Modified for wrappingAlignment

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9a87b90..2542216 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -408,7 +408,7 @@ public class AlignFrame extends GAlignFrame
   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
   {\r
     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
-    alignPanel.RefreshPanels();\r
+    alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
   }\r
 \r
 \r

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 9d6467a..de6e057 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -112,12 +112,17 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 \r
   public void setWrapAlignment(boolean wrap)\r
   {\r
-      scalePanelHolder.setVisible(!wrap);\r
-      scorePanelHolder.setVisible(!wrap);\r
+    scorePanelHolder.setVisible(!wrap);\r
+    scalePanelHolder.setVisible(!wrap);\r
+    secondaryPanelHolder.setVisible(!wrap);\r
+\r
+    hscroll.setVisible(!wrap);\r
+\r
+    idSpaceFillerPanel.setVisible(!wrap);\r
+    idSpaceFillerPanel1.setVisible(!wrap);\r
+\r
+    RefreshPanels();\r
 \r
-      hscroll.setVisible(!wrap);\r
-      idSpaceFillerPanel.setVisible(!wrap);\r
-      idSpaceFillerPanel1.setVisible(!wrap);\r
   }\r
 \r
 \r
@@ -151,6 +156,17 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     seqPanel.seqCanvas.paintFlag = true;\r
     idPanel.idCanvas.paintFlag = true;\r
     idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );\r
+\r
+    if(av.getWrapAlignment())\r
+    {\r
+      int max = av.alignment.getWidth()/ (seqPanel.seqCanvas.getWidth()/av.charWidth)+1;\r
+\r
+      int h  = (av.alignment.getHeight() + 2)*av.charHeight;\r
+      vextent = seqPanel.seqCanvas.getHeight()/h;\r
+      vscroll.setValues(0,vextent,0,max);\r
+    }\r
+    else\r
+\r
     setScrollValues(av.getStartRes(), av.getStartSeq());\r
     av.getConsensus(true);\r
     if(overviewPanel!=null)\r
@@ -202,9 +218,24 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 \r
     if (evt.getSource() == vscroll)\r
     {\r
-        int offy = vscroll.getValue();\r
+      int offy = vscroll.getValue();\r
+      if (av.getWrapAlignment())\r
+      {\r
+        av.setStartRes( vscroll.getValue() * av.getChunkWidth());\r
+        // System.out.println(vscroll.getValue()+" "+ av.getChunkWidth());\r
+      //  int resSpan = av.alignment.getWidth()/ (seqPanel.seqCanvas.getWidth()/av.charWidth)+1;\r
+     //   int h  = (av.alignment.getHeight() + 2)*av.charHeight;\r
+      //  vextent = seqPanel.seqCanvas.getHeight()/h;\r
+     //   vscroll.setValues(0,vextent,0,max);\r
+\r
+\r
+      // av.setStartSeq(  );\r
+      }\r
+      else\r
+      {\r
         av.setStartSeq(offy);\r
-        av.setEndSeq(offy + seqPanel.seqCanvas.getHeight()/av.getCharHeight());\r
+        av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight());\r
+      }\r
     }\r
 \r
 \r
@@ -216,8 +247,13 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   }\r
 \r
 \r
+\r
   public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException\r
   {\r
+    if(av.getWrapAlignment())\r
+    {\r
+     return PrintWrappedAlignment(pg, pf, pi);\r
+    }\r
 \r
     pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());\r
 \r
@@ -225,6 +261,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     int pheight = (int)pf.getImageableHeight();\r
     int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();\r
 \r
+\r
     pg.setColor(Color.white);\r
     pg.fillRect(0,0,pwidth, pheight);\r
     pg.setFont( av.getFont() );\r
@@ -296,6 +333,87 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     return Printable.PAGE_EXISTS;\r
   }\r
 \r
+  class VPanel extends javax.swing.JPanel\r
+  {\r
+    Image image;\r
+    public VPanel(Image i)\r
+    {\r
+      image = i;\r
+      repaint();\r
+    }\r
+    public void paintComponent(Graphics g)\r
+    {\r
+      if(image!=null)\r
+        g.drawImage(image,0,0,this);\r
+    }\r
+\r
+  }\r
+\r
+  public int PrintWrappedAlignment(Graphics pg, PageFormat pf, int pi)\r
+  {\r
+    pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());\r
+\r
+    int pwidth = (int)pf.getImageableWidth();\r
+    int pheight = (int)pf.getImageableHeight();\r
