X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FOverviewPanel.java;h=867ce56797cf768a81ca544e794b6a4ba6135a62;hb=ae83cc59079dc5374a41402889b6f4192f66e9e2;hp=93ff487b7734cf4f6d7167b2223852bb7f26a176;hpb=27b299821e542ddd590e3191682017c093fec14d;p=jalview.git

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 93ff487..867ce56 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.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
@@ -23,20 +23,27 @@ import java.awt.*;
 import java.awt.event.*;
 
 public class OverviewPanel
-    extends Panel implements Runnable
+    extends Panel implements Runnable, MouseMotionListener, MouseListener
 {
   Image miniMe;
+  Image offscreen;
   AlignViewport av;
   AlignmentPanel ap;
   float scalew = 1f;
   float scaleh = 1f;
 
   public int width, sequencesHeight;
-  int graphHeight = 30;
+  int graphHeight = 20;
   int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1;
 
   boolean resizing = false;
 
+  // Can set different properties in this seqCanvas than
+  // main visible SeqCanvas
+  SequenceRenderer sr;
+  FeatureRenderer fr;
+
+
   Frame nullFrame;
 
   public OverviewPanel(AlignmentPanel ap)
@@ -47,14 +54,30 @@ public class OverviewPanel
     nullFrame = new Frame();
     nullFrame.addNotify();
 
+
+    sr = new SequenceRenderer(av);
+    sr.graphics = nullFrame.getGraphics();
+    sr.renderGaps = false;
+    sr.forOverview = true;
+    fr = new FeatureRenderer(av);
+    fr.overview = true;
+
+
+
     // scale the initial size of overviewpanel to shape of alignment
     float initialScale = (float) av.alignment.getWidth() /
         (float) av.alignment.getHeight();
+
+    if(av.hconsensus==null)
+          graphHeight = 0;
+
     if (av.alignment.getWidth() > av.alignment.getHeight())
     {
       // wider
       width = 400;
       sequencesHeight = (int) (400f / initialScale);
+      if(sequencesHeight<40)
+              sequencesHeight = 40;
     }
     else
     {
@@ -81,87 +104,92 @@ public class OverviewPanel
       }
     });
 
-    addMouseMotionListener(new MouseMotionAdapter()
-    {
-      public void mouseDragged(MouseEvent evt)
-      {
-        doMouseDragged(evt);
-      }
-    });
+    addMouseMotionListener(this);
 
-    addMouseListener(new MouseAdapter()
-    {
-      public void mousePressed(MouseEvent evt)
-      {
-        doMousePressed(evt);
-      }
-
-      public void mouseReleased(MouseEvent evt)
-      {
-        doMouseReleased(evt);
-      }
-    });
+    addMouseListener(this);
 
     updateOverviewImage();
 
   }
 
-  public void doMousePressed(MouseEvent evt)
+
+  public void mouseEntered(MouseEvent evt)
+  {}
+  public void mouseExited(MouseEvent evt)
+  {}
+  public void mouseClicked(MouseEvent evt)
+  {}
+  public void mouseMoved(MouseEvent evt)
+  {}
+  public void mousePressed(MouseEvent evt)
   {
     boxX = evt.getX();
     boxY = evt.getY();
-
     checkValid();
-    repaint();
   }
 
-  public void doMouseReleased(MouseEvent evt)
+  public void mouseReleased(MouseEvent evt)
   {
     boxX = evt.getX();
     boxY = evt.getY();
     checkValid();
-    if (!resizing)
-    {
-      ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
-                         (int) (boxY / scaleh / av.getCharHeight()));
-    }
   }
 
-  public void doMouseDragged(MouseEvent evt)
+  public void mouseDragged(MouseEvent evt)
   {
     boxX = evt.getX();
     boxY = evt.getY();
     checkValid();
-    if (!resizing)
-    {
-      ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
-                         (int) (boxY / scaleh / av.getCharHeight()));
-    }
-    repaint();
-    ap.repaint();
   }
 
   void checkValid()
   {
     if (boxY < 0)
     {
-      boxY = 0;
+        boxY = 0;
     }
 
-    if (boxY > sequencesHeight - boxHeight)
+    if (boxY > (sequencesHeight - boxHeight))
     {
-      boxY = sequencesHeight - boxHeight + 1;
+        boxY = sequencesHeight - boxHeight + 1;
     }
 
     if (boxX < 0)
     {
-      boxX = 0;
+        boxX = 0;
     }
 
-    if (boxX > width - boxWidth)
+    if (boxX > (width - boxWidth))
     {
+      if(av.hasHiddenColumns)
+      {
+        //Try smallest possible box
+        boxWidth = (int) ( (av.endRes - av.startRes + 1) *
+                               av.getCharWidth() * scalew);
+      }
       boxX = width - boxWidth;
     }
+
+    int col = (int) (boxX / scalew / av.getCharWidth());
+    int row = (int) (boxY / scaleh / av.getCharHeight());
+
+    if (av.hasHiddenColumns)
+    {
+      if (!av.getColumnSelection().isVisible(col))
+      {
+        return;
+      }
+
+      col = av.getColumnSelection().findColumnPosition(col);
+    }
+
+    if( av.hasHiddenRows )
+    {
+      row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);
+    }
+
+    ap.setScrollValues( col, row );
+    ap.repaint();
   }
 
