X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=d7f2d5ed9790fd89df70203c4855e4244ccf656e;hb=ad66d7d56acd4063655df6a845e217683b88523e;hp=3ae0394f4ce9c62d72a28509013407363c101e41;hpb=2267fd4e6dd5e716ba5d89aef9c72c0bd21c6c0b;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 3ae0394..d7f2d5e 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -28,6 +28,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceI;
 import jalview.structure.StructureSelectionManager;
+import jalview.viewmodel.ViewportListenerI;
 import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BorderLayout;
@@ -42,10 +43,11 @@ import java.awt.event.AdjustmentEvent;
 import java.awt.event.AdjustmentListener;
 import java.awt.event.ComponentAdapter;
 import java.awt.event.ComponentEvent;
+import java.beans.PropertyChangeEvent;
 import java.util.List;
 
 public class AlignmentPanel extends Panel implements AdjustmentListener,
-        AlignmentViewPanel
+        AlignmentViewPanel, ViewportListenerI
 {
 
   public AlignViewport av;
@@ -131,7 +133,26 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       @Override
       public void componentResized(ComponentEvent evt)
       {
-        setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
+        // reset the viewport ranges when the alignment panel is resized
+        // in particular, this initialises the end residue value when Jalview
+        // is initialised
+        if (av.getWrapAlignment())
+        {
+          int widthInRes = seqPanel.seqCanvas
+                  .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+          vpRanges.setViewportWidth(widthInRes);
+        }
+        else
+        {
+          int widthInRes = seqPanel.seqCanvas.getWidth()
+                  / av.getCharWidth();
+          int heightInSeq = seqPanel.seqCanvas.getHeight()
+                  / av.getCharHeight();
+
+          vpRanges.setViewportWidth(widthInRes);
+          vpRanges.setViewportHeight(heightInSeq);
+        }
+        // setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
         if (getSize().height > 0
                 && annotationPanelHolder.getSize().height > 0)
         {
@@ -164,6 +185,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
         }
       }
     });
+    av.getRanges().addPropertyChangeListener(this);
   }
 
   @Override
@@ -230,11 +252,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     annotationPanel.repaint();
     validate();
     repaint();
-
-    if (overviewPanel != null)
-    {
-      overviewPanel.updateOverviewImage();
-    }
   }
 
   public void setIdWidth(int w, int h)
@@ -508,28 +525,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     }
     else
     {
-      scrollToWrappedVisible(start);
-    }
-    if (redrawOverview && overviewPanel != null)
-    {
-      overviewPanel.setBoxPosition();
+      vpRanges.scrollToWrappedVisible(start);
     }
+
     paintAlignment(redrawOverview);
     return true;
   }
 
-  void scrollToWrappedVisible(int res)
-  {
-    int cwidth = seqPanel.seqCanvas
-            .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
-    if (res <= vpRanges.getStartRes()
-            || res >= (vpRanges.getStartRes() + cwidth))
-    {
-      vscroll.setValue(res / cwidth);
-      vpRanges.setStartRes(vscroll.getValue() * cwidth);
-    }
-  }
-
   public OverviewPanel getOverviewPanel()
   {
     return overviewPanel;
@@ -671,126 +673,77 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
   int vextent = 0;
 
-  // return value is true if the scroll is valid
-  public boolean scrollUp(boolean up)
+  public void setScrollValues(int x, int y)
   {
-    if (up)
+    if (av.getWrapAlignment())
     {
-      if (vscroll.getValue() < 1)
-      {
-        return false;
-      }
-      setScrollValues(hscroll.getValue(), vscroll.getValue() - 1);
+      setScrollingForWrappedPanel(x);
     }
     else
     {
-      if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
-      {
-        return false;
-      }
-      setScrollValues(hscroll.getValue(), vscroll.getValue() + 1);
-    }
 
-    repaint();
-    return true;
-  }
+      int width = av.getAlignment().getWidth();
+      int height = av.getAlignment().getHeight();
 
-  public boolean scrollRight(boolean right)
-  {
-    if (!right)
-    {
-      if (hscroll.getValue() < 1)
+      if (av.hasHiddenColumns())
       {
-        return false;
+        width = av.getColumnSelection().findColumnPosition(width);
       }
-      setScrollValues(hscroll.getValue() - 1, vscroll.getValue());
-    }
-    else
-    {
-      if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
+      if (x < 0)
       {
-        return false;
+        x = 0;
       }
-      setScrollValues(hscroll.getValue() + 1, vscroll.getValue());
-    }
 
-    repaint();
-    return true;
-  }
-
-  public void setScrollValues(int x, int y)
-  {
-    int width = av.getAlignment().getWidth();
-    int height = av.getAlignment().getHeight();
-
-    if (av.hasHiddenColumns())
-    {
-      width = av.getColumnSelection().findColumnPosition(width);
-    }
-    if (x < 0)
-    {
-      x = 0;
-    }
-
-
-    hextent = seqPanel.seqCanvas.getSize().width / av.getCharWidth();
-    vextent = seqPanel.seqCanvas.getSize().height / av.getCharHeight();
-
-    if (hextent > width)
-    {
-      hextent = width;
-    }
+      hextent = seqPanel.seqCanvas.getSize().width / av.getCharWidth();
+      vextent = seqPanel.seqCanvas.getSize().height / av.getCharHeight();
 