+    int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();\r
+\r
+    if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)\r
+      pwidth = seqPanel.seqCanvas.getWidth() + idWidth;\r
+\r
+    Image image = createImage(pwidth, pheight);\r
+    pg = image.getGraphics();\r
+\r
+    pg.setColor(Color.white);\r
+    pg.fillRect(0,0,pwidth, pheight);\r
+    pg.setFont( av.getFont() );\r
+\r
+    ////////////////////////////////////\r
+    /// How many sequences and residues can we fit on a printable page?\r
+    AlignmentI da = av.alignment;\r
+    int endy   = da.getHeight();\r
+    int chunkHeight =  (da.getHeight() + 2)*av.charHeight;\r
+    int chunkWidth  =   (pwidth-idWidth)/av.charWidth;\r
+\r
+    int noChunksOnPage = pheight / chunkHeight;\r
+    int totalChunks = endy / chunkHeight;\r
+\r
+    if ( pi*noChunksOnPage > totalChunks )\r
+     return Printable.NO_SUCH_PAGE;\r
+\r
+    ////////////////\r
+    // Draw the ids\r
+    pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight);\r
+\r
+    int row = pi*noChunksOnPage;\r
+    pg.setColor(Color.black);\r
+    for(int ypos=2*av.charHeight;\r
+        ypos <= pheight && row*chunkWidth<da.getWidth();\r
+        ypos += chunkHeight, row++ )\r
+    {\r
+      for (int i = 0; i < endy; i++)\r
+      {\r
+        SequenceI s = da.getSequenceAt(i);\r
+        pg.drawString(s.getDisplayId(), 0,\r
+                      AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +\r
+                      av.charHeight - (av.charHeight / 5));\r
+      }\r
+    }\r
+\r
+    // draw main sequence panel\r
+    pg.translate(idWidth,0);\r
+    seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth-idWidth, pheight, pi*noChunksOnPage*chunkWidth);\r
+\r
+\r
+    javax.swing.JFrame frame = new javax.swing.JFrame();\r
+    frame.setSize(image.getWidth(null), image.getHeight(null));\r
+     frame.setVisible(true);\r
+     frame.getContentPane().setLayout(new BorderLayout());\r
+   VPanel pan = new VPanel(image);\r
+   frame.getContentPane().add(pan, BorderLayout.CENTER);\r
+   frame.validate();\r
+    return Printable.NO_SUCH_PAGE;//.PAGE_EXISTS;\r
+\r
+  }\r
 }\r
 \r
 \r

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 1bf5cc6..11d99d8 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -56,70 +56,25 @@ public class IdCanvas extends JPanel
 \r
     //Which ids are we printing\r
     int starty = av.getStartSeq();\r
-    int endy   = av.getEndSeq();\r
+    int endy   = da.getHeight();\r
 \r
     if (av.getWrapAlignment())\r
     {\r
-       starty = starty%av.getChunkHeight();\r
+          // Draw the rest of the panels\r
+          int chunkHeight =  (da.getHeight() + 2)*av.charHeight;\r
+          int row = av.getStartRes() / av.chunkWidth ;\r
+          for(int ypos=2*av.charHeight;\r
+              ypos <= getHeight() && row*av.chunkWidth<da.getWidth();\r
+              ypos += chunkHeight, row++ )\r
+          {\r
+            for (int i = starty; i < endy; i++)\r
+            {\r
+              SequenceI s = da.getSequenceAt(i);\r
+              drawIdString(gg, s, i, 0, ypos);\r
+            }\r
+          }\r
 \r
-       int ypos     = 0;\r
-       int rowstart = starty;\r
 \r
-       if (starty == 0)\r
-           ypos = 2*charHeight;\r
-       else if (starty == 1)\r
-       {\r
-           starty = 0;\r
-           ypos = charHeight;\r
-       }\r
-\r
-       endy   = starty + da.getHeight();\r
-\r
-       if (endy > da.getHeight()) {\r
-           endy = da.getHeight();\r
-       }\r
-\r
-       for (int i = starty; i < endy; i++) {\r
-         SequenceI s = da.getSequenceAt(i);\r
-         drawIdString(gg,s,i,starty,ypos);\r
-       }\r
-       if (rowstart == 0) {\r
-           ypos   = ypos +  av.getChunkHeight();\r
-       } else if (rowstart == 1) {\r
-           ypos   = ypos +  av.getChunkHeight();\r
-       } else {\r
-           ypos   = ypos +  av.getChunkHeight() - rowstart*charHeight;\r
-       }\r
-\r
-       starty = 0;\r
-\r
-       int chunkwidth = av.getChunkWidth();\r
-       int startx = (int)(av.getEndSeq()/chunkwidth)*chunkwidth;\r
-       int endx   = startx + chunkwidth;\r
-\r
-\r
-       while (ypos <= getHeight() && endx < da.getWidth()) {\r
-\r
-           for (int i = starty; i < endy; i++) {\r
