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Merge remote-tracking branch 'origin/alpha/JAL-3066_Jalview_212_slivka-integration...
[jalview.git] / src /
2019-09-06 Mateusz WarownyMerge remote-tracking branch 'origin/alpha/JAL-3066_Jal... tree | commitdiff
2019-09-06 Mateusz WarownyJAL-3066 Working custom parameters for clustalo tree | commitdiff
2019-09-06 Jim ProcterJAL-3066 fix compile error (@matesuz - this will confli... tree | commitdiff
2019-09-06 Jim ProcterJAL_1426 JAL-3066 update Apache James mime parser and... tree | commitdiff
2019-09-05 Mateusz WarownyJAL-3066 Implement clustaloWS using slivka system. tree | commitdiff
2019-08-13 Jim ProcterJAL-3362 keep Java 1.8 build happy by specifying generi... tree | commitdiff
2019-08-13 Jim ProcterMerge branch 'alpha/JAL-3362_Jalview_212_alpha' into... tree | commitdiff
2019-08-09 gmungocJAL-3187 removal of variant feature (non-virtual) trans... tree | commitdiff
2019-08-07 gmungocJAL-3187 (fudge) look in both alignments for stored... feature/JAL-3187linkedFeatures tree | commitdiff
2019-08-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures tree | commitdiff
2019-07-31 gmungocJAL-3389 add .py to restored Chimera session filename... tree | commitdiff
2019-07-31 gmungocMerge branch 'bug/JAL-3388structureChooserSorting'... tree | commitdiff
2019-07-30 gmungocJAL-3198 more efficient Sequence.getDisplayId() tree | commitdiff
2019-07-30 gmungocJAL-3388 correct class for column 0 Ref Sequence bug/JAL-3388structureChooserSorting tree | commitdiff
2019-07-29 gmungocJAL-3386 correct wrapped width calculation for headless... tree | commitdiff
2019-07-29 gmungocJAL-3377 more reused of SeqCanvas.computeWrappedGeometry tree | commitdiff
2019-07-29 gmungocJAL-3377 add seq-annotations gap to cheight not to... tree | commitdiff
2019-07-29 gmungocJAL-3377 Javadoc added for getWrappedHeight() tree | commitdiff
2019-07-29 gmungocJAL-3377 corrected wrapped widths height for IdCanvas tree | commitdiff
2019-07-29 gmungocJAL-3377 include seq-annotation spacing in getWrappedHe... tree | commitdiff
2019-07-26 gmungocMerge branch 'features/JAL-3375vcfValidation' into tree | commitdiff
2019-07-26 gmungocJAL-1793 only decode specific special characters in... tree | commitdiff
2019-07-26 gmungocJAL-3376 capture VCF POS, ID, QUAL, FILTER as feature... features/JAL-3375vcfValidation tree | commitdiff
2019-07-26 gmungocJAL-3375 format validate VCF Integer and Float fields tree | commitdiff
2019-07-25 gmungocJAL-3375 ignore '.' values for VCF data tree | commitdiff
2019-07-16 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures tree | commitdiff
2019-07-16 gmungocJAL-2987 tolerate null double values when formatting... tree | commitdiff
2019-07-15 Jim ProcterMerge branch 'merge/JAL-3285_mchmmer_with_211_develop... tree | commitdiff
2019-07-12 ThomasJAL-2629 can now choose number of jackhmmer iterations merge/JAL-3285_mchmmer_with_211_develop tree | commitdiff
2019-07-12 ThomasJAL-2629 fix faulty label in a MessageManager.getString... tree | commitdiff
2019-07-12 ThomasJAL-2629 add sort by evalue and bit score tree | commitdiff
2019-07-12 ThomasJAL-2629 hmmer searches now read domain rather than... tree | commitdiff
2019-07-11 Jim ProcterMerge branch 'merge/JAL-3285_mchmmer_with_211_develop... tree | commitdiff
2019-07-11 ThomasJAL-2629 hmmer searches include seqs past inclusion... tree | commitdiff
2019-07-11 ThomasJAL-2629 hmm search UI and structural improvements... tree | commitdiff
2019-07-10 Jim ProcterJAL-3070 standard way of storing/recovering documentati... tree | commitdiff
2019-07-10 Jim ProcterJAL-3070 remove final reference to Jws2Instance tree | commitdiff
2019-07-10 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures tree | commitdiff
2019-07-10 tvaJAL-2629 fix hmmsearch/jackhmmer assigning incorrect... tree | commitdiff
2019-07-10 Jim ProcterMerge branch 'tasks/JAL-3070_wsinterfaces' into alpha... tree | commitdiff
2019-07-10 tvaJAL-2629 fix hmsearch and jackhmmer not being able... tree | commitdiff
2019-07-10 tvaJAL-2629 hmmsearch # of new sequences now only displaye... tree | commitdiff
2019-07-10 tvaJAL-2629 fix incorrect hmmbuild on groups behaviour tree | commitdiff
2019-07-10 Jim ProcterMerge branch 'merge/JAL-3285_mchmmer_with_211_develop... tree | commitdiff
2019-07-10 tvaJAL-2629 fix hmmsearch/jackhmmer being unable to search... tree | commitdiff
2019-07-08 gmungocJAL-3187 derived peptide variants tweaks and tests tree | commitdiff
2019-07-05 tvaJAL-2629 uniquify all hmmer command sequence outputs tree | commitdiff
2019-07-05 gmungocJAL-3187 initial refactoring towards peptide variant... tree | commitdiff
2019-07-05 tvaJAL-2629 fix file format issues preventing hmmsearch... tree | commitdiff
