Overviewpanel allows for large alignments

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index f165bd3..b217e9c 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -579,8 +579,10 @@ public class AlignFrame extends GAlignFrame
     JInternalFrame frame = new JInternalFrame();\r
     FontChooser fc = new FontChooser( alignPanel, frame );\r
     frame.setContentPane(fc);\r
-    Desktop.addInternalFrame(frame, "Change Font", 480,100);\r
+    Desktop.addInternalFrame(frame, "Change Font", 480,100, false);\r
     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
+    if(alignPanel.getOverviewPanel()!=null)\r
+      alignPanel.getOverviewPanel().updateOverviewImage();\r
   }\r
 \r
   protected void fullSeqId_actionPerformed(ActionEvent e)\r
@@ -674,27 +676,20 @@ public class AlignFrame extends GAlignFrame
       return;\r
 \r
     JInternalFrame frame = new JInternalFrame();\r
-    OverviewPanel overview = alignPanel.getOverviewPanel();\r
-   try{\r
-     overview = new OverviewPanel(alignPanel, viewport);\r
+    OverviewPanel overview = new OverviewPanel(alignPanel);\r
      frame.setContentPane(overview);\r
     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
                              frame.getWidth(), frame.getHeight());\r
     frame.pack();\r
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
       {\r
             alignPanel.setOverviewPanel(null);\r
       };\r
     });\r
-    alignPanel.setOverviewPanel( overview );\r
 \r
-  }catch(java.lang.OutOfMemoryError ex)\r
-   {\r
-     JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
-                                   +"\nTry reducing the font size.",\r
-                                   "Out of memory", JOptionPane.WARNING_MESSAGE);\r
-   }\r
+    alignPanel.setOverviewPanel( overview );\r
 \r
 \r
   }\r
@@ -870,8 +865,8 @@ public class AlignFrame extends GAlignFrame
       }\r
     }\r
 \r
-\r
-\r
+    if(alignPanel.getOverviewPanel()!=null)\r
+      alignPanel.getOverviewPanel().updateOverviewImage();\r
     alignPanel.repaint();\r
   }\r
 \r

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 45edace..3257ce5 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -5,7 +5,7 @@ import java.awt.event.*;
 import java.awt.image.*;\r
 import java.awt.*;\r
 \r
-public class OverviewPanel extends JPanel\r
+public class OverviewPanel extends JPanel implements Runnable\r
 {\r
   BufferedImage miniMe;\r
   AlignViewport av;\r
@@ -13,49 +13,47 @@ public class OverviewPanel extends JPanel
   float scalew = 1f;\r
   float scaleh = 1f;\r
 \r
-  int sequencesWidth, sequencesHeight;\r
+  int width, sequencesHeight;\r
   int graphHeight=30;\r
   int boxX=-1, boxY=-1, boxWidth=-1, boxHeight=-1;\r
 \r
-  public OverviewPanel(AlignmentPanel ap, AlignViewport av)\r
+  boolean resizing = false;\r
+\r
+  public OverviewPanel(AlignmentPanel ap)\r
   {\r
-    this.av = av;\r
+    this.av = ap.av;\r
     this.ap = ap;\r
+    setLayout(null);\r
 \r
     // scale the initial size of overviewpanel to shape of alignment\r
-\r
-    float initialScale = (float)av.getAlignment().getWidth()/(float)av.getAlignment().getHeight();\r
-    if(av.getAlignment().getWidth() > av.getAlignment().getHeight())\r
+    float initialScale = (float)av.alignment.getWidth()/(float)av.alignment.getHeight();\r
