JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / schemes / UserColourScheme.java

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 61aed43..9ae14ca 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,31 +1,33 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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;
@@ -42,18 +44,22 @@ public class UserColourScheme extends ResidueColourScheme
     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);
@@ -61,7 +67,7 @@ public class UserColourScheme extends ResidueColourScheme
 
     if (col == null)
     {
-      System.out.println("Unknown colour!! " + colour);
+      System.out.println("Making colour from name: " + colour);
       col = createColourFromName(colour);
     }
 
@@ -93,8 +99,12 @@ public class UserColourScheme extends ResidueColourScheme
     return schemeName;
   }
 
-  public Color getColourFromString(String colour)
+  public static Color getColourFromString(String colour)
   {
+    if (colour == null)
+    {
+      return null;
+    }
     colour = colour.trim();
 
     Color col = null;
@@ -130,7 +140,7 @@ public class UserColourScheme extends ResidueColourScheme
 
   }
 
-  public Color createColourFromName(String name)
+  public static Color createColourFromName(String name)
   {
     int r, g, b;
 
@@ -158,6 +168,8 @@ 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;