X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=db3cb8c2837c28018dce334d8fddacec76b7e958;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=e0c327f769e17409f8dbf9f3df67102b55bc068a;hpb=49057b644ae4dc904a3245b695ba86678ac01ede;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index e0c327f..db3cb8c 100755
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -24,7 +24,8 @@ import java.awt.event.*;
 
 import jalview.datamodel.*;
 
-public class AlignmentPanel extends Panel implements AdjustmentListener
+public class AlignmentPanel
+    extends Panel implements AdjustmentListener
 {
 
   AlignViewport av;
@@ -40,8 +41,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
 
-  boolean MAC = false;
-
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
     try
@@ -53,9 +52,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       e.printStackTrace();
     }
 
-    if(System.getProperty("os.name").startsWith("Mac"))
-      MAC = true;
-
     alignFrame = af;
     this.av = av;
     seqPanel = new SeqPanel(av, this);
@@ -63,13 +59,15 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     scalePanel = new ScalePanel(av, this);
     idwidthAdjuster = new IdwidthAdjuster(this);
     annotationPanel = new AnnotationPanel(this);
+
+    sequenceHolderPanel.add(annotationPanel, BorderLayout.SOUTH);
+
     alabels = new AnnotationLabels(this);
 
     setAnnotationVisible(av.showAnnotation);
 
     idPanelHolder.add(idPanel, BorderLayout.CENTER);
     idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
-    annotationScroller.add(annotationPanel);
     annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
     seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
@@ -93,39 +91,70 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     idPanel.idCanvas.setSize(d);
 
     hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
-    annotationScroller.setSize(annotationPanel.getSize());
 
     idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
     annotationSpaceFillerHolder.setSize(d.width,
                                         annotationPanel.getSize().height);
     alabels.setSize(d.width, annotationPanel.getSize().height);
 
+    final AlignmentPanel ap = this;
+    av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
+    {
+      public void propertyChange(java.beans.PropertyChangeEvent evt)
+      {
+        if (evt.getPropertyName().equals("alignment"))
+        {
+          PaintRefresher.Refresh(ap,
+                                 av.getSequenceSetId(),
+                                 true,
+                                 true);
+          alignmentChanged();
+        }
+      }
+    });
+
   }
 
+  public void alignmentChanged()
+  {
+    av.alignmentChanged(this);
+
+    if (overviewPanel != null)
+    {
+      overviewPanel.updateOverviewImage();
+    }
+
+    alignFrame.updateEditMenuBar();
+
+    repaint();
+  }
 
   public void fontChanged()
   {
     // set idCanvas bufferedImage to null
     // to prevent drawing old image
-    idPanel.idCanvas.image =null;
+    idPanel.idCanvas.image = null;
     FontMetrics fm = getFontMetrics(av.getFont());
 
     scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
     idwidthAdjuster.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
 
+    annotationPanel.image = null;
     int ap = annotationPanel.adjustPanelHeight();
     annotationPanel.repaint();
     Dimension d = calculateIdWidth();
     d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
-    alabels.setSize(d.width+4, ap );
+    alabels.setSize(d.width + 4, ap);
     idPanel.idCanvas.setSize(d);
     hscrollFillerPanel.setSize(d);
 
     validate();
     repaint();
 
-    if(overviewPanel!=null)
-          overviewPanel.updateOverviewImage();
+    if (overviewPanel != null)
+    {
+      overviewPanel.updateOverviewImage();
+    }
   }
 
   public void setIdWidth(int w, int h)
@@ -138,16 +167,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
 
   Dimension calculateIdWidth()
   {
-    Frame frame = new Frame();
-    frame.addNotify();
-    Graphics g = frame.getGraphics();
-    if (g == null)
+    if (av.nullFrame == null)
     {
-      Frame f = new Frame();
-      f.addNotify();
-      g = f.getGraphics();
+      av.nullFrame = new Frame();
+      av.nullFrame.addNotify();
     }
 
+    Graphics g = av.nullFrame.getGraphics();
+
     FontMetrics fm = g.getFontMetrics(av.font);
     AlignmentI al = av.getAlignment();
 
