X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=9f9e32772af1ed82529773d94b96a5f9db518f58;hb=ac07859006686a2c62bcf57b24742eb610bc46f0;hp=f723fdc2673743c4ecb7517729cf72af3f5eebdd;hpb=764f4139569c1135e41348b24943c3e6d22f74ef;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index f723fdc..9f9e327 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -11,6 +11,10 @@ import jalview.util.*;
 import javax.swing.*;
 import java.awt.print.*;
 import java.awt.*;
+import java.awt.image.*;
+import org.jibble.epsgraphics.*;
+import javax.imageio.*;
+
 
 
 
@@ -25,15 +29,10 @@ public class TreePanel extends GTreePanel
   TreeCanvas treeCanvas;
   NJTree tree;
 
-  FileProperties       fp;
-  PostscriptProperties pp;
-
-  PrintWriter bw;
-  PrintStream ps;
-  boolean makeString = false;
-  StringBuffer out;
-
-
+  public NJTree getTree()
+  {
+    return tree;
+  }
 
   public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)
   {
@@ -55,9 +54,6 @@ public class TreePanel extends GTreePanel
     }
 
     tree = new NJTree(seq, type, pwtype, start, end);
-    av.setCurrentTree(tree);
-
-    propertiesInit();
 
     treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
 
@@ -66,197 +62,67 @@ public class TreePanel extends GTreePanel
     scrollPane.setViewportView(treeCanvas);
 
   }
+  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
+                   String type, String pwtype)
+    {
+      super();
+      // These are probably only  arbitrary strings reflecting source of tree
+      this.type = type;
+      this.pwtype = pwtype;
 
+      start = 0;
+      end = seqVector.size();
 
-public void drawPostscript(PostscriptProperties pp) {
-  try {
-    int width = 0;
-    int height = 0;
-
-    printout("%!\n");
-
-    printout("/" + pp.font + " findfont\n");
-    printout(pp.fsize + " scalefont setfont\n");
-
-    int offx = pp.xoffset;
-    int offy = pp.yoffset;
-
-    if (pp.orientation == PostscriptProperties.PORTRAIT) {
-      width = PostscriptProperties.SHORTSIDE;
-      height = PostscriptProperties.LONGSIDE;
-    } else {
-      height = PostscriptProperties.SHORTSIDE;
-      width = PostscriptProperties.LONGSIDE;
-      printout(height + " 0 translate\n90 rotate\n");
-    }
-    float wscale = (float)(width*.8-offx*2)/tree.getMaxHeight();
-    SequenceNode top = tree.getTopNode();
-
-    if (top.count == 0) {
-        top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;
-    }
-
-    float chunk = (float)(height-offy*2)/(((SequenceNode)top).count+1);
-
-    drawPostscriptNode(top,chunk,wscale,width,offx,offy);
-
-    printout("showpage\n");
-  } catch (java.io.IOException e) {
-    System.out.println("Exception " + e);
-  }
-}
-
-public void drawPostscriptNode(SequenceNode node, float chunk, float scale, int width, int offx, int offy) throws java.io.IOException {
-  if (node == null) {
-    return;
-  }
-
-  if (node.left() == null && node.right() == null) {
-    // Drawing leaf node
-
-    float height = node.height;
-    float dist = node.dist;
-
-    int xstart = (int)((height-dist)*scale) + offx;
-    int xend =   (int)(height*scale) + offx;
-
-    int ypos = (int)(node.ycount * chunk) + offy;
+      String longestName = "";
+      seq = new Sequence [seqVector.size()];
+      for (int i=0;i < seqVector.size();i++)
+      {
+        seq[i] = (Sequence) seqVector.elementAt(i);
+        if(seq[i].getName().length()>longestName.length())
+          longestName = seq[i].getName();
+      }
+      // This constructor matches sequence names to treenodes and sets up the tree layouts.
+      tree = new NJTree(seq, newtree);
 
-    // g.setColor(Color.black);
-    printout("\n" + new Format("%5.3f").form((double)node.color.getRed()/255) + " " +
-             new Format("%5.3f").form((double)node.color.getGreen()/255) + " " +
-             new Format("%5.3f").form((double)node.color.getBlue()/255) + " setrgbcolor\n");
+      tree.reCount(tree.getTopNode());
+      tree.findHeight(tree.getTopNode());
 
-    // Draw horizontal line
-    //  g.drawLine(xstart,ypos,xend,ypos);
-    printout(xstart + " " + ypos + " moveto " + xend + " " + ypos + " lineto stroke \n");
+      treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
+      treeCanvas.setShowBootstrap(newtree.HasBootstrap());
+      treeCanvas.setShowDistances(newtree.HasDistances());
+      scrollPane.setViewportView(treeCanvas);
 
