X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=45bcf66d4c7bbb62c62229db86ad53007fe25719;hb=d3760e28db022dd704f19d0e2df05af8675cf3c3;hp=b4ef770883b7d6947dd810d688dd4d1666219b12;hpb=c20e9d4ae9c98b093e74a10bf965e6d20d80fadf;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index b4ef770..45bcf66 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -62,7 +62,7 @@ public class SeqCanvas extends JComponent
         fr = new FeatureRenderer(av);
         sr = new SequenceRenderer(av);
         setLayout(new BorderLayout());
-        PaintRefresher.Register(this, av.alignment);
+        PaintRefresher.Register(this, av.getSequenceSetId());
         setBackground(Color.white);
     }
 
@@ -328,9 +328,34 @@ public class SeqCanvas extends JComponent
             return;
         }
 
-        img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);
-        gg = (Graphics2D) img.getGraphics();
-        gg.setFont(av.getFont());
+        if (img == null || imgWidth != img.getWidth() || imgHeight != img.getHeight())
+        {
+          try{
+            img = new BufferedImage(imgWidth, imgHeight,
+                                    BufferedImage.TYPE_INT_RGB);
+            gg = (Graphics2D) img.getGraphics();
+            gg.setFont(av.getFont());
+          }catch(OutOfMemoryError er)
+          {
+            System.gc();
+            System.out.println(er +" making image, SeqCanvas");
+            javax.swing.SwingUtilities.invokeLater(new Runnable()
+            {
+              public void run()
+              {
+                javax.swing.JOptionPane.showInternalMessageDialog(Desktop.
+                    desktop,
+                    "Out of memory creating alignment image!!"
+                    +
+                    "\nSee help files for increasing Java Virtual Machine memory."
+                    , "Out of memory",
+                    javax.swing.JOptionPane.WARNING_MESSAGE);
+              }
+            });
+
+            return;
+          }
+        }
 
         if (av.antiAlias)
           gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
@@ -393,7 +418,16 @@ public class SeqCanvas extends JComponent
     String getMask()
     {
       String mask = "00";
-      for (int i = av.alignment.getWidth(); i > 0; i /= 10)
+      int maxWidth = 0;
+      int tmp;
+      for(int i=0; i<av.alignment.getHeight(); i++)
+      {
+        tmp = av.alignment.getSequenceAt(i).getEnd();
+        if(tmp>maxWidth)
+          maxWidth = tmp;
+      }
+
+      for (int i = maxWidth; i > 0; i /= 10)
       {
         mask += "0";
       }
@@ -441,7 +475,7 @@ public class SeqCanvas extends JComponent
 
         int endx;
         int ypos = hgap;
-        int maxwidth = av.alignment.getWidth();
+        int maxwidth = av.alignment.getWidth()-1;
 
         if(av.hasHiddenColumns)
           maxwidth = av.getColumnSelection().findColumnPosition(maxwidth)-1;
@@ -529,14 +563,12 @@ public class SeqCanvas extends JComponent
                 annotations = new AnnotationPanel(av);
 
               annotations.drawComponent( (Graphics2D) g, startRes, endx+1);
-              g.translate(0, -cHeight - ypos);
+              g.translate(0, -cHeight - ypos -3);
             }
             g.setClip(clip);
             g.translate(-LABEL_WEST, 0);
 
             ypos += cHeight+getAnnotationHeight()+hgap;
-            if(av.showAnnotation)
-              ypos -= 3;
 
             startRes += cWidth;
         }
@@ -602,7 +634,7 @@ public class SeqCanvas extends JComponent
             g1.setColor(Color.blue);
 
             g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,
-                        0+offset,
+                        0 + offset,
                         (blockEnd - blockStart + 1) * av.charWidth - 1,
                         (endSeq - startSeq) * av.charHeight + offset);
           }
@@ -731,11 +763,11 @@ public class SeqCanvas extends JComponent
                     }
 
                     if ( (sx <= (endRes-startRes)*av.charWidth) &&
-                            group.getSequences(false).
+                            group.getSequences(null).
                             contains(av.alignment.getSequenceAt(i)))
                     {
                         if ((bottom == -1) &&
-                                !group.getSequences(false).contains(
+                                !group.getSequences(null).contains(
                                     av.alignment.getSequenceAt(i + 1)))
                         {
                             bottom = sy + av.charHeight;
@@ -744,7 +776,7 @@ public class SeqCanvas extends JComponent
                         if (!inGroup)
                         {
                             if (((top == -1) && (i == 0)) ||
-                                    !group.getSequences(false).contains(
+                                    !group.getSequences(null).contains(
                                         av.alignment.getSequenceAt(i - 1)))
                             {
                                 top = sy;