/*\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
-\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 javax.swing.*;\r
-import java.awt.*;\r
-import java.awt.image.*;\r
-import org.jibble.epsgraphics.*;\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
- public NJTree getTree()\r
- {\r
- return tree;\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
tree.reCount(tree.getTopNode());\r
tree.findHeight(tree.getTopNode());\r
scrollPane.setViewportView(treeCanvas);\r
-\r
}\r
- private void setViewStateFromTreeCanvas(TreeCanvas tree) {\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
- private void setTreeCanvasFromViewState(TreeCanvas tree) {\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
\r
public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
String type, String pwtype)\r
+ {\r
+ super();\r
+\r
+ // These are probably only arbitrary strings reflecting source of tree\r
+ this.type = type;\r
+ this.pwtype = pwtype;\r
+\r
+ start = 0;\r
+ end = seqVector.size();\r
+\r
+ String longestName = "";\r
+ seq = new Sequence[seqVector.size()];\r
+\r
+ for (int i = 0; i < seqVector.size(); i++)\r
{\r
- super();\r
- // These are probably only arbitrary strings reflecting source of tree\r
- this.type = type;\r
- this.pwtype = pwtype;\r
+ seq[i] = (Sequence) seqVector.elementAt(i);\r
+ }\r
+\r
+ // This constructor matches sequence names to treenodes and sets up the tree layouts.\r
+ tree = new NJTree(seq, newtree);\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
- start = 0;\r
- end = seqVector.size();\r
+ for (int i = 0; i < leaves.size(); i++)\r
+ {\r
+ SequenceNode lf = (SequenceNode) leaves.elementAt(i);\r
\r
- String longestName = "";\r
- seq = new Sequence [seqVector.size()];\r
- for (int i=0;i < seqVector.size();i++)\r
+ if (lf.isPlaceholder())\r
{\r
- seq[i] = (Sequence) seqVector.elementAt(i);\r
+ has_placeholders = true;\r
}\r
- // This constructor matches sequence names to treenodes and sets up the tree layouts.\r
- tree = new NJTree(seq, newtree);\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
- for (int i=0;i < leaves.size();i++) {\r
- SequenceNode lf = (SequenceNode) leaves.elementAt(i);\r
- if (lf.isPlaceholder())\r
- has_placeholders = true;\r
- if (longestName.length()<((Sequence) lf.element()).getName().length())\r
- longestName = TreeCanvas.PLACEHOLDER+((Sequence) lf.element()).getName();\r
+\r
+ if (longestName.length() < ( (Sequence) lf.element()).getName()\r
+ .length())\r
+ {\r
+ longestName = TreeCanvas.PLACEHOLDER +\r
+ ( (Sequence) lf.element()).getName();\r
}\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
-\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
- // JBPNote TODO: preference for always marking placeholders in new associated tree\r
}\r
\r
+ tree.reCount(tree.getTopNode());\r
+ tree.findHeight(tree.getTopNode());\r
\r
- public void textbox_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\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
+ // JBPNote TODO: preference for always marking placeholders in new associated tree\r
+ }\r
\r
- StringBuffer buffer = new StringBuffer();\r
+ public NJTree getTree()\r
+ {\r
+ return tree;\r
+ }\r
\r
- if(type.equals("AV"))\r
- buffer.append("Average distance tree using ");\r
- else\r
- buffer.append("Neighbour joining tree using ");\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
- if(pwtype.equals("BL"))\r
- buffer.append("BLOSUM62");\r
- else\r
- buffer.append("PID");\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
- Desktop.addInternalFrame(cap,buffer.toString(), 500, 100);\r
- jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
- cap.setText( fout.print(false,true) );\r
+ public void textbox_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
\r
- }\r
+ StringBuffer buffer = new StringBuffer();\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 void saveAsNewick_actionPerformed(ActionEvent e)\r
+ if (pwtype.equals("BL"))\r
+ {\r
+ buffer.append("BLOSUM62");\r
+ }\r
+ else\r
{\r
+ buffer.append("PID");\r
+ }\r
\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
- getProperty("LAST_DIRECTORY"));\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 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
int value = chooser.showSaveDialog(null);\r
- if (value == JalviewFileChooser.APPROVE_OPTION) {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());\r
- try{\r
+\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.FileWriter( choice ) );\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
- catch (Exception ex) {\r
+ catch (Exception ex)\r
+ {\r
ex.printStackTrace();\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
}\r
\r
protected void placeholdersMenu_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());\r
+ {\r
+ treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());\r
}\r
\r
protected void epsTree_actionPerformed(ActionEvent e)\r
{\r
- int width = treeCanvas.getWidth(), height=treeCanvas.getHeight();\r
+ int width = treeCanvas.getWidth();\r
+ int height = treeCanvas.getHeight();\r
+\r
try\r
{\r
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"),\r
- new String[]{"eps"},\r
- new String[]{"Encapsulated Postscript"},\r
- "Encapsulated Postscript");\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",chooser.getSelectedFile().getParent());\r
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
- EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);\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
+ pg.flush();\r
+ pg.close();\r
}\r
catch (Exception ex)\r
{\r
}\r
\r
protected void pngTree_actionPerformed(ActionEvent e)\r
- {\r
- int width = treeCanvas.getWidth(), height = treeCanvas.getHeight();\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("LAST_DIRECTORY"),\r
- new String[] {"png"},\r
- new String[] {"Portable network graphics"},\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.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
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());\r
FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
\r
- BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);\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
+ ImageIO.write(bi, "png", out);\r
+ out.close();\r
}\r
catch (Exception ex)\r
{\r
ex.printStackTrace();\r
}\r
}\r
-\r
}\r
git://source.jalview.org / jalview.git / blobdiff