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2019-07-10	tva	JAL-2629 fix hmsearch and jackhmmer not being able...	commit \| commitdiff \| tree
2019-07-10	tva	JAL-2629 hmmsearch # of new sequences now only displayed...	commit \| commitdiff \| tree
2019-07-10	tva	JAL-2629 fix incorrect hmmbuild on groups behaviour	commit \| commitdiff \| tree
2019-07-10	tva	JAL-2629 fix hmmsearch/jackhmmer being unable to search...	commit \| commitdiff \| tree
2019-07-05	tva	JAL-2629 uniquify all hmmer command sequence outputs	commit \| commitdiff \| tree
2019-07-05	tva	JAL-2629 fix file format issues preventing hmmsearch...	commit \| commitdiff \| tree
2019-07-03	tva	JAL-2629 fix search scores being read in incorrectly	commit \| commitdiff \| tree
2019-07-03	tva	JAL-2629 fix hmm on alignment being deleted upon running...	commit \| commitdiff \| tree
2019-07-03	tva	JAL-2629 evalues and bit scores now conserved after...	commit \| commitdiff \| tree
2019-07-03	tva	JAL-2629 removed empty line produced under sequence...	commit \| commitdiff \| tree
2019-07-03	tva	JAL-2629 can now filter by sequence e-value or bit...	commit \| commitdiff \| tree
2019-07-02	tva	JAL-2629 hmm match score colour scheme now colours...	commit \| commitdiff \| tree
2019-07-02	tva	JAL-2629 add simple jackhmmer functionality	commit \| commitdiff \| tree
2019-06-28	tva	JAL-2629 add ability to add background frequencies...	commit \| commitdiff \| tree
2019-06-28	tva	JAL-3336 add better method of determining where data...	commit \| commitdiff \| tree
2019-06-28	tva	JAL-3336 fix hmmsearch failing when parsing score table	commit \| commitdiff \| tree
2019-06-28	tva	JAL-2629 another file that should have been in previous...	commit \| commitdiff \| tree
2019-06-28	tva	JAL-2629 add file that should have been in previous...	commit \| commitdiff \| tree
2019-06-28	tva	JAL-2629 add HMM Match Score colour scheme	commit \| commitdiff \| tree
2019-06-10	tva	JAL-3297 pad gaps in alignment to ensure hmmalign runs	commit \| commitdiff \| tree
2019-06-07	tva	JAL-3291 issue fixed, passing tests added	commit \| commitdiff \| tree
2019-06-07	tva	JAL-3285 fix errors in tests introduced by merge	commit \| commitdiff \| tree
2019-06-06	tva	JAL-3285 build Jalview XML file for current version	commit \| commitdiff \| tree
2019-06-06	tva	JAL-3285 fix incorrect file paths on HMMAlign/Search...	commit \| commitdiff \| tree
2019-06-06	tva	JAL-3285 add Cygwin environment path fix for Windows	commit \| commitdiff \| tree
2019-06-06	tva	JAL-3285 code changes to HMMER colour schemes not included...	commit \| commitdiff \| tree
2019-06-06	tva	JAL-3285 fix FileLoader failing to load HMMER file	commit \| commitdiff \| tree
2019-06-05	tva	JAL-3285 method call change tin Information to match...	commit \| commitdiff \| tree
2019-06-05	tva	JAL-3285 delete duplicate variables in AlignmentViewport...	commit \| commitdiff \| tree
2019-06-05	tva	JAL-3285 method call change to HMMBuild not included...	commit \| commitdiff \| tree
2019-06-05	tva	JAL-3285 method call change in SeqPanel to match develop	commit \| commitdiff \| tree
2019-06-05	tva	JAL-3285 change method declaration in AAFrequency to...	commit \| commitdiff \| tree
2019-06-05	tva	JAL-3285 changed method call on AnnotationRenderer...	commit \| commitdiff \| tree
2019-06-05	tva	JAL-3285 code changes to Jalview2XML not included in...	commit \| commitdiff \| tree
2019-06-05	tva	JAL-3285 add unmerged code to AlignmentAnnotation	commit \| commitdiff \| tree
2019-06-05	tva	JAL-3285 method call name change to SeqPanel not included...	commit \| commitdiff \| tree
2019-06-05	tva	JAL-3285 method call name change in OverviewPanel not...	commit \| commitdiff \| tree
2019-06-05	tva	JAL-3285 small method call name change to AnnotationLabels	commit \| commitdiff \| tree
2019-06-05	tva	JAL-3285 add unmerged code to SequenceGroup	commit \| commitdiff \| tree
2019-06-05	tva	JAL-3285 small method call name change missed in ConsensusTh...	commit \| commitdiff \| tree
2019-06-05	tva	JAL-3285 small code changes to ConsensusThread not...	commit \| commitdiff \| tree
2019-06-05	tva	JAL-3285 small code changes to AnnotationRenderer not...	commit \| commitdiff \| tree
2019-06-05	tva	JAL-3285 code changes to AnnotationLabels not included...	commit \| commitdiff \| tree
2019-06-05	tva	JAL-3285 add unmerged features to AlignViewportI	commit \| commitdiff \| tree
2019-06-05	tva	JAL-3285 add unmerged features to AlignViewport	commit \| commitdiff \| tree
2019-06-05	tva	JAL-3285 add unmerged features into AlignmentViewport	commit \| commitdiff \| tree
2019-06-05	tva	JAL-3285 add methods and small changes to StockholmFile...	commit \| commitdiff \| tree

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