X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=90f4bd001b824678816b34181bfc60c2e1fee3db;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=e770a1688c1031eac22a9b20b7e4938b611944ab;hpb=0c0f58648af5512096275b634158c37c87989eaa;p=jalview.git diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java old mode 100755 new mode 100644 index e770a16..90f4bd0 --- a/src/jalview/appletgui/TreePanel.java +++ b/src/jalview/appletgui/TreePanel.java @@ -1,280 +1,390 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 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.appletgui; - -import java.util.*; - -import java.awt.event.*; -import java.awt.*; - -import jalview.analysis.*; -import jalview.datamodel.*; -import jalview.io.*; - -public class TreePanel extends Frame implements ActionListener, ItemListener -{ - SequenceI[] seq; - String type; - String pwtype; - int start; - int end; - TreeCanvas treeCanvas; - NJTree tree; - AlignViewport av; - - public NJTree getTree() - { - return tree; - } - - /** - * 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(AlignViewport av, String type, String pwtype) - { - try - { - jbInit(); - this.setMenuBar(jMenuBar1); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - - initTreePanel(av, type, pwtype, null); - } - - /** - * 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(AlignViewport av, - String type, - String pwtype, - NewickFile newtree) - { - try - { - jbInit(); - this.setMenuBar(jMenuBar1); - } - catch (Exception e) - { - e.printStackTrace(); - } - - initTreePanel(av, type, pwtype, newtree); - } - - - void initTreePanel(AlignViewport av, - String type, - String pwtype, - NewickFile newTree) - { - - this.av = av; - this.type = type; - this.pwtype = pwtype; - - treeCanvas = new TreeCanvas(av, scrollPane); - scrollPane.add(treeCanvas); - - - TreeLoader tl = new TreeLoader(newTree); - tl.start(); - - } - - class TreeLoader extends Thread - { - NewickFile newtree; - - public TreeLoader(NewickFile newtree) - { - this.newtree = newtree; - } - - public void run() - { - if (newtree != null) - tree = new NJTree(av.alignment.getSequencesArray(), - newtree); - else - { - int start, end; - SequenceI [] seqs; - String [] seqStrings = null; - // if (av.hasHiddenColumns) - { - // seqStrings = av.getSelectionAsString(); - } - - 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); - } - - tree.reCount(tree.getTopNode()); - tree.findHeight(tree.getTopNode()); - treeCanvas.setTree(tree); - if(newtree!=null) - { - distanceMenu.setState(newtree.HasDistances()); - bootstrapMenu.setState(newtree.HasBootstrap()); - treeCanvas.setShowBootstrap(newtree.HasBootstrap()); - treeCanvas.setShowDistances(newtree.HasDistances()); - } - - - treeCanvas.repaint(); - - av.setCurrentTree(tree); - - } - } - - public void actionPerformed(ActionEvent evt) - { - if(evt.getSource()==newickOutput) - newickOutput_actionPerformed(); - else if(evt.getSource()==fontSize) - fontSize_actionPerformed(); - } - - public void itemStateChanged(ItemEvent evt) - { - if(evt.getSource()==fitToWindow) - treeCanvas.fitToWindow = fitToWindow.getState(); - - else if(evt.getSource()==distanceMenu) - treeCanvas.setShowDistances(distanceMenu.getState()); - - else if(evt.getSource()==bootstrapMenu) - treeCanvas.setShowBootstrap(bootstrapMenu.getState()); - - else if(evt.getSource()==placeholdersMenu) - treeCanvas.setMarkPlaceholders(placeholdersMenu.getState()); - - treeCanvas.repaint(); - } - - - public void newickOutput_actionPerformed() - { - jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode()); - String output = fout.print(false, true); - CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null); - cap.setText(output); - java.awt.Frame frame = new java.awt.Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100); - } - - public java.awt.Font getTreeFont() - { - return treeCanvas.font; - } - - public void setTreeFont(java.awt.Font font) - { - treeCanvas.font = font; - treeCanvas.repaint(); - } - - protected void fontSize_actionPerformed() - { - if( treeCanvas==null ) - return; - - new FontChooser(this); - } - - - - - BorderLayout borderLayout1 = new BorderLayout(); - protected ScrollPane scrollPane = new ScrollPane(); - MenuBar jMenuBar1 = new MenuBar(); - Menu jMenu2 = new Menu(); - protected MenuItem fontSize = new MenuItem(); - protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem(); - protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem(); - protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem(); - protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem(); - Menu fileMenu = new Menu(); - MenuItem newickOutput = new MenuItem(); - - private void jbInit() throws Exception { - setLayout(borderLayout1); - this.setBackground(Color.white); - this.setFont(new java.awt.Font("Verdana", 0, 12)); - jMenu2.setLabel("View"); - fontSize.setLabel("Font..."); - fontSize.addActionListener(this); - bootstrapMenu.setLabel("Show Bootstrap Values"); - bootstrapMenu.addItemListener(this); - distanceMenu.setLabel("Show Distances"); - distanceMenu.addItemListener(this); - placeholdersMenu.setLabel("Mark Unassociated Leaves"); - placeholdersMenu.addItemListener(this); - fitToWindow.setState(true); - fitToWindow.setLabel("Fit To Window"); - fitToWindow.addItemListener(this); - fileMenu.setLabel("File"); - newickOutput.setLabel("Newick Format"); - newickOutput.addActionListener(this); - - add(scrollPane, BorderLayout.CENTER); - jMenuBar1.add(fileMenu); - jMenuBar1.add(jMenu2); - jMenu2.add(fitToWindow); - jMenu2.add(fontSize); - jMenu2.add(distanceMenu); - jMenu2.add(bootstrapMenu); - jMenu2.add(placeholdersMenu); - fileMenu.add(newickOutput); - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) + * Copyright (C) 2014 The Jalview Authors + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.appletgui; + +import java.awt.*; +import java.awt.event.*; + +import jalview.analysis.*; +import jalview.datamodel.*; +import jalview.io.*; +import jalview.util.MessageManager; + +public class TreePanel extends EmbmenuFrame implements ActionListener, + ItemListener +{ + SequenceI[] seq; + + String type; + + String pwtype; + + int start; + + int end; + + TreeCanvas treeCanvas; + + NJTree tree; + + AlignmentPanel ap; + + AlignViewport av; + + public NJTree getTree() + { + return tree; + } + + public void finalize() throws Throwable + { + ap = null; + av = null; + super.finalize(); + } + + /** + * 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) + { + try + { + jbInit(); + this.setMenuBar(jMenuBar1); + } catch (Exception ex) + { + ex.printStackTrace(); + } + + initTreePanel(ap, type, pwtype, null); + } + + /** + * 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) + { + try + { + jbInit(); + this.setMenuBar(jMenuBar1); + } catch (Exception e) + { + e.printStackTrace(); + } + + initTreePanel(ap, type, pwtype, newtree); + } + + void initTreePanel(AlignmentPanel ap, String type, String pwtype, + NewickFile newTree) + { + + this.ap = ap; + this.av = ap.av; + this.type = type; + this.pwtype = pwtype; + + treeCanvas = new TreeCanvas(ap, scrollPane); + TreeLoader tl = new TreeLoader(newTree); + tl.start(); + embedMenuIfNeeded(treeCanvas); + scrollPane.add(treeCanvas, BorderLayout.CENTER); + } + + void showOriginalData() + { + // 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[]) + if (tree.seqData != null) + { + 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) + { + Alignment al = new Alignment((SequenceI[]) alAndColsel[0]); + AlignFrame af = new AlignFrame(al, av.applet, + "Original Data for Tree", false); + + af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]); + } + } + else + { + System.out.println("Original Tree Data not available"); + } + } + + class TreeLoader extends Thread + { + NewickFile newtree; + + jalview.datamodel.AlignmentView odata = null; + + public TreeLoader(NewickFile newtree) + { + this.newtree = newtree; + } + + public void run() + { + if (newtree != null) + { + if (odata == null) + { + tree = new NJTree(av.getAlignment().getSequencesArray(), newtree); + } + else + { + tree = new NJTree(av.getAlignment().getSequencesArray(), odata, + newtree); + } + + } + else + { + int start, end; + SequenceI[] seqs; + boolean selview = (av.getSelectionGroup() != null) + && (av.getSelectionGroup().getSize() > 1); + AlignmentView seqStrings = av.getAlignmentView(selview); + if (!selview) + { + start = 0; + end = av.getAlignment().getWidth(); + seqs = av.getAlignment().getSequencesArray(); + } + else + { + start = av.getSelectionGroup().getStartRes(); + end = av.getSelectionGroup().getEndRes() + 1; + seqs = av.getSelectionGroup().getSequencesInOrder( + av.getAlignment()); + } + + tree = new NJTree(seqs, seqStrings, type, pwtype, start, end); + } + + tree.reCount(tree.getTopNode()); + tree.findHeight(tree.getTopNode()); + treeCanvas.setTree(tree); + if (newtree != null) + { + // Set default view, paying lip service to any overriding tree view + // parameter settings + boolean showDist = newtree.HasDistances() + && av.applet.getDefaultParameter("showTreeDistances", + newtree.HasDistances()); + boolean showBoots = newtree.HasBootstrap() + && av.applet.getDefaultParameter("showTreeBootstraps", + newtree.HasBootstrap()); + distanceMenu.setState(showDist); + bootstrapMenu.setState(showBoots); + treeCanvas.setShowBootstrap(showBoots); + treeCanvas.setShowDistances(showDist); + treeCanvas.setMarkPlaceholders(av.applet.getDefaultParameter( + "showUnlinkedTreeNodes", false)); + } + + treeCanvas.repaint(); + + av.setCurrentTree(tree); + + } + } + + public void actionPerformed(ActionEvent evt) + { + if (evt.getSource() == newickOutput) + { + newickOutput_actionPerformed(); + } + else if (evt.getSource() == fontSize) + { + fontSize_actionPerformed(); + } + else if (evt.getSource() == inputData) + { + showOriginalData(); + } + } + + public void itemStateChanged(ItemEvent evt) + { + if (evt.getSource() == fitToWindow) + { + treeCanvas.fitToWindow = fitToWindow.getState(); + } + + else if (evt.getSource() == distanceMenu) + { + treeCanvas.setShowDistances(distanceMenu.getState()); + } + + else if (evt.getSource() == bootstrapMenu) + { + treeCanvas.setShowBootstrap(bootstrapMenu.getState()); + } + + else if (evt.getSource() == placeholdersMenu) + { + treeCanvas.setMarkPlaceholders(placeholdersMenu.getState()); + } + + treeCanvas.repaint(); + } + + public void newickOutput_actionPerformed() + { + jalview.io.NewickFile fout = new jalview.io.NewickFile( + tree.getTopNode()); + String output = fout.print(false, true); + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null); + cap.setText(output); + java.awt.Frame frame = new java.awt.Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100); + } + + public java.awt.Font getTreeFont() + { + return treeCanvas.font; + } + + public void setTreeFont(java.awt.Font font) + { + treeCanvas.font = font; + treeCanvas.repaint(); + } + + protected void fontSize_actionPerformed() + { + if (treeCanvas == null) + { + return; + } + + new FontChooser(this); + } + + BorderLayout borderLayout1 = new BorderLayout(); + + protected ScrollPane scrollPane = new ScrollPane(); + + MenuBar jMenuBar1 = new MenuBar(); + + Menu jMenu2 = new Menu(); + + protected MenuItem fontSize = new MenuItem(); + + protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem(); + + protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem(); + + protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem(); + + protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem(); + + Menu fileMenu = new Menu(); + + MenuItem newickOutput = new MenuItem(); + + MenuItem inputData = new MenuItem(); + + private void jbInit() throws Exception + { + setLayout(borderLayout1); + this.setBackground(Color.white); + this.setFont(new java.awt.Font("Verdana", 0, 12)); + jMenu2.setLabel(MessageManager.getString("action.view")); + fontSize.setLabel(MessageManager.getString("action.font")); + fontSize.addActionListener(this); + bootstrapMenu.setLabel(MessageManager + .getString("label.show_bootstrap_values")); + bootstrapMenu.addItemListener(this); + distanceMenu.setLabel(MessageManager.getString("label.show_distances")); + distanceMenu.addItemListener(this); + placeholdersMenu.setLabel(MessageManager + .getString("label.mark_unassociated_leaves")); + placeholdersMenu.addItemListener(this); + fitToWindow.setState(true); + fitToWindow.setLabel(MessageManager.getString("label.fit_to_window")); + fitToWindow.addItemListener(this); + fileMenu.setLabel(MessageManager.getString("action.file")); + newickOutput.setLabel(MessageManager.getString("label.newick_format")); + newickOutput.addActionListener(this); + inputData.setLabel(MessageManager.getString("label.input_data")); + + add(scrollPane, BorderLayout.CENTER); + jMenuBar1.add(fileMenu); + jMenuBar1.add(jMenu2); + jMenu2.add(fitToWindow); + jMenu2.add(fontSize); + jMenu2.add(distanceMenu); + jMenu2.add(bootstrapMenu); + jMenu2.add(placeholdersMenu); + fileMenu.add(newickOutput); + fileMenu.add(inputData); + inputData.addActionListener(this); + } + +}