X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=26b470a3d546e4162debb1c4114a63841dad4217;hb=9be2898dd1635c87539a90de321975f043d005f3;hp=02330a58e5b492cc99630abb98539d6ef7152d1e;hpb=8e67558df4403377d98e3efb232a10bf72fbcdbf;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 02330a5..26b470a 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -11,6 +11,7 @@ import java.io.*;
 import java.awt.image.*;
 import org.jibble.epsgraphics.*;
 import javax.imageio.*;
+import javax.swing.*;
 
 
 
@@ -72,32 +73,13 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
            av.setSelectionGroup(null);
            repaint();
            break;
-         case KeyEvent.VK_X:
-           if(evt.isControlDown())
-           alignFrame.cut_actionPerformed(null);
-           break;
-         case KeyEvent.VK_C:
-         if(evt.isControlDown())
-           alignFrame.copy_actionPerformed(null);
-           break;
-         case KeyEvent.VK_V:
-          if(evt.isControlDown())
-           alignFrame.paste(true);
-           break;
-         case KeyEvent.VK_A:
-         if(evt.isControlDown())
-           alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
-           break;
+
         case KeyEvent.VK_DOWN:
           alignFrame.moveSelectedSequences(false);
           break;
         case KeyEvent.VK_UP:
           alignFrame.moveSelectedSequences(true);
           break;
-        case KeyEvent.VK_F:
-         if(evt.isControlDown())
-          alignFrame.findMenuItem_actionPerformed(null);
-          break;
        }
      }
    });
@@ -107,6 +89,11 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   {
     // set idCanvas bufferedImage to null
     // to prevent drawing old image
+    FontMetrics fm = getFontMetrics(av.getFont());
+
+    scalePanelHolder.setPreferredSize(new Dimension(10, av.charHeight+fm.getDescent()));
+    idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight+fm.getDescent()));
+
     idPanel.idCanvas.gg = null;
     annotationPanel.adjustPanelHeight();
     Dimension d = calculateIdWidth();
@@ -285,6 +272,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
   public void setScrollValues(int x, int y)
   {
+    av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
+
     hextent = seqPanel.seqCanvas.getWidth()/av.charWidth;
     vextent = seqPanel.seqCanvas.getHeight()/av.charHeight;
 
@@ -308,6 +297,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
     vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
 
+
+
   }
 
 
@@ -339,7 +330,6 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       }
     }
 
-
     if(overviewPanel!=null)
       overviewPanel.setBoxPosition();
 
@@ -376,8 +366,6 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     }
     else
     {
-      if (overviewPanel != null)
-        overviewPanel.updateOverviewImage();
       setScrollValues(av.getStartRes(), av.getStartSeq());
     }
 
@@ -401,149 +389,159 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
   {
 
-    int idWidth = calculateIdWidth().width + 4;
+      int idWidth = calculateIdWidth().width + 4;
+      FontMetrics fm = getFontMetrics(av.getFont());
+      int scaleHeight = av.charHeight + fm.getDescent();
 
+      pg.setColor(Color.white);
+      pg.fillRect(0, 0, pwidth, pheight);
+      pg.setFont(av.getFont());
 
-    pg.setColor(Color.white);
-    pg.fillRect(0,0,pwidth, pheight);
-    pg.setFont( av.getFont() );
+      ////////////////////////////////////
+      /// How many sequences and residues can we fit on a printable page?
+      int totalRes = (pwidth - idWidth) / av.getCharWidth();
 
-    ////////////////////////////////////
-    /// How many sequences and residues can we fit on a printable page?
-    int totalRes = (pwidth - idWidth)/av.getCharWidth();
-    int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;
-    int pagesWide = av.getAlignment().getWidth() / totalRes +1;
-    int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;
+      int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) - 1;
 
-    if (pi >= pagesWide*pagesHigh)
-     return Printable.NO_SUCH_PAGE;
+      int pagesWide = av.getAlignment().getWidth() / totalRes + 1;
 
-    /////////////////////////////
-    /// Only print these sequences and residues on this page
-    int startRes, endRes, startSeq, endSeq;
-    startRes = (pi % pagesWide) * totalRes;
-    endRes = startRes + totalRes-1;
-    if(endRes>av.getAlignment().getWidth())
-      endRes = av.getAlignment().getWidth();
+      /////////////////////////////
+      /// Only print these sequences and residues on this page
+      int startRes, endRes, startSeq, endSeq;
+      startRes = (pi % pagesWide) * totalRes;
+      endRes = startRes + totalRes - 1;
+      if (endRes > av.getAlignment().getWidth()-1)
+        endRes = av.getAlignment().getWidth()-1;
 
