X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=d3f513b3e263b8123469eb8da564457621af91e1;hb=efbf36f3efcd7a971a6ca33d098f54b204f2cae9;hp=62f8ca9fb31f8f6e50b58be7f51d81215b32d96b;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 62f8ca9..d3f513b 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -40,13 +40,18 @@ public class OverviewPanel extends JPanel implements Runnable
     float scaleh = 1f;
     int width;
     int sequencesHeight;
-    int graphHeight = 30;
+    int graphHeight = 20;
     int boxX = -1;
     int boxY = -1;
     int boxWidth = -1;
     int boxHeight = -1;
     boolean resizing = false;
 
+    // Can set different properties in this seqCanvas than
+    // main visible SeqCanvas
+    SequenceRenderer sr;
+    FeatureRenderer fr;
+
     /**
      * Creates a new OverviewPanel object.
      *
@@ -58,14 +63,25 @@ public class OverviewPanel extends JPanel implements Runnable
         this.ap = ap;
         setLayout(null);
 
+        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.conservation==null)
+          graphHeight = 0;
+
+
         if (av.alignment.getWidth() > av.alignment.getHeight())
         {
             // wider
             width = 400;
             sequencesHeight = (int) (400f / initialScale);
+            if(sequencesHeight<40)
+              sequencesHeight = 40;
         }
         else
         {
@@ -95,6 +111,7 @@ public class OverviewPanel extends JPanel implements Runnable
             {
                 public void mouseDragged(MouseEvent evt)
                 {
+                  if(!av.wrapAlignment)
                     doMouseDragged(evt);
                 }
             });
@@ -103,11 +120,13 @@ 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);
                 }
             });
@@ -140,11 +159,22 @@ public class OverviewPanel extends JPanel implements Runnable
         boxY = evt.getY();
         checkValid();
 
-        if (!resizing)
+        if(av.hasHiddenColumns)
         {
-            ap.setScrollValues((int) (boxX / scalew / av.getCharWidth()),
+          int col = (int) ( boxX / scalew / av.getCharWidth());
+
+          if(av.getColumnSelection().isVisible(col))
+          {
+            ap.setScrollValues(
+                av.getColumnSelection().findColumnPosition(col),
                 (int) (boxY / scaleh / av.getCharHeight()));
+          }
+          else
+            System.out.println(col +" not visible");
         }
+        else
+          ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
+                            (int) (boxY / scaleh / av.getCharHeight()));
     }
 
     /**
@@ -158,11 +188,23 @@ public class OverviewPanel extends JPanel implements Runnable
         boxY = evt.getY();
         checkValid();
 
-        if (!resizing)
+        if(av.hasHiddenColumns)
         {
-            ap.setScrollValues((int) (boxX / scalew / av.getCharWidth()),
+          int col = (int) ( boxX / scalew / av.getCharWidth());
+
+          if(!av.getColumnSelection().isVisible(col))
+          {
+            return;
+          }
+
+            ap.setScrollValues(
+               av.getColumnSelection().findColumnPosition( col ),
                 (int) (boxY / scaleh / av.getCharHeight()));
         }
+        else
+        ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
+                            (int) (boxY / scaleh / av.getCharHeight()));
+       repaint();
     }
 
     /**
@@ -187,7 +229,14 @@ 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;
         }
     }
 
@@ -198,16 +247,29 @@ public class OverviewPanel extends JPanel implements Runnable
     {
         if (resizing)
         {
+            resizeAgain = true;
             return;
         }
 
         resizing = true;
 
+        if ( (getWidth() > 0) && (getHeight() > 0))
+        {
+          width = getWidth();
+          sequencesHeight = getHeight() - graphHeight;
+        }
+
+        setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
+
         Thread thread = new Thread(this);
         thread.start();
         repaint();
     }
 
+    // This is set true if the user resizes whilst
+    // the overview is being calculated
+    boolean resizeAgain = false;
+
     /**
      * DOCUMENT ME!
      */
@@ -215,14 +277,14 @@ public class OverviewPanel extends JPanel implements Runnable
     {
         miniMe = null;
 
-        int alwidth = av.alignment.getWidth();
-        int alheight = av.alignment.getHeight();
+       if (av.showSequenceFeatures)
+       {
+         fr.transferSettings( ap.seqPanel.seqCanvas.getFeatureRenderer() );
+       }
 
-        if ((getWidth() > 0) && (getHeight() > 0))
-        {
-            width = getWidth();
-            sequencesHeight = getHeight() - graphHeight;
-        }
+        int alwidth = av.alignment.getWidth();
+        int alheight = av.alignment.getHeight()
+            +av.alignment.getHiddenSequences().getSize();
 
         setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
 
@@ -235,90 +297,125 @@ public class OverviewPanel extends JPanel implements Runnable
         miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
                 BufferedImage.TYPE_INT_RGB);
 
