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jalview.git
2019-09-16 Mateusz WarownySet the initial value of the choice field to the defaul... commit | commitdiff | tree | snapshot
2019-09-16 Mateusz WarownyAdd the remaining msa services to the Discoverer commit | commitdiff | tree | snapshot
2019-09-11 Mateusz WarownyChange choice field to use dropbox instead of radio... commit | commitdiff | tree | snapshot
2019-09-11 Mateusz WarownyCreate generic msa service instance commit | commitdiff | tree | snapshot
2019-09-06 Mateusz WarownyMerge remote-tracking branch 'origin/alpha/JAL-3066_Jal... commit | commitdiff | tree | snapshot
2019-09-06 Mateusz WarownyJAL-3066 Working custom parameters for clustalo commit | commitdiff | tree | snapshot
2019-09-06 Jim ProcterJAL-3066 fix compile error (@matesuz - this will confli... commit | commitdiff | tree | snapshot
2019-09-06 Jim ProcterJAL_1426 JAL-3066 update Apache James mime parser and... commit | commitdiff | tree | snapshot
2019-09-06 Mateusz WarownyJAL-1426 Replacing old apache-http jars. commit | commitdiff | tree | snapshot
2019-09-05 Mateusz WarownyJAL-3066 Implement clustaloWS using slivka system. commit | commitdiff | tree | snapshot
2019-08-13 Jim ProcterJAL-3362 keep Java 1.8 build happy by specifying generi... commit | commitdiff | tree | snapshot
2019-08-13 Jim ProcterMerge branch 'alpha/JAL-3362_Jalview_212_alpha' into... commit | commitdiff | tree | snapshot
2019-08-09 gmungocJAL-3187 removal of variant feature (non-virtual) trans... commit | commitdiff | tree | snapshot
2019-08-07 gmungocJAL-3187 (fudge) look in both alignments for stored... feature/JAL-3187linkedFeatures commit | commitdiff | tree | snapshot
2019-08-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures commit | commitdiff | tree | snapshot
2019-07-31 gmungocJAL-3389 add .py to restored Chimera session filename... commit | commitdiff | tree | snapshot
2019-07-31 gmungocMerge branch 'bug/JAL-3388structureChooserSorting'... commit | commitdiff | tree | snapshot
2019-07-30 gmungocJAL-3198 more efficient Sequence.getDisplayId() commit | commitdiff | tree | snapshot
2019-07-30 gmungocJAL-3388 correct class for column 0 Ref Sequence bug/JAL-3388structureChooserSorting commit | commitdiff | tree | snapshot
2019-07-29 gmungocJAL-3386 correct wrapped width calculation for headless... commit | commitdiff | tree | snapshot
2019-07-29 gmungocJAL-3377 more reused of SeqCanvas.computeWrappedGeometry commit | commitdiff | tree | snapshot
2019-07-29 gmungocJAL-3377 add seq-annotations gap to cheight not to... commit | commitdiff | tree | snapshot
2019-07-29 gmungocJAL-3377 Javadoc added for getWrappedHeight() commit | commitdiff | tree | snapshot
2019-07-29 gmungocJAL-3377 corrected wrapped widths height for IdCanvas commit | commitdiff | tree | snapshot
2019-07-29 gmungocJAL-3377 include seq-annotation spacing in getWrappedHe... commit | commitdiff | tree | snapshot
2019-07-26 gmungocMerge branch 'features/JAL-3375vcfValidation' into commit | commitdiff | tree | snapshot
2019-07-26 gmungocJAL-1793 only decode specific special characters in... commit | commitdiff | tree | snapshot
2019-07-26 gmungocJAL-3376 capture VCF POS, ID, QUAL, FILTER as feature... features/JAL-3375vcfValidation commit | commitdiff | tree | snapshot
2019-07-26 gmungocJAL-3375 format validate VCF Integer and Float fields commit | commitdiff | tree | snapshot
2019-07-25 gmungocJAL-3375 ignore '.' values for VCF data commit | commitdiff | tree | snapshot
2019-07-16 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures commit | commitdiff | tree | snapshot
2019-07-16 gmungocJAL-2987 tolerate null double values when formatting... commit | commitdiff | tree | snapshot
