-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
-\r
-\r
-\r
-public class TreePanel extends GTreePanel\r
-{\r
- SequenceI[] seq;\r
- String type;\r
- String pwtype;\r
- AlignViewport av;\r
- int start;\r
- int end;\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
- {\r
- super();\r
-\r
- this.type = type;\r
- this.pwtype = pwtype;\r
-\r
- start = s;\r
- end = e;\r
-\r
- String longestName = "";\r
- seq = new Sequence [seqVector.size()];\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
- longestName = seq[i].getName();\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
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
- scrollPane.setViewportView(treeCanvas);\r
-\r
- }\r
-\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
-\r
- int offx = pp.xoffset;\r
- int offy = pp.yoffset;\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
-\r
- if (top.count == 0) {\r
- top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;\r
- }\r
-\r
- float chunk = (float)(height-offy*2)/(((SequenceNode)top).count+1);\r
-\r
- drawPostscriptNode(top,chunk,wscale,width,offx,offy);\r
-\r
- printout("showpage\n");\r
- } catch (java.io.IOException e) {\r
- System.out.println("Exception " + e);\r
- }\r
-}\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
-\r
- int xstart = (int)((height-dist)*scale) + offx;\r
- int xend = (int)(height*scale) + offx;\r
-\r
- int ypos = (int)(node.ycount * chunk) + offy;\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
-\r
- // Draw horizontal line\r
- // g.drawLine(xstart,ypos,xend,ypos);\r
- printout(xstart + " " + ypos + " moveto " + xend + " " + ypos + " lineto stroke \n");\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
- }\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
- }\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
-\r
-public String getText(String format) {\r
- return null;\r
-}\r
-\r
-public void getPostscript(PrintWriter bw) {\r
- this.bw = bw;\r
- drawPostscript(pp);\r
-\r
-}\r
-\r
-public void getPostscript(PrintStream bw) {\r
- this.ps = bw;\r
- drawPostscript(pp);\r
- bw.flush();\r
-}\r
-\r
-public StringBuffer getPostscript() {\r
- makeString = true;\r
- out = new StringBuffer();\r
- drawPostscript(pp);\r
- return out;\r
-}\r
-\r
-public void propertiesInit() {\r
- this.pp = new PostscriptProperties();\r
- this.fp = new FileProperties();\r
-}\r
-\r
-\r
- public void saveButton_actionPerformed(ActionEvent e)\r
- {\r
-\r
- try{\r
- JFileChooser chooser = new JFileChooser(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 == JFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
-\r
- bw = new PrintWriter(new FileWriter(choice));\r
- getPostscript(bw);\r
- bw.close();\r
-\r
- }\r
-\r
- }catch(Exception ex){ex.printStackTrace();}\r
-\r
- }\r
-\r
-\r
- protected void saveMenu_actionPerformed(ActionEvent e)\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
-\r
- protected void fitToWindow_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.fitToWindow = fitToWindow.isSelected();\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
-\r
- }\r
-\r
- protected void distanceMenu_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.setShowDistances(distanceMenu.isSelected());\r
- }\r
-\r
- protected void bootstrapMenu_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());\r
- }\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.gui;
+
+import java.beans.*;
+import java.io.*;
+import java.util.*;
+import javax.imageio.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.image.*;
+import javax.swing.*;
+
+import org.jibble.epsgraphics.*;
+import jalview.analysis.*;
+import jalview.commands.CommandI;
+import jalview.commands.OrderCommand;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbgui.*;
+
+/**
+ * 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(this, ap, scrollPane);
+ scrollPane.setViewportView(treeCanvas);
+
+ PaintRefresher.Register(this, ap.av.getSequenceSetId());
+
+ buildAssociatedViewMenu();
+
+ 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");
+ // TODO: deal with case when a change event is received whilst a
+ // tree is still being calculated - should save reference for
+ // processing message later.
+ return;
+ }
+ if (evt.getNewValue() == null)
+ {
+ System.out
+ .println("new alignment sequences vector value is null");
+ }
+
+ tree.UpdatePlaceHolders((Vector) evt.getNewValue());
+ treeCanvas.nameHash.clear(); // reset the mapping between canvas
+ // rectangles and leafnodes
+ repaint();
+ }
+ }
+ });
+
+ TreeLoader tl = new TreeLoader(newTree);
+ if (inputData != null)
+ {
+ tl.odata = inputData;
+ }
+ tl.start();
+
+ }
+
+ public void viewMenu_menuSelected()
+ {
+ buildAssociatedViewMenu();
+ }
+
+ void buildAssociatedViewMenu()
+ {
+ AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
+ .getSequenceSetId());
+ if (aps.length == 1 && treeCanvas.ap == aps[0])
+ {
+ associateLeavesMenu.setVisible(false);
+ return;
+ }
+
+ associateLeavesMenu.setVisible(true);
+
+ if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
+ {
+ viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
+ }
+
+ associateLeavesMenu.removeAll();
+
+ JRadioButtonMenuItem item;
+ ButtonGroup buttonGroup = new ButtonGroup();
+ int i, iSize = aps.length;
+ final TreePanel thisTreePanel = this;
+ for (i = 0; i < iSize; i++)
+ {
+ final AlignmentPanel ap = aps[i];
+ item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
+ buttonGroup.add(item);
+ item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ treeCanvas.applyToAllViews = false;
+ treeCanvas.ap = ap;
+ treeCanvas.av = ap.av;
+ PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
+ }
+ });
+
+ associateLeavesMenu.add(item);
+ }
+
+ final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
+ buttonGroup.add(itemf);
+ itemf.setSelected(treeCanvas.applyToAllViews);
+ itemf.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ treeCanvas.applyToAllViews = itemf.isSelected();
+ }
+ });
+ associateLeavesMenu.add(itemf);
+
+ }
+
+ 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);
+ if (av.getSortByTree())
+ {
+ sortByTree_actionPerformed(null);
+ }
+ }
+ }
+
+ 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");
+ }
+
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(
+ tree.getTopNode());
+ try
+ {
+ cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
+ tree.isHasRootDistance()));
+ Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("generating newick tree file", oom);
+ cap.dispose();
+ }
+
+ }
+
+ /**
+ * 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[])
+ char gc = '-';
+ try
+ {
+ // we try to get the associated view's gap character
+ // but this may fail if the view was closed...
