X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=bcdffa095f04cd590a4f0aa227c7f33e81cbf84f;hb=c20e9d4ae9c98b093e74a10bf965e6d20d80fadf;hp=19308660c35cba64bff5f208b7385de29b89c619;hpb=13561ba5431a3befd5b0e08824ea50f90b23df0e;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 1930866..bcdffa0 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) 2006 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
@@ -22,13 +22,9 @@ package jalview.appletgui;
 import java.awt.*;
 import java.awt.event.*;
 
-import jalview.analysis.*;
 import jalview.datamodel.*;
-import jalview.jbappletgui.*;
-import jalview.schemes.*;
 
-public class AlignmentPanel
-    extends GAlignmentPanel implements AdjustmentListener
+public class AlignmentPanel extends Panel implements AdjustmentListener
 {
 
   AlignViewport av;
@@ -44,12 +40,19 @@ public class AlignmentPanel
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
 
-  boolean MAC = false;
+
 
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
-    if(System.getProperty("os.name").startsWith("Mac"))
-      MAC = true;
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
 
     alignFrame = af;
     this.av = av;
@@ -58,11 +61,15 @@ public class AlignmentPanel
     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);
@@ -73,9 +80,6 @@ public class AlignmentPanel
     hscroll.addAdjustmentListener(this);
     vscroll.addAdjustmentListener(this);
 
-    seqPanel.seqCanvas.addKeyListener(new MyKeyAdapter());
-    idPanel.idCanvas.addKeyListener(new MyKeyAdapter());
-
     addComponentListener(new ComponentAdapter()
     {
       public void componentResized(ComponentEvent evt)
@@ -89,7 +93,6 @@ public class AlignmentPanel
     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,
@@ -98,80 +101,31 @@ public class AlignmentPanel
 
   }
 
-  class MyKeyAdapter
-      extends KeyAdapter
-  {
-    public void keyPressed(KeyEvent evt)
-    {
-      // System.out.println(evt.getKeyCode()); log.
-      switch (evt.getKeyCode())
-      {
-        case 27: // escape key
-          av.setSelectionGroup(null);
-          alignFrame.alignPanel.repaint();
-          break;
-        case KeyEvent.VK_X:
-          if (evt.isControlDown())
-          {
-            alignFrame.cut_actionPerformed(null);
-          }
-          break;
-        case KeyEvent.VK_C:
-          if (evt.isControlDown())
-          {
-            alignFrame.copy_actionPerformed(null);
-          }
-          break;
-        case KeyEvent.VK_V:
-          if (evt.isControlDown())
-          {
-            alignFrame.paste(true);
-          }
-          break;
-        case KeyEvent.VK_A:
-          if (evt.isControlDown())
-          {
-            alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
-          }
-          break;
-        case KeyEvent.VK_DOWN:
-          alignFrame.moveSelectedSequences(false);
-          break;
-        case KeyEvent.VK_UP:
-          alignFrame.moveSelectedSequences(true);
-          break;
-        case KeyEvent.VK_F:
-          if (evt.isControlDown())
-          {
-            alignFrame.findMenuItem_actionPerformed(null);
-          }
-          break;
-        case KeyEvent.VK_BACK_SPACE:
-        case KeyEvent.VK_DELETE:
-          alignFrame.cut_actionPerformed(null);
-          break;
-
-      }
-    }
-  }
 
   public void fontChanged()
   {
     // set idCanvas bufferedImage to null
     // to prevent drawing old image
+    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.adjustPanelHeight();
+    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 );
     idPanel.idCanvas.setSize(d);
     hscrollFillerPanel.setSize(d);
 
-    alignFrame.pack();
+    validate();
+    repaint();
+
+    if(overviewPanel!=null)
+          overviewPanel.updateOverviewImage();
   }
 
   public void setIdWidth(int w, int h)
@@ -184,16 +138,14 @@ public class AlignmentPanel
 
   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();
 
@@ -203,14 +155,7 @@ public class AlignmentPanel
     while (i < al.getHeight() && al.getSequenceAt(i) != null)
     {
       SequenceI s = al.getSequenceAt(i);
-      if (av.getShowFullId())
-      {
-        id = s.getDisplayId();
-      }
-      else
-      {
-        id = s.getName();
-      }
+      id = s.getDisplayId(av.getShowJVSuffix());
 
       if (fm.stringWidth(id) > idWidth)
       {
@@ -223,7 +168,7 @@ public class AlignmentPanel
     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;
@@ -238,27 +183,58 @@ public class AlignmentPanel
     return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
   }
 
