jalview

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JAL-2629 can now choose number of jackhmmer iterations

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    /src/jalview/hmmer/HMMERParamStore.java
JAL-2629 fix faulty label in a MessageManager.getString() call

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    /src/jalview/hmmer/HMMERParamStore.java
JAL-2629 add sort by evalue and bit score

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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/jbgui/GAlignFrame.java
JAL-2629 hmmer searches now read domain rather than full scores

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    /src/jalview/hmmer/Search.java
JAL-2629 hmmer searches include seqs past inclusion threshold in output

JAL-2629 hmm search UI and structural improvements, inclusion thresholds

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    /resources/lang/Messages.properties
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    /src/jalview/hmmer/HMMERParamStore.java
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    /src/jalview/hmmer/HMMSearch.java
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    /src/jalview/hmmer/HmmerCommand.java
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    /src/jalview/hmmer/JackHMMER.java
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    /src/jalview/hmmer/Search.java
JAL-2629 fix hmmsearch/jackhmmer assigning incorrect evalues and scores

JAL-2629 fix hmsearch and jackhmmer not being able to search alignment

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    /src/jalview/hmmer/HMMERParamStore.java
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    /src/jalview/hmmer/HMMSearch.java
JAL-2629 hmmsearch # of new sequences now only displayed when specified

JAL-2629 fix incorrect hmmbuild on groups behaviour

JAL-2629 fix hmmsearch/jackhmmer being unable to search through DB file

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    /src/jalview/hmmer/HMMERParamStore.java
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    /src/jalview/hmmer/HMMSearch.java
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    /src/jalview/hmmer/JackHMMER.java
JAL-2629 uniquify all hmmer command sequence outputs

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    /src/jalview/hmmer/HmmerCommand.java
JAL-2629 fix file format issues preventing hmmsearch, jackhmmer running

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    /src/jalview/hmmer/HmmerCommand.java
JAL-2629 fix search scores being read in incorrectly

JAL-2629 fix hmm on alignment being deleted upon running jackhmmer

JAL-2629 evalues and bit scores now conserved after hmmalign is run

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    /src/jalview/analysis/SeqsetUtils.java
JAL-2629 removed empty line produced under sequence report

JAL-2629 can now filter by sequence e-value or bit score

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    /src/jalview/hmmer/HMMSearch.java
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    /src/jalview/hmmer/HmmerCommand.java
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    /src/jalview/hmmer/JackHMMER.java
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    /src/jalview/jbgui/GAlignFrame.java
JAL-2629 hmm match score colour scheme now colours by length

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    /resources/ProbabilityOfMatch
JAL-2629 add simple jackhmmer functionality

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    /src/jalview/hmmer/HMMERParamStore.java
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    /src/jalview/hmmer/HmmerCommand.java
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    /src/jalview/hmmer/JackHMMER.java
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    /src/jalview/io/StockholmFile.java
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    /src/jalview/jbgui/GAlignFrame.java
JAL-2629 add ability to add background frequencies to a HMM

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    /src/jalview/io/CountReader.java
JAL-3336 add better method of determining where data table begins

JAL-3336 fix hmmsearch failing when parsing score table

JAL-2629 another file that should have been in previous commit

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    /resources/ProbabilityOfMatch
JAL-2629 add file that should have been in previous commit

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    /src/jalview/schemes/HMMMatchScoreColourScheme.java
JAL-2629 add HMM Match Score colour scheme

JAL-3297 pad gaps in alignment to ensure hmmalign runs

JAL-3291 issue fixed, passing tests added

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    /test/jalview/io/HMMAlignmentTest.sto
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    /test/jalview/io/HMMAlignmentTestHMM.hmm
JAL-3285 fix errors in tests introduced by merge

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    /test/jalview/gui/AlignViewportTest.java
JAL-3285 build Jalview XML file for current version

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    /src/jalview/gui/OptsAndParamsPage.java
  1. … 12 more files in changeset.