-    if (vextent > height)
-    {
-      vextent = height;
-    }
+      if (hextent > width)
+      {
+        hextent = width;
+      }
 
-    if ((hextent + x) > width)
-    {
-      System.err.println("hextent was " + hextent + " and x was " + x);
+      if (vextent > height)
+      {
+        vextent = height;
+      }
 
-      x = width - hextent;
-    }
+      if ((hextent + x) > width)
+      {
+        System.err.println("hextent was " + hextent + " and x was " + x);
 
-    if ((vextent + y) > height)
-    {
-      y = height - vextent;
-    }
+        x = width - hextent;
+      }
 
-    if (y < 0)
-    {
-      y = 0;
-    }
+      if ((vextent + y) > height)
+      {
+        y = height - vextent;
+      }
 
-    if (x < 0)
-    {
-      System.err.println("x was " + x);
-      x = 0;
-    }
+      if (y < 0)
+      {
+        y = 0;
+      }
 
-    vpRanges.setStartSeq(y);
-    vpRanges.setEndSeq(y + vextent);
-    vpRanges.setStartRes(x);
-    vpRanges.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av
-            .getCharWidth())) - 1);
+      if (x < 0)
+      {
+        System.err.println("x was " + x);
+        x = 0;
+      }
 
-    hscroll.setValues(x, hextent, 0, width);
-    vscroll.setValues(y, vextent, 0, height);
+      hscroll.setValues(x, hextent, 0, width);
+      vscroll.setValues(y, vextent, 0, height);
 
-    if (overviewPanel != null)
-    {
-      overviewPanel.setBoxPosition();
+      sendViewPosition();
     }
-    sendViewPosition();
-
   }
 
   @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     int oldX = vpRanges.getStartRes();
+    int oldwidth = vpRanges.getViewportWidth();
     int oldY = vpRanges.getStartSeq();
+    int oldheight = vpRanges.getViewportHeight();
 
     if (evt == null || evt.getSource() == apvscroll)
     {
@@ -804,9 +757,16 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     if (evt == null || evt.getSource() == hscroll)
     {
       int x = hscroll.getValue();
-      vpRanges.setStartRes(x);
-      vpRanges.setEndRes(x + seqPanel.seqCanvas.getSize().width
-              / av.getCharWidth() - 1);
+      int width = seqPanel.seqCanvas.getWidth() / av.getCharWidth();
+
+      // if we're scrolling to the position we're already at, stop
+      // this prevents infinite recursion of events when the scroll/viewport
+      // ranges values are the same
+      if ((x == oldX) && (width == oldwidth))
+      {
+        return;
+      }
+      vpRanges.setViewportStartAndWidth(x, width);
     }
 
     if (evt == null || evt.getSource() == vscroll)
@@ -815,67 +775,84 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       if (av.getWrapAlignment())
       {
         int rowSize = seqPanel.seqCanvas
-                .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
-        vpRanges.setStartRes(vscroll.getValue() * rowSize);
-        vpRanges.setEndRes((vscroll.getValue() + 1) * rowSize);
+                .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+
+        // if we're scrolling to the position we're already at, stop
+        // this prevents infinite recursion of events when the scroll/viewport
+        // ranges values are the same
+        if ((offy * rowSize == oldX) && (oldwidth == rowSize))
+        {
+          return;
+        }
+        else if (offy > -1)
+        {
+          vpRanges.setViewportStartAndWidth(offy * rowSize, rowSize);
+        }
       }
       else
       {
-        vpRanges.setStartSeq(offy);
-        vpRanges.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
-                / av.getCharHeight() - 1);
-      }
-    }
+        int height = seqPanel.seqCanvas.getHeight() / av.getCharHeight();
 
-    if (overviewPanel != null)
-    {
-      overviewPanel.setBoxPosition();
+        // if we're scrolling to the position we're already at, stop
+        // this prevents infinite recursion of events when the scroll/viewport
+        // ranges values are the same
+        if ((offy == oldY) && (height == oldheight))
+        {
+          return;
+        }
+        vpRanges.setViewportStartAndHeight(offy, height);
+      }
     }
 
-    int scrollX = vpRanges.getStartRes() - oldX;
-    int scrollY = vpRanges.getStartSeq() - oldY;
+    /*    if (overviewPanel != null)
+        {
+          overviewPanel.setBoxPosition();
+        }
 