2019-07-05 gmungocJAL-1793 apply URL decoding when saving VCF attribute... tree | commitdiff
2019-07-03 tvaJAL-2629 fix search scores being read in incorrectly tree | commitdiff
2019-07-03 tvaJAL-2629 fix hmm on alignment being deleted upon runnin... tree | commitdiff
2019-07-03 tvaJAL-2629 evalues and bit scores now conserved after... tree | commitdiff
2019-07-03 tvaJAL-2629 removed empty line produced under sequence... tree | commitdiff
2019-07-03 tvaJAL-2629 can now filter by sequence e-value or bit... tree | commitdiff
2019-07-02 Jim ProcterJAL-3111 JAL-3280 hide the version check preference... tree | commitdiff
2019-07-02 Jim ProcterMerge branch 'develop' into tasks/JAL-3311_removeVamsasMenu tree | commitdiff
2019-07-02 tvaJAL-2629 hmm match score colour scheme now colours... tree | commitdiff
2019-07-02 tvaJAL-2629 add simple jackhmmer functionality tree | commitdiff
2019-07-01 Ben SoaresJAL-3333 removed unused variable tree | commitdiff
2019-07-01 Ben SoaresJAL-3333 using floats for smoother weighting tree | commitdiff
2019-06-29 Ben SoaresJAL-3333 Sorry couldn't resist adding a bit of weightin... tree | commitdiff
2019-06-29 Ben SoaresJAL-3333 Title text now appears instantly. Altering... tree | commitdiff
2019-06-28 Ben SoaresMerge branch 'bug/JAL-3333_Blurry_fonts_in_WebServiceIn... tree | commitdiff
2019-06-28 Ben SoaresJAL-3333 changed RGB model. Tested in mojave and Windo... tree | commitdiff
2019-06-28 tvaJAL-2629 add ability to add background frequencies... tree | commitdiff
2019-06-28 Jim ProcterMerge branch 'bug/JAL-3333_Blurry_fonts_in_WebServiceIn... tree | commitdiff
2019-06-28 Ben SoaresJAL-3333 Smooth rotation of image now too tree | commitdiff
2019-06-28 Ben SoaresJAL-3333 added height to rotating image preferred size tree | commitdiff
2019-06-28 tvaJAL-3336 add better method of determining where data... tree | commitdiff
2019-06-28 Jim ProcterJAL-3330 apply Ensembl feature settings when showing... bug/JAL-3330_backpropagateEnsemblFeatureColours tree | commitdiff
2019-06-28 tvaJAL-3336 fix hmmsearch failing when parsing score table tree | commitdiff
2019-06-28 Ben SoaresJAL-3333 Replaced title text rendered in animated image... tree | commitdiff
2019-06-28 tvaJAL-2629 add file that should have been in previous... tree | commitdiff
2019-06-28 tvaJAL-2629 add HMM Match Score colour scheme tree | commitdiff
2019-06-26 Jim ProcterJAL-3334 fix - always load full SO to resolve the seque... tree | commitdiff
2019-06-26 Jim ProcterJAL-3111 get rid of nasty tab characters tree | commitdiff
2019-06-26 Jim ProcterJAL-3332 test to check for duplicate db sources and... tree | commitdiff
2019-06-26 Jim ProcterJAL-3330 javadoc tree | commitdiff
2019-06-24 Jim ProcterJAL-3330 merge styles onto originating view after fetch... tree | commitdiff
2019-06-24 Jim ProcterJAL-3330 dbreffetcher: record any feature display model... tree | commitdiff
2019-06-24 Jim ProcterJAL-3330 merge styles onto originating views when show... tree | commitdiff
2019-06-24 Jim ProcterJAL-3330 mergeFeatureStyles - needs test coverage tree | commitdiff
2019-06-19 Ben SoaresMerge branch 'merge/JAL-3310_and_JAL-3300' into develop tree | commitdiff
2019-06-19 Ben SoaresJAL-3321 Last pieces of the getdown-launcher.jar upgrad... tree | commitdiff
2019-06-19 Jim ProcterMerge branch 'develop' into documentation/JAL-3111_rele... tree | commitdiff
2019-06-18 gmungocJAL-3313 don't double count mapped codons tree | commitdiff
2019-06-18 Jim ProcterMerge branch 'bug/JAL-2830_editManglesDatasetSequence... tree | commitdiff
2019-06-18 Ben SoaresMerge branch 'develop' into merge/JAL-3310_and_JAL... tree | commitdiff
2019-06-18 gmungocJAL-3187 javadoc tree | commitdiff
2019-06-18 Jim ProcterMerge branch 'bug/JAL-3286duplicatePdbQuery' into develop tree | commitdiff
2019-06-18 gmungocJAL-3304 option to export linked features also for... tree | commitdiff
2019-06-18 Ben SoaresJAL-3312 Fixed SHIFT-CMD/SHIFT-CTRL Key combinations... tree | commitdiff
2019-06-18 gmungocJAL-3304 option to export linked features in Jalview... tree | commitdiff
2019-06-18 gmungocJAL-3187 i18n show linked features checkboxes tree | commitdiff
2019-06-18 gmungocJAL-3305 mirror popup menu column selections in split... tree | commitdiff
2019-06-17 Ben SoaresJAL-3310 JAL-3300 two getdown fixes merged tree | commitdiff
2019-06-17 gmungocJAL-2792 JAL-3187 linked features (if shown) in Feature... tree | commitdiff
2019-06-17 gmungocJAL-3187 update alignAs code and unit tests for 'shared... tree | commitdiff
2019-06-17 gmungocJAL-3187 add sequence to feature details table (and... tree | commitdiff
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