-     startSeq = (pi / pagesWide) * totalSeq;
-     endSeq = startSeq + totalSeq;
-     if(endSeq > av.getAlignment().getHeight())
-       endSeq = av.getAlignment().getHeight();
+      startSeq = (pi / pagesWide) * totalSeq;
+      endSeq = startSeq + totalSeq;
+      if (endSeq > av.getAlignment().getHeight())
+        endSeq = av.getAlignment().getHeight();
 
+      int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
 
-    ////////////////
-    //draw Scale
-    pg.translate(idWidth,0);
-    scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth);
+      if (av.showAnnotation)
+        pagesHigh += annotationPanel.getHeight();
 
-    pg.translate(-idWidth, 30);
-    ////////////////
-    // Draw the ids
-    Color currentColor=null;
-    Color currentTextColor=null;
-    for(int i=startSeq; i<endSeq; i++)
-    {
-      if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(av.getAlignment().getSequenceAt(i)))
-      {
-        currentColor = Color.gray;
-        currentTextColor = Color.black;
-      }
-      else
+      pagesHigh /= pheight;
+
+      if (pi >= pagesWide * pagesHigh)
+        return Printable.NO_SUCH_PAGE;
+
+        //draw Scale
+      pg.translate(idWidth, 0);
+      scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
+      pg.translate( -idWidth, scaleHeight);
+      ////////////////
+      // Draw the ids
+      Color currentColor = null;
+      Color currentTextColor = null;
+      for (int i = startSeq; i < endSeq; i++)
       {
-        currentColor = av.getAlignment().getSequenceAt(i).getColor();
-        currentTextColor = Color.black;
-      }
+        if (av.getSelectionGroup() != null &&
+            av.getSelectionGroup().sequences.
+            contains(av.getAlignment().getSequenceAt(i)))
+        {
+          currentColor = Color.gray;
+          currentTextColor = Color.black;
+        }
+        else
+        {
+          currentColor = av.getAlignment().getSequenceAt(i).getColor();
+          currentTextColor = Color.black;
+        }
 
-      pg.setColor(currentColor);
-      pg.fillRect(0,  jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
-                              idWidth,
-                              av.getCharHeight());
+        pg.setColor(currentColor);
+        pg.fillRect(0,
+                    jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,
+            av.getCharHeight()),
+                    idWidth,
+                    av.getCharHeight());
 
-      pg.setColor(currentTextColor);
+        pg.setColor(currentTextColor);
 
-      String string = av.getAlignment().getSequenceAt(i).getName();
-      if(av.getShowFullId())
-        string = av.getAlignment().getSequenceAt(i).getDisplayId();
+        String string = av.getAlignment().getSequenceAt(i).getName();
+        if (av.getShowFullId())
+          string = av.getAlignment().getSequenceAt(i).getDisplayId();
 
-      pg.drawString(string, 0,  jalview.analysis.AlignmentUtil.getPixelHeight
-                    (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));
-    }
+        pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight
+                      (startSeq, i, av.getCharHeight()) + av.getCharHeight() -
+                      (av.getCharHeight() / 5));
+      }
 
-    // draw main sequence panel
-    pg.translate(idWidth,0);
-    seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);
+      // draw main sequence panel
+      pg.translate(idWidth, 0);
+      seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,
+                                   startRes, startSeq, 0);
 
 
-    if(av.getShowAnnotation())
+      if (av.showAnnotation && endSeq == av.alignment.getHeight())
       {
-        pg.translate(-idWidth,(endSeq-startSeq)*av.charHeight);
-        alabels.drawComponent((Graphics2D)pg);
-        pg.translate(idWidth,0);
-        annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes+1);
+        pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight);
+        alabels.drawComponent( (Graphics2D) pg);
+        pg.translate(idWidth, 0);
+        annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes+1);
       }
 
-    return Printable.PAGE_EXISTS;
+      return Printable.PAGE_EXISTS;
+
   }
 
 
   public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
   {
+      int idWidth = calculateIdWidth().width + 4;
 
