X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=997966fa97e8e0fc17bc886afcfced1ff2b4512f;hb=ff2e8d0b23e91c4d7f19dd1922e48e5a718ee0f1;hp=296bb80cd7224af3030611f3d705c60ab23fe64c;hpb=e61e2b53cc88a6dd4dd5abe857b19172f253ba11;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 296bb80..997966f 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -12,6 +12,9 @@ import com.sun.image.codec.jpeg.*;
 import java.io.*;
 import java.awt.image.*;
 
+import org.jibble.epsgraphics.*;
+import javax.imageio.*;
+
 
 public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
 {
@@ -31,30 +34,21 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     this.av         = av;
     seqPanel        = new SeqPanel  (av, this);
     idPanel         = new IdPanel   (av, this);
+
     scalePanel = new ScalePanel(av, this);
     scorePanel = new ScorePanel(av);
     ssPanel = new SecondaryStructurePanel(av);
 
     secondaryPanelHolder.add(ssPanel, BorderLayout.CENTER);
-    idPanelHolder.add(idPanel, BorderLayout.CENTER);
-    idPanel.addNotify();
 
-    javax.swing.JFrame f = new javax.swing.JFrame();
-    f.addNotify();
-    FontMetrics fm = f.getGraphics().getFontMetrics(av.font);
-    AlignmentI al = av.getAlignment();
+    idPanelHolder.add(idPanel, BorderLayout.CENTER);
+    IdwidthAdjuster iap = new IdwidthAdjuster(this);
+    idSpaceFillerPanel1.add(iap, BorderLayout.CENTER);
 
-    int i   = 0;
-    int idWidth = 0;
-    while (i < al.getHeight() && al.getSequenceAt(i) != null)
-    {
-      SequenceI s   = al.getSequenceAt(i);
-      String str   = s.getDisplayId();
-      if (fm.stringWidth(str) > idWidth)
-        idWidth = fm.stringWidth(str);
-      i++;
-    }
-    hscrollFillerPanel.setPreferredSize(new Dimension(idWidth, 12));
+    Dimension d = calculateIdWidth();
+    d.setSize( d.width+4, d.height);
+    idPanel.idCanvas.setPreferredSize( d );
+    hscrollFillerPanel.setPreferredSize( d );
 
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
     scorePanelHolder.add(scorePanel, BorderLayout.CENTER);
@@ -113,6 +107,38 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
    });
   }
 
+  Dimension calculateIdWidth()
+  {
+    Graphics g = this.getGraphics();
+    if(g==null)
+    {
+      javax.swing.JFrame f = new javax.swing.JFrame();
+      f.addNotify();
+      g = f.getGraphics();
+    }
+
+    FontMetrics fm = g.getFontMetrics(av.font);
+    AlignmentI al = av.getAlignment();
+
+       int i   = 0;
+       int idWidth = 0;
+       String id;
+       while (i < al.getHeight() && al.getSequenceAt(i) != null)
+       {
+         SequenceI s   = al.getSequenceAt(i);
+         if(av.getShowFullId())
+           id   = s.getDisplayId();
+         else
+           id = s.getName();
+
+         if (fm.stringWidth(id) > idWidth)
+           idWidth = fm.stringWidth(id);
+         i++;
+       }
+
+       return new Dimension(idWidth, 12);
+  }
+
 
  public void highlightSearchResults(int [] results)
  {
@@ -340,7 +366,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
   {
 
-    int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();
+    int idWidth = calculateIdWidth().width;
 
 
     pg.setColor(Color.white);
@@ -373,17 +399,17 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     ////////////////
     //draw Scale
-    pg.translate(idWidth,0);
+    pg.translate(30,0);
     scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth);
 
-    pg.translate(-idWidth, 30);
+    pg.translate(-30, 30);
     ////////////////
     // Draw the ids
     Color currentColor=null;
     Color currentTextColor=null;
     for(int i=startSeq; i<endSeq; i++)
     {
-      if (av.alignment.findGroup(av.getAlignment().getSequenceAt(i))==null)
+      if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(av.getAlignment().getSequenceAt(i)))
       {
         currentColor = Color.gray;
         currentTextColor = Color.black;
@@ -401,7 +427,10 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
       pg.setColor(currentTextColor);
 
-      String 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));
     }
@@ -418,7 +447,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
   {
 
-    int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();
+    int idWidth = calculateIdWidth().width;
 
     if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)
       pwidth = seqPanel.seqCanvas.getWidth() + idWidth;
@@ -454,7 +483,11 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       for (int i = 0; i < endy; i++)
       {
         SequenceI s = da.getSequenceAt(i);
-        pg.drawString(s.getDisplayId(), 0,
+        String string = s.getName();
+        if (av.getShowFullId())
+          string = s.getDisplayId();
+
+        pg.drawString(string, 0,
                       AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
                       av.charHeight - (av.charHeight / 5));
       }
@@ -469,48 +502,72 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
   }
 
-  public void makeJPG(int width, int height)
+
+  public void makeEPS(int width, int height)
   {
     try
     {
+      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
+          "LAST_DIRECTORY"), new String[]{"eps"}, "Encapsulated Postscript");
+      chooser.setFileView(new jalview.io.JalviewFileView());
+      chooser.setDialogTitle("Create EPS file from alignment");
+      chooser.setToolTipText("Save");
 
-      BufferedImage bi = new BufferedImage(width, height,
-                                           BufferedImage.TYPE_INT_RGB);
-      Graphics pg = bi.getGraphics();
+      int value = chooser.showSaveDialog(this);
+      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+        return;
+
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
+      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+      EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, height);
 
-      try
-      {
         if (av.getWrapAlignment())
           printWrappedAlignment(pg, width, height, 0);
         else
           printUnwrapped(pg, width, height, 0);
-      }
-      catch (Exception ex)
-      {}
 
-      javax.swing.JFileChooser chooser = new javax.swing.JFileChooser(jalview.bin.Cache.getProperty(
-          "LAST_DIRECTORY"));
+
+        pg.flush();
+        pg.close();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  public void makePNG(int width, int height)
+  {
+    try
+    {
+      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
+          "LAST_DIRECTORY"), new String[]{"png"}, "Portable network graphics");
       chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle("Create JPG image from alignment");
+      chooser.setDialogTitle("Create EPS file from alignment");
       chooser.setToolTipText("Save");
 
       int value = chooser.showSaveDialog(this);
-      if (value == javax.swing.JFileChooser.APPROVE_OPTION)
-      {
+      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+        return;
 
-        FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
-        JPEGImageEncoder jie = JPEGCodec.createJPEGEncoder(out);
-        JPEGEncodeParam param = JPEGCodec.getDefaultJPEGEncodeParam(bi);
-        param.setQuality(1.0f, true);
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
+      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+
+      BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
+      Graphics png = bi.getGraphics();
 
-        jie.encode(bi, param);
-        out.close();
-      }
 
+        if (av.getWrapAlignment())
+          printWrappedAlignment(png, width, height, 0);
+        else
+          printUnwrapped(png, width, height, 0);
+
+        ImageIO.write(bi, "png", out);
+        out.close();
     }
-    catch (IOException ex)
+    catch (Exception ex)
     {
-      System.out.println("ex Writing image ");
+      ex.printStackTrace();
     }
   }
 
@@ -518,3 +575,4 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
 
 
+