+
         Graphics mg = miniMe.getGraphics();
-        BufferedImage consensus = new BufferedImage(fullsizeWidth, 60,
-                BufferedImage.TYPE_3BYTE_BGR);
-        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);
+        mg.setColor(Color.orange);
+        mg.fillRect(0,0,width, miniMe.getHeight());
+
+        float sampleCol = (float) alwidth / (float) width;
+        float sampleRow = (float) alheight / (float) sequencesHeight;
+
+        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++)
+        {
+          if((int)(row*sampleRow)==lastrow)
+          {
+            //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;
+          }
 
-        boolean oldRenderGaps = av.renderGaps;
+          lastrow = (int)(row*sampleRow);
 
-        try
-        {
-            // 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();
-            BufferedImage block;
-            int blockx = 0;
-            int blocky = 0;
-            int blockw = 0;
-            int blockh = 0;
-            int eRes = 0;
-            int eSeq = 0;
-
-            av.setRenderGaps(false);
-
-            for (int sRes = 0, chunkx = 0; sRes < alwidth;
-                    sRes += maxSize, chunkx++)
+          hiddenRow = false;
+          if (av.hasHiddenRows)
+          {
+            seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
+            if (seq == null)
             {
-                eSeq = 0;
-                eRes += maxSize;
 
-                if (eRes > alwidth)
-                {
-                    eRes = alwidth;
-                }
+              int index =
+                 av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(lastrow);
 
-                for (int sSeq = 0, chunky = 0; sSeq < alheight;
-                        sSeq += maxSize, chunky++)
-                {
-                    eSeq += maxSize;
 
-                    if (eSeq > alheight)
-                    {
-                        eSeq = alheight;
-                    }
+             seq = av.alignment.getSequenceAt(index);
+            }
+            else
+            {
+              hiddenRow = true;
+            }
+          }
+          else
+            seq = av.alignment.getSequenceAt(lastrow);
 
-                    blocky = 0;
-                    blockx = (int) ((float) sRes / (float) alwidth * width);
+          if(seq==null)
+          {
+            System.out.println(lastrow+" null");
+            continue;
+          }
 
-                    block = new BufferedImage((eRes - sRes) * av.charWidth,
-                            (eSeq - sSeq) * av.charHeight,
-                            BufferedImage.TYPE_3BYTE_BGR);
-                    g = block.getGraphics();
+            for (col = 0; col < width; col++)
+            {
+            if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)
+            {
+              miniMe.setRGB(col,row,color);
+              continue;
+            }
 
-                    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).getRGB();
 
-                    mg.drawImage(block, blockx, blocky, blockx + blockw,
-                        blocky + blockh, 0, 0, block.getWidth(),
-                        block.getHeight(), this);
+              if (av.showSequenceFeatures)
+                color = fr.findFeatureColour(color, lastrow, lastcol);
+            }
+            else
+            {
+              color = -1; //White
+            }
 
-                    block = null;
-                }
+            if(hiddenRow ||
+               (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
+            {
+              color = new Color(color).darker().darker().getRGB();
             }
+
+
+            miniMe.setRGB(col,row,color);
+
+
+          }
         }
-        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();
+
+        if(resizeAgain)
+        {
+          resizeAgain = false;
+          updateOverviewImage();
+        }
     }
 
     /**
@@ -326,9 +423,31 @@ public class OverviewPanel extends JPanel implements Runnable
      */
     public void setBoxPosition()
     {
-        boxX = (int) (av.getStartRes() * av.getCharWidth() * scalew);
+      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);
+      }
+
+
+      scalew = (float) width / (float) fullsizeWidth;
+      scaleh = (float) sequencesHeight / (float) fullsizeHeight;
+
+        boxX = (int) (startRes * av.getCharWidth() * scalew);
         boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh);
-        boxWidth = (int) ((av.getEndRes() - av.getStartRes() + 1) * av.getCharWidth() * scalew);
+
+        if(av.hasHiddenColumns)
+          boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+        else
+          boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+
         boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) -
             boxY;
         repaint();
@@ -341,26 +460,24 @@ public class OverviewPanel extends JPanel implements Runnable
      */
     public void paintComponent(Graphics g)
     {
-        g.setColor(Color.white);
-        g.fillRect(0, 0, getWidth(), getHeight());
-        g.setColor(Color.black);
-
-        if (resizing)
+        if (miniMe != null && !resizing)
         {
-            g.setFont(new Font("Verdana", Font.BOLD, 15));
-            g.drawString("Recalculating", 5, sequencesHeight / 2);
-            g.drawString("Overview.....", 5, (sequencesHeight / 2) + 20);
+          g.drawImage(miniMe, 0, 0, this);
         }
         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.setColor(Color.white);
+          g.fillRect(0, 0, getWidth(), getHeight());
+          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);
+
     }
 }