X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=89f3eed3a72e8ac78599640ec1897704e75fae7e;hb=9876fdccf311378e690c1f9e18db52675d427b89;hp=82a5871eafd14bd083d6d6c30acb9c7cf75615eb;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 82a5871..89f3eed 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,26 +1,32 @@
/*
- * 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 2.9)
+ * Copyright (C) 2015 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 jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
import java.awt.Color;
+import java.util.Map;
import java.util.StringTokenizer;
-import jalview.datamodel.SequenceI;
public class UserColourScheme extends ResidueColourScheme
{
@@ -39,6 +45,21 @@ public class UserColourScheme extends ResidueColourScheme
colors = newColors;
}
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map hiddenRepSequences)
+ {
+ UserColourScheme usc = new UserColourScheme(colors);
+ if (lowerCaseColours != null)
+ {
+ usc.schemeName = new String(schemeName);
+ usc.lowerCaseColours = new Color[lowerCaseColours.length];
+ System.arraycopy(lowerCaseColours, 0, usc.lowerCaseColours, 0,
+ lowerCaseColours.length);
+ }
+ return usc;
+ }
+
public UserColourScheme(String colour)
{
super(ResidueProperties.aaIndex);
@@ -143,6 +164,8 @@ public class UserColourScheme extends ResidueColourScheme
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;