+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-import jalview.jbgui.GTreePanel;\r
-import jalview.io.*;\r
-import java.awt.event.*;\r
-import java.util.*;\r
import java.io.*;\r
-import jalview.util.*;\r
-import javax.swing.*;\r
-import java.awt.print.*;\r
-import java.awt.*;\r
+import java.util.*;\r
+import javax.imageio.*;\r
\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+import java.awt.image.*;\r
+import javax.swing.*;\r
\r
+import org.jibble.epsgraphics.*;\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
+import jalview.jbgui.*;\r
\r
-public class TreePanel extends GTreePanel\r
+public class TreePanel\r
+ extends GTreePanel\r
{\r
SequenceI[] seq;\r
String type;\r
TreeCanvas treeCanvas;\r
NJTree tree;\r
\r
- FileProperties fp;\r
- PostscriptProperties pp;\r
-\r
- PrintWriter bw;\r
- PrintStream ps;\r
- boolean makeString = false;\r
- StringBuffer out;\r
-\r
-\r
-\r
- public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)\r
+ public TreePanel(AlignViewport av, Vector seqVector, String type,\r
+ String pwtype, int s, int e)\r
{\r
super();\r
\r
end = e;\r
\r
String longestName = "";\r
- seq = new Sequence [seqVector.size()];\r
- for (int i=0;i < seqVector.size();i++)\r
+ seq = new Sequence[seqVector.size()];\r
+\r
+ for (int i = 0; i < seqVector.size(); i++)\r
{\r
seq[i] = (Sequence) seqVector.elementAt(i);\r
- if(seq[i].getName().length()>longestName.length())\r
+\r
+ if (seq[i].getName().length() > longestName.length())\r
+ {\r
longestName = seq[i].getName();\r
+ }\r
}\r
\r
tree = new NJTree(seq, type, pwtype, start, end);\r
- av.setCurrentTree(tree);\r
-\r
- propertiesInit();\r
\r
treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
-\r
+ treeCanvas.setShowDistances(true); // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default\r
+ setViewStateFromTreeCanvas(treeCanvas);\r
tree.reCount(tree.getTopNode());\r
tree.findHeight(tree.getTopNode());\r
scrollPane.setViewportView(treeCanvas);\r
-\r
}\r
\r
+ public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
+ String type, String pwtype)\r
+ {\r
+ super();\r
\r
-public void drawPostscript(PostscriptProperties pp) {\r
- try {\r
- int width = 0;\r
- int height = 0;\r
-\r
- printout("%!\n");\r
-\r
- printout("/" + pp.font + " findfont\n");\r
- printout(pp.fsize + " scalefont setfont\n");\r
+ // These are probably only arbitrary strings reflecting source of tree\r
+ this.type = type;\r
+ this.pwtype = pwtype;\r
\r
- int offx = pp.xoffset;\r
- int offy = pp.yoffset;\r
+ start = 0;\r
+ end = seqVector.size();\r
\r
- if (pp.orientation == PostscriptProperties.PORTRAIT) {\r
- width = PostscriptProperties.SHORTSIDE;\r
- height = PostscriptProperties.LONGSIDE;\r
- } else {\r
- height = PostscriptProperties.SHORTSIDE;\r
- width = PostscriptProperties.LONGSIDE;\r
- printout(height + " 0 translate\n90 rotate\n");\r
- }\r
- float wscale = (float)(width*.8-offx*2)/tree.getMaxHeight();\r
- SequenceNode top = tree.getTopNode();\r
+ String longestName = "";\r
+ seq = new Sequence[seqVector.size()];\r
\r
- if (top.count == 0) {\r
- top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;\r
+ for (int i = 0; i < seqVector.size(); i++)\r
+ {\r
+ seq[i] = (Sequence) seqVector.elementAt(i);\r
}\r
\r
- float chunk = (float)(height-offy*2)/(((SequenceNode)top).count+1);\r
-\r
- drawPostscriptNode(top,chunk,wscale,width,offx,offy);\r
+ // This constructor matches sequence names to treenodes and sets up the tree layouts.\r
+ tree = new NJTree(seq, newtree);\r
\r
- printout("showpage\n");\r
- } catch (java.io.IOException e) {\r
- System.out.println("Exception " + e);\r
- }\r
-}\r
+ // Now have to calculate longest name based on the leaves\r
+ Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());\r
+ boolean has_placeholders = false;\r
\r
-public void drawPostscriptNode(SequenceNode node, float chunk, float scale, int width, int offx, int offy) throws java.io.IOException {\r
- if (node == null) {\r
- return;\r
- }\r
-\r
- if (node.left() == null && node.right() == null) {\r
- // Drawing leaf node\r
-\r
- float height = node.height;\r
- float dist = node.dist;\r
+ for (int i = 0; i < leaves.size(); i++)\r
+ {\r
+ SequenceNode lf = (SequenceNode) leaves.elementAt(i);\r
\r
- int xstart = (int)((height-dist)*scale) + offx;\r
- int xend = (int)(height*scale) + offx;\r
+ if (lf.isPlaceholder())\r
+ {\r
+ has_placeholders = true;\r
+ }\r
\r
- int ypos = (int)(node.ycount * chunk) + offy;\r
+ if (longestName.length() < ( (Sequence) lf.element()).getName()\r
+ .length())\r
+ {\r
+ longestName = TreeCanvas.PLACEHOLDER +\r
+ ( (Sequence) lf.element()).getName();\r
+ }\r
+ }\r
\r
- // g.setColor(Color.black);\r
- printout("\n" + new Format("%5.3f").form((double)node.color.getRed()/255) + " " +\r
- new Format("%5.3f").form((double)node.color.getGreen()/255) + " " +\r
- new Format("%5.3f").form((double)node.color.getBlue()/255) + " setrgbcolor\n");\r
+ tree.reCount(tree.getTopNode());\r
+ tree.findHeight(tree.getTopNode());\r
\r
- // Draw horizontal line\r
- // g.drawLine(xstart,ypos,xend,ypos);\r
- printout(xstart + " " + ypos + " moveto " + xend + " " + ypos + " lineto stroke \n");\r
+ treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
+ treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
+ treeCanvas.setShowDistances(newtree.HasDistances());\r
+ scrollPane.setViewportView(treeCanvas);\r
+ treeCanvas.setMarkPlaceholders(has_placeholders);\r
+ setViewStateFromTreeCanvas(treeCanvas);\r
\r
- if (treeCanvas.showDistances && node.dist > 0) {\r
- // g.drawString(new Format("%5.2f").form(node.dist),xstart,ypos - 5);\r
- printout("(" + new Format("%5.2f").form(node.dist) + ") " + xstart + " " + (ypos+5) + " moveto show\n");\r
- }\r
- //g.drawString((String)node.element(),xend+20,ypos);\r
- printout("(" + (((SequenceI)node.element()).getName()) + ") " + (xend+20) + " " + (ypos) + " moveto show\n");\r
- } else {\r
- drawPostscriptNode((SequenceNode)node.left(),chunk,scale,width,offx,offy);\r
- drawPostscriptNode((SequenceNode)node.right(),chunk,scale,width,offx,offy);\r
-\r
-\r
- float height = node.height;\r
- float dist = node.dist;\r
-\r
- int xstart = (int)((height-dist)*scale) + offx;\r
- int xend = (int)(height*scale) + offx;\r
- int ypos = (int)(node.ycount * chunk) + offy;\r
-\r
- printout("\n" + new Format("%5.3f").form((double)node.color.getRed()/255) + " " +\r
- new Format("%5.3f").form((double)node.color.getGreen()/255) + " " +\r
- new Format("%5.3f").form((double)node.color.getBlue()/255) + " setrgbcolor\n");\r
- // g.setColor(Color.black);\r
- // bw.append("\nblack setrgbcolor\n");\r
- // Draw horizontal line\r
- // g.drawLine(xstart,ypos,xend,ypos);\r
- printout(xstart + " " + ypos + " moveto " + xend + " " + ypos + " lineto stroke\n");\r
- int ystart = (int)(((SequenceNode)node.left()).ycount * chunk) + offy;\r
- int yend = (int)(((SequenceNode)node.right()).ycount * chunk) + offy;\r
-\r
- // g.drawLine((int)(height*scale) + offx, ystart,\r
- // (int)(height*scale) + offx, yend);\r
- printout\r
- (((int)(height*scale) + offx) + " " + ystart + " moveto " + ((int)(height*scale) + offx) + " " +\r
- yend + " lineto stroke\n");\r
- if (treeCanvas.showDistances && node.dist > 0) {\r
- // g.drawString(new Format("%5.2f").form(node.dist),xstart,ypos - 5);\r
- printout("(" +new Format("%5.2f").form(node.dist) + ") " + (xstart) + " " + (ypos+5) + " moveto show\n");\r
