/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
-import java.awt.Color;
-import java.util.Map;
-import java.util.StringTokenizer;
-
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
+import java.awt.Color;
+import java.util.Map;
+import java.util.StringTokenizer;
+
public class UserColourScheme extends ResidueColourScheme
{
Color[] lowerCaseColours;
super(ResidueProperties.aaIndex);
colors = newColors;
}
+
@Override
public ColourSchemeI applyTo(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
UserColourScheme usc = new UserColourScheme(colors);
- if (lowerCaseColours!=null) {
+ if (lowerCaseColours != null)
+ {
usc.schemeName = new String(schemeName);
usc.lowerCaseColours = new Color[lowerCaseColours.length];
- System.arraycopy(lowerCaseColours, 0, usc.lowerCaseColours, 0, lowerCaseColours.length);
+ System.arraycopy(lowerCaseColours, 0, usc.lowerCaseColours, 0,
+ lowerCaseColours.length);
}
return usc;
}
+
public UserColourScheme(String colour)
{
super(ResidueProperties.aaIndex);
public void parseAppletParameter(String paramValue)
{
+ // TODO: need a function to generate appletParameter colour string from a
+ // UCS
StringTokenizer st = new StringTokenizer(paramValue, ";");
StringTokenizer st2;
String token = null, colour, residues;