X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=98e90bdf769f07363b4b8bb598d97a5edf6d3db2;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=3e8e87a2d148949f3feb3625425112ad72d36e1b;hpb=b0832234b2a89510d715951d94ae213e449ca6b2;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 3e8e87a..98e90bd 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.util.ColorUtils;
 
@@ -44,7 +45,8 @@ public class ColourSchemeProperty
    * Returns a colour scheme for the given name, with which the given data may
    * be coloured. The name is not case-sensitive, and may be one of
    * <ul>
-   * <li>any currently registered colour scheme; Jalview by default provides</li>
+   * <li>any currently registered colour scheme; Jalview by default
+   * provides</li>
    * <ul>
    * <li>Clustal</li>
    * <li>Blosum62</li>
@@ -61,9 +63,11 @@ public class ColourSchemeProperty
    * <li>T-Coffee Scores</li>
    * <li>RNA Helices</li>
    * </ul>
-   * <li>the name of a programmatically added colour scheme</li> <li>an AWT
-   * colour name e.g. red</li> <li>an AWT hex rgb colour e.g. ff2288</li> <li>
-   * residue colours list e.g. D,E=red;K,R,H=0022FF;c=yellow</li> </ul>
+   * <li>the name of a programmatically added colour scheme</li>
+   * <li>an AWT colour name e.g. red</li>
+   * <li>an AWT hex rgb colour e.g. ff2288</li>
+   * <li>residue colours list e.g. D,E=red;K,R,H=0022FF;c=yellow</li>
+   * </ul>
    * 
    * If none of these formats is matched, the string is converted to a colour
    * using a hashing algorithm. For name "None", returns null.
@@ -72,8 +76,8 @@ public class ColourSchemeProperty
    * @param name
    * @return
    */
-  public static ColourSchemeI getColourScheme(AnnotatedCollectionI forData,
-          String name)
+  public static ColourSchemeI getColourScheme(AlignViewportI view,
+          AnnotatedCollectionI forData, String name)
   {
     if (ResidueColourScheme.NONE.equalsIgnoreCase(name))
     {
@@ -85,8 +89,8 @@ public class ColourSchemeProperty
      * if this is the name of a registered colour scheme, just
      * create a new instance of it
      */
-    ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(
-            name, forData, null);
+    ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(name,
+            view, forData, null);
     if (scheme != null)
     {
       return scheme;
@@ -146,8 +150,7 @@ public class ColourSchemeProperty
    */
   public static String getColourName(ColourSchemeI cs)
   {
-    return cs == null ? ResidueColourScheme.NONE : cs
-            .getSchemeName();
+    return cs == null ? ResidueColourScheme.NONE : cs.getSchemeName();
   }
 
 }