*/
package jalview.schemes;
+import java.util.Locale;
+
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
import jalview.util.ColorUtils;
import jalview.util.StringUtils;
}
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI sg)
{
return new UserColourScheme(this);
}
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);
}
if (col == null)
{
- System.out.println("Making colour from name: " + colour);
+ jalview.bin.Console.outPrintln("Making colour from name: " + colour);
col = ColorUtils.createColourFromName(colour);
}
continue;
}
- if (residue.equals(residue.toLowerCase()))
+ if (residue.equals(residue.toLowerCase(Locale.ROOT)))
{
if (lowerCaseColours == null)
{
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);
+ jalview.bin.Console.outPrintln(
+ "Error parsing userDefinedColours:\n" + token + "\n" + ex);
}
}
- @Override
- public Color findColour(char c, int j, SequenceI seq)
- {
- Color colour;
- int index = ResidueProperties.aaIndex[c];
-
- if (lowerCaseColours != null && 'a' <= c && c <= 'z')
- {
- colour = lowerCaseColours[index];
- }
- else
- {
- colour = colors[index];
- }
-
- return colour;
- }
-
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++)
{
c = lowerCaseColours[index];
if (c != null && !c.equals(Color.white))
{
- residue = residue.toLowerCase();
+ residue = residue.toLowerCase(Locale.ROOT);
if (colours.get(c) == null)
{
colours.put(c, new ArrayList<String>());
/*
* 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);
+ }
}