added commented out seqStrings comment.

[jalview.git] / src / jalview / appletgui / AlignViewport.java

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 152966e..9f6448d 100755 (executable)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -56,7 +56,7 @@ public class AlignViewport
   boolean conservationColourSelected = false;\r
   boolean abovePIDThreshold = false;\r
 \r
-  SequenceGroup selectionGroup = new SequenceGroup();\r
+  SequenceGroup selectionGroup;\r
 \r
   int charHeight;\r
   int charWidth;\r
@@ -141,14 +141,34 @@ public class AlignViewport
     updateConservation();\r
     updateConsensus();\r
 \r
-    if (applet != null && applet.getParameter("defaultColour") != null)\r
+\r
+    if (applet != null)\r
     {\r
-      globalColourScheme = ColourSchemeProperty.getColour(alignment,\r
-          applet.getParameter("defaultColour"));\r
-      if (globalColourScheme != null)\r
+      String colour = applet.getParameter("defaultColour");\r
+\r
+      if(colour == null)\r
+      {\r
+        colour = applet.getParameter("userDefinedColour");\r
+        if(colour !=null)\r
+          colour = "User Defined";\r
+      }\r
+\r
+      if(colour != null)\r
+      {\r
+        globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);\r
+        if (globalColourScheme != null)\r
+        {\r
+          globalColourScheme.setConsensus(vconsensus);\r
+        }\r
+      }\r
+\r
+      if(applet.getParameter("userDefinedColour")!=null)\r
       {\r
-        globalColourScheme.setConsensus(vconsensus);\r
+        ((UserColourScheme)globalColourScheme).parseAppletParameter(\r
+            applet.getParameter("userDefinedColour"));\r
       }\r
+\r
+\r
     }\r
   }\r
 \r
@@ -561,32 +581,6 @@ public class AlignViewport
     return increment;\r
   }\r
 \r
-  public int getIndex(int y)\r
-  {\r
-    int y1 = 0;\r
-    int starty = getStartSeq();\r
-    int endy = getEndSeq();\r
-\r
-    for (int i = starty; i <= endy; i++)\r
-    {\r
-      if (i < alignment.getHeight() && alignment.getSequenceAt(i) != null)\r
-      {\r
-        int y2 = y1 + getCharHeight();\r
-\r
-        if (y >= y1 && y <= y2)\r
-        {\r
-          return i;\r
-        }\r
-        y1 = y2;\r
-      }\r
-      else\r
-      {\r
-        return -1;\r
-      }\r
-    }\r
-    return -1;\r
-  }\r
-\r
   public ColumnSelection getColumnSelection()\r
   {\r
     return colSel;\r