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Merge branch 'merge/JAL-3285_mchmmer_with_211_develop' into alpha/JAL-3362_Jalview_21...
[jalview.git] / src /
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 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
2019-07-05 tvaJAL-2629 uniquify all hmmer command sequence outputs tree | commitdiff
2019-07-05 tvaJAL-2629 fix file format issues preventing hmmsearch... 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 Jim ProcterMerge branch 'bug/JAL-3286duplicatePdbQuery' into develop tree | commitdiff
2019-06-18 Ben SoaresJAL-3312 Fixed SHIFT-CMD/SHIFT-CTRL Key combinations... tree | commitdiff
2019-06-17 Ben SoaresJAL-3310 JAL-3300 two getdown fixes merged tree | commitdiff
2019-06-17 Jim ProcterJAL-3311 remove menus and documentation relating to... tasks/JAL-3311_removeVamsasMenu tree | commitdiff
2019-06-14 Ben SoaresJAL-3295 pre-merged code with JAL-3295 branch which... tree | commitdiff
2019-06-14 Ben SoaresJAL-3278 A system.out.println turned into a cache.log... tree | commitdiff
2019-06-14 Jim ProcterJAL-3111 report build type and commit in stdout from... tree | commitdiff
2019-06-14 Jim ProcterJAL-3299 JAL-3280 javadoc on BuildDetails bean tree | commitdiff
2019-06-13 Jim ProcterMerge branch 'bug/JAL-3295_CMD_select_not_working_in_se... tree | commitdiff
2019-06-13 gmungocJAL-3143 recognise lnc_RNA as transcript tree | commitdiff
2019-06-12 Ben SoaresJAL-3295 Fixed CMD-select of sequences in alignment... tree | commitdiff
2019-06-11 gmungocJAL-3143 also parse "phase" from JSON response if present tree | commitdiff
2019-06-11 gmungocJAL-3288 fixes for gain/lose focus tree | commitdiff
2019-06-10 tvaJAL-3297 pad gaps in alignment to ensure hmmalign runs tree | commitdiff
2019-06-07 gmungocMerge branch 'bug/JAL-3288splitFrameMenusJava11' into... tree | commitdiff
2019-06-07 tvaJAL-3291 issue fixed, passing tests added tree | commitdiff
2019-06-07 gmungocJAL-3187 Viewport schema attributes for showComplementF... tree | commitdiff
2019-06-07 gmungocJAL-3251 added optional attributes Sequence.biotype... tree | commitdiff
2019-06-07 gmungocJAL-2738 use GeneLocus extends DBRefEntry to hold chrom... tree | commitdiff
2019-06-06 tvaJAL-3285 build Jalview XML file for current version tree | commitdiff
2019-06-06 tvaJAL-3285 fix incorrect file paths on HMMAlign/Search... tree | commitdiff
2019-06-06 tvaJAL-3285 add Cygwin environment path fix for Windows tree | commitdiff
2019-06-06 tvaJAL-3285 code changes to HMMER colour schemes not inclu... tree | commitdiff
2019-06-06 tvaJAL-3285 fix FileLoader failing to load HMMER file tree | commitdiff
2019-06-05 tvaJAL-3285 method call change tin Information to match... tree | commitdiff
2019-06-05 tvaJAL-3285 delete duplicate variables in AlignmentViewpor... tree | commitdiff
2019-06-05 tvaJAL-3285 method call change to HMMBuild not included... tree | commitdiff
2019-06-05 gmungocJAL-3288 override JInternalFrame.setSelected() to avoid... bug/JAL-3288splitFrameMenusJava11 tree | commitdiff
2019-06-05 tvaJAL-3285 method call change in SeqPanel to match develop tree | commitdiff
2019-06-05 tvaJAL-3285 change method declaration in AAFrequency to... tree | commitdiff
2019-06-05 tvaJAL-3285 changed method call on AnnotationRenderer... tree | commitdiff
2019-06-05 tvaJAL-3285 code changes to Jalview2XML not included in... tree | commitdiff
2019-06-05 tvaJAL-3285 add unmerged code to AlignmentAnnotation tree | commitdiff
2019-06-05 tvaJAL-3285 method call name change to SeqPanel not includ... tree | commitdiff
2019-06-05 tvaJAL-3285 method call name change in OverviewPanel not... tree | commitdiff
2019-06-05 tvaJAL-3285 small method call name change to AnnotationLabels tree | commitdiff
2019-06-05 tvaJAL-3285 add unmerged code to SequenceGroup tree | commitdiff
2019-06-05 tvaJAL-3285 small method call name change missed in Consen... tree | commitdiff
2019-06-05 tvaJAL-3285 small code changes to ConsensusThread not... tree | commitdiff
2019-06-05 tvaJAL-3285 small code changes to AnnotationRenderer not... tree | commitdiff
2019-06-05 tvaJAL-3285 code changes to AnnotationLabels not included... tree | commitdiff
2019-06-05 tvaJAL-3285 add unmerged features to AlignViewportI tree | commitdiff
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