X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=c5adccbf39ca08be6c60887ab44ade8245b10f31;hb=d15e991c6f3930ab77e3082b97a18e5ef7f3b571;hp=60e8cb1a7ead8319ca565beabc1e6ab870a23d5d;hpb=b949d2a0b53aa810d1f3dbfad21f5f0324bbf44c;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 60e8cb1..c5adccb 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -177,6 +177,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     Dimension d = calculateIdWidth();
     d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
     alabels.setSize(d.width + 4, ap);
+    
     idPanel.idCanvas.setSize(d);
     hscrollFillerPanel.setSize(d);
     
@@ -281,6 +282,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
   public boolean scrollToPosition(SearchResults results,
           boolean redrawOverview)
   {
+	  
     // do we need to scroll the panel?
     if (results != null && results.getSize() > 0)
     {
@@ -300,10 +302,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
       }
       if (av.applet.debug) {
         // DEBUG
-        System.out.println("DEBUG: scroll: start=" + r[0]
+        /*System.out.println("DEBUG: scroll: start=" + r[0]
                 + " av.getStartRes()=" + av.getStartRes() + " end=" + r[1]
                 + " seq.end=" + seq.getEnd() + " av.getEndRes()="
                 + av.getEndRes() + " hextent=" + hextent);
+         */
       }
       int start = r[0];
       int end = r[1];
@@ -321,7 +324,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
   }
   public boolean scrollTo(int ostart, int end, int seqIndex, boolean scrollToNearest, boolean redrawOverview)
   {
-    int start=-1;
+	    int startv, endv, starts, ends, width;
+
+	  int start=-1;
     if (av.hasHiddenColumns)
     {
       start = av.getColumnSelection().findColumnPosition(ostart);
@@ -333,10 +338,37 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
           // don't scroll - position isn't visible
           return false;
         }
-        }
       }
-      if (!av.wrapAlignment)
-      {
+    }
+    else
+    {
+      start = ostart;
+    }
+    if (!av.wrapAlignment)
+    {
+    	  /*
+    	  int spos=av.getStartRes(),sqpos=av.getStartSeq();
+          if ((startv = av.getStartRes()) >= start)
+          {
+        	  spos=start-1;
+//        	  seqIn
+//            setScrollValues(start - 1, seqIndex);
+          }
+          else if ((endv = av.getEndRes()) <= end)
+          {
+//            setScrollValues(spos=startv + 1 + end - endv, seqIndex);
+        	  spos=startv + 1 + end - endv;
+          }
+          else if ((starts = av.getStartSeq()) > seqIndex)
+          {
+            setScrollValues(av.getStartRes(), seqIndex);
+          }
+          else if ((ends = av.getEndSeq()) <= seqIndex)
+          {
+            setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+          }
+
+    	  /* */
         if ((av.getStartRes() > end)
                 || (av.getEndRes() < start)
                 || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
@@ -358,8 +390,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
               seqIndex = 0;
             }
           }
+          // System.out.println("trying to scroll to: "+start+" "+seqIndex);
           setScrollValues(start, seqIndex);
-        }
+        }/**/
       }
       else
       {
@@ -422,7 +455,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     apvscroll.addNotify();
     hscroll.addNotify();
     validate();
-    repaint();
+    paintAlignment(true);
   }
   /**
    * calculate the annotation dimensions and refresh slider values accordingly.
@@ -462,6 +495,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     annotationSpaceFillerHolder.setSize(new Dimension(e.width, height));
     annotationPanelHolder.setSize(new Dimension(d.width, height));
     seqPanelHolder.setSize(d.width,seqandannot-height);
+    seqPanel.seqCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
     int s=apvscroll.getValue();
     if (s>mheight-height)
     {
@@ -561,9 +595,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     {
       width = av.getColumnSelection().findColumnPosition(width);
     }
-
-    av.setStartRes(x);
-    av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
+    if (x<0) { x = 0; };
 
     hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
     vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
@@ -580,6 +612,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
 
     if ((hextent + x) > width)
     {
+      System.err.println("hextent was "+hextent+" and x was "+x);
+
       x = width - hextent;
     }
 
@@ -595,6 +629,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
 
     if (x < 0)
     {
+      System.err.println("x was "+x);
       x = 0;
     }
 
@@ -607,6 +642,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     }
 
     av.setEndSeq(endSeq);
+    av.setStartRes(x);
+    av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
+
     hscroll.setValues(x, hextent, 0, width);
     vscroll.setValues(y, vextent, 0, height);
 
@@ -941,5 +979,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
   {
     return StructureSelectionManager.getStructureSelectionManager(av.applet);
   }
+  @Override
+  public void raiseOOMWarning(String string, OutOfMemoryError error)
+  {
+    // TODO: JAL-960
+    System.err.println("Out of memory whilst '"+string+"'");
+    error.printStackTrace();
+  }
 
 }