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