X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=78bef801cda4eab910621a740031829d16d70773;hb=fe5db5e87fc726b1560d21f97f19b0e04963b72c;hp=73ef46bb3445886457db3820a99a281cc327e057;hpb=3e63bb86ad0e6f4bc86197053f921cb67b341567;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 73ef46b..78bef80 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -7,10 +7,11 @@ import jalview.io.*;
 import java.awt.event.*;
 import java.util.*;
 import java.io.*;
-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 +26,10 @@ 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)
   {
@@ -55,17 +51,30 @@ public class TreePanel extends GTreePanel
     }
 
     tree = new NJTree(seq, type, pwtype, start, end);
-    av.setCurrentTree(tree);
-
-    propertiesInit();
 
     treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
-
+    treeCanvas.setShowDistances(true); // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
+    setViewStateFromTreeCanvas(treeCanvas);
     tree.reCount(tree.getTopNode());
     tree.findHeight(tree.getTopNode());
     scrollPane.setViewportView(treeCanvas);
 
   }
+  private void setViewStateFromTreeCanvas(TreeCanvas tree) {
+    // update view menu state from treeCanvas render state
+    distanceMenu.setSelected(tree.showDistances);
+    bootstrapMenu.setSelected(tree.showBootstrap);
+    placeholdersMenu.setSelected(tree.markPlaceholders);
+  }
+
+  private void setTreeCanvasFromViewState(TreeCanvas tree) {
+      // update view menu state from treeCanvas render state
+      tree.showDistances = distanceMenu.isSelected();
+      tree.showBootstrap = bootstrapMenu.isSelected();
+      tree.markPlaceholders = placeholdersMenu.isSelected();
+    }
+
+
   public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
                    String type, String pwtype)
     {
@@ -82,213 +91,61 @@ public class TreePanel extends GTreePanel
       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);
-      av.setCurrentTree(tree);
-
-      propertiesInit();
-
+      // Now have to calculate longest name based on the leaves
+      Vector leaves = tree.findLeaves(tree.getTopNode(),new Vector());
+      boolean has_placeholders = false;
+      for (int i=0;i < leaves.size();i++) {
+        SequenceNode lf = (SequenceNode) leaves.elementAt(i);
+        if (lf.isPlaceholder())
+          has_placeholders = true;
+        if (longestName.length()<((Sequence) lf.element()).getName().length())
+          longestName = TreeCanvas.PLACEHOLDER+((Sequence) lf.element()).getName();
+      }
       tree.reCount(tree.getTopNode());
       tree.findHeight(tree.getTopNode());
 
       treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
+      treeCanvas.setShowBootstrap(newtree.HasBootstrap());
+      treeCanvas.setShowDistances(newtree.HasDistances());
       scrollPane.setViewportView(treeCanvas);
-
+      treeCanvas.setMarkPlaceholders(has_placeholders);
+      setViewStateFromTreeCanvas(treeCanvas);
+      // JBPNote TODO: preference for always marking placeholders in new associated tree
     }
 
 
-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;
+    public void textbox_actionPerformed(ActionEvent e)
+    {
+      CutAndPasteTransfer cap = new CutAndPasteTransfer();
+      JInternalFrame frame = new JInternalFrame();
+      frame.setContentPane(cap);
 
-    int xstart = (int)((height-dist)*scale) + offx;
-    int xend =   (int)(height*scale) + offx;
+      StringBuffer buffer = new StringBuffer();
 
-    int ypos = (int)(node.ycount * chunk) + offy;
+      if(type.equals("AV"))
+        buffer.append("Average distance tree using ");
+      else
+        buffer.append("Neighbour joining tree using ");
 
-    // 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");
+      if(pwtype.equals("BL"))
+       buffer.append("BLOSUM62");
+      else
+        buffer.append("PID");
 
-    // Draw horizontal line
-    //  g.drawLine(xstart,ypos,xend,ypos);
-    printout(xstart + " " + ypos + " moveto " + xend + " " + ypos + " lineto stroke \n");
+      Desktop.addInternalFrame(frame,buffer.toString(), 500, 100);
+      jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+      cap.setText(  fout.print(false,true) );
 
-    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{
-      JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-      chooser.setDialogTitle("Save Tree as postscript file");
-      chooser.setToolTipText("Save");
-      int value = chooser.showSaveDialog(this);
-      if (value == JalviewFileChooser.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();}
-
-  }
 
+    public void saveAsNewick_actionPerformed(ActionEvent e)
+    {
 
-  protected void saveMenu_actionPerformed(ActionEvent e)
-  {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+  JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
         getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save tree as newick file");
@@ -296,7 +153,7 @@ public void propertiesInit() {
     int value = chooser.showSaveDialog(null);
     if (value == JalviewFileChooser.APPROVE_OPTION) {
       String choice =  chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",  choice);
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",  chooser.getSelectedFile().getParent());
       try{
         jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
         String output = fout.print(false,true); // distances only
@@ -358,5 +215,79 @@ public void propertiesInit() {
     treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
   }
 
+  protected void placeholdersMenu_actionPerformed(ActionEvent e)
+    {
+      treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
+  }
+
+  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"},
+              new String[]{"Encapsulated Postscript"},
+              "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().getParent());
+      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"},
+          new String[] {"Portable network graphics"},
+          "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().getParent());
+      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();
+    }
+  }
 
 }