-             SequenceI s = da.getSequenceAt(i);\r
-             drawIdString(gg,s,i,starty,ypos);\r
-           }\r
-\r
-           ypos   += av.getChunkHeight();\r
-           startx += chunkwidth;\r
-           endx = startx + chunkwidth;\r
-\r
-           if (endx > da.getWidth()) {\r
-               endx = da.getWidth();\r
-           }\r
-\r
-           starty = 0;\r
-\r
-           if (endy > da.getHeight()) {\r
-               endy = da.getHeight();\r
-           }\r
-\r
-       }\r
     } else\r
     {\r
 \r

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 939a65e..0e528a2 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -73,6 +73,8 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene
 \r
   public void mouseDragged(MouseEvent e) {\r
     int y = e.getY();\r
+    if(av.getWrapAlignment())\r
+      y-=2*av.charHeight;\r
     int seq = av.getIndex(y);\r
 \r
     if (seq < lastid)\r
@@ -89,7 +91,11 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene
   {\r
     if (e.getClickCount() == 2)\r
     {\r
-       int seq = av.getIndex(e.getY());\r
+       int y = e.getY();\r
+       if(av.getWrapAlignment())\r
+         y-=2*av.charHeight;\r
+\r
+       int seq = av.getIndex(y);\r
        String id = av.getAlignment().getSequenceAt(seq).getName();\r
 \r
        try{\r
@@ -108,6 +114,9 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene
       return;\r
 \r
     int y = e.getY();\r
+    if(av.getWrapAlignment())\r
+      y-=2*av.charHeight;\r
+\r
     int seq = av.getIndex(y);\r
 \r
     if (javax.swing.SwingUtilities.isRightMouseButton(e))\r

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 27a8a9c..3c9bf51 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -35,15 +35,21 @@ public class SeqCanvas extends JPanel
 \r
     }\r
 \r
-  public void drawScale(int startx, int endx,int charWidth, int charHeight,int ypos) {\r
+  public void drawScale(Graphics g, int startx, int endx,int ypos) {\r
       int scalestartx = startx - startx%10 + 10;\r
 \r
-      gg.setColor(Color.black);\r
+      g.setColor(Color.black);\r
+\r
+      for (int i=scalestartx;i < endx;i+= 10)\r
+      {\r
+          String string = String.valueOf(i);\r
+          g.drawString(string,(i-startx-1)*av.charWidth,ypos - av.charHeight/2);\r
+\r
+          g.drawLine( (i-startx-1)*av.charWidth +av.charWidth/2, ypos+2 - av.charHeight/2,\r
+                    (i-startx-1)*av.charWidth +av.charWidth/2, ypos-2 );\r
 \r
-      for (int i=scalestartx;i < endx;i+= 10) {\r
-         String string = String.valueOf(i);\r
-         gg.drawString(string,(int)((i-startx-1)*charWidth),ypos+15 - charHeight*(2));\r
       }\r
+\r
   }\r
 \r
 \r
@@ -58,119 +64,62 @@ public class SeqCanvas extends JPanel
  * in the adjustment listener in SeqPanel when the scrollbars move.\r
  */\r
 \r
-  public void paintComponent(Graphics g) {\r
-\r
-    AlignmentI da = av.getAlignment();\r
+  public void paintComponent(Graphics g)\r
+  {\r
 \r
-    if (img == null ||\r
-        imgWidth  !=  getWidth()  ||\r
-        imgHeight !=  getHeight()\r
-        || paintFlag)\r
+    if (img==null ||  imgWidth!=getWidth() || imgHeight!=getHeight() || paintFlag)\r
     {\r
-\r
       imgWidth  = getWidth();\r
       imgHeight = getHeight();\r
-\r
       img = createImage(imgWidth,imgHeight);\r
       gg  = img.getGraphics();\r
-\r
       gg.setFont(av.getFont());\r
-\r
       paintFlag = false;\r
     }\r
 \r
+\r
     chunkWidth  =   getWidth()/av.charWidth;\r
-    chunkHeight =  (da.getHeight() + 2)*av.charHeight;\r
+    chunkHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;\r
 \r
     av.setChunkHeight(chunkHeight);\r
     av.setChunkWidth(chunkWidth);\r
 \r
-\r
-\r
     fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight);\r
 \r
-    /* if (av.getWrapAlignment()) {\r
-        int offy = av.getStartSeq();\r
-         startx = (int)(offy/chunkWidth)*chunkWidth;\r
-         endx   = startx + chunkWidth;\r
-         starty = offy%chunkHeight;\r
-         endy   = starty + da.getHeight();\r
-\r
-         int ypos     = 0;\r
-         int rowstart = starty;\r
-\r
-         if (starty == 0) {\r
-             ypos = 2*charHeight;\r
-         } else if (starty == 1) {\r
-             starty = 0;\r