2019-07-15 Jim ProcterMerge branch 'merge/JAL-3285_mchmmer_with_211_develop... commit | commitdiff | tree | snapshot
2019-07-12 ThomasJAL-2629 can now choose number of jackhmmer iterations merge/JAL-3285_mchmmer_with_211_develop commit | commitdiff | tree | snapshot
2019-07-12 ThomasJAL-2629 fix faulty label in a MessageManager.getString... commit | commitdiff | tree | snapshot
2019-07-12 ThomasJAL-2629 add sort by evalue and bit score commit | commitdiff | tree | snapshot
2019-07-12 ThomasJAL-2629 hmmer searches now read domain rather than... commit | commitdiff | tree | snapshot
2019-07-11 Jim ProcterMerge branch 'merge/JAL-3285_mchmmer_with_211_develop... commit | commitdiff | tree | snapshot
2019-07-11 ThomasJAL-2629 hmmer searches include seqs past inclusion... commit | commitdiff | tree | snapshot
2019-07-11 ThomasJAL-2629 hmm search UI and structural improvements... commit | commitdiff | tree | snapshot
2019-07-10 Jim ProcterJAL-3070 standard way of storing/recovering documentati... commit | commitdiff | tree | snapshot
2019-07-10 Jim ProcterJAL-3070 remove final reference to Jws2Instance commit | commitdiff | tree | snapshot
2019-07-10 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures commit | commitdiff | tree | snapshot
2019-07-10 tvaJAL-2629 fix hmmsearch/jackhmmer assigning incorrect... commit | commitdiff | tree | snapshot
2019-07-10 Jim ProcterMerge branch 'tasks/JAL-3070_wsinterfaces' into alpha... commit | commitdiff | tree | snapshot
2019-07-10 tvaJAL-2629 fix hmsearch and jackhmmer not being able... commit | commitdiff | tree | snapshot
2019-07-10 Jim ProcterJAL-3289 bamboo properties for ‘BUILD’ getdown channel... commit | commitdiff | tree | snapshot
2019-07-10 Jim ProcterJAL-3289 bamboo properties for ‘BUILD’ getdown channel commit | commitdiff | tree | snapshot
2019-07-10 tvaJAL-2629 hmmsearch # of new sequences now only displaye... commit | commitdiff | tree | snapshot
2019-07-10 tvaJAL-2629 fix incorrect hmmbuild on groups behaviour commit | commitdiff | tree | snapshot
2019-07-10 Jim ProcterJAL-3289 bamboo properties for ‘BUILD’ getdown channel... commit | commitdiff | tree | snapshot
2019-07-10 Jim ProcterJAL-3289 bamboo properties for ‘BUILD’ getdown channel commit | commitdiff | tree | snapshot
2019-07-10 Jim ProcterMerge branch 'merge/JAL-3285_mchmmer_with_211_develop... commit | commitdiff | tree | snapshot
2019-07-10 tvaJAL-2629 fix hmmsearch/jackhmmer being unable to search... commit | commitdiff | tree | snapshot
2019-07-08 gmungocJAL-3187 derived peptide variants tweaks and tests commit | commitdiff | tree | snapshot
2019-07-05 tvaJAL-2629 uniquify all hmmer command sequence outputs commit | commitdiff | tree | snapshot
2019-07-05 gmungocJAL-3187 initial refactoring towards peptide variant... commit | commitdiff | tree | snapshot
2019-07-05 tvaJAL-2629 fix file format issues preventing hmmsearch... commit | commitdiff | tree | snapshot
2019-07-05 Ben SoaresJAL-1544 fixed a html encoding of '<' (%lt; -> &lt... commit | commitdiff | tree | snapshot
2019-07-05 gmungocJAL-1793 apply URL decoding when saving VCF attribute... commit | commitdiff | tree | snapshot
2019-07-04 Jim ProcterJAL-3111 correct JVL appbase for 2.10.5 via getdown commit | commitdiff | tree | snapshot
2019-07-04 Jim ProcterMerge branch 'task/JAL-3337-rm-lib-update-sourceDist... commit | commitdiff | tree | snapshot
2019-07-04 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie... commit | commitdiff | tree | snapshot
2019-07-04 Jim ProcterJAL-3337 round-and-round the process source files again commit | commitdiff | tree | snapshot
2019-07-04 Jim ProcterJAL-3337 more includes and excludes commit | commitdiff | tree | snapshot
2019-07-04 Jim ProcterJAL-3337 remove the old lib directory ! task/JAL-3337-rm-lib-update-sourceDist commit | commitdiff | tree | snapshot