-  public void highlightSearchResults(int[] results)
+  public void highlightSearchResults(SearchResults results)
   {
     seqPanel.seqCanvas.highlightSearchResults(results);
 
-    // do we need to scroll the panel?
+   // do we need to scroll the panel?
     if (results != null)
     {
-      SequenceI seq = av.alignment.getSequenceAt(results[0]);
-      int start = seq.findIndex(results[1]) - 1;
-      int end = seq.findIndex(results[2]) - 1;
-      if (av.getStartRes() > start
-          || av.getEndRes() < end
-          || (av.getStartSeq() > results[0]
-              || av.getEndSeq() < results[0]))
-      {
-        setScrollValues(start, results[0]);
-      }
+      SequenceI seq = results.getResultSequence(0);
+      int seqIndex = av.alignment.findIndex(seq);
+      int start = seq.findIndex(results.getResultStart(0)) - 1;
+      int end = seq.findIndex(results.getResultEnd(0)) - 1;
+
+        if(!av.wrapAlignment)
+        {
+          if ( (av.getStartRes() > end)  || (av.getEndRes() < start) ||
+             ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+          {
+            if (start > av.alignment.getWidth() - hextent)
+            {
+              start = av.alignment.getWidth() - hextent;
+              if (start < 0)
+                start = 0;
+            }
+            if (seqIndex > av.alignment.getHeight() - vextent)
+            {
+              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;
@@ -271,8 +247,11 @@ public class AlignmentPanel
 
   public void setAnnotationVisible(boolean b)
   {
-    annotationSpaceFillerHolder.setVisible(b);
-    annotationScroller.setVisible(b);
+    if (!av.wrapAlignment)
+    {
+      annotationSpaceFillerHolder.setVisible(b);
+      annotationPanel.setVisible(b);
+    }
     validate();
     repaint();
   }
@@ -281,14 +260,27 @@ public class AlignmentPanel
   {
     av.startSeq = 0;
     scalePanelHolder.setVisible(!wrap);
+
+
     hscroll.setVisible(!wrap);
     idwidthAdjuster.setVisible(!wrap);
 
-    av.setShowAnnotation(!wrap);
-    annotationScroller.setVisible(!wrap);
-    annotationSpaceFillerHolder.setVisible(!wrap);
+    if (wrap)
+    {
+      annotationPanel.setVisible(false);
+      annotationSpaceFillerHolder.setVisible(false);
+    }
+    else if (av.showAnnotation)
+    {
+      annotationPanel.setVisible(true);
+      annotationSpaceFillerHolder.setVisible(true);
+    }
+
+
     idSpaceFillerPanel1.setVisible(!wrap);
 
+    fontChanged();//This is so that the scalePanel is resized correctly
+
     validate();
     repaint();
 
@@ -307,8 +299,7 @@ public class AlignmentPanel
       {
         return false;
       }
-      fastPaint = false;
-      vscroll.setValue(vscroll.getValue() - 1);
+      setScrollValues(hscroll.getValue(), vscroll.getValue()-1);
     }
     else
     {
@@ -316,24 +307,22 @@ public class AlignmentPanel
       {
         return false;
       }
-      fastPaint = false;
-      vscroll.setValue(vscroll.getValue() + 1);
+      setScrollValues(hscroll.getValue(), vscroll.getValue()+1);
     }
-    fastPaint = true;
+
+    repaint();
     return true;
   }
 
   public boolean scrollRight(boolean right)
   {
-
-    if (right)
+    if (!right)
     {
       if (hscroll.getValue() < 1)
       {
         return false;
       }
-      fastPaint = false;
-      hscroll.setValue(hscroll.getValue() - 1);
+      setScrollValues(hscroll.getValue()-1, vscroll.getValue());
     }
     else
     {
@@ -341,40 +330,47 @@ public class AlignmentPanel
       {
         return false;
       }
-      fastPaint = false;
-      hscroll.setValue(hscroll.getValue() + 1);
+      setScrollValues(hscroll.getValue()+1, vscroll.getValue());
     }
-    fastPaint = true;
+
+    repaint();
     return true;
   }
 
   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)
@@ -397,6 +393,9 @@ public class AlignmentPanel
     hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
     vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
 