@@ -170,7 +197,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     i = 0;
     if (al.getAlignmentAnnotation() != null)
     {
-      fm = g.getFontMetrics(frame.getFont());
+      fm = g.getFontMetrics(av.nullFrame.getFont());
       while (i < al.getAlignmentAnnotation().length)
       {
         String label = al.getAlignmentAnnotation()[i].label;
@@ -189,7 +216,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
   {
     seqPanel.seqCanvas.highlightSearchResults(results);
 
-   // do we need to scroll the panel?
+    // do we need to scroll the panel?
     if (results != null)
     {
       SequenceI seq = results.getResultSequence(0);
@@ -197,41 +224,50 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       int start = seq.findIndex(results.getResultStart(0)) - 1;
       int end = seq.findIndex(results.getResultEnd(0)) - 1;
 
-        if(!av.wrapAlignment)
+      if (!av.wrapAlignment)
+      {
+        if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||
+            ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
         {
-          if ( (av.getStartRes() > end)  || (av.getEndRes() < start) ||
-             ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+          if (start > av.alignment.getWidth() - hextent)
           {
-            if (start > av.alignment.getWidth() - hextent)
-            {
-              start = av.alignment.getWidth() - hextent;
-              if (start < 0)
-                start = 0;
-            }
-            if (seqIndex > av.alignment.getHeight() - vextent)
+            start = av.alignment.getWidth() - hextent;
+            if (start < 0)
             {
-              seqIndex = av.alignment.getHeight() - vextent;
-              if (seqIndex < 0)
-                seqIndex = 0;
+              start = 0;
             }
-            setScrollValues(start, seqIndex);
           }
-        }
-        else
-        {
-          int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
-              seqCanvas.getSize().width);
-          if (start < av.getStartRes() || start > (av.getStartRes() + cwidth))
+          if (seqIndex > av.alignment.getHeight() - vextent)
           {
-            vscroll.setValue(start / cwidth);
-            av.startRes = vscroll.getValue() * cwidth;
+            seqIndex = av.alignment.getHeight() - vextent;
+            if (seqIndex < 0)
+            {
+              seqIndex = 0;
+            }
           }
+          setScrollValues(start, seqIndex);
         }
+      }
+      else
+      {
+        scrollToWrappedVisible(start);
+      }
     }
 
     repaint();
   }
 
+  void scrollToWrappedVisible(int res)
+  {
+    int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
+        getSize().width);
+    if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
+    {
+      vscroll.setValue(res / cwidth);
+      av.startRes = vscroll.getValue() * cwidth;
+    }
+  }
+
   public OverviewPanel getOverviewPanel()
   {
     return overviewPanel;
@@ -247,7 +283,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     if (!av.wrapAlignment)
     {
       annotationSpaceFillerHolder.setVisible(b);
-      annotationScroller.setVisible(b);
+      annotationPanel.setVisible(b);
     }
     validate();
     repaint();
@@ -256,34 +292,32 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
   public void setWrapAlignment(boolean wrap)
   {
     av.startSeq = 0;
+    av.startRes = 0;
     scalePanelHolder.setVisible(!wrap);
 
-
     hscroll.setVisible(!wrap);
     idwidthAdjuster.setVisible(!wrap);
 
     if (wrap)
     {
-      annotationScroller.setVisible(false);
+      annotationPanel.setVisible(false);
       annotationSpaceFillerHolder.setVisible(false);
     }
     else if (av.showAnnotation)
     {
-      annotationScroller.setVisible(true);
+      annotationPanel.setVisible(true);
       annotationSpaceFillerHolder.setVisible(true);
     }
 
-
     idSpaceFillerPanel1.setVisible(!wrap);
 
-    fontChanged();//This is so that the scalePanel is resized correctly
+    fontChanged(); //This is so that the scalePanel is resized correctly
 
     validate();
     repaint();
 
   }
 
-
   int hextent = 0;
   int vextent = 0;
 