+ gc = av.getGapCharacter();
+
+ } catch (Exception ex)
+ {
+ }
+ ;
+ Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
+
+ if (alAndColsel != null && alAndColsel[0] != null)
+ {
+ // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
+
+ Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+ Alignment dataset = (av != null && av.getAlignment() != null) ? av
+ .getAlignment().getDataset() : null;
+ 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();
+ }
+
+ /**
+ * sort the associated alignment view by the current tree.
+ *
+ * @param e
+ */
+ public void sortByTree_actionPerformed(ActionEvent e)
+ {
+
+ if (treeCanvas.applyToAllViews)
+ {
+ final ArrayList<CommandI> commands = new ArrayList<CommandI>();
+ for (AlignmentPanel ap: PaintRefresher.getAssociatedPanels(av
+ .getSequenceSetId()))
+ {
+ commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
+ }
+ av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
+ {
+
+ @Override
+ public void undoCommand(AlignmentI[] views)
+ {
+ for (CommandI tsort:commands)
+ {
+ tsort.undoCommand(views);
+ }
+ }
+
+ @Override
+ public int getSize()
+ {
+ return commands.size();
+ }
+
+ @Override
+ public String getDescription()
+ {
+ return "Tree Sort (many views)";
+ }
+
+ @Override
+ public void doCommand(AlignmentI[] views)
+ {
+
+ for (CommandI tsort:commands)
+ {
+ tsort.doCommand(views);
+ }
+ }
+ });
+ for (AlignmentPanel ap: PaintRefresher.getAssociatedPanels(av
+ .getSequenceSetId()))
+ {
+ // ensure all the alignFrames refresh their GI after adding an undo item
+ ap.alignFrame.updateEditMenuBar();
+ }
+ } else {
+ treeCanvas.ap.alignFrame.addHistoryItem(sortAlignmentIn(treeCanvas.ap));
+ }
+
+ }
+ public CommandI sortAlignmentIn(AlignmentPanel ap)
+ {
+ AlignViewport av = ap.av;
+ SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByTree(av.getAlignment(), tree);
+ CommandI undo;
+ undo=new OrderCommand("Tree Sort", oldOrder,
+ av.alignment);
+
+ ap.paintAlignment(true);
+ return undo;
+ }
+ /**
+ * 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();
+ }
+ }
+
+ /**
+ * change node labels to the annotation referred to by labelClass TODO:
+ * promote to a datamodel modification that can be undone TODO: make argument
+ * one case of a generic transformation function ie { undoStep = apply(Tree,
+ * TransformFunction)};
+ *
+ * @param labelClass
+ */
+ public void changeNames(final String labelClass)
+ {
+ tree.applyToNodes(new NodeTransformI()
+ {
+
+ public void transform(BinaryNode node)
+ {
+ if (node instanceof SequenceNode
+ && !((SequenceNode) node).isPlaceholder()
+ && !((SequenceNode) node).isDummy())
+ {
+ String newname = null;
+ SequenceI sq = (SequenceI) ((SequenceNode) node).element();
+ if (sq != null)
+ {
+ // search dbrefs, features and annotation
+ DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
+ sq.getDBRef(), new String[]
+ { labelClass.toUpperCase() });
+ if (refs != null)
+ {
+ for (int i = 0; i < refs.length; i++)
+ {
+ if (newname == null)
+ {
+ newname = new String(refs[i].getAccessionId());
+ }
+ else
+ {
+ newname = newname + "; " + refs[i].getAccessionId();
+ }
+ }
+ }
+ if (newname == null)
+ {
+ SequenceFeature sf[] = sq.getSequenceFeatures();
+ for (int i = 0; sf != null && i < sf.length; i++)
+ {
+ if (sf[i].getType().equals(labelClass))
+ {
+ if (newname == null)
+ {
+ newname = new String(sf[i].getDescription());
+ }
+ else
+ {
+ newname = newname + "; " + sf[i].getDescription();
+ }
+ }
+ }
+ }
+ }
+ if (newname != null)
+ {
+ String oldname = ((SequenceNode) node).getName();
+ // TODO : save in the undo object for this modification.
+ ((SequenceNode) node).setName(newname);
+ }
+ }
+ }
+ });
+ }
+}
git://source.jalview.org / jalview.git / blobdiff