[UGENE-6548] Add "Weak similarities" color scheme to the Alignment Editor Created: 22/Aug/19  Updated: 05/Dec/20  Resolved: 03/Nov/20

Status: Closed
Project: UGENE
Component/s: Basic-MSA
Affects Version/s: 1.32
Fix Version/s: 35

Type: New Feature Priority: Critical
Reporter: Olga Golosova Assignee: Yuliya Algaer
Resolution: Fixed  
Labels: request
Remaining Estimate: Not Specified
Time Spent: Not Specified
Original Estimate: Not Specified

Issue Links:
Relates
relates to UGENE-6474 Add "Percentage Identity (colored)" c... Closed
Story Points: 1
Assigned Tester: Yuliya Algaer
Sprint: DEV-35-1, DEV-35-2, DEV-37-1, DEV-37-2, DEV-37-3
Affect Type: Userdefined

 Description   

Add a new color scheme "Weak similarities" to the color schemes in the Alignment Editor ("Color" combo box on the "Highlighting" tab on the options panel, "Colors" menu in the "Actions" main menu and the Alignment Editor context menu).

Alphabets

The color scheme should be available for alignments of the following alphabets:

  • Standard DNA
  • Standard RNA
  • Extended DNA
  • Extended RNA

Characters priority

When there is a choice between two characters and and it is not specified by other rules which character to color, follow priorities: T>U>G>C>A>B>D>H>K>M>R>S>V>W>Y>N.

Coloring rules

  1. Do not color gaps ("-"), i.e. use black font and white background.
  2. Residues should be colored according to their percentage number in the column (use the priorities, described above, in case of equal percentage numbers):
    • Residues with the most frequency/priority in the column:
      • background color: light blue (#00FFFF)
      • font color: blue (#0000FF)
    • Residues with the 2nd frequency/priority:
      • background color: white (#FFFFFF)
      • font color: crimson (#FF00FF)
    • Residues with the 3rd frequency/priority:
      • background color: white (#FFFFFF)
      • font color: black (#000000)
    • Residues with the 4th frequency/priority:
      • background color: gray (#C0C0C0)
      • font color: black (#000000)
    • Other residues:
      • background color: white (#FFFFFF)
      • font color: orange (#FF6600)

 Comments   
Comment by Kirill Rasputin [ 24/Mar/20 ]

Gui tests added. Test scenarios added.

Comment by Olga Golosova [ 26/Mar/20 ]

Colors for the most frequent characters should be the following:

background color: light blue (#00FFFF)
font color: blue (#0000FF)

In the current version they are mixed up.

Comment by Kirill Rasputin [ 02/Apr/20 ]

Font and background color changed.
GUI tests and manual test data updated.

Comment by Svetlana Samoilenko [ 13/Apr/20 ]

GUITest_regression_scenarios_test_6548_1
stably falls on Windows10 (suite3) only with message " wrong color".

Comment by Svetlana Samoilenko [ 05/Jun/20 ]

Add please Russian translation for "Weak similarities".

Comment by Yuliya Algaer [ 06/Jun/20 ]

Done

Comment by Yuliya Algaer [ 07/Jul/20 ]

Please update the documentation

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