Goal and implementation review for hmmer3 model import and visualisation
Activity
CR-JAL-72 13
- Details
- Objectives
- General Comments 0
- Unresolved
- Resolved
- Number of files included: 79
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jalview
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examples
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- File uniref50_hmm 0 Remove
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resources/lang
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- File Messages.properties 0 Remove
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src/jalview
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Folder
analysis
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- File AAFrequency.java 1 Remove
- File SeqsetUtils.java 0 Remove
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api
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- File AlignViewportI.java 0 Remove
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appletgui
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- File AlignFrame.java 0 Remove
- File AlignViewport.java 0 Remove
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bin
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- File Cache.java 0 Remove
- File Jalview.java 0 Remove
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datamodel
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- File Alignment.java 0 Remove
- File AlignmentAnnotation.java 0 Remove
- File AlignmentI.java 0 Remove
- File AlignmentOrder.java 0 Remove
- File AnnotatedCollectionI.java 0 Remove
- File EValueStatistic.java 0 Remove
- File HMMNode.java 0 Remove
- File HiddenMarkovModel.java 7 Remove
- File ResidueCount.java 0 Remove
- File Sequence.java 0 Remove
- File SequenceCollectionI.java 0 Remove
- File SequenceGroup.java 0 Remove
- File SequenceI.java 0 Remove
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gui
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- File AlignFrame.java 2 Remove
- File AlignViewport.java 0 Remove
- File AnnotationLabels.java 1 Remove
- File OptsAndParamsPage.java 0 Remove
- File PopupMenu.java 0 Remove
- File Preferences.java 0 Remove
- File WsJobParameters.java 0 Remove
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Folder
hmmer
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- File HMMAlignThread.java 0 Remove
- File HMMBuildThread.java 0 Remove
- File HMMERCommands.java 0 Remove
- File HMMERParamStore.java 0 Remove
- File HMMERPreset.java 0 Remove
- File HMMSearchThread.java 0 Remove
- File alignment_buffer.sto 0 Remove
- File alignment_input.sto 0 Remove
- File hmm_buffer.hmm 0 Remove
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io
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- File AlignFile.java 0 Remove
- File FileFormat.java 1 Remove
- File FileLoader.java 0 Remove
- File HMMFile.java 1 Remove
- File IdentifyFile.java 0 Remove
- File StockholmFile.java 0 Remove
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jbgui
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- File GAlignFrame.java 0 Remove
- File GPreferences.java 0 Remove
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renderer
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- File AnnotationRenderer.java 0 Remove
- File ResidueShader.java 0 Remove
- File ResidueShaderI.java 0 Remove
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schemes
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- File HMMERAlignmentColourScheme.java 0 Remove
- File HMMERColourScheme.java 0 Remove
- File JalviewColourScheme.java 0 Remove
- File ResidueProperties.java 0 Remove
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util
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- File HMMProbabilityDistributionAnalyser.java 0 Remove
- File ProbabilityAnalyserKickstarter.java 0 Remove
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viewmodel
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- File AlignmentViewport.java 0 Remove
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workers
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- File AlignCalcManager.java 0 Remove
- File InformationThread.java 0 Remove
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ws
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jws2
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- File MsaWSThread.java 0 Remove
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params
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Folder
simple
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- File DoubleParameter.java 0 Remove
- File LogarithmicParameter.java 0 Remove
- File StringParameter.java 0 Remove
- File ValueConstrainI.java 0 Remove
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simple
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jws2
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analysis
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test/jalview
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Folder
analysis
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- File AAFrequencyTest.java 0 Remove
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datamodel
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- File HiddenMarkovModelTest.java 0 Remove
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Folder
hmmer
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- File HMMERTest.java 0 Remove
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Folder
io
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- File FileFormatsTest.java 0 Remove
- File FormatAdapterTest.java 0 Remove
- File HMMFileTest.java 0 Remove
- File test_MADE1_hmm.txt 0 Remove
- File test_PKinase_hmm.txt 0 Remove
- File test_export_hmm.txt 0 Remove
- File test_fn3_hmm.txt 0 Remove
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schemes
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- File HMMERColourSchemeTest.java 0 Remove
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Folder
util
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- File Binned.csv 0 Remove
- File HMMProbabilityDistributionAnalyserTest.java 0 Remove
- File Raw.csv 0 Remove
- File test_Fams_for_probability_analysis 0 Remove
- File test_hmms_for_probability_analysis 0 Remove
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Folder
analysis
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Folder
examples
0
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Participant | Role | Time Spent | Comments | Latest Comment |
---|---|---|---|---|
Author | 44m | |||
Reviewer - 0% reviewed | 1h 12m | 13 | this looks particularly weird - what's going on ? | |
Total | 1h 56m | 13 |
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Linked Issue:
JAL-2599
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#permalink
Objectives
- Add HiddenMarkovModel class
- Update HiddenMarkovModel class
- add HMMFile class to read and write HMM files
- add tests for HMMFile class
- restructure file exporter
- create method to test HMM model as string
- fully integrate HMMER3 file format into Jalview
- add HMMER colour scheme
- test HMMER colour scheme
- transferred the storage position of the HMM to annotations
