X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=92989fbfe3f5a51abec8d2f4389e3eb080cae161;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=d73bed2d62e7e95224561cc8d91144652ba1929a;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index d73bed2..92989fb 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,31 +1,33 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* 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;
@@ -42,18 +44,22 @@ public class UserColourScheme extends ResidueColourScheme
super(ResidueProperties.aaIndex);
colors = newColors;
}
+
@Override
public ColourSchemeI applyTo(AnnotatedCollectionI sg,
Map 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);
@@ -158,7 +164,8 @@ public class UserColourScheme extends ResidueColourScheme
public void parseAppletParameter(String paramValue)
{
- // TODO: need a function to generate appletParameter colour string from a UCS
+ // TODO: need a function to generate appletParameter colour string from a
+ // UCS
StringTokenizer st = new StringTokenizer(paramValue, ";");
StringTokenizer st2;
String token = null, colour, residues;