From fddbe4cfde483f487a99b30f4a44100112995193 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 17 Mar 2009 16:50:48 +0000
Subject: [PATCH] fixes launchApp bug where user defined colourscheme defined
 in applet parameter does not get passed to application

---
 src/jalview/schemes/ColourSchemeProperty.java |   63 +++++++++++++++----------
 1 file changed, 38 insertions(+), 25 deletions(-)

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 6fc4e2b..dd4eb53 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -77,7 +77,7 @@ public class ColourSchemeProperty
    * DOCUMENT ME!
    * 
    * @param name
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -145,7 +145,7 @@ public class ColourSchemeProperty
    * DOCUMENT ME!
    * 
    * @param cs
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -216,7 +216,7 @@ public class ColourSchemeProperty
    * DOCUMENT ME!
    * 
    * @param index
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -298,9 +298,9 @@ public class ColourSchemeProperty
    * DOCUMENT ME!
    * 
    * @param al
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param name
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -313,33 +313,46 @@ public class ColourSchemeProperty
   /**
    * retrieve or create colourscheme associated with name
    * 
-   * @param seqs sequences to colour
-   * @param width range of sequences to colour
-   * @param name colourscheme name, applet colour parameter specification, or string to parse as colour for new coloursheme
+   * @param seqs
+   *          sequences to colour
+   * @param width
+   *          range of sequences to colour
+   * @param name
+   *          colourscheme name, applet colour parameter specification, or
+   *          string to parse as colour for new coloursheme
    * @return Valid Colourscheme
    */
   public static ColourSchemeI getColour(java.util.Vector seqs, int width,
           String name)
   {
     int colindex = getColourIndexFromName(name);
-    if (colindex == UNDEFINED) // USER_DEFINED)
+    if (colindex == UNDEFINED)
     {
-      try
+      if (name.indexOf('=') == -1)
       {
-        return new UserColourScheme(name);
-      } catch (Exception e)
-      {
-        // System.err.println("Ignoring unknown colourscheme name");
+        // try to build a colour from the string directly
+        try
+        {
+          return new UserColourScheme(name);
+        } catch (Exception e)
+        {
+          // System.err.println("Ignoring unknown colourscheme name");
+        }
       }
-      try {
-        // fix the launchApp user defined coloursheme transfer bug
-        jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
-                "white");
-        ucs.parseAppletParameter(name);
-
-      } catch (Exception e)
+      else
       {
-        // System.err.println("Ignoring exception when parsing colourscheme as applet-parameter");
+        // try to parse the string as a residue colourscheme
+        try
+        {
+          // fix the launchApp user defined coloursheme transfer bug
+          jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
+                  "white");
+          ucs.parseAppletParameter(name);
+
+        } catch (Exception e)
+        {
+          // System.err.println("Ignoring exception when parsing colourscheme as applet-parameter");
+        }
       }
     }
     return getColour(seqs, width, getColourIndexFromName(name));
@@ -349,11 +362,11 @@ public class ColourSchemeProperty
    * DOCUMENT ME!
    * 
    * @param seqs
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param width
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param index
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
-- 
1.7.10.2