-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 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.analysis.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.io.*;\r
-\r
-import jalview.jbgui.*;\r
-\r
-import org.jibble.epsgraphics.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import java.awt.image.*;\r
-\r
-import java.io.*;\r
-\r
-import java.util.*;\r
-\r
-import javax.imageio.*;\r
-\r
-import java.beans.PropertyChangeEvent;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class TreePanel extends GTreePanel\r
-{\r
- String type;\r
- String pwtype;\r
- TreeCanvas treeCanvas;\r
- NJTree tree;\r
- AlignViewport av;\r
-\r
- /**\r
- * Creates a new TreePanel object.\r
- *\r
- * @param av DOCUMENT ME!\r
- * @param seqVector DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- * @param pwtype DOCUMENT ME!\r
- * @param s DOCUMENT ME!\r
- * @param e DOCUMENT ME!\r
- */\r
- public TreePanel(AlignmentPanel ap, String type, String pwtype)\r
- {\r
- super();\r
- initTreePanel(ap, type, pwtype, null);\r
-\r
- // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default\r
- // showDistances(true);\r
- }\r
-\r
- /**\r
- * Creates a new TreePanel object.\r
- *\r
- * @param av DOCUMENT ME!\r
- * @param seqVector DOCUMENT ME!\r
- * @param newtree DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- * @param pwtype DOCUMENT ME!\r
- */\r
- public TreePanel(AlignmentPanel ap,\r
- String type,\r
- String pwtype,\r
- NewickFile newtree)\r
- {\r
- super();\r
- initTreePanel(ap, type, pwtype, newtree);\r
- }\r
-\r
- public AlignmentI getAlignment()\r
- {\r
- return treeCanvas.av.getAlignment();\r
- }\r
-\r
-\r
- void initTreePanel(AlignmentPanel ap, String type, String pwtype,\r
- NewickFile newTree)\r
- {\r
-\r
- av = ap.av;\r
- this.type = type;\r
- this.pwtype = pwtype;\r
-\r
- treeCanvas = new TreeCanvas(ap, scrollPane);\r
- scrollPane.setViewportView(treeCanvas);\r
-\r
- av.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
- {\r
- public void propertyChange(PropertyChangeEvent evt)\r
- {\r
- if (evt.getPropertyName().equals("alignment"))\r
- {\r
- if(tree==null)\r
- System.out.println("tree is null");\r
- if(evt.getNewValue()==null)\r
- System.out.println("new value is null");\r
-\r
- tree.UpdatePlaceHolders( (Vector) evt.getNewValue());\r
-\r
- repaint();\r
- }\r
- }\r
- });\r
-\r
- this.av = av;\r
-\r
-\r
- TreeLoader tl = new TreeLoader(newTree);\r
- tl.start();\r
-\r
- }\r
-\r
- class TreeLoader extends Thread\r
- {\r
- NewickFile newtree;\r
- jalview.datamodel.AlignmentView odata=null;\r
- public TreeLoader(NewickFile newtree)\r
- {\r
- this.newtree = newtree;\r
- if (newtree != null)\r
- {\r
- // Must be outside run(), as Jalview2XML tries to\r
- // update distance/bootstrap visibility at the same time\r
- showBootstrap(newtree.HasBootstrap());\r
- showDistances(newtree.HasDistances());\r
- }\r
- }\r
-\r
- public void run()\r
- {\r
-\r
- if(newtree!=null)\r
- {\r
- if (odata==null) {\r
- tree = new NJTree(av.alignment.getSequencesArray(),\r
- newtree);\r
- } else {\r
- tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);\r
- }\r
- if (!tree.hasOriginalSequenceData())\r
- allowOriginalSeqData(false);\r
- }\r
- else\r
- {\r
- int start, end;\r
- SequenceI [] seqs;\r
- AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);\r
- if(av.getSelectionGroup()==null)\r
- {\r
- start = 0;\r
- end = av.alignment.getWidth();\r
- seqs = av.alignment.getSequencesArray();\r
- }\r
- else\r
- {\r
- start = av.getSelectionGroup().getStartRes();\r
- end = av.getSelectionGroup().getEndRes()+1;\r
- seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
- }\r
-\r
- tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);\r
- showDistances(true);\r
- }\r
-\r
-\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
- treeCanvas.setTree(tree);\r
- treeCanvas.repaint();\r
- av.setCurrentTree(tree);\r
-\r
- }\r
- }\r
-\r
- public void showDistances(boolean b)\r
- {\r
- treeCanvas.setShowDistances(b);\r
- distanceMenu.setSelected(b);\r
- }\r
-\r
- public void showBootstrap(boolean b)\r
- {\r
- treeCanvas.setShowBootstrap(b);\r
- bootstrapMenu.setSelected(b);\r
- }\r
-\r
- public void showPlaceholders(boolean b)\r
- {\r
- placeholdersMenu.setState(b);\r
- treeCanvas.setMarkPlaceholders(b);\r
- }\r
-\r
- private void allowOriginalSeqData(boolean b) {\r
- originalSeqData.setVisible(b);\r
- }\r
-\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public NJTree getTree()\r
- {\r
- return tree;\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void textbox_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\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
- if (pwtype.equals("BL"))\r
- {\r
- buffer.append("BLOSUM62");\r
- }\r
- else\r
- {\r
- buffer.append("PID");\r
