X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=2d5b23dfa343f3b55284a07b944c6df4563a896e;hb=refs%2Fheads%2Fdoc%2FJAL-3746_Release_2_11_2;hp=425b3a1c964cf0e2fc6bb781cf910e0a7f13924f;hpb=320c96aed11f5c396a9efd9ea83b0e35f05e21e4;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 425b3a1..2d5b23d 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;
 
@@ -44,6 +45,9 @@ 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>
+   * <ul>
    * <li>Clustal</li>
    * <li>Blosum62</li>
    * <li>% Identity</li>
@@ -58,10 +62,13 @@ public class ColourSchemeProperty
    * <li>Purine/Pyrimidine</li>
    * <li>T-Coffee Scores</li>
    * <li>RNA Helices</li>
-   * <li>User Defined</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.
    * 
@@ -69,7 +76,8 @@ public class ColourSchemeProperty
    * @param name
    * @return
    */
-  public static ColourSchemeI getColourScheme(AnnotatedCollectionI forData,
+  public static ColourSchemeI getColourScheme(AlignViewportI view,
+          AnnotatedCollectionI forData,
           String name)
   {
     if (ResidueColourScheme.NONE.equalsIgnoreCase(name))
@@ -77,36 +85,27 @@ public class ColourSchemeProperty
       return null;
 
     }
-    JalviewColourScheme scheme = JalviewColourScheme.forName(name);
-    if (scheme != null)
-    {
-      return scheme.getColourScheme(forData);
-    }
 
-    if (name.indexOf('=') == -1)
+    /*
+     * if this is the name of a registered colour scheme, just
+     * create a new instance of it
+     */
+    ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(name,
+            view,
+            forData, null);
+    if (scheme != null)
     {
-      /*
-       * parse the name as a colour specification
-       * e.g. "red" or "ff00ed",
-       * or failing that hash the name to a colour
-       */
-      return new UserColourScheme(name);
+      return scheme;
     }
 
     /*
      * try to parse the string as a residues colour scheme
      * e.g. A=red;T,G=blue etc
+     * else parse the name as a colour specification
+     * e.g. "red" or "ff00ed",
+     * or failing that hash the name to a colour
      */
-    UserColourScheme ucs = null;
-    try
-    {
-      // fix the launchApp user defined colourscheme transfer bug
-      ucs = new UserColourScheme("white");
-      ucs.parseAppletParameter(name);
-    } catch (Exception e)
-    {
-      // System.err.println("Ignoring exception when parsing colourscheme as applet-parameter");
-    }
+    UserColourScheme ucs = new UserColourScheme(name);
     return ucs;
   }
 
@@ -153,8 +152,7 @@ public class ColourSchemeProperty
    */
   public static String getColourName(ColourSchemeI cs)
   {
-    return cs == null ? ResidueColourScheme.NONE : cs
-            .getSchemeName();
+    return cs == null ? ResidueColourScheme.NONE : cs.getSchemeName();
   }
 
 }