@@ -296,7 +330,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       {
         return false;
       }
-      setScrollValues(hscroll.getValue(), vscroll.getValue()-1);
+      setScrollValues(hscroll.getValue(), vscroll.getValue() - 1);
     }
     else
     {
@@ -304,22 +338,22 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       {
         return false;
       }
-      setScrollValues(hscroll.getValue(), vscroll.getValue()+1);
+      setScrollValues(hscroll.getValue(), vscroll.getValue() + 1);
     }
+
     repaint();
     return true;
   }
 
   public boolean scrollRight(boolean right)
   {
-
-    if (right)
+    if (!right)
     {
       if (hscroll.getValue() < 1)
       {
         return false;
       }
-      setScrollValues(hscroll.getValue()-1, vscroll.getValue());
+      setScrollValues(hscroll.getValue() - 1, vscroll.getValue());
     }
     else
     {
@@ -327,7 +361,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       {
         return false;
       }
-      setScrollValues(hscroll.getValue()+1, vscroll.getValue());
+      setScrollValues(hscroll.getValue() + 1, vscroll.getValue());
     }
 
     repaint();
@@ -336,30 +370,38 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
 
   public void setScrollValues(int x, int y)
   {
+    int width = av.alignment.getWidth();
+    int height = av.alignment.getHeight();
+
+    if (av.hasHiddenColumns)
+    {
+      width = av.getColumnSelection().findColumnPosition(width);
+    }
+
     av.setStartRes(x);
-    av.setStartSeq(y);
-    av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() - 1);
+    av.setEndRes( (x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
 
     hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
     vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
 
-    if (hextent > av.alignment.getWidth())
+    if (hextent > width)
     {
-      hextent = av.alignment.getWidth();
+      hextent = width;
     }
-    if (vextent > av.alignment.getHeight())
+
+    if (vextent > height)
     {
-      vextent = av.alignment.getHeight();
+      vextent = height;
     }
 
-    if (hextent + x > av.getAlignment().getWidth())
+    if ( (hextent + x) > width)
     {
-      x = av.getAlignment().getWidth() - hextent;
+      x = width - hextent;
     }
 
-    if (vextent + y > av.getAlignment().getHeight())
+    if ( (vextent + y) > height)
     {
-      y = av.getAlignment().getHeight() - vextent;
+      y = height - vextent;
     }
 
     if (y < 0)
@@ -372,6 +414,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       x = 0;
     }
 
+    av.setStartSeq(y);
+
     int endSeq = y + vextent;
     if (endSeq > av.alignment.getHeight())
     {
@@ -379,8 +423,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     }
 
     av.setEndSeq(endSeq);
-    hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
-    vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
+    hscroll.setValues(x, hextent, 0, width);
+    vscroll.setValues(y, vextent, 0, height);
+
+    if (overviewPanel != null)
+    {
+      overviewPanel.setBoxPosition();
+    }
+
   }
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
@@ -388,8 +438,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     int oldX = av.getStartRes();
     int oldY = av.getStartSeq();
 
-
-    if (evt==null || evt.getSource() == hscroll)
+    if (evt == null || evt.getSource() == hscroll)
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
@@ -397,8 +446,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
                    1);
     }
 
-
-    if (evt==null || evt.getSource() == vscroll)
+    if (evt == null || evt.getSource() == vscroll)
     {
       int offy = vscroll.getValue();
       if (av.getWrapAlignment())
@@ -424,7 +472,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     int scrollX = av.startRes - oldX;
     int scrollY = av.startSeq - oldY;
 
-    if (av.getWrapAlignment() || !fastPaint || MAC)
+    if (av.getWrapAlignment() || !fastPaint || av.MAC)
     {
       repaint();
     }
@@ -432,12 +480,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     {
       // Make sure we're not trying to draw a panel
       // larger than the visible window
-      if(scrollX>av.endRes-av.startRes)
+      if (scrollX > av.endRes - av.startRes)
       {
         scrollX = av.endRes - av.startRes;
       }
-      else if(scrollX<av.startRes-av.endRes)
+      else if (scrollX < av.startRes - av.endRes)
+      {
         scrollX = av.startRes - av.endRes;
+      }
 
       idPanel.idCanvas.fastPaint(scrollY);
       seqPanel.seqCanvas.fastPaint(scrollX,
@@ -469,12 +519,23 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
 
     if (av.getWrapAlignment())
     {
-      int max = av.alignment.getWidth() /
-          seqPanel.seqCanvas.
-          getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width) +1;
-      vscroll.setMaximum(max);
-      vscroll.setUnitIncrement(1);
-      vscroll.setVisibleAmount(1);
+      int maxwidth = av.alignment.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(max);
+        vscroll.setUnitIncrement(1);
+        vscroll.setVisibleAmount(1);
+      }
     }
     else
     {
@@ -491,7 +552,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     if (getBounds() == g.getClipBounds())
     {
       if (overviewPanel != null)
+      {
         overviewPanel.updateOverviewImage();
+      }
     }
 