-    int idWidth = calculateIdWidth().width+4;
-
-    if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)
-      pwidth = seqPanel.seqCanvas.getWidth() + idWidth;
+      int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth - idWidth);
+      int totalHeight = totalHeight = (av.alignment.getHeight() + 2) *
+          ( (av.alignment.getWidth()
+             / resWidth) + 1) * av.charHeight;
 
 
-    pg.setColor(Color.white);
-    pg.fillRect(0,0,pwidth, pheight);
-    pg.setFont( av.getFont() );
+      pg.setColor(Color.white);
+      pg.fillRect(0, 0, pwidth, pheight);
+      pg.setFont(av.getFont());
 
-    ////////////////////////////////////
-    /// How many sequences and residues can we fit on a printable page?
-    AlignmentI da = av.alignment;
-    int endy   = da.getHeight();
-    int chunkHeight =  (da.getHeight() + 2)*av.charHeight;
-    int chunkWidth  =   (pwidth-idWidth)/av.charWidth;
+      ////////////////
+      // Draw the ids
+      pg.setColor(Color.black);
 
-    int noChunksOnPage = pheight / chunkHeight;
-    int totalChunks = da.getWidth() / chunkWidth;
+      pg.translate(0, -pi * pheight);
 
-    if ( pi*noChunksOnPage > totalChunks )
-     return Printable.NO_SUCH_PAGE;
+      pg.setClip(0,pi*pheight,pwidth, pheight);
 
-    ////////////////
-    // Draw the ids
-    pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight);
+      int ypos = 2 * av.charHeight;
+      do
+      {
+        for (int i = 0; i < av.alignment.getHeight(); i++)
+        {
+          SequenceI s = av.alignment.getSequenceAt(i);
+          String string = s.getName();
+          if (av.getShowFullId())
+            string = s.getDisplayId();
 
-    pg.setColor(Color.black);
+          pg.drawString(string, 0,
+                        AlignmentUtil.getPixelHeight(0, i, av.charHeight) +
+                        ypos +
+                        av.charHeight - (av.charHeight / 5));
 
-    int rowSize =  av.getEndRes() - av.getStartRes();
-    // Draw the rest of the panels
+        }
 
-    for(int ypos=2*av.charHeight, row=av.getEndRes(); row<av.alignment.getWidth();
-        ypos += av.chunkHeight, row+=rowSize )
-    {
-      for (int i = 0; i < endy; i++)
-      {
-        SequenceI s = da.getSequenceAt(i);
-        String string = s.getName();
-        if (av.getShowFullId())
-          string = s.getDisplayId();
+        ypos += (av.alignment.getHeight() + 2) * av.charHeight;
 
-        pg.drawString(string, 0,
-                      AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
-                      av.charHeight - (av.charHeight / 5));
       }
-    }
+      while (ypos < totalHeight);
+
+      pg.translate(idWidth, 0);
 
-    // draw main sequence panel
-    pg.translate(idWidth,0);
-    seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth-idWidth, pheight, pi*noChunksOnPage*chunkWidth);
+      seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
+
+      if (pi * pheight < totalHeight)
+        return Printable.PAGE_EXISTS;
+      else
+        return Printable.NO_SUCH_PAGE;
 
 
-    return Printable.PAGE_EXISTS;
 
   }
 
@@ -611,7 +609,6 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       }
 
 
-System.out.println(width +" "+height);
 
     try
     {
@@ -629,8 +626,9 @@ System.out.println(width +" "+height);
       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 
       BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
-      Graphics png = bi.getGraphics();
+      Graphics2D png = (Graphics2D)bi.getGraphics();
 
+      png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
 
         if (av.getWrapAlignment())
           printWrappedAlignment(png, width, height, 0);
@@ -648,6 +646,37 @@ System.out.println(width +" "+height);
 
 }
 
+class Preview extends JFrame
+{
+
+  public Preview(Image image)
+  {
+    setResizable(true);
+    setSize(image.getWidth(this), image.getHeight(this));
+    setVisible(true);
+    getContentPane().setLayout(new BorderLayout());
+    getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);
+    validate();
+    repaint();
+  }
+}
+
+class PreviewPanel extends JPanel
+{
+  Image image;
+  public PreviewPanel(Image image)
+  {
+    this.image = image;
+  }
+  public void paintComponent(Graphics g)
+  {
+    if(image!=null)
+      g.drawImage(image,0,0,this);
+    else
+      System.out.println("image is null");
+  }
+}
+