CR-JAL-59 JAL-2544: Sort by features buggy with gapped selection region

open for 4 years

Author

Reviewers

JAL-2544: Sort by features buggy with gapped selection region

Activity

Details
Objectives
General Comments 0
Unresolved
Resolved
Number of files included: 3

jalview 0
- Folder src/jalview/analysis 0
  - File AlignmentSorter.java 0 Remove
  - File AlignmentSorter.java 0 Remove
- Folder test/jalview/analysis 0
  - File AlignmentSorterTest.java 0 Remove

#permalink

Details

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

Participant	Role	Time Spent	Comments
Mungo Carstairs	Author
Kira Mourão	Reviewer - 100% reviewed	6m
Total		6m	0

Linked Issue:
JAL-2544

#permalink

Objectives

If Sort by Feature Density (or Score) is on a selection region, and the region includes trailing spaces, then features to the right of the region may be counted.
Example: uniref50.fa + exampleFeatures.txt.
Select columns 8-10 (only FER1_MAIZE has 1 feature) and Sequence sort by Density in Feature Settings. Sure enough FER1_MAIZE sorts to the bottom (or the top on a second, inverting sort).
Now insert one ore more gaps before the first features in FER1_SPIOL (at column 11).
Widen the selection region to include one or more of the gapped columns (but not the SPIOL features).
Sort by Density again - FER1_SPIOL is now sorted to bottom / top.

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-59

JAL-2544: Sort by features buggy with gapped selection region

CR-JAL-59 0

Details

Objectives

Branches in review

Issues Raised From Comments

General Comments

Log time against

JAL-2544: Sort by features buggy with gapped selection region

CR-JAL-59 0

Summarize the review outcomes (optional)

Details

Objectives

Branches in review

Issues Raised From Comments

General Comments

Log time against