schemeName = from.schemeName;
if (from.lowerCaseColours != null)
{
- lowerCaseColours = new Color[lowerCaseColours.length];
+ lowerCaseColours = new Color[from.lowerCaseColours.length];
System.arraycopy(from.lowerCaseColours, 0, lowerCaseColours, 0,
from.lowerCaseColours.length);
}
{
lowerCaseColours = new Color[colors.length];
}
- lowerCaseColours[colIndex] = ColorUtils.parseColourString(colour);
+ lowerCaseColours[colIndex] = ColorUtils
+ .parseColourString(colour);
}
else
{
}
} catch (Exception ex)
{
- System.out.println("Error parsing userDefinedColours:\n" + token
- + "\n" + ex);
+ System.out.println(
+ "Error parsing userDefinedColours:\n" + token + "\n" + ex);
}
}
- @Override
- public Color findColour(char c, int j, SequenceI seq)
- {
- Color currentColour;
- int index = ResidueProperties.aaIndex[c];
-
- if ((threshold == 0) || aboveThreshold(c, j))
- {
- if (lowerCaseColours != null && 'a' <= c && c <= 'z')
- {
- currentColour = lowerCaseColours[index];
- }
- else
- {
- currentColour = colors[index];
- }
- }
- else
- {
- currentColour = Color.white;
- }
-
- if (conservationColouring)
- {
- currentColour = applyConservation(currentColour, j);
- }
-
- return currentColour;
- }
-
public void setLowerCaseColours(Color[] lcolours)
{
lowerCaseColours = lcolours;
}
/**
- * Answers the customised name of the colour scheme, if it has one, else
- * "User Defined"
+ * Answers the customised name of the colour scheme, if it has one, else "User
+ * Defined"
*/
@Override
public String getSchemeName()
{
return schemeName;
}
- return "User Defined";
+ return ResidueColourScheme.USER_DEFINED;
}
/**
/*
* step 1: build a map from colours to the symbol(s) that have the colour
*/
- Map<Color, List<String>> colours = new HashMap<Color, List<String>>();
+ Map<Color, List<String>> colours = new HashMap<>();
for (char symbol = 'A'; symbol <= 'Z'; symbol++)
{
/*
* step 2: make a list of { A,G,R=12f9d6 } residues/colour specs
*/
- List<String> residueColours = new ArrayList<String>();
+ List<String> residueColours = new ArrayList<>();
for (Entry<Color, List<String>> cols : colours.entrySet())
{
boolean first = true;
Collections.sort(residueColours);
return StringUtils.listToDelimitedString(residueColours, ";");
}
+
+ @Override
+ public boolean hasGapColour()
+ {
+ return (findColour(' ') != null);
+ }
}