X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FOverviewPanel.java;h=72654893e7efe75edce5d3967a32daa468fff902;hb=2c99f6f286b5a4bb09b79131f620eb44d70ee3fe;hp=e8f9f9f07ddb818ac483fc2c743ea02cef2624f2;hpb=1f705a7597d9558cbb6962826bfdc2f0ac2c6a50;p=jalview.git

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index e8f9f9f..7265489 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) 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
@@ -26,6 +26,7 @@ public class OverviewPanel
     extends Panel implements Runnable, MouseMotionListener, MouseListener
 {
   Image miniMe;
+  Image offscreen;
   AlignViewport av;
   AlignmentPanel ap;
   float scalew = 1f;
@@ -42,7 +43,6 @@ public class OverviewPanel
   SequenceRenderer sr;
   FeatureRenderer fr;
 
-
   Frame nullFrame;
 
   public OverviewPanel(AlignmentPanel ap)
@@ -53,30 +53,31 @@ public class OverviewPanel
     nullFrame = new Frame();
     nullFrame.addNotify();
 
-
     sr = new SequenceRenderer(av);
     sr.graphics = nullFrame.getGraphics();
-    sr.renderGaps( false );
+    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.vconsensus==null)
-          graphHeight = 0;
+    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;
+      if (sequencesHeight < 40)
+      {
+        sequencesHeight = 40;
+      }
     }
     else
     {
@@ -111,22 +112,23 @@ public class OverviewPanel
 
   }
 
-
   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 mouseReleased(MouseEvent evt)
@@ -134,8 +136,6 @@ public class OverviewPanel
     boxX = evt.getX();
     boxY = evt.getY();
     checkValid();
-    ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
-                         (int) (boxY / scaleh / av.getCharHeight()));
   }
 
   public void mouseDragged(MouseEvent evt)
@@ -143,11 +143,6 @@ public class OverviewPanel
     boxX = evt.getX();
     boxY = evt.getY();
     checkValid();
-    ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
-                         (int) (boxY / scaleh / av.getCharHeight()));
-
-    repaint();
-    ap.repaint();
   }
 
   void checkValid()
@@ -157,7 +152,7 @@ public class OverviewPanel
       boxY = 0;
     }
 
-    if (boxY > sequencesHeight - boxHeight)
+    if (boxY > (sequencesHeight - boxHeight))
     {
       boxY = sequencesHeight - boxHeight + 1;
     }
@@ -167,10 +162,37 @@ public class OverviewPanel
       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.paintAlignment(false);
   }
 
   /**
@@ -180,16 +202,17 @@ public class OverviewPanel
   {
     if (resizing)
     {
-        resizeAgain = true;
-        return;
+      resizeAgain = true;
+      return;
     }
 
     if (av.showSequenceFeatures)
-   {
-     fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
-     fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
-     fr.sequenceFeatures = ap.seqPanel.seqCanvas.getFeatureRenderer().sequenceFeatures;
-   }
+    {
+      fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().
+          featureGroups;
+      fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().
+          featureColours;
+    }
 
     resizing = true;
 
@@ -199,16 +222,15 @@ public class OverviewPanel
       sequencesHeight = getSize().height - graphHeight;
     }
     setSize(new Dimension(width, sequencesHeight + graphHeight));
-    setBoxPosition();
 
     Thread thread = new Thread(this);
     thread.start();
-        repaint();
+    repaint();
   }
 
   // This is set true if the user resizes whilst
   // the overview is being calculated
-    boolean resizeAgain = false;
+  boolean resizeAgain = false;
 
   public void run()
   {
@@ -218,10 +240,7 @@ public class OverviewPanel
 
     if (av.showSequenceFeatures)
     {
-      fr.renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
-      fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
-      fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
-      fr.sequenceFeatures = ap.seqPanel.seqCanvas.getFeatureRenderer().sequenceFeatures;
+      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
     }
 
     if (getSize().width > 0 && getSize().height > 0)
@@ -239,61 +258,94 @@ public class OverviewPanel
     scaleh = (float) sequencesHeight / (float) fullsizeHeight;
 
     miniMe = nullFrame.createImage(width, sequencesHeight + graphHeight);
+    offscreen = nullFrame.createImage(width, sequencesHeight + graphHeight);
 
