CR-JAL-11 JAL-2379: Improve PCA memory management

closed on 07 Feb 17

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JAL-2379: Improve PCA memory management

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General Comments 2
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Number of files included: 12

jalview 0
- Folder src/jalview 0
  - Folder analysis 0
    - File PCA.java 0 Remove
  - Folder datamodel 0
    - File BinarySequence.java 0 Remove
  - Folder ext/android 0
    - File ContainerHelpers.java 0 Remove
    - File SparseDoubleArray.java 0 Remove
  - Folder gui 0
    - File PCAPanel.java 0 Remove
  - Folder math 0
    - File Matrix.java 2 Remove
    - File MatrixI.java 0 Remove
    - File SparseMatrix.java 0 Remove
  - Folder viewmodel 0
    - File PCAModel.java 1 Remove
- Folder test/jalview 0
  - Folder ext/android 0
    - File SparseDoubleArrayTest.java 0 Remove
  - Folder math 0
    - File MatrixTest.java 0 Remove
    - File SparseMatrixTest.java 0 Remove

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Participant	Role	Time Spent	Comments	Latest Comment
Mungo Carstairs	Author	11m	1	The original changes (to encode sequences as SparseMatrix...
Kira Mourão	Reviewer - Complete	32m	4	I"ve only found some very minor tidies
Total		44m	5

Linked Issue:
JAL-2379

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Objectives

Investigate possible improvements to the memory footprint of the PCA calculation.

Branches in review

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Issues Raised From Comments

Key	Summary	State	Assignee

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General Comments

Kira Mourão

I"ve only found some very minor tidies

27 Jan 17

Mungo Carstairs

The original changes (to encode sequences as SparseMatrix using SparseDoubleA...

The original changes (to encode sequences as SparseMatrix using SparseDoubleArray) got superseded by a further refactoring.
This skips encoding and instead does the Blosum (or other) score matrix lookup while computing an NxN (N = number of seqs) pairwise similarity score matrix.

Reviews of these changes under CR-JAL-13.

07 Feb 17

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CR-JAL-11

JAL-2379: Improve PCA memory management

CR-JAL-11 5

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Objectives

Branches in review

Issues Raised From Comments

General Comments

Kira Mourão

Mungo Carstairs

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JAL-2379: Improve PCA memory management

CR-JAL-11 5

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Details

Objectives

Branches in review

Issues Raised From Comments

General Comments

Kira Mourão

Mungo Carstairs

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