- add information content calculations
- complete Information Content annotation
- test HMM annotaTION
Branches in review
Repository | Branch to review | Branched from |
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/examples/uniref50_hmm
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/resources/lang/Messages.properties
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/src/jalview/analysis/AAFrequency.java
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/src/jalview/analysis/SeqsetUtils.java
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/src/jalview/api/AlignViewportI.java
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/src/jalview/appletgui/AlignFrame.java
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/src/jalview/appletgui/AlignViewport.java
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/src/jalview/bin/Cache.java
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/src/jalview/bin/Jalview.java
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/src/jalview/datamodel/Alignment.java
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/src/.../datamodel/AlignmentAnnotation.java
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/src/jalview/datamodel/AlignmentI.java
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/src/jalview/datamodel/AlignmentOrder.java
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/src/.../datamodel/AnnotatedCollectionI.java
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/src/.../datamodel/EValueStatistic.java
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/src/jalview/datamodel/HMMNode.java
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/src/.../datamodel/HiddenMarkovModel.java
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/src/jalview/datamodel/ResidueCount.java
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/src/jalview/datamodel/Sequence.java
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/src/.../datamodel/SequenceCollectionI.java
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/src/jalview/datamodel/SequenceGroup.java
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/src/jalview/datamodel/SequenceI.java
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/src/jalview/gui/AlignFrame.java
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/src/jalview/gui/AlignViewport.java
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/src/jalview/gui/AnnotationLabels.java
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/src/jalview/gui/OptsAndParamsPage.java
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/src/jalview/gui/PopupMenu.java
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/src/jalview/gui/Preferences.java
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/src/jalview/gui/WsJobParameters.java
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/src/jalview/hmmer/HMMAlignThread.java
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/src/jalview/hmmer/HMMBuildThread.java
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/src/jalview/hmmer/HMMERCommands.java
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/src/jalview/hmmer/HMMERParamStore.java
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/src/jalview/hmmer/HMMERPreset.java
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/src/jalview/hmmer/HMMSearchThread.java
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/src/jalview/hmmer/alignment_buffer.sto
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/src/jalview/hmmer/alignment_input.sto
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/src/jalview/hmmer/hmm_buffer.hmm
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/src/jalview/io/AlignFile.java
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/src/jalview/io/FileFormat.java
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/src/jalview/io/FileLoader.java
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/src/jalview/io/HMMFile.java
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/src/jalview/io/IdentifyFile.java
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/src/jalview/io/StockholmFile.java
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/src/jalview/jbgui/GAlignFrame.java
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/src/jalview/jbgui/GPreferences.java
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/src/.../renderer/AnnotationRenderer.java
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/src/jalview/renderer/ResidueShader.java
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/src/jalview/renderer/ResidueShaderI.java
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/src/.../schemes/HMMERAlignmentColourScheme.java
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/src/.../schemes/HMMERColourScheme.java
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/src/.../schemes/JalviewColourScheme.java
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/src/.../schemes/ResidueProperties.java
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/src/.../util/HMMProbabilityDistributionAnalyser.java
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/src/.../util/ProbabilityAnalyserKickstarter.java
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/src/.../viewmodel/AlignmentViewport.java
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/src/jalview/workers/AlignCalcManager.java
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/src/.../workers/InformationThread.java
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/src/jalview/ws/jws2/MsaWSThread.java
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/src/jalview/.../simple/DoubleParameter.java
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/src/.../simple/LogarithmicParameter.java
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/src/jalview/.../simple/StringParameter.java
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/src/jalview/.../params/ValueConstrainI.java
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/test/.../analysis/AAFrequencyTest.java
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/test/.../datamodel/HiddenMarkovModelTest.java
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/test/jalview/hmmer/HMMERTest.java
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/test/jalview/io/FileFormatsTest.java
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/test/jalview/io/FormatAdapterTest.java
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/test/jalview/io/HMMFileTest.java
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/test/jalview/io/test_MADE1_hmm.txt
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/test/jalview/io/test_PKinase_hmm.txt
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/test/jalview/io/test_export_hmm.txt
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/test/jalview/io/test_fn3_hmm.txt
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/test/.../schemes/HMMERColourSchemeTest.java
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/test/jalview/util/Binned.csv
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/test/.../util/HMMProbabilityDistributionAnalyserTest.java
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