X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FOverviewPanel.java;h=54e1ac2b68b2b85aa6773e83d2ce22cba11ac95d;hb=b169b1a49c078d123feb729db6acb9779f50e7d6;hp=c5789fe0ba3eb555cd9b318a920c3597e376baf1;hpb=de468b0bf50850a89c6a8a7acfa4ff5b689ffed1;p=jalview.git

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index c5789fe..54e1ac2 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -26,6 +26,7 @@ public class OverviewPanel
     extends Panel implements Runnable, MouseMotionListener, MouseListener
 {
   Image miniMe;
+  Image offscreen;
   AlignViewport av;
   AlignmentPanel ap;
   float scalew = 1f;
@@ -40,7 +41,7 @@ public class OverviewPanel
   // Can set different properties in this seqCanvas than
   // main visible SeqCanvas
   SequenceRenderer sr;
-  //FeatureRenderer fr;
+  FeatureRenderer fr;
 
 
   Frame nullFrame;
@@ -56,10 +57,10 @@ public class OverviewPanel
 
     sr = new SequenceRenderer(av);
     sr.graphics = nullFrame.getGraphics();
-    sr.renderGaps( false );
-    //fr = new FeatureRenderer(av);
-    //fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;
-    //fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed;
+    sr.renderGaps = false;
+    sr.forOverview = true;
+    fr = new FeatureRenderer(av);
+    fr.overview = true;
 
 
 
@@ -124,9 +125,7 @@ public class OverviewPanel
   {
     boxX = evt.getX();
     boxY = evt.getY();
-
     checkValid();
-    repaint();
   }
 
   public void mouseReleased(MouseEvent evt)
@@ -134,8 +133,6 @@ 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)
@@ -143,34 +140,56 @@ 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()
   {
     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();
   }
 
   /**
@@ -184,6 +203,12 @@ public class OverviewPanel
         return;
     }
 
+    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))
@@ -192,11 +217,10 @@ 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
@@ -209,6 +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;
@@ -224,33 +253,93 @@ 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=-1, lastrow=-1;
-    Color color = Color.white;
-    for (int col = 0; col < width; col++)
+    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++)
     {
-      for (int row = 0; row < sequencesHeight; row++)
+      if((int)(row*sampleRow)==lastrow)
+      {
+        sameRow ++;
+        continue;
+      }
+
+      hiddenRow = false;
+      if (av.hasHiddenRows)
       {
-        if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)
+        seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
+        if (seq == null)
         {
-          mg.setColor(color);
-          mg.fillRect(col,row,1,1);
-          continue;
+          int index =
+             av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(lastrow);
+
+         seq = av.alignment.getSequenceAt(index);
+        }
+        else
+        {
+          hiddenRow = true;
         }
+      }
+      else
+        seq = av.alignment.getSequenceAt(lastrow);
 
-        lastrow = (int)(row*sampleRow);
-        lastcol = (int)(col*sampleCol);
+        for (col = 0; col < width; col++)
+        {
+          if ( (int) (col * sampleCol) == lastcol && (int) (row * sampleRow) == lastrow)
+          {
+            sameCol ++;
+            continue;
+          }
+
+          lastcol = (int) (col * sampleCol);
+
+          if (seq.getLength() > lastcol)
+          {
+            color = sr.getResidueBoxColour(
+                seq, lastcol);
+
+            if (av.showSequenceFeatures)
+              color = fr.findFeatureColour(color, seq, lastcol);
+          }
+          else
+          {
+            color = Color.white; //White
+          }
+
+          if (hiddenRow ||
+              (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
+          {
+            color = color.darker().darker();
+          }
 
-        color = sr.findSequenceColour(av.alignment.getSequenceAt(lastrow), lastcol);
+          mg.setColor(color);
+          if (sameCol == 1 && sameRow == 1)
+            mg.drawLine(xstart, ystart, xstart, ystart);
+          else
+            mg.fillRect(xstart, ystart, sameCol, sameRow);
 
-        mg.setColor(color);
-        mg.fillRect(col,row,1,1);
+          xstart = col;
+          sameCol = 1;
+      }
+      lastrow = (int)(row*sampleRow);
+      ystart = row;
+      sameRow = 1;
+    }
 
-        if (av.conservation != null)
+    if (av.conservation != null)
+    {
+      for (col = 0; col < width; col++)
+      {
+        lastcol = (int) (col * sampleCol);
         {
           mg.translate(col, sequencesHeight);
           ap.annotationPanel.drawGraph(mg, av.conservation,
@@ -258,11 +347,10 @@ public class OverviewPanel
                                        graphHeight,
                                        (int) (col * sampleCol),
                                        (int) (col * sampleCol) + 1);
-          mg.translate(-col, -sequencesHeight);
+          mg.translate( -col, -sequencesHeight);
         }
       }
     }
-
     System.gc();
 
     resizing = false;
@@ -274,21 +362,50 @@ public class OverviewPanel
       resizeAgain = false;
       updateOverviewImage();
     }
-  }
+}
 
   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();
   }
 
@@ -299,9 +416,14 @@ 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
     {
@@ -312,10 +434,6 @@ public class OverviewPanel
       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);
   }
 
 }