header updated

[jalview.git] / src / jalview / gui / FeatureRenderer.java

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 628de4e..afe29a0 100755 (executable)
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -54,7 +54,6 @@ public class FeatureRenderer
 \r
     String [] renderOrder;\r
 \r
-\r
     /**\r
      * Creates a new FeatureRenderer object.\r
      *\r
@@ -77,33 +76,30 @@ public class FeatureRenderer
     boolean offscreenRender = false;\r
     public Color findFeatureColour(Color initialCol, SequenceI seq, int res)\r
     {\r
-      int seqindex = av.alignment.findIndex(seq);\r
-\r
       return new Color( findFeatureColour (initialCol.getRGB(),\r
-                        seqindex, res ));\r
+                        seq, res ));\r
     }\r
 \r
     /**\r
-     * This is used by the Molecule Viewer to get the accurate colour\r
-     * of the rendered sequence\r
+     * This is used by the Molecule Viewer and Overview to\r
+     * get the accurate colourof the rendered sequence\r
      */\r
-    public int findFeatureColour(int initialCol, int seqIndex, int column)\r
+    public int findFeatureColour(int initialCol, SequenceI seq, int column)\r
     {\r
       if(!av.showSequenceFeatures)\r
         return initialCol;\r
 \r
-      if(seqIndex!=lastSequenceIndex)\r
+      if(seq!=lastSeq)\r
       {\r
-        lastSequence = av.alignment.getSequenceAt(seqIndex);\r
-        lastSequenceIndex = seqIndex;\r
-        sequenceFeatures = lastSequence.getDatasetSequence().getSequenceFeatures();\r
+        lastSeq = seq;\r
+        sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();\r
         if(sequenceFeatures==null)\r
           return initialCol;\r
 \r
         sfSize = sequenceFeatures.length;\r
       }\r
 \r
-      if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))\r
+      if(jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))\r
         return Color.white.getRGB();\r
 \r
 \r
@@ -121,7 +117,7 @@ public class FeatureRenderer
       {\r
         offscreenImage.setRGB(0,0,initialCol);\r
         drawSequence(offscreenImage.getGraphics(),\r
-                     lastSequence,\r
+                     lastSeq,\r
                      column,column,0);\r
 \r
         return offscreenImage.getRGB(0,0);\r
@@ -129,8 +125,8 @@ public class FeatureRenderer
       else\r
       {\r
         drawSequence(null,\r
-                    lastSequence,\r
-                    lastSequence.findPosition(column),\r
+                    lastSeq,\r
+                    lastSeq.findPosition(column),\r
                     -1, -1);\r
 \r
         if (currentColour == null)\r
@@ -158,8 +154,7 @@ public class FeatureRenderer
      */\r
    // String type;\r
    // SequenceFeature sf;\r
-    int lastSequenceIndex=-1;\r
-    SequenceI lastSequence;\r
+    SequenceI lastSeq;\r
     SequenceFeature [] sequenceFeatures;\r
     int sfSize, sfindex, spos, epos;\r
 \r
@@ -170,12 +165,13 @@ public class FeatureRenderer
           || seq.getDatasetSequence().getSequenceFeatures().length==0)\r
         return;\r
 \r
-\r
       if(g!=null)\r
         fm = g.getFontMetrics();\r
 \r
 \r
-      if (av.featuresDisplayed == null || renderOrder==null)\r
+      if (av.featuresDisplayed == null\r
+          || renderOrder==null\r
+          || newFeatureAdded)\r
        {\r
          findAllFeatures();\r
          if(av.featuresDisplayed.size()<1)\r
@@ -185,9 +181,9 @@ public class FeatureRenderer
          sfSize = sequenceFeatures.length;\r
        }\r
 \r
-       if(lastSequence==null || seq!=lastSequence)\r
+       if(lastSeq==null || seq!=lastSeq)\r
       {\r
-        lastSequence = seq;\r
+        lastSeq = seq;\r
         sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
         sfSize = sequenceFeatures.length;\r
       }\r
@@ -203,8 +199,8 @@ public class FeatureRenderer
 \r
       if(!offscreenRender)\r
       {\r
-        spos = lastSequence.findPosition(start);\r
-        epos = lastSequence.findPosition(end);\r
+        spos = lastSeq.findPosition(start);\r
+        epos = lastSeq.findPosition(end);\r
       }\r
 \r
 \r
@@ -212,6 +208,7 @@ public class FeatureRenderer
       for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)\r
        {\r
         type =  renderOrder[renderIndex];\r
+\r
         if(!av.featuresDisplayed.containsKey(type))\r
           continue;\r
 \r
@@ -333,12 +330,34 @@ public class FeatureRenderer
       }\r
     }\r
 \r
-    synchronized void findAllFeatures()\r
+\r
+    boolean newFeatureAdded = false;\r
+\r
+    public void featuresAdded()\r
     {\r
+      findAllFeatures();\r
+    }\r
+\r
+   boolean findingFeatures = false;\r
+   synchronized void findAllFeatures()\r
+   {\r
+      newFeatureAdded = false;\r
+\r
+      if(findingFeatures)\r
+      {\r
+        newFeatureAdded = true;\r
+        return;\r
+      }\r
+\r
+      findingFeatures = true;\r
       jalview.schemes.UserColourScheme ucs = new\r
           jalview.schemes.UserColourScheme();\r
 \r
-          av.featuresDisplayed = new Hashtable();\r
+      if(av.featuresDisplayed==null)\r
+        av.featuresDisplayed = new Hashtable();\r
+\r
+      av.featuresDisplayed.clear();\r
+\r
       Vector allfeatures = new Vector();\r
       for (int i = 0; i < av.alignment.getHeight(); i++)\r
       {\r
@@ -383,6 +402,8 @@ public class FeatureRenderer
         renderOrder[i] = en.nextElement().toString();\r
         i--;\r
       }\r
+\r
+      findingFeatures = false;\r
     }\r
 \r
     public Color getColour(String featureType)\r