   /**
@@ -169,17 +197,30 @@ public class OverviewPanel
    */
   public void updateOverviewImage()
   {
-      if (resizing)
-      {
-          resizeAgain = true;
-          return;
-      }
+    if (resizing)
+    {
+        resizeAgain = true;
+        return;
+    }
 
-      resizing = true;
+    if (av.showSequenceFeatures)
+   {
+     fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
+     fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
+   }
+
+    resizing = true;
+
+    if ( (getSize().width > 0) && (getSize().height > 0))
+    {
+      width = getSize().width;
+      sequencesHeight = getSize().height - graphHeight;
+    }
+    setSize(new Dimension(width, sequencesHeight + graphHeight));
 
-      Thread thread = new Thread(this);
-      thread.start();
-      repaint();
+    Thread thread = new Thread(this);
+    thread.start();
+    repaint();
   }
 
   // This is set true if the user resizes whilst
@@ -192,6 +233,11 @@ public class OverviewPanel
     int alwidth = av.alignment.getWidth();
     int alheight = av.alignment.getHeight();
 
+    if (av.showSequenceFeatures)
+    {
+      fr.transferSettings( ap.seqPanel.seqCanvas.getFeatureRenderer() );
+    }
+
     if (getSize().width > 0 && getSize().height > 0)
     {
       width = getSize().width;
@@ -207,85 +253,106 @@ public class OverviewPanel
     scaleh = (float) sequencesHeight / (float) fullsizeHeight;
 
     miniMe = nullFrame.createImage(width, sequencesHeight + graphHeight);
+    offscreen = nullFrame.createImage(width, sequencesHeight + graphHeight);
 
     Graphics mg = miniMe.getGraphics();
-    Image consensus = nullFrame.createImage(fullsizeWidth, 60);
-    Graphics g = consensus.getGraphics();
-    ap.annotationPanel.drawGraph(g, av.conservation, fullsizeWidth, 60);
-    mg.drawImage(consensus, 0, sequencesHeight, width,
-                 sequencesHeight + graphHeight, 0, 0, fullsizeWidth, 60, this);
-
-    boolean oldRenderGaps = av.renderGaps;
-    try
+    float sampleCol = (float) alwidth / (float) width;
+    float sampleRow = (float) alheight / (float) sequencesHeight;
+
+    int lastcol=0, lastrow=0;
+    int xstart=0, ystart=0;
+    Color color = Color.yellow;
+    int row, col, sameRow = 0, sameCol = 0;
+    jalview.datamodel.SequenceI seq;
+    boolean hiddenRow = false;
+    for (row = 0; row <= sequencesHeight; row++)
     {
-      // We'll have to draw the full size alignment in chunks, as an image of the
-      // whole alignment requires too much memory
-
-      // Max size depends on the font size, the following is a
-      // guess at a size which works
-      int maxSize = 2000 / av.getFont().getSize();
-      Image block;
-      int blockx = 0, blocky = 0, blockw = 0, blockh = 0, eRes = 0, eSeq = 0;
+      if((int)(row*sampleRow)==lastrow)
+      {
+        sameRow ++;
+        continue;
+      }
 
-      av.setRenderGaps(false);
-      for (int sRes = 0, chunkx = 0; sRes < alwidth; sRes += maxSize, chunkx++)
+      hiddenRow = false;
+      if (av.hasHiddenRows)
       {
-        eSeq = 0;
-        eRes += maxSize;
-        if (eRes > alwidth)
+        seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
+        if (seq == null)
         {
-          eRes = alwidth;
-        }
+          int index =
+             av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(lastrow);
 
-        for (int sSeq = 0, chunky = 0; sSeq < alheight; sSeq += maxSize, chunky++)
+         seq = av.alignment.getSequenceAt(index);
+        }
+        else
         {
-          if(resizeAgain)
-                  break;
+          hiddenRow = true;
+        }
+      }
+      else
+        seq = av.alignment.getSequenceAt(lastrow);
 
-          eSeq += maxSize;
-          if (eSeq > alheight)
+        for (col = 0; col < width; col++)
+        {
+          if ( (int) (col * sampleCol) == lastcol && (int) (row * sampleRow) == lastrow)
           {
-            eSeq = alheight;
+            sameCol ++;
+            continue;
           }
 
-          blocky = 0;
-          blockx = (int) ( (float) sRes / (float) alwidth * width);
-
-          block = nullFrame.createImage( (eRes - sRes) * av.charWidth,
-                                        (eSeq - sSeq) * av.charHeight);
-          g = block.getGraphics();
-
-          ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq, sRes, sSeq,
-                                          0);
-
-          blockh = (int) ( (float) (eSeq - sSeq) / (float) alheight *
-                          sequencesHeight) + 1;
-          blockw = (int) ( (float) (eRes - sRes) / (float) alwidth * width) + 1;
+          lastcol = (int) (col * sampleCol);
 