     Graphics mg = miniMe.getGraphics();
     float sampleCol = (float) alwidth / (float) width;
     float sampleRow = (float) alheight / (float) sequencesHeight;
 
-    int lastcol=0, lastseq=0;
-    int xstart=0, ystart=0;
+    int lastcol = 0, lastrow = 0;
+    int xstart = 0, ystart = 0;
     Color color = Color.yellow;
-    int col, sameRow = 0, sameCol = 0;
-    jalview.datamodel.SequenceI sequence;
-
-    for (int row = 0; row <= sequencesHeight; row++)
+    int row, col, sameRow = 0, sameCol = 0;
+    jalview.datamodel.SequenceI seq;
+    boolean hiddenRow = false;
+    for (row = 0; row <= sequencesHeight; row++)
     {
-      if((int)(row*sampleRow)==lastseq)
+      if ( (int) (row * sampleRow) == lastrow)
       {
-        sameRow ++;
+        sameRow++;
         continue;
       }
 
-      sequence = av.getAlignment().getSequenceAt(lastseq);
+      hiddenRow = false;
+      if (av.hasHiddenRows)
+      {
+        seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
+        if (seq == null)
+        {
+          int index =
+              av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(
+              lastrow);
+
+          seq = av.alignment.getSequenceAt(index);
+        }
+        else
+        {
+          hiddenRow = true;
+        }
+      }
+      else
+      {
+        seq = av.alignment.getSequenceAt(lastrow);
+      }
 
       for (col = 0; col < width; col++)
       {
-        if((int)(col*sampleCol) == lastcol)
+        if ( (int) (col * sampleCol) == lastcol &&
+            (int) (row * sampleRow) == lastrow)
         {
-          sameCol ++;
+          sameCol++;
           continue;
         }
 
-        lastcol = (int)(col*sampleCol);
+        lastcol = (int) (col * sampleCol);
 
-        if(sequence.getLength()>lastcol)
+        if (seq.getLength() > lastcol)
         {
-          color = sr.findSequenceColour(sequence, lastcol);
+          color = sr.getResidueBoxColour(
+              seq, lastcol);
 
           if (av.showSequenceFeatures)
-            color = fr.findFeatureColour(color,
-                                        sequence,
-                                        lastcol);
+          {
+            color = fr.findFeatureColour(color, seq, lastcol);
+          }
         }
         else
-          color = color.white;
+        {
+          color = Color.white; //White
+        }
+
+        if (hiddenRow ||
+            (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
+        {
+          color = color.darker().darker();
+        }
 
         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;
       }
-
-
-      lastseq = (int)(row*sampleRow);
+      lastrow = (int) (row * sampleRow);
       ystart = row;
       sameRow = 1;
     }
@@ -314,16 +366,13 @@ public class OverviewPanel
         }
       }
     }
-
-
-
     System.gc();
 
     resizing = false;
 
     setBoxPosition();
 
-    if(resizeAgain)
+    if (resizeAgain)
     {
       resizeAgain = false;
       updateOverviewImage();
@@ -333,16 +382,49 @@ public class OverviewPanel
   public void setBoxPosition()
   {
     int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
-    int fullsizeHeight = av.alignment.getHeight() * av.getCharHeight();
+    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) (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;
+    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();
   }
 
@@ -353,23 +435,15 @@ public class OverviewPanel
 
   public void paint(Graphics g)
   {
+    Graphics og = offscreen.getGraphics();
     if (miniMe != null)
     {
-      g.drawImage(miniMe, 0, 0, this);
+      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);
-    }
-
-    g.setColor(Color.red);
-    g.drawRect(boxX, boxY, boxWidth, boxHeight);
-    g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
   }
 
 }