-             ypos = charHeight;\r
-         }\r
-\r
-         if (endy > da.getHeight()) {\r
-             endy = da.getHeight();\r
-         }\r
-\r
-         if (endx > da.getWidth()) {\r
-             endx = da.getWidth();\r
-         }\r
-\r
-         if (rowstart < 2) {\r
-             drawScale(startx,endx,charWidth,charHeight,ypos);\r
-         }\r
-\r
-         drawPanel(gg,startx,endx,starty,endy,startx,starty,ypos);\r
-\r
-         if (rowstart == 0) {\r
-             ypos = ypos + chunkHeight;\r
-         } else if (rowstart == 1) {\r
-             ypos = ypos + chunkHeight;\r
-         } else {\r
-             ypos   = ypos + chunkHeight - rowstart*charHeight;\r
-         }\r
-\r
-         startx += chunkWidth;\r
-         endx   = startx + chunkWidth;\r
-         starty = 0;\r
-\r
-         if (endx > da.getWidth()) {\r
-             endx = da.getWidth();\r
-         }\r
-         // Draw the rest of the panels\r
-\r
-         while (ypos <= getHeight()) {\r
-             drawScale(startx,endx,charWidth,charHeight,ypos);\r
-             drawPanel(gg,startx,endx,0,da.getHeight(),startx,starty,ypos);\r
-\r
-             ypos   += chunkHeight;\r
-             startx += chunkWidth;\r
-             endx   = startx + chunkWidth;\r
-\r
-             if (endy > da.getHeight()) {\r
-                 endy = da.getHeight();\r
-             }\r
-\r
-             if (endx > da.getWidth()) {\r
-                 endx = da.getWidth();\r
-             }\r
-\r
-         }\r
-      }\r
-      else*/\r
-      {\r
-         drawPanel(gg,av.startRes,av.endRes,av.startSeq,av.endSeq,av.startRes,av.startSeq,0);\r
-      }\r
-\r
+    if (av.getWrapAlignment())\r
+      drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);\r
+    else\r
+      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes, av.startSeq, 0);\r
 \r
-  /*  if ((oldendy -oldstarty) > (getWidth() / av.getCharWidth())) {\r
-      System.out.println("LIMITS ERROR LIMITS ERROR");\r
-      System.out.println("Corrds " + (oldendy-oldstarty) + " " + (getWidth()/av.getCharWidth()) + " " + getWidth() + " " + av.getCharWidth());\r
-    }*/\r
 \r
     g.drawImage(img,0,0,this);\r
 \r
   }\r
 \r
+  public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)\r
+  {\r
+      AlignmentI da = av.getAlignment();\r
+\r
+      int cWidth  =   canvasWidth/av.charWidth;\r
+      int cHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;\r
 \r
+      int  endx   = startRes+cWidth-1;\r
+      int ypos  = 2*av.charHeight;\r
+\r
+      while (ypos <= canvasHeight)\r
+      {\r
+        drawScale(g, startRes, endx, ypos);\r
+        drawPanel(g, startRes, endx, 0, da.getHeight(), startRes, 0, ypos);\r
+\r
+        ypos += cHeight;\r
+        startRes += cWidth;\r
+        endx = startRes + cWidth - 1;\r
+\r
+        if (endx > da.getWidth())\r
+          endx = da.getWidth();\r
+      }\r
+\r
+  }\r
 \r
 \r
   public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {\r

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index ab2e1ef..aa4a456 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -38,10 +38,15 @@ public class SeqPanel extends JPanel
     addMouseMotionListener( new MouseMotionAdapter()\r
     {\r
       public void mouseMoved(MouseEvent evt)\r
-      {   doMouseMoved(evt);    }\r
+      {\r
+       if(av.getWrapAlignment())\r
+         return;\r
+        doMouseMoved(evt);    }\r
 \r
       public void mouseDragged(MouseEvent evt)\r
       {\r
+        if(av.getWrapAlignment())\r
+         return;\r
         if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
           doMouseDragged(evt);\r
         else\r
@@ -53,6 +58,8 @@ public class SeqPanel extends JPanel
     {\r
       public void mouseReleased(MouseEvent evt)\r
       {\r
+        if(av.getWrapAlignment())\r
+         return;\r
         if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
           doMouseReleased(evt);\r
         else\r
@@ -60,6 +67,8 @@ public class SeqPanel extends JPanel
       }\r
       public void mousePressed(MouseEvent evt)\r
       {\r
+        if(av.getWrapAlignment())\r
+         return;\r
         if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
           doMousePressed(evt);\r
         else\r