-    if (treeCanvas.showDistances && node.dist > 0) {
-      //	g.drawString(new Format("%5.2f").form(node.dist),xstart,ypos - 5);
-      printout("(" + new Format("%5.2f").form(node.dist) + ") " + xstart + " " + (ypos+5) + " moveto show\n");
-    }
-    //g.drawString((String)node.element(),xend+20,ypos);
-    printout("(" + (((SequenceI)node.element()).getName()) + ") " + (xend+20) + " " + (ypos) + " moveto show\n");
-  } else {
-    drawPostscriptNode((SequenceNode)node.left(),chunk,scale,width,offx,offy);
-    drawPostscriptNode((SequenceNode)node.right(),chunk,scale,width,offx,offy);
-
-
-    float height = node.height;
-    float dist = node.dist;
-
-    int xstart = (int)((height-dist)*scale) + offx;
-    int xend =   (int)(height*scale) + offx;
-    int ypos = (int)(node.ycount * chunk) + offy;
-
-    printout("\n" + new Format("%5.3f").form((double)node.color.getRed()/255) + " " +
-             new Format("%5.3f").form((double)node.color.getGreen()/255) + " " +
-             new Format("%5.3f").form((double)node.color.getBlue()/255) + " setrgbcolor\n");
-    //      g.setColor(Color.black);
-    //      bw.append("\nblack setrgbcolor\n");
-    // Draw horizontal line
-    //      g.drawLine(xstart,ypos,xend,ypos);
-    printout(xstart + " " + ypos + " moveto " + xend + " " + ypos + " lineto stroke\n");
-    int ystart = (int)(((SequenceNode)node.left()).ycount * chunk) + offy;
-    int yend = (int)(((SequenceNode)node.right()).ycount * chunk) + offy;
-
-    //      g.drawLine((int)(height*scale) + offx, ystart,
-    //		 (int)(height*scale) + offx, yend);
-    printout
-    (((int)(height*scale) + offx) + " " + ystart + " moveto " +  ((int)(height*scale) + offx) + " " +
-     yend + " lineto stroke\n");
-    if (treeCanvas.showDistances && node.dist > 0) {
-      //	g.drawString(new Format("%5.2f").form(node.dist),xstart,ypos - 5);
-      printout("(" +new Format("%5.2f").form(node.dist) + ") " + (xstart) + " " + (ypos+5) + " moveto show\n");
     }
-  }
-}
-
-public void printout(String s) throws IOException {
-  if (bw != null) {
-    bw.write(s);
-  }
-  if (ps != null) {
-    ps.print(s);
-  }
-  if (makeString == true) {
-    out.append(s);
-  }
-}
 
 
-public PostscriptProperties getPostscriptProperties() {
-  return pp;
-}
-
-public FileProperties getFileProperties() {
-  return fp;
-}
-
-public void setPostscriptProperties(PostscriptProperties pp) {
-  this.pp = pp;
-}
-
-public void setFileProperties(FileProperties fp) {
-  this.fp = fp;
-}
 
 public String getText(String format) {
   return null;
 }
 
-public void getPostscript(PrintWriter bw) {
-  this.bw = bw;
-  drawPostscript(pp);
-
-}
-
-public void getPostscript(PrintStream bw) {
-  this.ps = bw;
-  drawPostscript(pp);
-  bw.flush();
-}
-
-public StringBuffer getPostscript() {
-  makeString = true;
-  out = new StringBuffer();
-  drawPostscript(pp);
-  return out;
-}
-
-public void propertiesInit() {
-  this.pp = new PostscriptProperties();
-  this.fp = new FileProperties();
-}
-
-
-  public void saveButton_actionPerformed(ActionEvent e)
-  {
-
-    try{
-      JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-      chooser.setDialogTitle("Save Tree as postscript file");
-      chooser.setToolTipText("Save");
-      int value = chooser.showSaveDialog(this);
-      if (value == JFileChooser.APPROVE_OPTION)
-      {
-        String choice = chooser.getSelectedFile().getPath();
-        jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-
-        bw = new PrintWriter(new FileWriter(choice));
-        getPostscript(bw);
-        bw.close();
-
-      }
-
-    }catch(Exception ex){ex.printStackTrace();}
-
-  }
-
 
   protected void saveMenu_actionPerformed(ActionEvent e)
   {
-
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty("LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Save tree as newick file");
+    chooser.setToolTipText("Save");
+    int value = chooser.showSaveDialog(null);
+    if (value == JalviewFileChooser.APPROVE_OPTION) {
+      String choice =  chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",  choice);
+      try{
+        jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+        String output = fout.print(false,true); // distances only
+        java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );
+        out.println(output);
+        out.close();
+      }
+      catch (Exception ex) {
+        ex.printStackTrace();
+      }
+    }
   }
 
   protected void printMenu_actionPerformed(ActionEvent e)
@@ -308,4 +174,67 @@ public void propertiesInit() {
   }
 
 
+  protected void epsTree_actionPerformed(ActionEvent e)
+  {
+    int width = treeCanvas.getWidth(), height=treeCanvas.getHeight();
+    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 tree");
+      chooser.setToolTipText("Save");
+
+      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("Tree", out, 0, 0, width, height);
+
+
+      treeCanvas.draw(pg, width, height);
+
+        pg.flush();
+        pg.close();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  protected void pngTree_actionPerformed(ActionEvent e)
+ {
+  int width = treeCanvas.getWidth(), height = treeCanvas.getHeight();
+    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 PNG image from tree");
+      chooser.setToolTipText("Save");
+
+      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());
+
+      BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
+      Graphics png = bi.getGraphics();
+
+      treeCanvas.draw(png, width, height);
+
+        ImageIO.write(bi, "png", out);
+        out.close();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
 }