X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=fae6dfc9fcd149b2d14ac019c5abb6eb31591050;hb=7e129811d6ff01074428462284dffc2a6c2395a4;hp=d1b9350782948a6fd8675e8772b6e58a3c62c6e3;hpb=3402d066dbd7667cd805e6d78ac5eca66e237c72;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index d1b9350..fae6dfc 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -18,8 +18,6 @@
  */
 package jalview.gui;
 
-import jalview.analysis.*;
-
 import jalview.datamodel.*;
 
 import jalview.jbgui.*;
@@ -151,12 +149,30 @@ public class AlignmentPanel extends GAlignmentPanel
                 av.charHeight + fm.getDescent()));
 
         idPanel.idCanvas.gg = null;
+        seqPanel.seqCanvas.img = null;
         annotationPanel.adjustPanelHeight();
 
         Dimension d = calculateIdWidth();
         d.setSize(d.width + 4, d.height);
         idPanel.idCanvas.setPreferredSize(d);
         hscrollFillerPanel.setPreferredSize(d);
+
+        if (av.getWrapAlignment())
+        {
+          int max = av.alignment.getWidth() /
+              seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+          vscroll.setMaximum(max);
+          vscroll.setUnitIncrement(1);
+          vscroll.setVisibleAmount(1);
+        }
+        else
+        {
+          setScrollValues(av.getStartRes(), av.getStartSeq());
+        }
+
+        if(overviewPanel!=null)
+          overviewPanel.setBoxPosition();
+
         repaint();
     }
 
@@ -167,16 +183,9 @@ public class AlignmentPanel extends GAlignmentPanel
      */
     public Dimension calculateIdWidth()
     {
-        Graphics g = this.getGraphics();
-
-        if (g == null)
-        {
-            javax.swing.JFrame f = new javax.swing.JFrame();
-            f.addNotify();
-            g = f.getGraphics();
-        }
+      Container c = new Container();
 
-        FontMetrics fm = g.getFontMetrics(av.font);
+        FontMetrics fm = c.getFontMetrics(av.font);
         AlignmentI al = av.getAlignment();
 
         int i = 0;
@@ -209,7 +218,7 @@ public class AlignmentPanel extends GAlignmentPanel
 
         if (al.getAlignmentAnnotation() != null)
         {
-            fm = g.getFontMetrics(alabels.getFont());
+            fm = c.getFontMetrics(alabels.getFont());
 
             while (i < al.getAlignmentAnnotation().length)
             {
@@ -290,43 +299,28 @@ public class AlignmentPanel extends GAlignmentPanel
      */
     public void setWrapAlignment(boolean wrap)
     {
+        av.startSeq = 0;
         scalePanelHolder.setVisible(!wrap);
         hscroll.setVisible(!wrap);
         idwidthAdjuster.setVisible(!wrap);
 
-        av.setShowAnnotation(!wrap);
-        annotationScroller.setVisible(!wrap);
-        annotationSpaceFillerHolder.setVisible(!wrap);
-        idSpaceFillerPanel1.setVisible(!wrap);
-
-        repaint();
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void setColourScheme()
-    {
-        ColourSchemeI cs = av.getGlobalColourScheme();
-
-        if (av.getConservationSelected())
-        {
-            Alignment al = (Alignment) av.getAlignment();
-            Conservation c = new Conservation("All",
-                    ResidueProperties.propHash, 3, al.getSequences(), 0,
-                    al.getWidth());
-
-            c.calculate();
-            c.verdict(false, av.ConsPercGaps);
+       if(wrap)
+       {
+         annotationScroller.setVisible(false);
+         annotationSpaceFillerHolder.setVisible(false);
+       }
+       else if(av.showAnnotation)
+       {
+         annotationScroller.setVisible(true);
+         annotationSpaceFillerHolder.setVisible(true);
+       }
 
-            ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
-
-            av.setGlobalColourScheme(ccs);
-        }
+       idSpaceFillerPanel1.setVisible(!wrap);
 
         repaint();
     }
 
+
     // return value is true if the scroll is valid
     public boolean scrollUp(boolean up)
     {
@@ -439,14 +433,6 @@ public class AlignmentPanel extends GAlignmentPanel
         vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
     }
 
-    public void this_mouseWheelMoved(MouseWheelEvent e)
-    {
-      if(e.getWheelRotation()>0)
-        scrollUp(false);
-      else
-        scrollUp(true);
-    }
-
 
     /**
      * DOCUMENT ME!
@@ -455,6 +441,7 @@ public class AlignmentPanel extends GAlignmentPanel
      */
     public void adjustmentValueChanged(AdjustmentEvent evt)
     {
+
         int oldX = av.getStartRes();
         int oldY = av.getStartSeq();
 
@@ -489,21 +476,28 @@ public class AlignmentPanel extends GAlignmentPanel
             overviewPanel.setBoxPosition();
         }
 
-        if (av.getWrapAlignment() || !fastPaint)
+        int xShift = av.getStartRes() - oldX;
+        int yShift = av.getStartSeq() - oldY;
+
+        if ( (xShift == 0 && yShift == 0) ||
+            (Math.abs(xShift) > av.getEndRes() - av.getStartRes()
+             || Math.abs(yShift) > av.getEndSeq() - av.getStartSeq())
+             || av.getWrapAlignment()
+             || !fastPaint)
         {
-            repaint();
+          // Either no shift at all, or shift greater than visible amount
+          repaint();
         }
         else
         {
-            idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
-            seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
-                av.getStartSeq() - oldY);
+            idPanel.idCanvas.fastPaint(yShift);
+            seqPanel.seqCanvas.fastPaint(xShift, yShift);
 
             scalePanel.repaint();
 
             if (av.getShowAnnotation())
             {
-                annotationPanel.fastPaint(av.getStartRes() - oldX);
+                annotationPanel.fastPaint(xShift);
             }
         }
     }