commitdiff
2019-03-19 gmungocJAL-3210 code formatting only tree | commitdiff
2019-03-13 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2019-03-08 gmungocJAL-3193 defensive trim of URL read from properties... tree | commitdiff
2019-02-28 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into merge... tree | commitdiff
2019-02-20 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into feature... tree | commitdiff
2019-02-19 gmungocJAL-3187 hacks to get peptide variant in to Jmol hover... tree | commitdiff
2019-01-29 gmungocMerge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of... tree | commitdiff
2019-01-29 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into trialMerge tree | commitdiff
2019-01-29 gmungocJAL-3143 format alleles array for feature description tree | commitdiff
2019-01-29 hansonrtime check, iterators tree | commitdiff
2019-01-29 hansonrmore iterators out; some time checks tree | commitdiff
2019-01-26 hansonrPlatform.timecheck calls removed or commented out. tree | commitdiff
2019-01-26 hansonrJalview.isJS() --> Platform.isJS(), DBRefEntry[] -... tree | commitdiff
2019-01-25 hansonrJSON refactoring tree | commitdiff
2019-01-25 gmungocJAL-3187 don't compute variant features on peptide... tree | commitdiff
2019-01-24 gmungocJAL-3018 Ensembl version updated to 9.0 tree | commitdiff
2019-01-18 gmungocJAL-3143 'id' not 'ID' attribute drives generation... tree | commitdiff
2018-12-25 hansonrbetter Jmol help link tree | commitdiff
2018-12-06 gmungocMerge branch 'develop' into Jalview-BH/JAL-3026-JAL... tree | commitdiff
2018-12-06 gmungocJAL-1854 fix Checkstyle import violations tree | commitdiff
2018-11-19 gmungocJAL-3032 reinstate methods now available in SwingJS tree | commitdiff
2018-11-14 gmungocJAL-3032 don't throw Exception to signal chain not... tree | commitdiff
2018-11-14 gmungocJAL-3152 holding patch for colour Jmol by sequence tree | commitdiff
2018-11-12 gmungocJAL-3076 JalviewJS requires lower case content-type... tree | commitdiff
2018-11-11 hansonradds explicit AJAX-allowed tree | commitdiff
2018-11-01 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into tree | commitdiff
2018-11-01 gmungocMerge branch 'Jalview-BH/JAL-3026' into tree | commitdiff
2018-10-31 gmungocMerge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' into... feature/JAL-3144noJTree tree | commitdiff
2018-10-31 gmungocJAL-3026 skip unsupported HttpURLConnection methods... tree | commitdiff
2018-10-25 gmungocJAL-3143 comma-delimited feature attributes for alleles, tree | commitdiff
2018-10-25 gmungocJAL-3143 fetch Ensembl(Genomes) features as JSON not GFF tree | commitdiff
2018-10-17 Jim ProcterMerge branch 'feature/JAL-3063JAXB' into Jalview-BH... tree | commitdiff
2018-09-03 gmungocJAL-3076 fetch Ensembl sequence as JSON instead of... tree | commitdiff
2018-09-03 Jim ProcterJAL-3076 clarify javadoc handling single sequence respo... bug/JAL-3076ensemblGeneId tree | commitdiff
2018-08-27 hansonrJAL-3026 Jmol functioning; some issues tree | commitdiff
2018-08-24 hansonrJAL-3026 GD#107,128,130,139 build-site.xml tree | commitdiff
2018-08-21 hansonrmc_view references were MCview tree | commitdiff
2018-08-10 gmungocJAL-3018 updated to Ensembl REST 7.0 tree | commitdiff
2018-08-10 gmungocJAL-3076 refactor for more efficient scan of 'gene... tree | commitdiff
2018-08-10 gmungocJAL-3076 fetch Ensembl sequence as JSON instead of... tree | commitdiff
2018-07-22 hansonrallows for null Jmol viewer tree | commitdiff
2018-06-28 hansonrJAL-3032 DND enabled; additional io changes for File... tree | commitdiff
2018-06-07 gmungocJAL-2755 correct Javadoc and error handling tree | commitdiff
2018-06-04 gmungocJAL-3018 updated REST versions to 6.3 tree | commitdiff
2018-05-28 gmungocMerge remote-tracking branch 'origin/releases/Release_2... tree | commitdiff
2018-05-07 Jim ProcterJAL-2321 use StructureImportSettings singleton settings... tree | commitdiff
2018-05-07 Jim ProcterJAL-2321 allow JmolParser to be configured before parsi... tree | commitdiff
2018-05-07 gmungocMerge branch 'releases/Release_2_10_4_Branch' into... tree | commitdiff
2018-05-04 Jim ProcterMerge branch 'bug/JAL-2899' into releases/Release_2_10_... tree | commitdiff
2018-05-01 Jim ProcterJAL-2899 colouring moved from SwingWorker to a backgrou... tree | commitdiff
2018-04-30 Jim ProcterMerge branch 'bug/JAL-2899' into releases/Release_2_10_... tree | commitdiff
2018-04-05 Jim ProcterJAL-2945 resolve model as PDB file. Need to verify... tree | commitdiff
2018-03-16 gmungocJAL-2679 getGeneId() now uses the same pattern as getGe... tree | commitdiff
2018-03-16 gmungocMerge remote-tracking branch 'origin/releases/Release_2... tree | commitdiff
2018-03-15 gmungocJAL-2893 enabling Get Crossreferences to ENSEMBLGENOMES tree | commitdiff
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