CR-JAL-51 4
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- Objectives
- General Comments 0
- Unresolved
- Resolved
- Number of files included: 14
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jalview
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src/jalview
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analysis/scoremodels
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- File PIDModel.java 0 Remove
- File ScoreMatrix.java 0 Remove
- File ScoreModels.java 4 Remove
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appletgui
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- File TreePanel.java 0 Remove
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gui
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- File AlignFrame.java 0 Remove
- File CalculationChooser.java 0 Remove
- File CalculationChooser.java 0 Remove
- File PCAPanel.java 0 Remove
- File TreePanel.java 0 Remove
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io
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- File ScoreMatrixFile.java 0 Remove
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jbgui
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- File GAlignFrame.java 0 Remove
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viewmodel
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- File PCAModel.java 0 Remove
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analysis/scoremodels
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test/jalview
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analysis/scoremodels
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- File ScoreMatrixTest.java 0 Remove
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io
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- File ScoreMatrixFileTest.java 0 Remove
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analysis/scoremodels
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src/jalview
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Participant | Role | Time Spent | Comments | Latest Comment |
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Author | 10m | 1 | sorry to be curmudgeonly - but by getting rid of ViewBase... | |
Reviewer - Complete | 11m | 2 | I should clarify that here ugly meant: instanceof + downc... | |
Total | 20m | 4 |
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Linked Issue:
JAL-2499
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Objectives
1. load uniref50.fa and exampleFeatures.txt
2. Compute a PCA with the Sequence Features Similarity score
On features/JAL-2393customMatrices (f647b9ceacdc464621491653cfb3382b42ca14a5) this results in a PCA viewer where all the points lie at the origin. File->Output Values shows the input matrix for PCA to be all zeros.
Branches in review
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/src/jalview/.../scoremodels/PIDModel.java
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/src/jalview/.../scoremodels/ScoreMatrix.java
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/src/jalview/.../scoremodels/ScoreModels.java
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4
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/src/jalview/appletgui/TreePanel.java
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/src/jalview/gui/AlignFrame.java
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/src/jalview/gui/CalculationChooser.java
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/src/jalview/gui/CalculationChooser.java
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/src/jalview/gui/PCAPanel.java
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/src/jalview/gui/TreePanel.java
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/src/jalview/io/ScoreMatrixFile.java
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/src/jalview/jbgui/GAlignFrame.java
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/src/jalview/viewmodel/PCAModel.java
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/test/.../scoremodels/ScoreMatrixTest.java
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/test/jalview/io/ScoreMatrixFileTest.java
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