X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=aa98e76cdef6b2c32069cea96d313b2c5a9992be;hb=d1a58585358deed317674daeeac5fb5be66637ab;hp=50d1f7b9cefb7886242ba52801479f009dc8225c;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 50d1f7b..aa98e76 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,
@@ -529,7 +554,7 @@ 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);
@@ -600,10 +625,11 @@ public class SeqCanvas extends JComponent
           if(av.getShowHiddenMarkers())
           {
             g1.setColor(Color.blue);
+
             g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,
-                        startSeq + offset,
+                        0 + offset,
                         (blockEnd - blockStart + 1) * av.charWidth - 1,
-                        startSeq + (endSeq - startSeq) * av.charHeight + offset);
+                        (endSeq - startSeq) * av.charHeight + offset);
           }
 
           g1.translate( -screenY * av.charWidth, 0);
@@ -698,6 +724,7 @@ public class SeqCanvas extends JComponent
         int sy = -1;
         int ex = -1;
         int groupIndex = -1;
+        int visWidth = (endRes - startRes +1) * av.charWidth;
 
         if ((group == null) && (av.alignment.getGroups().size() > 0))
         {
@@ -705,6 +732,7 @@ public class SeqCanvas extends JComponent
             groupIndex = 0;
         }
 
+
         if (group != null)
         {
             do
@@ -722,7 +750,7 @@ public class SeqCanvas extends JComponent
                     ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -
                         1;
 
-                    if(sx+ex<0 || sx>imgWidth)
+                    if(sx+ex<0 || sx>visWidth)
                     {
                       continue;
                     }
@@ -769,10 +797,10 @@ public class SeqCanvas extends JComponent
                     {
                       if (inGroup)
                       {
-                        if (sx >= 0 && sx < imgWidth)
+                        if (sx >= 0 && sx < visWidth)
                           g.drawLine(sx, oldY, sx, sy);
 
-                        if (sx + ex < imgWidth)
+                        if (sx + ex < visWidth)
                           g.drawLine(sx + ex, oldY, sx + ex, sy);
 
                         if (sx < 0)
@@ -781,8 +809,8 @@ public class SeqCanvas extends JComponent
                           sx = 0;
                         }
 
-                        if (sx + ex > imgWidth)
-                          ex = imgWidth;
+                        if (sx + ex > visWidth)
+                          ex = visWidth;
 
                         else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
                           ex = (endRes - startRes + 1) * av.charWidth;
@@ -807,10 +835,10 @@ public class SeqCanvas extends JComponent
                 if (inGroup)
                 {
                   sy = offset + ( (i - startSeq) * av.charHeight);
-                  if (sx >= 0 && sx < imgWidth)
+                  if (sx >= 0 && sx < visWidth)
                     g.drawLine(sx, oldY, sx, sy);
 
-                  if (sx + ex < imgWidth)
+                  if (sx + ex < visWidth)
                     g.drawLine(sx + ex, oldY, sx + ex, sy);
 
                   if (sx < 0)
@@ -819,8 +847,8 @@ public class SeqCanvas extends JComponent
                     sx = 0;
                   }
 
-                  if (sx + ex > imgWidth)
-                    ex = imgWidth;
+                  if (sx + ex > visWidth)
+                    ex = visWidth;
                   else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
                     ex = (endRes - startRes + 1) * av.charWidth;
 
@@ -841,6 +869,8 @@ public class SeqCanvas extends JComponent
 
                 groupIndex++;
 
+                g.setStroke(new BasicStroke());
+
                 if (groupIndex >= av.alignment.getGroups().size())
                 {
                     break;
@@ -848,7 +878,7 @@ public class SeqCanvas extends JComponent
 
                 group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
 
-                g.setStroke(new BasicStroke());
+
             }
             while (groupIndex < av.alignment.getGroups().size());