- }\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(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void saveAsNewick_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.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
-\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(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());\r
- java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(\r
- choice));\r
- out.println(output);\r
- out.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void printMenu_actionPerformed(ActionEvent e)\r
- {\r
- //Putting in a thread avoids Swing painting problems\r
- treeCanvas.startPrinting();\r
- }\r
-\r
-\r
- public void originalSeqData_actionPerformed(ActionEvent e)\r
- {\r
- if (!tree.hasOriginalSequenceData())\r
- {\r
- jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");\r
- return;\r
- }\r
- // decide if av alignment is sufficiently different to original data to warrant a new window to be created\r
- // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)\r
- // or create a selection box around columns in alignment view\r
- // test Alignment(SeqCigar[])\r
- Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.\r
- getGapCharacter());\r
-\r
-\r
- if (alAndColsel != null && alAndColsel[0]!=null)\r
- {\r
- // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);\r
-\r
- Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);\r
- Alignment dataset = av.getAlignment().getDataset();\r
- if (dataset != null)\r
- {\r
- al.setDataset(dataset);\r
- }\r
-\r
- if (true)\r
- {\r
- // make a new frame!\r
- AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],\r
- AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT\r
-);\r
-\r
- //>>>This is a fix for the moment, until a better solution is found!!<<<\r
- // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());\r
-\r
- // af.addSortByOrderMenuItem(ServiceName + " Ordering",\r
- // msaorder);\r
-\r
- Desktop.addInternalFrame(af, "Original Data for " + this.title,\r
- AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\r
- }\r
- }\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void fitToWindow_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.fitToWindow = fitToWindow.isSelected();\r
- repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void font_actionPerformed(ActionEvent e)\r
- {\r
- if (treeCanvas == null)\r
- {\r
- return;\r
- }\r
-\r
- new FontChooser(this);\r
- }\r
-\r
- public Font getTreeFont()\r
- {\r
- return treeCanvas.font;\r
- }\r
-\r
- public void setTreeFont(Font font)\r
- {\r
- if(treeCanvas!=null)\r
- treeCanvas.setFont(font);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void distanceMenu_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.setShowDistances(distanceMenu.isSelected());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void bootstrapMenu_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void placeholdersMenu_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void epsTree_actionPerformed(ActionEvent e)\r
- {\r
- boolean accurateText = true;\r
-\r
- String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",\r
- "Prompt each time");\r
-\r
- // If we need to prompt, and if the GUI is visible then\r
- // Prompt for EPS rendering style\r
- if (renderStyle.equalsIgnoreCase("Prompt each time")\r
- && !\r
- (System.getProperty("java.awt.headless") != null\r
- && System.getProperty("java.awt.headless").equals("true")))\r
- {\r
- EPSOptions eps = new EPSOptions();\r
- renderStyle = eps.getValue();\r
-\r
- if (renderStyle==null || eps.cancelled)\r
- return;\r
-\r
-\r
- }\r
-\r
- if (renderStyle.equalsIgnoreCase("text"))\r
- {\r
- accurateText = false;\r
- }\r
-\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"), new String[] { "eps" },\r
- new String[] { "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
- pg.setAccurateTextMode(accurateText);\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public 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(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[] { "png" },\r
- new String[] { "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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.gui;
+
+import jalview.analysis.*;
+
+import jalview.datamodel.*;
+
+import jalview.io.*;
+
+import jalview.jbgui.*;
+
+import org.jibble.epsgraphics.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.image.*;
+
+import java.io.*;
+
+import java.util.*;
+
+import javax.imageio.*;
+
+import java.beans.PropertyChangeEvent;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class TreePanel extends GTreePanel
+{
+ String type;
+ String pwtype;
+ TreeCanvas treeCanvas;
+ NJTree tree;
+ AlignViewport av;
+
+ /**
+ * Creates a new TreePanel object.
