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tva <tva@10.205.251.175> in jalview

not related to JAL-3765 ! Actually related to JAL-3675!

not related to JAL-3765 ! Actually related to JAL-3675!

relevant issue is JAL-3626

relevant issue is JAL-3626

Would be nicer. Currently the getdown-launcher is agnostic of which CHANNEL the Jalview version it's in was created with. This seemed like a quick way to achieve almost the same, but longer term a ...

Would be nicer. Currently the getdown-launcher is agnostic of which CHANNEL the Jalview version it's in was created with.
This seemed like a quick way to achieve almost the same, but longer term a getdown created visibile indicator would be ideal. I'll create an issue.

Hi Ben Soares - maybe nicer to have these generated by the getdown launcher in the future ? Worth an issue perhaps ?

Hi Ben Soares - maybe nicer to have these generated by the getdown launcher in the future ? Worth an issue perhaps ?

Ben Soares reported JAL-3514 about this build

Ben Soares reported JAL-3514 about this build

JAL-2629 fix hmmsearch/jackhmmer assigning incorrect evalues and scores

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

    • -3
    • +4
    /src/jalview/hmmer/HMMERParamStore.java
    • -11
    • +11
    /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

    • -15
    • +10
    /src/jalview/hmmer/HMMERParamStore.java
    • -14
    • +43
    /src/jalview/hmmer/HMMSearch.java
    • -17
    • +13
    /src/jalview/hmmer/JackHMMER.java
JAL-2629 uniquify all hmmer command sequence outputs

    • -15
    • +35
    /src/jalview/hmmer/HmmerCommand.java
JAL-2629 fix file format issues preventing hmmsearch, jackhmmer running

    • -26
    • +50
    /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

    • -0
    • +18
    /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

    • -52
    • +22
    /src/jalview/hmmer/HMMSearch.java
    • -3
    • +38
    /src/jalview/hmmer/HmmerCommand.java
    • -58
    • +28
    /src/jalview/hmmer/JackHMMER.java
    • -0
    • +47
    /src/jalview/jbgui/GAlignFrame.java
JAL-2629 hmm match score colour scheme now colours by length

    • -138
    • +261
    /resources/ProbabilityOfMatch
JAL-2629 add simple jackhmmer functionality

    • -0
    • +80
    /src/jalview/hmmer/HMMERParamStore.java
    • -0
    • +94
    /src/jalview/hmmer/HmmerCommand.java
    • -0
    • +406
    /src/jalview/hmmer/JackHMMER.java
    • -26
    • +27
    /src/jalview/io/StockholmFile.java
    • -0
    • +53
    /src/jalview/jbgui/GAlignFrame.java
JAL-2629 add ability to add background frequencies to a HMM

    • -0
    • +63
    /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

    • -0
    • +138
    /resources/ProbabilityOfMatch
JAL-2629 add file that should have been in previous commit

    • -0
    • +265
    /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

    • -0
    • +16
    /test/jalview/io/HMMAlignmentTest.sto
    • -0
    • +478
    /test/jalview/io/HMMAlignmentTestHMM.hmm
JAL-3285 fix errors in tests introduced by merge

    • -3
    • +5
    /test/jalview/gui/AlignViewportTest.java
JAL-3285 build Jalview XML file for current version

    • -5
    • +7
    /src/jalview/gui/OptsAndParamsPage.java
  1. … 12 more files in changeset.
JAL-3285 fix incorrect file paths on HMMAlign/Search results