CR-JAL-39 JAL-1632: Dialog to create/edit tree calculation settings

closed on 16 May 17

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JAL-1632: Dialog to create/edit tree calculation settings

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Number of files included: 46

jalview 0
- Folder resources 0
  - Folder lang 0
    - File Messages.properties 0 Remove
    - File Messages_es.properties 0 Remove
  - Folder scoreModel 0
    - File blosum62.scm 0 Remove
    - File dna.scm 0 Remove
    - File pam250.scm 0 Remove
- Folder src 0
  - Folder MCview 0
    - File AppletPDBCanvas.java 0 Remove
    - File PDBCanvas.java 0 Remove
  - Folder jalview 0
    - Folder analysis 0
      - Folder scoremodels 0
        
        File FeatureDistanceModel.java 0 Remove
        
        File PIDModel.java 0 Remove
        
        File PairwiseSeqScoreModel.java 0 Remove
        
        File ScoreMatrix.java 0 Remove
        
        File ScoreModels.java 0 Remove
        
        File SimilarityParams.java 0 Remove
      - File AlignSeq.java 0 Remove
      - File Conservation.java 0 Remove
      - File NJTree.java 0 Remove
      - File PCA.java 0 Remove
    - Folder api/analysis 0
      - File ScoreModelI.java 0 Remove
      - File SimilarityParamsI.java 0 Remove
    - Folder appletgui 0
      - File AlignFrame.java 0 Remove
      - File PCAPanel.java 0 Remove
      - File TreePanel.java 0 Remove
    - Folder bin 0
      - File Jalview.java 0 Remove
    - Folder datamodel 0
      - File BinarySequence.java 0 Remove
    - Folder gui 0
      - File AlignFrame.java 0 Remove
      - File AlignmentPanel.java 0 Remove
      - File CalculationChooser.java 0 Remove
      - File Jalview2XML.java 0 Remove
      - File Jalview2XML_V1.java 0 Remove
      - File PCAPanel.java 0 Remove
      - File SeqPanel.java 0 Remove
      - File TreeChooser.java 0 Remove
      - File TreePanel.java 0 Remove
    - Folder io 0
      - Folder vamsas 0
        
        File Tree.java 0 Remove
      - File VamsasAppDatastore.java 0 Remove
    - Folder jbgui 0
      - File GAlignFrame.java 0 Remove
    - Folder schemes 0
      - File Blosum62ColourScheme.java 0 Remove
      - File ResidueProperties.java 0 Remove
      - File ScoreMatrix.java 0 Remove
    - Folder structure 0
      - File StructureSelectionManager.java 0 Remove
    - Folder viewmodel 0
      - File PCAModel.java 0 Remove
    - Folder ws/jws1 0
      - File SeqSearchWSThread.java 0 Remove
- Folder test/jalview 0
  - Folder analysis 0
    - Folder scoremodels 0
      - File FeatureDistanceModelTest.java 0 Remove
      - File ScoreMatrixTest.java 0 Remove
    - File TestAlignSeq.java 0 Remove
  - Folder schemes 0
    - File ScoreMatrixPrinter.java 0 Remove

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Participant	Role	Time Spent	Comments
Mungo Carstairs	Author	0m
Kira Mourão	Reviewer - Complete	1m
Total		1m	0

Linked Issue:
JAL-1632

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Objectives

The number of score models make the existing tree calculation submenu unwieldly since it is at least 2*(PAM, Blosum, PID, etc) long. It would be better to be able to open a parameter settings dialog to configure a particular tree building calculation which provides the option to create favourite settings combinations.

Branches in review

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Issues Raised From Comments

Key	Summary	State	Assignee

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General Comments

There are no general comments on this review.

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CR-JAL-39

JAL-1632: Dialog to create/edit tree calculation settings

CR-JAL-39 0

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JAL-1632: Dialog to create/edit tree calculation settings

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