+    if(av.alignment.getWidth() > av.alignment.getHeight())\r
     {\r
       // wider\r
-      sequencesWidth = 400;\r
+      width = 400;\r
       sequencesHeight = (int)(400f/initialScale);\r
     }\r
     else\r
     {\r
       // taller\r
-      sequencesWidth = (int)(400f*initialScale);\r
+      width = (int)(400f*initialScale);\r
       sequencesHeight = 300;\r
+      if(width<120)\r
+        width = 120;\r
     }\r
 \r
-\r
-\r
-    setSize(sequencesWidth, sequencesHeight+graphHeight);\r
-    setLayout(null);\r
-\r
-    updateOverviewImage();\r
-\r
     addComponentListener(new ComponentAdapter()\r
    {\r
 \r
        public void componentResized(ComponentEvent evt)\r
        {\r
-         if( getWidth()!=sequencesWidth || getHeight()!=sequencesHeight+graphHeight)\r
+         if( getWidth()!=width || getHeight()!=sequencesHeight+graphHeight)\r
+         {\r
            updateOverviewImage();\r
+         }\r
        }\r
    });\r
 \r
-\r
     addMouseMotionListener(new MouseMotionAdapter()\r
            {\r
              public void mouseDragged(MouseEvent evt)\r
@@ -70,112 +68,169 @@ public class OverviewPanel extends JPanel
       { doMouseReleased(evt);}\r
     });\r
 \r
+    updateOverviewImage();\r
+\r
   }\r
 \r
   public void doMousePressed(MouseEvent evt)\r
   {\r
-    checkValid(evt.getX(), evt.getY());\r
+    boxX = evt.getX();\r
+    boxY = evt.getY();\r
+\r
+    checkValid();\r
     repaint();\r
   }\r
 \r
   public void doMouseReleased(MouseEvent evt)\r
   {\r
-    int x = evt.getX();\r
-    int y = evt.getY();\r
-    checkValid(x, y);\r
-    ap.setScrollValues( (int)(x/scalew/av.getCharWidth()), (int)(y/scaleh/av.getCharHeight()) );\r
+    boxX = evt.getX();\r
+    boxY = evt.getY();\r
+    checkValid();\r
+    if(!resizing)\r
+    ap.setScrollValues( (int)(boxX/scalew/av.getCharWidth()),\r
+                        (int)(boxY/scaleh/av.getCharHeight()) );\r
   }\r
 \r
   public void doMouseDragged(MouseEvent evt)\r
   {\r
-    int x = evt.getX();\r
-    int y = evt.getY();\r
-    checkValid(x, y);\r
-    ap.setScrollValues( (int)(x/scalew/av.getCharWidth()), (int)(y/scaleh/av.getCharHeight()) );\r
-    repaint();\r
+    boxX = evt.getX();\r
+    boxY = evt.getY();\r
+    checkValid();\r
+    if(!resizing)\r
+    ap.setScrollValues( (int)(boxX/scalew/av.getCharWidth()),\r
+                        (int)(boxY/scaleh/av.getCharHeight()) );\r
   }\r
 \r
-  void checkValid(int x, int y)\r
+  void checkValid()\r
   {\r
+    if (boxY < 0)\r
+      boxY = 0;\r
 \r
-    if (y < 0)\r
-      y = 0;\r
-    if (y > sequencesHeight - boxHeight)\r
-      y = sequencesHeight- boxHeight;\r
+    if (boxY > sequencesHeight - boxHeight)\r
+      boxY = sequencesHeight - boxHeight+1;\r
 \r
+    if (boxX < 0)\r
+      boxX = 0;\r
 \r
-    if (x < 0)\r
-      x = 0;\r
+    if (boxX > width - boxWidth)\r
+      boxX = width - boxWidth;\r
+  }\r
 \r
-    if (x > sequencesWidth - boxWidth)\r
-      x = sequencesWidth - boxWidth;\r
+  public void updateOverviewImage()\r
+  {\r
+    if(resizing)\r
+    {\r
+      return;\r
+    }\r
 \r
-    boxX = x;\r
-    boxY = y;\r
+    resizing = true;\r
+    Thread thread = new Thread(this);\r
+    thread.start();\r
+    repaint();\r
   }\r