- }\r
+ // JBPNote TODO: preference for always marking placeholders in new associated tree\r
}\r
-}\r
\r
-public void printout(String s) throws IOException {\r
- if (bw != null) {\r
- bw.write(s);\r
- }\r
- if (ps != null) {\r
- ps.print(s);\r
- }\r
- if (makeString == true) {\r
- out.append(s);\r
+ public NJTree getTree()\r
+ {\r
+ return tree;\r
}\r
-}\r
-\r
\r
-public PostscriptProperties getPostscriptProperties() {\r
- return pp;\r
-}\r
-\r
-public FileProperties getFileProperties() {\r
- return fp;\r
-}\r
-\r
-public void setPostscriptProperties(PostscriptProperties pp) {\r
- this.pp = pp;\r
-}\r
-\r
-public void setFileProperties(FileProperties fp) {\r
- this.fp = fp;\r
-}\r
+ private void setViewStateFromTreeCanvas(TreeCanvas tree)\r
+ {\r
+ // update view menu state from treeCanvas render state\r
+ distanceMenu.setSelected(tree.showDistances);\r
+ bootstrapMenu.setSelected(tree.showBootstrap);\r
+ placeholdersMenu.setSelected(tree.markPlaceholders);\r
+ }\r
\r
-public String getText(String format) {\r
- return null;\r
-}\r
+ private void setTreeCanvasFromViewState(TreeCanvas tree)\r
+ {\r
+ // update view menu state from treeCanvas render state\r
+ tree.showDistances = distanceMenu.isSelected();\r
+ tree.showBootstrap = bootstrapMenu.isSelected();\r
+ tree.markPlaceholders = placeholdersMenu.isSelected();\r
+ }\r
\r
-public void getPostscript(PrintWriter bw) {\r
- this.bw = bw;\r
- drawPostscript(pp);\r
+ public void textbox_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
\r
-}\r
+ StringBuffer buffer = new StringBuffer();\r
\r
-public void getPostscript(PrintStream bw) {\r
- this.ps = bw;\r
- drawPostscript(pp);\r
- bw.flush();\r
-}\r
+ if (type.equals("AV"))\r
+ {\r
+ buffer.append("Average distance tree using ");\r
+ }\r
+ else\r
+ {\r
+ buffer.append("Neighbour joining tree using ");\r
+ }\r
\r
-public StringBuffer getPostscript() {\r
- makeString = true;\r
- out = new StringBuffer();\r
- drawPostscript(pp);\r
- return out;\r
-}\r
+ if (pwtype.equals("BL"))\r
+ {\r
+ buffer.append("BLOSUM62");\r
+ }\r
+ else\r
+ {\r
+ buffer.append("PID");\r
+ }\r
\r
-public void propertiesInit() {\r
- this.pp = new PostscriptProperties();\r
- this.fp = new FileProperties();\r
-}\r
+ Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);\r
\r
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
+ cap.setText(fout.print(false, true));\r
+ }\r
\r
- public void saveButton_actionPerformed(ActionEvent e)\r
+ public void saveAsNewick_actionPerformed(ActionEvent e)\r
{\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty(\r
+ "LAST_DIRECTORY"));\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Save tree as newick file");\r
+ chooser.setToolTipText("Save");\r
\r
- try{\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
- chooser.setDialogTitle("Save Tree as postscript file");\r
- chooser.setToolTipText("Save");\r
- int value = chooser.showSaveDialog(this);\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
+ int value = chooser.showSaveDialog(null);\r
\r
- bw = new PrintWriter(new FileWriter(choice));\r
- getPostscript(bw);\r
- bw.close();\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
\r
+ try\r
+ {\r
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
+ String output = fout.print(false, true); // distances only\r
+ java.io.PrintWriter out = new java.io.PrintWriter(new java.io.\r
+ FileWriter(\r
+ choice));\r
+ out.println(output);\r
+ out.close();\r
}\r
-\r
- }catch(Exception ex){ex.printStackTrace();}\r
-\r
- }\r
-\r
-\r
- protected void saveMenu_actionPerformed(ActionEvent e)\r
- {\r
-\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
}\r
\r
protected void printMenu_actionPerformed(ActionEvent e)\r
