Add "Percentage Identity (colored)" color scheme to the Alignment Editor

Add a new color scheme "Percentage Identity (colored)" to the color schemes in the Alignment Editor ("Color" combo box on the "Highlighting" tab on the options panel in the Alignment Editor, "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

Additional widgets in the GUI

When the "Percentage Identity (colored)" color scheme is selected, there are should be the following additional widgets on the options panel a slider and an editable spin box to set the "Threshold" parameter: min value - 0.1%, max value - 99.9%, step - 0.1%, default value - 50%.

Characters priority

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

General rules for highlighting

When the color scheme is selected, use the following rules for coloring a character background and font depending on the percentage of characters presence in a column:

1. If all characters (100%) are the same and there are no gaps in the column:
   • background color: yellow (#FFFF00)
   • font color: red (#FF0000)
2. If there are 50% of one character in a column and 50% of another (gaps are not taken into account) in the column, then only half of the characters should be highlighted as follows:
   • background color: green (#00FF00)
   • font color: black (#000000)
3. If there are one or several characters in a column with percentage number more or equal to the threshold value (see "Threshold" parameter above), gaps are considered as character when calculating percentage number in the column, then the most frequent of the characters (in case of the same number of most frequent characters follow the priorities described above) should be highlighted as follows:
   • background color: light blue (#00FFFF)
   • font color: blue (#0000FF)
4. If other rules are not applied, use the following colors:
   • background color: white (#FFFFFF)
   • font color: black (#000000)