2019-07-04 Jim ProcterJAL-3337 rejig the source distribution generation to... commit | commitdiff | tree | snapshot
2019-07-04 Jim ProcterJAL-3111 replace year in header for help pages and... commit | commitdiff | tree | snapshot
2019-07-04 Ben SoaresJAL-3225 try/catch for non-deprecated/deprecated proper... commit | commitdiff | tree | snapshot
2019-07-04 Ben SoaresJAL-3353 Change to build.gradle to use the file://... commit | commitdiff | tree | snapshot
2019-07-04 gmungocMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2019-07-04 gmungocJAL-3111 help pages minor corrections commit | commitdiff | tree | snapshot
2019-07-04 Ben SoaresJAL-3348 fixed an internal href in help to allow building commit | commitdiff | tree | snapshot
2019-07-04 Ben SoaresJAL-3337 adjusted building doc as sourceDist uses gradl... commit | commitdiff | tree | snapshot
2019-07-04 Jim ProcterMerge branch 'task/JAL-3348_document_cli_memory_setting... commit | commitdiff | tree | snapshot
2019-07-04 Jim ProcterJAL-3111 JAL-3348 JVL file documentation commit | commitdiff | tree | snapshot
2019-07-04 Jim ProcterJAL-3348 revised bsoares memory settings documentation... commit | commitdiff | tree | snapshot
2019-07-04 Ben SoaresMerge branch 'develop' into task/JAL-3348_document_cli_... commit | commitdiff | tree | snapshot
2019-07-03 Ben SoaresJAL-3348 memory.html documentation finished for 2.11.0 commit | commitdiff | tree | snapshot
2019-07-03 Ben SoaresJAL-3348 jvmmempc in jvl file now works in linux commit | commitdiff | tree | snapshot
2019-07-03 Ben SoaresJAL-3348 jvmmempc multiple values shouldn't be merged commit | commitdiff | tree | snapshot
2019-07-03 Jim ProcterJAL-3111 tidy up lists/indentation for release notes commit | commitdiff | tree | snapshot
2019-07-03 Jim ProcterJAL-3111 Java 11 only and 'onwards' commit | commitdiff | tree | snapshot
2019-07-03 Jim ProcterJAL-3111 more whatsNew tweaks commit | commitdiff | tree | snapshot
2019-07-03 Jim ProcterMerge branch 'task/JAL-3337_gradle_tasks_sourceDist_and... commit | commitdiff | tree | snapshot
2019-07-03 Jim ProcterJAL-3111 more whats new commit | commitdiff | tree | snapshot
2019-07-03 Ben SoaresJAL-3348 start of new memory setting text commit | commitdiff | tree | snapshot
2019-07-03 Ben SoaresJAL-3348 jvmmempc allowed in jvl file commit | commitdiff | tree | snapshot
2019-07-03 Ben SoaresMerge branch 'develop' into task/JAL-3348_document_cli_... commit | commitdiff | tree | snapshot
2019-07-03 Jim ProcterMerge branch 'documentation/JAL-2843_featureFiltersForm... commit | commitdiff | tree | snapshot
2019-07-03 tvaJAL-2629 fix search scores being read in incorrectly commit | commitdiff | tree | snapshot
2019-07-03 tvaJAL-2629 fix hmm on alignment being deleted upon runnin... commit | commitdiff | tree | snapshot
2019-07-03 tvaJAL-2629 evalues and bit scores now conserved after... commit | commitdiff | tree | snapshot
2019-07-03 tvaJAL-2629 removed empty line produced under sequence... commit | commitdiff | tree | snapshot
2019-07-03 tvaJAL-2629 can now filter by sequence e-value or bit... commit | commitdiff | tree | snapshot
2019-07-03 Ben SoaresJAL-3348 prepping getdown to pass JVM command line... commit | commitdiff | tree | snapshot
2019-07-02 Jim ProcterJAL-3111 updated what’s new… still more to come ! commit | commitdiff | tree | snapshot
2019-07-02 Jim ProcterJAL-3111 updated privacy statement to remove mention... commit | commitdiff | tree | snapshot
2019-07-02 Jim ProcterJAL-3111 JAL-3150 revised Jalview archive documentation... commit | commitdiff | tree | snapshot
2019-07-02 Jim ProcterJAL-3111 JAL-3348 removed pre 2.11 instructions on... commit | commitdiff | tree | snapshot
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