CR-JAL-51 JAL-2499: fix Sequence Features PCA calculation

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JAL-2499: fix Sequence Features PCA calculation

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Number of files included: 14

jalview 0
- Folder src/jalview 0
  - Folder analysis/scoremodels 0
    - File PIDModel.java 0 Remove
    - File ScoreMatrix.java 0 Remove
    - File ScoreModels.java 4 Remove
  - Folder appletgui 0
    - File TreePanel.java 0 Remove
  - Folder gui 0
    - 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
  - Folder io 0
    - File ScoreMatrixFile.java 0 Remove
  - Folder jbgui 0
    - File GAlignFrame.java 0 Remove
  - Folder viewmodel 0
    - File PCAModel.java 0 Remove
- Folder test/jalview 0
  - Folder analysis/scoremodels 0
    - File ScoreMatrixTest.java 0 Remove
  - Folder io 0
    - File ScoreMatrixFileTest.java 0 Remove

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Participant	Role	Time Spent	Comments	Latest Comment
Jim Procter	Author	10m	1	sorry to be curmudgeonly - but by getting rid of ViewBase...
Kira Mourão	Reviewer - Complete	11m	2	I should clarify that here ugly meant: instanceof + downc...
Total		20m	4

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.

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CR-JAL-51

JAL-2499: fix Sequence Features PCA calculation

CR-JAL-51 4

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JAL-2499: fix Sequence Features PCA calculation

CR-JAL-51 4

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