+    if(overviewPanel!=null)
+          overviewPanel.setBoxPosition();
+
   }
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
@@ -404,7 +403,8 @@ public class AlignmentPanel
     int oldX = av.getStartRes();
     int oldY = av.getStartSeq();
 
-    if (evt.getSource() == hscroll)
+
+    if (evt==null || evt.getSource() == hscroll)
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
@@ -412,7 +412,8 @@ public class AlignmentPanel
                    1);
     }
 
-    if (evt.getSource() == vscroll)
+
+    if (evt==null || evt.getSource() == vscroll)
     {
       int offy = vscroll.getValue();
       if (av.getWrapAlignment())
@@ -435,15 +436,27 @@ public class AlignmentPanel
       overviewPanel.setBoxPosition();
     }
 
-    if (av.getWrapAlignment() || !fastPaint || MAC)
+    int scrollX = av.startRes - oldX;
+    int scrollY = av.startSeq - oldY;
+
+    if (av.getWrapAlignment() || !fastPaint || av.MAC)
     {
       repaint();
     }
     else
     {
-      idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
-      seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
-                                   av.getStartSeq() - oldY);
+      // Make sure we're not trying to draw a panel
+      // larger than the visible window
+      if(scrollX>av.endRes-av.startRes)
+      {
+        scrollX = av.endRes - av.startRes;
+      }
+      else if(scrollX<av.startRes-av.endRes)
+        scrollX = av.startRes - av.endRes;
+
+      idPanel.idCanvas.fastPaint(scrollY);
+      seqPanel.seqCanvas.fastPaint(scrollX,
+                                   scrollY);
 
       scalePanel.repaint();
       if (av.getShowAnnotation())
@@ -461,23 +474,25 @@ public class AlignmentPanel
 
   public void paint(Graphics g)
   {
+    invalidate();
     Dimension d = idPanel.idCanvas.getSize();
     idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
     annotationSpaceFillerHolder.setSize(d.width,
                                         annotationPanel.getSize().height);
-    alabels.setSize(d.width, annotationPanel.getSize().height);
 
-    alabels.repaint();
-    idPanel.idCanvas.repaint();
-    seqPanel.seqCanvas.repaint();
-    scalePanel.repaint();
-    annotationPanel.repaint();
+    alabels.setSize(d.width, annotationPanel.getSize().height);
 
     if (av.getWrapAlignment())
     {
-      int max = av.alignment.getWidth() /
-          seqPanel.seqCanvas.
-          getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
+      int maxwidth = av.alignment.getWidth();
+
+      if (av.hasHiddenColumns)
+        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+
+      int max = maxwidth /
+          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width) +
+          1;
+
       vscroll.setMaximum(max);
       vscroll.setUnitIncrement(1);
       vscroll.setVisibleAmount(1);
@@ -487,5 +502,84 @@ public class AlignmentPanel
       setScrollValues(av.getStartRes(), av.getStartSeq());
     }
 
+    alabels.repaint();
+
+    seqPanel.seqCanvas.repaint();
+    scalePanel.repaint();
+    annotationPanel.repaint();
+    idPanel.idCanvas.repaint();
+
+    if (getBounds() == g.getClipBounds())
+    {
+      if (overviewPanel != null)
+        overviewPanel.updateOverviewImage();
+    }
+
   }
+
+  protected Panel sequenceHolderPanel = new Panel();
+  protected Scrollbar vscroll = new Scrollbar();
+  protected Scrollbar hscroll = new Scrollbar();
+  protected Panel seqPanelHolder = new Panel();
+  BorderLayout borderLayout1 = new BorderLayout();
+  BorderLayout borderLayout3 = new BorderLayout();
+  protected Panel scalePanelHolder = new Panel();
+  protected Panel idPanelHolder = new Panel();
+  BorderLayout borderLayout5 = new BorderLayout();
+  protected Panel idSpaceFillerPanel1 = new Panel();
+  public Panel annotationSpaceFillerHolder = new Panel();
+  BorderLayout borderLayout6 = new BorderLayout();
+  BorderLayout borderLayout7 = new BorderLayout();
+  Panel hscrollHolder = new Panel();
+  BorderLayout borderLayout10 = new BorderLayout();
+  protected Panel hscrollFillerPanel = new Panel();
+  BorderLayout borderLayout11 = new BorderLayout();
+  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);
+      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);
+  }
+
 }