{\r
-\r
//Putting in a thread avoids Swing painting problems\r
treeCanvas.startPrinting();\r
}\r
repaint();\r
}\r
\r
-\r
protected void fontSize_actionPerformed(ActionEvent e)\r
{\r
- if( treeCanvas==null )\r
- return;\r
-\r
- String size = fontSize.getText().substring( fontSize.getText().indexOf("-")+1);\r
-\r
- Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
- "Select font size",\r
- "Font size",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
- ,"Font Size - "+size);\r
- if(selection!=null)\r
- {\r
- fontSize.setText("Font Size - " + selection);\r
-\r
- int i = Integer.parseInt(selection.toString());\r
- treeCanvas.setFontSize(i);\r
- }\r
- scrollPane.setViewportView(treeCanvas);\r
+ if (treeCanvas == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ String size = fontSize.getText().substring(fontSize.getText().indexOf("-") +\r
+ 1);\r
+\r
+ Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
+ "Select font size", "Font size", JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ new String[]\r
+ {\r
+ "1", "2", "4", "6", "8", "10", "12", "14", "16", "18", "20"\r
+ }, "Font Size - " + size);\r
+\r
+ if (selection != null)\r
+ {\r
+ fontSize.setText("Font Size - " + selection);\r
\r
+ int i = Integer.parseInt(selection.toString());\r
+ treeCanvas.setFontSize(i);\r
+ }\r
+\r
+ scrollPane.setViewportView(treeCanvas);\r
}\r
\r
protected void distanceMenu_actionPerformed(ActionEvent e)\r
treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());\r
}\r
\r
+ protected void placeholdersMenu_actionPerformed(ActionEvent e)\r
+ {\r
+ treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());\r
+ }\r
+\r
+ protected void epsTree_actionPerformed(ActionEvent e)\r
+ {\r
+ int width = treeCanvas.getWidth();\r
+ int height = treeCanvas.getHeight();\r
+\r
+ try\r
+ {\r
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
+ jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"eps"},\r
+ new String[]\r
+ {"Encapsulated Postscript"},\r
+ "Encapsulated Postscript");\r
+ chooser.setFileView(new jalview.io.JalviewFileView());\r
+ chooser.setDialogTitle("Create EPS file from tree");\r
+ chooser.setToolTipText("Save");\r
+\r
+ int value = chooser.showSaveDialog(this);\r
+\r
+ if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ return;\r
+ }\r
+\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
+\r
+ FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
+ EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,\r
+ height);\r
+\r
+ treeCanvas.draw(pg, width, height);\r
+\r
+ pg.flush();\r
+ pg.close();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
\r
+ protected void pngTree_actionPerformed(ActionEvent e)\r
+ {\r
+ int width = treeCanvas.getWidth();\r
+ int height = treeCanvas.getHeight();\r
+\r
+ try\r
+ {\r
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
+ jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"png"},\r
+ new String[]\r
+ {"Portable network graphics"},\r
+ "Portable network graphics");\r
+\r
+ chooser.setFileView(new jalview.io.JalviewFileView());\r
+ chooser.setDialogTitle("Create PNG image from tree");\r
+ chooser.setToolTipText("Save");\r
+\r
+ int value = chooser.showSaveDialog(this);\r
+\r
+ if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ return;\r
+ }\r
+\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
+\r
+ FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
+\r
+ BufferedImage bi = new BufferedImage(width, height,\r
+ BufferedImage.TYPE_INT_RGB);\r
+ Graphics png = bi.getGraphics();\r
+\r
+ treeCanvas.draw(png, width, height);\r
+\r
+ ImageIO.write(bi, "png", out);\r
+ out.close();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff