X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=c9ed3051c6790c454183b10d6faf8fd5db4dfeb3;hb=3e3378e2ccfea39a2b161600c5a2029716acd1b7;hp=5959493fa0cbe6b739a33b9907378dddd310eabb;hpb=628a29c56cc280f434f3568f3bf79555e1c77726;p=jalview.git

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 5959493..c9ed305 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -53,7 +53,7 @@ public class IdCanvas extends JPanel
     {
         setLayout(new BorderLayout());
         this.av = av;
-        PaintRefresher.Register(this, av.alignment);
+        PaintRefresher.Register(this, av.getSequenceSetId());
     }
 
     /**
@@ -86,7 +86,7 @@ public class IdCanvas extends JPanel
         }
         else
         {
-            gg.setColor(s.getColor());
+            gg.setColor(av.getSequenceColour(s));
             gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
                 charHeight);
             gg.setColor(Color.black);
@@ -173,6 +173,8 @@ public class IdCanvas extends JPanel
             return;
         }
 
+        int oldHeight = imgHeight;
+
         imgHeight = getHeight();
         imgHeight -= (imgHeight % av.charHeight);
 
@@ -181,15 +183,17 @@ public class IdCanvas extends JPanel
             return;
         }
 
-        image = new BufferedImage(getWidth(), imgHeight,
-                BufferedImage.TYPE_INT_RGB);
-        gg = (Graphics2D) image.getGraphics();
+        if(oldHeight!=imgHeight || image.getWidth(this)!=getWidth())
+        {
+          image = new BufferedImage(getWidth(), imgHeight,
+                                    BufferedImage.TYPE_INT_RGB);
+        }
 
+        gg = (Graphics2D) image.getGraphics();
         //Fill in the background
         gg.setColor(Color.white);
         gg.fillRect(0, 0, getWidth(), imgHeight);
 
-
         drawIds(av.getStartSeq(), av.endSeq);
 
         g.drawImage(image, 0, 0, this);
@@ -276,9 +280,15 @@ public class IdCanvas extends JPanel
         {
           //Now draw the id strings
 
+            SequenceI sequence;
             //Now draw the id strings
             for (int i = starty; i < endy; i++)
             {
+              sequence = av.alignment.getSequenceAt(i);
+
+              if(sequence==null)
+                continue;
+
               if (av.hasHiddenRows)
               {
                 setHiddenFont(i);
@@ -286,21 +296,21 @@ public class IdCanvas extends JPanel
 
                 // Selected sequence colours
                 if ( (searchResults != null) &&
-                    searchResults.contains(av.alignment.getSequenceAt(i)))
+                    searchResults.contains(sequence))
                 {
                   currentColor = Color.black;
                   currentTextColor = Color.white;
                 }
                 else if ( (av.getSelectionGroup() != null) &&
                          av.getSelectionGroup().getSequences(false).contains(
-                             av.alignment.getSequenceAt(i)))
+                             sequence))
                 {
                   currentColor = Color.lightGray;
                   currentTextColor = Color.black;
                 }
                 else
                 {
-                  currentColor = av.alignment.getSequenceAt(i).getColor();
+                  currentColor = av.getSequenceColour(sequence);
                   currentTextColor = Color.black;
                 }
 
@@ -311,7 +321,7 @@ public class IdCanvas extends JPanel
 
                 gg.setColor(currentTextColor);
 
-                String string = av.alignment.getSequenceAt(i).getDisplayId( av.getShowJVSuffix());
+                String string = sequence.getDisplayId( av.getShowJVSuffix());
 
                 gg.drawString(string, 0,
                     (((i - starty) * av.charHeight) + av.charHeight) -
@@ -327,12 +337,32 @@ public class IdCanvas extends JPanel
 
     void drawMarker(int i, int starty, int yoffset)
     {
-      int hiddenIndex = av.adjustForHiddenSeqs(i);
-      int lastIndex = av.adjustForHiddenSeqs(i - 1);
-      int nextIndex = av.adjustForHiddenSeqs(i + 1);
+
+      SequenceI [] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
+      //Use this method here instead of calling hiddenSeq adjust
+      //3 times.
+      int hSize = hseqs.length;
+
+      int hiddenIndex = i;
+      int lastIndex = i - 1;
+      int nextIndex = i + 1;
+
+      for(int j=0; j<hSize; j++)
+      {
+        if (hseqs[j] != null)
+        {
+          if(j-1<hiddenIndex)
+            hiddenIndex++;
+          if(j-1<lastIndex)
+            lastIndex++;
+          if(j-1<nextIndex)
+            nextIndex++;
+        }
+      }
 
       boolean below = (hiddenIndex > lastIndex + 1);
-      boolean above = (nextIndex>hiddenIndex+1);
+      boolean above = (nextIndex > hiddenIndex+1);
+
 
         gg.setColor(Color.blue);
         if(below)
@@ -371,7 +401,9 @@ public class IdCanvas extends JPanel
       Font bold = new Font(av.getFont().getName(), Font.BOLD,
                            av.getFont().getSize());
 
-      if (av.alignment.getSequenceAt(i).getHiddenSequences() != null)
+
+      if (av.alignment.getSequenceAt(i)!=null
+          && av.alignment.getSequenceAt(i).getHiddenSequences() != null)
         gg.setFont(bold);
       else
         gg.setFont(italic);