 \r
-  public void updateOverviewImage()\r
+  public void run()\r
   {\r
+    miniMe = null;\r
+    int alwidth = av.alignment.getWidth();\r
+    int alheight = av.alignment.getHeight();\r
 \r
-  boolean oldRenderGaps = av.renderGaps;\r
-  av.setRenderGaps(false);\r
-   miniMe = null;\r
-   setPreferredSize (new Dimension(sequencesWidth, sequencesHeight+graphHeight));\r
-   sequencesWidth=getWidth();\r
-   sequencesHeight=this.getHeight()-graphHeight;\r
+    if(getWidth()>0 && getHeight()>0)\r
+    {\r
+      width = getWidth();\r
+      sequencesHeight = getHeight() - graphHeight;\r
+    }\r
 \r
+    setPreferredSize (new Dimension(width, sequencesHeight+graphHeight));\r
 \r
-    int fullsizeWidth  = av.getAlignment().getWidth() * av.getCharWidth();\r
-    int fullsizeHeight = av.getAlignment().getHeight()* av.getCharHeight();\r
+    int fullsizeWidth  = alwidth * av.getCharWidth();\r
+    int fullsizeHeight = alheight * av.getCharHeight();\r
 \r
+    scalew = (float) width / (float) fullsizeWidth;\r
+    scaleh = (float) sequencesHeight / (float) fullsizeHeight;\r
 \r
-    BufferedImage fullSize = new BufferedImage(fullsizeWidth,\r
-                                               fullsizeHeight,\r
-                                               BufferedImage.TYPE_INT_RGB);\r
+    miniMe = new BufferedImage(width, sequencesHeight + graphHeight,\r
+                               BufferedImage.TYPE_INT_RGB);\r
 \r
+    Graphics mg = miniMe.getGraphics();\r
     BufferedImage consensus = new BufferedImage(fullsizeWidth,\r
-                                               60,\r
-                                               BufferedImage.TYPE_INT_RGB);\r
+                                           60,\r
+                                           BufferedImage.TYPE_3BYTE_BGR);\r
+    Graphics g = consensus.getGraphics();\r
+    ap.annotationPanel.drawGraph(g, av.conservation, fullsizeWidth, 60);\r
+    mg.drawImage(consensus, 0, sequencesHeight, width,\r
+             sequencesHeight + graphHeight, 0, 0, fullsizeWidth, 60, this);\r
 \r
 \r
-    Graphics g = fullSize.getGraphics();\r
-    ap.seqPanel.seqCanvas.drawPanel(g,0,av.getAlignment().getWidth(),0,av.getAlignment().getHeight(),0,0,0);\r
+    boolean oldRenderGaps = av.renderGaps;\r
+    try{\r
+    // We'll have to draw the full size alignment in chunks, as an image of the\r
+    // whole alignment requires too much memory\r
 \r
-    g = consensus.getGraphics();\r
+      // Max size depends on the font size, the following is a\r
+      // guess at a size which works\r
+      int maxSize = 2000 /  av.getFont().getSize();\r
+      BufferedImage block;\r
+      int blockx=0, blocky=0, blockw=0, blockh=0, eRes=0, eSeq=0;\r
 \r
-    ap.annotationPanel.drawGraph(g, av.conservation, fullsizeWidth, 60);\r
+      av.setRenderGaps(false);\r
+      for(int sRes=0, chunkx=0; sRes<alwidth; sRes+=maxSize, chunkx++)\r
+      {\r
+          eSeq = 0;\r
+          eRes+=maxSize;\r
+          if(eRes>alwidth)\r
+            eRes = alwidth;\r
+\r
+          for(int sSeq=0, chunky=0; sSeq<alheight; sSeq+=maxSize, chunky++)\r
+          {\r
+            eSeq+=maxSize;\r
+            if(eSeq>alheight)\r
+              eSeq = alheight;\r
+\r
+            blocky = 0;\r
