X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=714eec688ce9f2a27463b8b4ee7a25c071c7e934;hb=3bff9f93376444b36ca6b69d30193e10ea3c07ab;hp=635e4550591766e076fb979312246ccb701981fe;hpb=2ffe2deedb1527c067060646055bddd18d41d367;p=jalview.git

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 635e455..714eec6 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -49,7 +49,8 @@ public class OverviewPanel extends JPanel implements Runnable
 
     // Can set different properties in this seqCanvas than
     // main visible SeqCanvas
-    SeqCanvas overviewSeq;
+    SequenceRenderer sr;
+    FeatureRenderer fr;
 
     /**
      * Creates a new OverviewPanel object.
@@ -62,14 +63,15 @@ public class OverviewPanel extends JPanel implements Runnable
         this.ap = ap;
         setLayout(null);
 
-        overviewSeq = new SeqCanvas(av);
-        overviewSeq.isOverview = true;
-        overviewSeq.sr.renderGaps = false;
+        sr = new SequenceRenderer(av);
+        sr.renderGaps = false;
+        sr.forOverview = true;
+        fr = new FeatureRenderer(av);
 
         // scale the initial size of overviewpanel to shape of alignment
         float initialScale = (float) av.alignment.getWidth() / (float) av.alignment.getHeight();
 
-        if(av.vconsensus==null)
+        if(av.conservation==null)
           graphHeight = 0;
 
 
@@ -109,8 +111,12 @@ public class OverviewPanel extends JPanel implements Runnable
             {
                 public void mouseDragged(MouseEvent evt)
                 {
-                  if(!av.wrapAlignment)
-                    doMouseDragged(evt);
+                  if (!av.wrapAlignment)
+                  {
+                    boxX = evt.getX();
+                    boxY = evt.getY();
+                    checkValid();
+                  }
                 }
             });
 
@@ -119,63 +125,17 @@ public class OverviewPanel extends JPanel implements Runnable
                 public void mousePressed(MouseEvent evt)
                 {
                   if(!av.wrapAlignment)
-                    doMousePressed(evt);
-                }
-
-                public void mouseReleased(MouseEvent evt)
-                {
-                  if(!av.wrapAlignment)
-                    doMouseReleased(evt);
+                  {
+                    boxX = evt.getX();
+                    boxY = evt.getY();
+                    checkValid();
+                  }
                 }
             });
 
         updateOverviewImage();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void doMousePressed(MouseEvent evt)
-    {
-        boxX = evt.getX();
-        boxY = evt.getY();
-
-        checkValid();
-        repaint();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void doMouseReleased(MouseEvent evt)
-    {
-        boxX = evt.getX();
-        boxY = evt.getY();
-        checkValid();
-
-        ap.setScrollValues((int) (boxX / scalew / av.getCharWidth()),
-                (int) (boxY / scaleh / av.getCharHeight()));
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void doMouseDragged(MouseEvent evt)
-    {
-        boxX = evt.getX();
-        boxY = evt.getY();
-        checkValid();
-
-        ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
-                           (int) (boxY / scaleh / av.getCharHeight()));
-       repaint();
-    }
 
     /**
      * DOCUMENT ME!
@@ -199,8 +159,35 @@ public class OverviewPanel extends JPanel implements Runnable
 
         if (boxX > (width - boxWidth))
         {
-            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 );
+
     }
 
     /**
@@ -223,7 +210,6 @@ public class OverviewPanel extends JPanel implements Runnable
         }
 
         setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
-        setBoxPosition();
 
         Thread thread = new Thread(this);
         thread.start();
@@ -241,8 +227,14 @@ public class OverviewPanel extends JPanel implements Runnable
     {
         miniMe = null;
 
+       if (av.showSequenceFeatures)
+       {
+         fr.transferSettings( ap.seqPanel.seqCanvas.getFeatureRenderer() );
+       }
+
         int alwidth = av.alignment.getWidth();
-        int alheight = av.alignment.getHeight();
+        int alheight = av.alignment.getHeight()
+            +av.alignment.getHiddenSequences().getSize();
 
         setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
 
@@ -257,36 +249,112 @@ public class OverviewPanel extends JPanel implements Runnable
 
 
         Graphics mg = miniMe.getGraphics();
+        mg.setColor(Color.orange);
+        mg.fillRect(0,0,width, miniMe.getHeight());
 
         float sampleCol = (float) alwidth / (float) width;
         float sampleRow = (float) alheight / (float) sequencesHeight;
 
-        for (int col = 0; col < width; col++)
+        int lastcol=-1, lastrow=-1;
+        int color = Color.white.getRGB();
+        int row, col;
+        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)
           {
-            overviewSeq.drawPanel(mg,
-                                            (int) (col * sampleCol),
-                                            (int) (col * sampleCol),
-                                            (int) (row * sampleRow),
-                                            (int) (row * sampleRow) + 1,
-                                            (int) (col * sampleCol),
-                                            (int) (row * sampleRow), 0);
-            mg.translate(0, 1);
-
-            if (av.conservation != null)
+            //No need to recalculate the colours,
+            //Just copy from the row above
+            for (col = 0; col < width; col++)
+            {
+              miniMe.setRGB(col, row, miniMe.getRGB(col, row-1));
+            }
+            continue;
+          }
+
+          lastrow = (int)(row*sampleRow);
+
+          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);
+
+          if(seq==null)
+          {
+            System.out.println(lastrow+" null");
+            continue;
+          }
+
+            for (col = 0; col < width; col++)
+            {
+            if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)
+            {
+              miniMe.setRGB(col,row,color);
+              continue;
+            }
+
+
+            lastcol = (int)(col*sampleCol);
+
+            if (seq.getLength() > lastcol)
+            {
+              color = sr.getResidueBoxColour(
+                  seq, lastcol).getRGB();
+
+              if (av.showSequenceFeatures)
+                color = fr.findFeatureColour(color, lastrow, lastcol);
+            }
+            else
+            {
+              color = -1; //White
+            }
+
+            if(hiddenRow ||
+               (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
+            {
+              color = new Color(color).darker().darker().getRGB();
+            }
+
+
+            miniMe.setRGB(col,row,color);
+
+
+          }
+        }
+
+        if (av.conservation != null)
+        {
+          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);
+            }
           }
-          mg.translate(0, -sequencesHeight);
-          mg.translate(1, 0);
-
         }
-
         System.gc();
 
         resizing = false;
@@ -306,16 +374,49 @@ public class OverviewPanel extends JPanel implements Runnable
     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();
     }