+        int scrollX = vpRanges.getStartRes() - oldX;
+        int scrollY = vpRanges.getStartSeq() - oldY;
+    */
     if (av.getWrapAlignment() || !fastPaint || av.MAC)
     {
       repaint();
     }
-    else
-    {
-      // Make sure we're not trying to draw a panel
-      // larger than the visible window
-      if (scrollX > vpRanges.getEndRes() - vpRanges.getStartRes())
-      {
-        scrollX = vpRanges.getEndRes() - vpRanges.getStartRes();
-      }
-      else if (scrollX < vpRanges.getStartRes() - vpRanges.getEndRes())
-      {
-        scrollX = vpRanges.getStartRes() - vpRanges.getEndRes();
-      }
-
-      idPanel.idCanvas.fastPaint(scrollY);
-      seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
-
-      scalePanel.repaint();
-      if (av.isShowAnnotation())
-      {
-        annotationPanel.fastPaint(vpRanges.getStartRes() - oldX);
-      }
-    }
+    /*    else
+        {
+          // Make sure we're not trying to draw a panel
+          // larger than the visible window
+          if (scrollX > vpRanges.getEndRes() - vpRanges.getStartRes())
+          {
+            scrollX = vpRanges.getEndRes() - vpRanges.getStartRes();
+          }
+          else if (scrollX < vpRanges.getStartRes() - vpRanges.getEndRes())
+          {
+            scrollX = vpRanges.getStartRes() - vpRanges.getEndRes();
+          }
+
+          idPanel.idCanvas.fastPaint(scrollY);
+          seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
+
+          scalePanel.repaint();
+          if (av.isShowAnnotation())
+          {
+            annotationPanel.fastPaint(vpRanges.getStartRes() - oldX);
+          }
+        }*/
     sendViewPosition();
 
     /*
      * If there is one, scroll the (Protein/cDNA) complementary alignment to
      * match, unless we are ourselves doing that.
      */
-    if (isFollowingComplementScroll())
-    {
-      setFollowingComplementScroll(false);
-    }
-    else
-    {
-      AlignmentPanel ap = getComplementPanel();
-      av.scrollComplementaryAlignment(ap);
-    }
+    /*    if (isFollowingComplementScroll())
+        {
+          setFollowingComplementScroll(false);
+        }
+        else
+        {
+          AlignmentPanel ap = getComplementPanel();
+          av.scrollComplementaryAlignment(ap);
+        }*/
 
   }
 
@@ -927,7 +904,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
      * This is like AlignmentI.findIndex(seq) but here we are matching the
      * dataset sequence not the aligned sequence
      */
-    int sequenceIndex = 0;
     boolean matched = false;
     for (SequenceI seq : seqs)
     {
@@ -936,7 +912,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
         matched = true;
         break;
       }
-      sequenceIndex++;
     }
     if (!matched)
     {
@@ -1003,30 +978,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       idPanel.idCanvas.setSize(d.width, canvasHeight);
     }
 
-    if (av.getWrapAlignment())
-    {
-      int maxwidth = av.getAlignment().getWidth();
-
-      if (av.hasHiddenColumns())
-      {
-        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
-      }
-
-      int canvasWidth = seqPanel.seqCanvas
-              .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
-
-      if (canvasWidth > 0)
-      {
-        int max = maxwidth / canvasWidth;
-        vscroll.setMaximum(1 + max);
-        vscroll.setUnitIncrement(1);
-        vscroll.setVisibleAmount(1);
-      }
-    }
-    else
-    {
-      setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
-    }
+    setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
 
     seqPanel.seqCanvas.repaint();
     idPanel.idCanvas.repaint();
@@ -1042,6 +994,36 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
   }
 
+  /*
+   * Set vertical scroll bar parameters for wrapped panel
+   * @param res 
+   *    the residue to scroll to
+   */
+  private void setScrollingForWrappedPanel(int res)
+  {
+    // get the width of the alignment in residues
+    int maxwidth = av.getAlignment().getWidth();
+    if (av.hasHiddenColumns())
+    {
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+    }
+
+    // get the width of the canvas in residues
+    int canvasWidth = seqPanel.seqCanvas
+            .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
+    if (canvasWidth > 0)
+    {
+      // position we want to scroll to is number of canvasWidth's to get there
+      int current = res / canvasWidth;
+
+      // max scroll position: add one because extent is 1 and scrollbar value
+      // can only be set to at most max - extent
+      int max = maxwidth / canvasWidth + 1;
+      vscroll.setUnitIncrement(1);
+      vscroll.setValues(current, 1, 0, max);
+    }
+  }
+
   protected Panel sequenceHolderPanel = new Panel();
 
   protected Scrollbar vscroll = new Scrollbar();
@@ -1187,4 +1169,27 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     return this.followingComplementScroll;
   }
 
+  @Override
+  /**
+   * Property change event fired when a change is made to the viewport ranges 
+   * object associated with this alignment panel's viewport
+   */
+  public void propertyChange(PropertyChangeEvent evt)
+  {
+    // update this panel's scroll values based on the new viewport ranges values
+    int x = vpRanges.getStartRes();
+    int y = vpRanges.getStartSeq();
+    setScrollValues(x, y);
+
+    // now update any complementary alignment (its viewport ranges object
+    // is different so does not get automatically updated)
+    if (isFollowingComplementScroll())
+    {
+      setFollowingComplementScroll(false);
+      av.scrollComplementaryAlignment(getComplementPanel());
+      setFollowingComplementScroll(true);
+    }
+
+  }
+
 }