+ *
+ * @param av DOCUMENT ME!
+ * @param seqVector DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ * @param pwtype DOCUMENT ME!
+ * @param s DOCUMENT ME!
+ * @param e DOCUMENT ME!
+ */
+ public TreePanel(AlignmentPanel ap, String type, String pwtype)
+ {
+ super();
+ initTreePanel(ap, type, pwtype, null, null);
+
+ // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
+ // showDistances(true);
+ }
+
+ /**
+ * Creates a new TreePanel object.
+ *
+ * @param av DOCUMENT ME!
+ * @param seqVector DOCUMENT ME!
+ * @param newtree DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ * @param pwtype DOCUMENT ME!
+ */
+ public TreePanel(AlignmentPanel ap,
+ String type,
+ String pwtype,
+ NewickFile newtree)
+ {
+ super();
+ initTreePanel(ap, type, pwtype, newtree, null);
+ }
+
+ public TreePanel(AlignmentPanel av,
+ String type,
+ String pwtype,
+ NewickFile newtree, AlignmentView inputData) {
+ super();
+ initTreePanel(av,type,pwtype,newtree,inputData);
+ }
+
+ public AlignmentI getAlignment()
+ {
+ return treeCanvas.av.getAlignment();
+ }
+ public AlignViewport getViewPort() {
+ return treeCanvas.av;
+ }
+
+ void initTreePanel(AlignmentPanel ap, String type, String pwtype,
+ NewickFile newTree, AlignmentView inputData)
+ {
+
+ av = ap.av;
+ this.type = type;
+ this.pwtype = pwtype;
+
+ treeCanvas = new TreeCanvas(ap, scrollPane);
+ scrollPane.setViewportView(treeCanvas);
+
+ av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
+ {
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ if (evt.getPropertyName().equals("alignment"))
+ {
+ if(tree==null)
+ System.out.println("tree is null");
+ if(evt.getNewValue()==null)
+ System.out.println("new value is null");
+
+ tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
+
+ repaint();
+ }
+ }
+ });
+
+ this.av = av;
+
+
+ TreeLoader tl = new TreeLoader(newTree);
+ if (inputData!=null) {
+ tl.odata=inputData;
+ }
+ tl.start();
+
+ }
+
+ class TreeLoader extends Thread
+ {
+ NewickFile newtree;
+ jalview.datamodel.AlignmentView odata=null;
+ public TreeLoader(NewickFile newtree)
+ {
+ this.newtree = newtree;
+ if (newtree != null)
+ {
+ // Must be outside run(), as Jalview2XML tries to
+ // update distance/bootstrap visibility at the same time
+ showBootstrap(newtree.HasBootstrap());
+ showDistances(newtree.HasDistances());
+ }
+ }
+
+ public void run()
+ {
+
+ if(newtree!=null)
+ {
+ if (odata==null) {
+ tree = new NJTree(av.alignment.getSequencesArray(),
+ newtree);
+ } else {
+ tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
+ }
+ if (!tree.hasOriginalSequenceData())
+ allowOriginalSeqData(false);
+ }
+ else
+ {
+ int start, end;
+ SequenceI [] seqs;
+ AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);
+ if(av.getSelectionGroup()==null)
+ {
+ start = 0;
+ end = av.alignment.getWidth();
+ seqs = av.alignment.getSequencesArray();
+ }
+ else
+ {
+ start = av.getSelectionGroup().getStartRes();
+ end = av.getSelectionGroup().getEndRes()+1;
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+ }
+
+ tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+ showDistances(true);
+ }
+
+
+ tree.reCount(tree.getTopNode());
+ tree.findHeight(tree.getTopNode());
+ treeCanvas.setTree(tree);
+ treeCanvas.repaint();
+ av.setCurrentTree(tree);
+
+ }
+ }
+
+ public void showDistances(boolean b)
+ {
+ treeCanvas.setShowDistances(b);
+ distanceMenu.setSelected(b);
+ }
+
+ public void showBootstrap(boolean b)
+ {
+ treeCanvas.setShowBootstrap(b);
+ bootstrapMenu.setSelected(b);
+ }
+
+ public void showPlaceholders(boolean b)
+ {
+ placeholdersMenu.setState(b);
+ treeCanvas.setMarkPlaceholders(b);
+ }
+
+ private void allowOriginalSeqData(boolean b) {
+ originalSeqData.setVisible(b);
+ }
+
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public NJTree getTree()
+ {
+ return tree;
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void textbox_actionPerformed(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+
+ StringBuffer buffer = new StringBuffer();
+
+ if (type.equals("AV"))
+ {
+ buffer.append("Average distance tree using ");
+ }
+ else
