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

open for 4 years

Author

Reviewers

JAL-2499: fix Sequence Features PCA calculation

Activity

Details
Objectives
General Comments 0
Unresolved
Resolved
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

#permalink

Details

Warning: no files are visible, they have all been filtered.

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

#permalink

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

#permalink

Issues Raised From Comments

Key	Summary	State	Assignee

#permalink

General Comments

There are no general comments on this review.

Click to load diff

Notation	Description
[Crucible Review CR-1\|CR-1]	Creates a link to a Crucible review or FishEye artifact using the internal key reference for the item. Example: Crucible Review CR-1
[Atlassian Crucible\|http://atlassian.com/crucible]	Creates a link to an external resource, special characters that come after the URL and are not part of it must be separated with a space. External links are denoted with an arrow icon. Example: Atlassian Crucible
{cs:id=1\|rep=repository-key}	Render a link to the changeset Example: 1
bold	Makes text appear bold.
_italic_	Makes text appear in italics.
+underline+	Makes text appear underlined.
??citation??	Makes text appear in citation form.
-strikethrough-	Makes text appear ~~struck through~~.
^superscript^	Makes text appear in ^superscript.
~subscript~	Makes text appear in _subscript.
{{ monospaced }}	Placing double curly-brackets around text makes it appear `monospaced`.
{code} // Some comments here public String getFoo() { return foo; } {code}	The code macro displays a preformatted block for showing code with syntax highlighting. Example: // Some comments here public String getFoo() { return foo; }
bq. Block Quote	To make an entire paragraph into a block quotation, place "bq. " before it. Example: Block Quote
{quote} here is quoteable content to be quoted {quote}	Quote a block of text that's longer than one paragraph. Example: here is quoteable content to be quoted
{color:red} look ma, red text!{color}	Changes the color of a block of text. Example: look ma, red text!
* A list with bullets * Second item ** Indented item	Example: A list with bullets Second item Indented item
# A list with numbers # Second item ## Indented item	Example: A list with numbers Second item Indented item

CR-JAL-51

JAL-2499: fix Sequence Features PCA calculation

CR-JAL-51 4

Details

Objectives

Branches in review

Issues Raised From Comments

General Comments

Log time against

JAL-2499: fix Sequence Features PCA calculation

CR-JAL-51 4

Summarize the review outcomes (optional)

Details

Objectives

Branches in review

Issues Raised From Comments

General Comments

Log time against