-          blocky += (int) ( (float) sSeq / (float) alheight * sequencesHeight);
+          if (seq.getLength() > lastcol)
+          {
+            color = sr.getResidueBoxColour(
+                seq, lastcol);
 
-          mg.drawImage(block, blockx,
-                       blocky,
-                       blockx + blockw,
-                       blocky + blockh,
+            if (av.showSequenceFeatures)
+              color = fr.findFeatureColour(color, seq, lastcol);
+          }
+          else
+          {
+            color = Color.white; //White
+          }
 
-                       0, 0, block.getWidth(null), block.getHeight(null), this);
+          if (hiddenRow ||
+              (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
+          {
+            color = color.darker().darker();
+          }
 
-          block = null;
-        }
+          mg.setColor(color);
+          if (sameCol == 1 && sameRow == 1)
+            mg.drawLine(xstart, ystart, xstart, ystart);
+          else
+            mg.fillRect(xstart, ystart, sameCol, sameRow);
 
+          xstart = col;
+          sameCol = 1;
       }
-
+      lastrow = (int)(row*sampleRow);
+      ystart = row;
+      sameRow = 1;
     }
-    catch (OutOfMemoryError error)
+
+    if (av.conservation != null)
     {
-      System.err.println(
-          "Out of memory when trying to calculate the overview window image!");
+      for (col = 0; col < width; col++)
+      {
+        lastcol = (int) (col * sampleCol);
+        {
+          mg.translate(col, sequencesHeight);
+          ap.annotationPanel.drawGraph(mg, av.conservation,
+                                       (int) (sampleCol) + 1,
+                                       graphHeight,
+                                       (int) (col * sampleCol),
+                                       (int) (col * sampleCol) + 1);
+          mg.translate( -col, -sequencesHeight);
+        }
+      }
     }
-
     System.gc();
 
-    av.setRenderGaps(oldRenderGaps);
     resizing = false;
 
     setBoxPosition();
@@ -295,15 +362,50 @@ public class OverviewPanel
       resizeAgain = false;
       updateOverviewImage();
     }
-  }
+}
 
   public void setBoxPosition()
   {
-    boxX = (int) (av.getStartRes() * av.getCharWidth() * scalew);
-    boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh);
-    boxWidth = (int) ( (av.getEndRes() - av.getStartRes() + 1) *
-                      av.getCharWidth() * scalew);
-    boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) - boxY;
+    int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
+    int fullsizeHeight = (av.alignment.getHeight()
+                          + av.alignment.getHiddenSequences().getSize()) *
+        av.getCharHeight();
+
+    int startRes = av.getStartRes();
+    int endRes = av.getEndRes();
+
+    if (av.hasHiddenColumns)
+    {
+      startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
+      endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
+    }
+
+    int startSeq = av.startSeq;
+    int endSeq = av.endSeq;
+
+    if (av.hasHiddenRows)
+    {
+      startSeq =
+          av.alignment.getHiddenSequences().adjustForHiddenSeqs(startSeq);
+
+      endSeq =
+          av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);
+
+    }
+
+    scalew = (float) width / (float) fullsizeWidth;
+    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
+
+    boxX = (int) (startRes * av.getCharWidth() * scalew);
+    boxY = (int) (startSeq * av.getCharHeight() * scaleh);
+
+    if (av.hasHiddenColumns)
+      boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
+    else
+      boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
+
+    boxHeight = (int) ( (endSeq - startSeq) * av.getCharHeight() * scaleh);
+
     repaint();
   }
 
@@ -314,26 +416,23 @@ public class OverviewPanel
 
   public void paint(Graphics g)
   {
-    if (resizing)
+    Graphics og = offscreen.getGraphics();
+    if (miniMe != null)
+    {
+      og.drawImage(miniMe, 0, 0, this);
+      og.setColor(Color.red);
+      og.drawRect(boxX, boxY, boxWidth, boxHeight);
+      og.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+      g.drawImage(offscreen, 0,0, this);
+    }
+    else
     {
       g.setColor(Color.white);
       g.fillRect(0, 0, getSize().width, getSize().height);
       g.setColor(Color.black);
-
       g.setFont(new Font("Verdana", Font.BOLD, 15));
       g.drawString("Recalculating", 5, sequencesHeight / 2);
-      g.drawString("Overview.....", 5, sequencesHeight / 2 + 20);
-    }
-    else
-    {
-      if (miniMe != null)
-      {
-        g.drawImage(miniMe, 0, 0, this);
-      }
-
-      g.setColor(Color.red);
-      g.drawRect(boxX, boxY, boxWidth, boxHeight);
-      g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+      g.drawString("Overview.....", 5, (sequencesHeight / 2) + 20);
     }
   }