+            blockx = (int)((float)sRes/(float)alwidth * width);\r
+\r
+            block = new BufferedImage((eRes-sRes)*av.charWidth,\r
+              (eSeq-sSeq)*av.charHeight,\r
+              BufferedImage.TYPE_3BYTE_BGR);\r
+            g = block.getGraphics();\r
+\r
+           ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq, sRes, sSeq, 0);\r
+\r
+           blockh = (int)( (float)(eSeq-sSeq)/(float)alheight *  sequencesHeight  )+1 ;\r
+           blockw = (int)( (float)(eRes-sRes)/(float)alwidth  *   width )+1;\r
+\r
+           blocky += (int) ((float)sSeq/(float)alheight* sequencesHeight);\r
+\r
+           mg.drawImage(block,  blockx,\r
+                              blocky ,\r
+                            blockx + blockw,\r
+                            blocky + blockh,\r
+\r
+                         0, 0, block.getWidth(),block.getHeight(), this);\r
+\r
+          block = null;\r
+          }\r
+\r
+      }\r
+\r
+    }catch(OutOfMemoryError error)\r
+    {     System.out.println("out of memory");   }\r
 \r
-    try{\r
-      miniMe = new BufferedImage(sequencesWidth, sequencesHeight + graphHeight,\r
-                                 BufferedImage.TYPE_INT_RGB);\r
-      Graphics mg = miniMe.getGraphics();\r
-\r
-      mg.drawImage(fullSize, 0, 0, sequencesWidth, sequencesHeight, 0, 0,\r
-                   fullsizeWidth, fullsizeHeight, this);\r
-      mg.drawImage(consensus, 0, sequencesHeight, sequencesWidth,\r
-                   sequencesHeight + graphHeight, 0, 0, fullsizeWidth, 60, this);\r
-\r
-      scalew = (float) sequencesWidth / (float) fullsizeWidth;\r
-      scaleh = (float) sequencesHeight / (float) fullsizeHeight;\r
-\r
-      setBoxPosition();\r
-    }catch(Exception ex)\r
-    {// most likely the frame size is zero\r
-      miniMe = null;\r
-    }\r
 \r
     av.setRenderGaps(oldRenderGaps);\r
+    resizing = false;\r
 \r
+    setBoxPosition();\r
   }\r
 \r
   public void setBoxPosition()\r
   {\r
       boxX = (int) (av.getStartRes() * av.getCharWidth() * scalew);\r
       boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh);\r
-      boxWidth = (int) (av.getEndRes() * av.getCharWidth() * scalew) - boxX;\r
+      boxWidth = (int) ((av.getEndRes()-av.getStartRes()+1)* av.getCharWidth() * scalew) ;\r
       boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) - boxY;\r
       repaint();\r
-\r
   }\r
 \r
 \r
@@ -183,13 +238,23 @@ public class OverviewPanel extends JPanel
   {\r
     g.setColor(Color.white);\r
     g.fillRect(0,0,getWidth(),getHeight());\r
-    if(miniMe!=null)\r
-      g.drawImage(miniMe, 0,0,this);\r
+    g.setColor(Color.black);\r
 \r
-    g.setColor(Color.red);\r
+    if(resizing)\r
+    {\r
+      g.setFont(new Font("Verdana", Font.BOLD, 15));\r
+      g.drawString("Recalculating", 5, sequencesHeight/2);\r
+      g.drawString("Overview.....", 5, sequencesHeight/2 +20);\r
+    }\r
+    else\r
+    {\r
+      if(miniMe!=null)\r
+        g.drawImage(miniMe, 0,0,this);\r
 \r
-    g.drawRect(boxX, boxY, boxWidth, boxHeight);\r
-    g.drawRect(boxX+1, boxY+1, boxWidth-2, boxHeight-2);\r
+      g.setColor(Color.red);\r
+      g.drawRect(boxX, boxY, boxWidth, boxHeight);\r
+      g.drawRect(boxX+1, boxY+1, boxWidth-2, boxHeight-2);\r
+    }\r
   }\r
 \r
 }\r