+ {
+ buffer.append("Neighbour joining tree using ");
+ }
+
+ if (pwtype.equals("BL"))
+ {
+ buffer.append("BLOSUM62");
+ }
+ else
+ {
+ buffer.append("PID");
+ }
+
+ Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+ cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void saveAsNewick_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",
+ chooser.getSelectedFile().getParent());
+
+ try
+ {
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+ String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());
+ java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
+ choice));
+ out.println(output);
+ out.close();
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void printMenu_actionPerformed(ActionEvent e)
+ {
+ //Putting in a thread avoids Swing painting problems
+ treeCanvas.startPrinting();
+ }
+
+
+ public void originalSeqData_actionPerformed(ActionEvent e)
+ {
+ if (!tree.hasOriginalSequenceData())
+ {
+ jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+ return;
+ }
+ // decide if av alignment is sufficiently different to original data to warrant a new window to be created
+ // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
+ // or create a selection box around columns in alignment view
+ // test Alignment(SeqCigar[])
+ Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
+ getGapCharacter());
+
+
+ if (alAndColsel != null && alAndColsel[0]!=null)
+ {
+ // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
+
+ Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+ Alignment dataset = av.getAlignment().getDataset();
+ if (dataset != null)
+ {
+ al.setDataset(dataset);
+ }
+
+ if (true)
+ {
+ // make a new frame!
+ AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT
+);
+
+ //>>>This is a fix for the moment, until a better solution is found!!<<<
+ // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
+
+ // af.addSortByOrderMenuItem(ServiceName + " Ordering",
+ // msaorder);
+
+ Desktop.addInternalFrame(af, "Original Data for " + this.title,
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+ }
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void fitToWindow_actionPerformed(ActionEvent e)
+ {
+ treeCanvas.fitToWindow = fitToWindow.isSelected();
+ repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void font_actionPerformed(ActionEvent e)
+ {
+ if (treeCanvas == null)
+ {
+ return;
+ }
+
+ new FontChooser(this);
+ }
+
+ public Font getTreeFont()
+ {
+ return treeCanvas.font;
+ }
+
+ public void setTreeFont(Font font)
+ {
+ if(treeCanvas!=null)
+ treeCanvas.setFont(font);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void distanceMenu_actionPerformed(ActionEvent e)
+ {
+ treeCanvas.setShowDistances(distanceMenu.isSelected());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void bootstrapMenu_actionPerformed(ActionEvent e)
+ {
+ treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void placeholdersMenu_actionPerformed(ActionEvent e)
+ {
+ treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void epsTree_actionPerformed(ActionEvent e)
+ {
+ boolean accurateText = true;
+
+ String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
+ "Prompt each time");
+
+ // If we need to prompt, and if the GUI is visible then
+ // Prompt for EPS rendering style
+ if (renderStyle.equalsIgnoreCase("Prompt each time")
+ && !
+ (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true")))
+ {
+ EPSOptions eps = new EPSOptions();
+ renderStyle = eps.getValue();
+
+ if (renderStyle==null || eps.cancelled)
+ return;
+
+
+ }
+
+ if (renderStyle.equalsIgnoreCase("text"))
+ {
+ accurateText = false;
+ }
+
+ int width = treeCanvas.getWidth();
+ int 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);
+
+ pg.setAccurateTextMode(accurateText);
+
+ treeCanvas.draw(pg, width, height);
+
+ pg.flush();
+ pg.close();
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void pngTree_actionPerformed(ActionEvent e)
+ {
+ int width = treeCanvas.getWidth();
+ int 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();
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff