sequence is char []

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

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 551dea7..47fbb0d 100755 (executable)
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,7 +1,7 @@
 \r
 /*\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
@@ -78,6 +78,7 @@ public class FeatureRenderer
       renderOrder = fr.renderOrder;\r
       featureGroups = fr.featureGroups;\r
       featureColours = fr.featureColours;\r
+      transparency =  fr.transparency;\r
     }\r
 \r
 \r
@@ -99,7 +100,7 @@ public class FeatureRenderer
 \r
       currentColour = null;\r
 \r
-      drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1, -1, -1);\r
+      drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1);\r
 \r
       if(currentColour==null)\r
         return initialCol;\r
@@ -136,7 +137,7 @@ public class FeatureRenderer
 \r
       currentColour = null;\r
 \r
-      drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1, -1, -1);\r
+      drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1);\r
 \r
       if(currentColour==null)\r
         return initialCol;\r
@@ -166,7 +167,7 @@ public class FeatureRenderer
     int sfSize, sfindex, spos, epos;\r
 \r
     public void drawSequence(Graphics g, SequenceI seq,\r
-                             int start, int end, int y1, int width, int height)\r
+                             int start, int end, int y1)\r
     {\r
       if (   seq.getSequenceFeatures() == null\r
           || seq.getSequenceFeatures().length==0)\r
@@ -246,13 +247,13 @@ public class FeatureRenderer
                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
                           new Color( ( (Integer) av.featuresDisplayed.get(\r
                 sequenceFeatures[sfindex].type)).intValue()),\r
-                          start, end, y1, width, height);\r
+                          start, end, y1);\r
             renderFeature(g, seq,\r
                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
                           new Color( ( (Integer) av.featuresDisplayed.get(\r
                 sequenceFeatures[sfindex].type)).intValue()),\r
-                          start, end, y1, width, height);\r
+                          start, end, y1);\r
 \r
           }\r
           else\r
@@ -260,7 +261,7 @@ public class FeatureRenderer
                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
                           getColour(sequenceFeatures[sfindex].type),\r
-                          start, end, y1, width, height);\r
+                          start, end, y1);\r
 \r
         }\r
       }\r
@@ -275,7 +276,7 @@ public class FeatureRenderer
     char s;\r
     int i;\r
     void renderFeature(Graphics g, SequenceI seq,\r
-                       int fstart, int fend, Color featureColour, int start, int end,  int y1, int width, int height)\r
+                       int fstart, int fend, Color featureColour, int start, int end,  int y1)\r
     {\r
 \r
       if (((fstart <= end) && (fend >= start)))\r
@@ -292,7 +293,7 @@ public class FeatureRenderer
 \r
           for (i = fstart; i <= fend; i++)\r
           {\r
-            s = seq.getSequence().charAt(i);\r
+            s = seq.getCharAt(i);\r
 \r
             if (jalview.util.Comparison.isGap(s))\r
             {\r
@@ -301,16 +302,16 @@ public class FeatureRenderer
 \r
             g.setColor(featureColour);\r
 \r
-            g.fillRect( (i - start) * width, y1, width, height);\r
+            g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);\r
 \r
             if(!av.validCharWidth)\r
               continue;\r
 \r
             g.setColor(Color.white);\r
-            charOffset = (width - fm.charWidth(s)) / 2;\r
+            charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
             g.drawString(String.valueOf(s),\r
-                         charOffset + (width * (i - start)),\r
-                         (y1 + height) - height / 5); //pady = height / 5;\r
+                         charOffset + (av.charWidth * (i - start)),\r
+                         (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;\r
 \r
           }\r
       }\r
@@ -318,6 +319,9 @@ public class FeatureRenderer
 \r
     void findAllFeatures()\r
     {\r
+      jalview.schemes.UserColourScheme ucs = new\r
+          jalview.schemes.UserColourScheme();\r
+\r
       av.featuresDisplayed = new Hashtable();\r
       Vector allfeatures = new Vector();\r
       for (int i = 0; i < av.alignment.getHeight(); i++)\r
@@ -332,6 +336,14 @@ public class FeatureRenderer
         {\r
           if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
           {\r
+            if (getColour(features[index].getType()) == null)\r
+            {\r
+              featureColours.put(features[index].getType(),\r
+                                 ucs.createColourFromName(features[index].\r
+                  getType()));\r
+            }\r
+\r
+\r
             av.featuresDisplayed.put(features[index].getType(),\r
                                   new Integer( getColour(features[index].getType()).getRGB()) );\r
             allfeatures.addElement(features[index].getType());\r
@@ -400,10 +412,10 @@ public class FeatureRenderer
   {\r
     void setTransparency(Graphics g, float value)\r
     {\r
-  //    Graphics2D g2 = (Graphics2D) g;\r
-   //   g2.setComposite(\r
-    //      AlphaComposite.getInstance(\r
-    //          AlphaComposite.SRC_OVER, value));\r
+    /* Graphics2D g2 = (Graphics2D) g;\r
+     g2.setComposite(\r
+        AlphaComposite.getInstance(\r
+             AlphaComposite.SRC_OVER, value));*/\r
     }\r
   }\r
 \r