   }
@@ -513,55 +576,54 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
   BorderLayout borderLayout10 = new BorderLayout();
   protected Panel hscrollFillerPanel = new Panel();
   BorderLayout borderLayout11 = new BorderLayout();
-  public Panel annotationScroller = new Panel();
   BorderLayout borderLayout4 = new BorderLayout();
   BorderLayout borderLayout2 = new BorderLayout();
 
-  private void jbInit() throws Exception {
-      //  idPanelHolder.setPreferredSize(new Dimension(70, 10));
-      this.setLayout(borderLayout7);
-
-      //   sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
-      sequenceHolderPanel.setLayout(borderLayout3);
-      seqPanelHolder.setLayout(borderLayout1);
-      scalePanelHolder.setBackground(Color.white);
-
-      // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
-      scalePanelHolder.setLayout(borderLayout6);
-      idPanelHolder.setLayout(borderLayout5);
-      idSpaceFillerPanel1.setBackground(Color.white);
-
-      //  idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
-      idSpaceFillerPanel1.setLayout(borderLayout11);
-      annotationSpaceFillerHolder.setBackground(Color.white);
-
-      //  annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
-      annotationSpaceFillerHolder.setLayout(borderLayout4);
-      hscroll.setOrientation(Scrollbar.HORIZONTAL);
-      hscrollHolder.setLayout(borderLayout10);
-      hscrollFillerPanel.setBackground(Color.white);
-
-      //  hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
-      hscrollHolder.setBackground(Color.white);
-
-      //    annotationScroller.setPreferredSize(new Dimension(10, 80));
-      //  this.setPreferredSize(new Dimension(220, 166));
-      seqPanelHolder.setBackground(Color.white);
-      idPanelHolder.setBackground(Color.white);
-      annotationScroller.setLayout(borderLayout2);
-      sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
-      sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
-      seqPanelHolder.add(vscroll, BorderLayout.EAST);
-      sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);
-
-      //  Panel3.add(secondaryPanelHolder,  BorderLayout.SOUTH);
-      this.add(idPanelHolder, BorderLayout.WEST);
-      idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
-      idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
-      this.add(hscrollHolder, BorderLayout.SOUTH);
-      hscrollHolder.add(hscroll, BorderLayout.CENTER);
-      hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
-      this.add(sequenceHolderPanel, BorderLayout.CENTER);
+  private void jbInit()
+      throws Exception
+  {
+    //  idPanelHolder.setPreferredSize(new Dimension(70, 10));
+    this.setLayout(borderLayout7);
+
+    //   sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
+    sequenceHolderPanel.setLayout(borderLayout3);
+    seqPanelHolder.setLayout(borderLayout1);
+    scalePanelHolder.setBackground(Color.white);
+
+    // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
+    scalePanelHolder.setLayout(borderLayout6);
+    idPanelHolder.setLayout(borderLayout5);
+    idSpaceFillerPanel1.setBackground(Color.white);
+
+    //  idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
+    idSpaceFillerPanel1.setLayout(borderLayout11);
+    annotationSpaceFillerHolder.setBackground(Color.white);
+
+    //  annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
+    annotationSpaceFillerHolder.setLayout(borderLayout4);
+    hscroll.setOrientation(Scrollbar.HORIZONTAL);
+    hscrollHolder.setLayout(borderLayout10);
+    hscrollFillerPanel.setBackground(Color.white);
+
+    //  hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
+    hscrollHolder.setBackground(Color.white);
+
+    //    annotationScroller.setPreferredSize(new Dimension(10, 80));
+    //  this.setPreferredSize(new Dimension(220, 166));
+    seqPanelHolder.setBackground(Color.white);
+    idPanelHolder.setBackground(Color.white);
+    sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
+    sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
+    seqPanelHolder.add(vscroll, BorderLayout.EAST);
+
+    //  Panel3.add(secondaryPanelHolder,  BorderLayout.SOUTH);
+    this.add(idPanelHolder, BorderLayout.WEST);
+    idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
+    idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
+    this.add(hscrollHolder, BorderLayout.SOUTH);
+    hscrollHolder.add(hscroll, BorderLayout.CENTER);
+    hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
+    this.add(sequenceHolderPanel, BorderLayout.CENTER);
   }
 
 }