X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=64716b0c53d604e2360deb627ff9e0bffa05ad28;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=58da0748dcf176ace9c2f484eb36084f6dd3cf55;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java old mode 100755 new mode 100644 index 58da074..64716b0 --- a/src/jalview/appletgui/TreePanel.java +++ b/src/jalview/appletgui/TreePanel.java @@ -1,191 +1,424 @@ -/* - * 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 jalview.analysis.*; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.jbappletgui.*; - -public class TreePanel - extends GTreePanel -{ - SequenceI[] seq; - String type; - String pwtype; - AlignViewport av; - int start; - int end; - TreeCanvas treeCanvas; - NJTree tree; - - public NJTree getTree() - { - return tree; - } - - public TreePanel(AlignViewport av, Vector seqVector, String type, - String pwtype, int s, int e) - { - super(); - - this.type = type; - this.pwtype = pwtype; - - start = s; - end = e; - - String longestName = ""; - seq = new Sequence[seqVector.size()]; - for (int i = 0; i < seqVector.size(); i++) - { - seq[i] = (Sequence) seqVector.elementAt(i); - if (seq[i].getName().length() > longestName.length()) - { - longestName = seq[i].getName(); - } - } - - tree = new NJTree(seq, type, pwtype, start, end); - - treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName); - - tree.reCount(tree.getTopNode()); - tree.findHeight(tree.getTopNode()); - scrollPane.add(treeCanvas); - - } - - public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree, - String type, String pwtype) - { - super(); - // These are probably only arbitrary strings reflecting source of tree - this.type = type; - this.pwtype = pwtype; - - start = 0; - end = seqVector.size(); - - String longestName = ""; - seq = new Sequence[seqVector.size()]; - for (int i = 0; i < seqVector.size(); i++) - { - seq[i] = (Sequence) seqVector.elementAt(i); - } - // This constructor matches sequence names to treenodes and sets up the tree layouts. - tree = new NJTree(seq, newtree); - // Now have to calculate longest name based on the leaves - Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector()); - - for (int i = 0; i < leaves.size(); i++) - { - if (longestName.length() < - ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()).getName(). - length()) - { - longestName = TreeCanvas.PLACEHOLDER + - ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()). - getName(); - } - } - - tree.reCount(tree.getTopNode()); - tree.findHeight(tree.getTopNode()); - - treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName); - treeCanvas.setShowBootstrap(newtree.HasBootstrap()); - treeCanvas.setShowDistances(newtree.HasDistances()); - distanceMenu.setState(newtree.HasDistances()); - bootstrapMenu.setState(newtree.HasBootstrap()); - if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree - { - placeholdersMenu.setState(treeCanvas.markPlaceholders); - } - scrollPane.add(treeCanvas); - - } - - public String getText(String format) - { - return null; - } - - protected void fitToWindow_actionPerformed(ActionEvent e) - { - treeCanvas.fitToWindow = fitToWindow.getState(); - repaint(); - } - - public void newickOutput_actionPerformed(ActionEvent actionEvent) - { - jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode()); - String output = fout.print(false, true); - CutAndPasteTransfer cap = new CutAndPasteTransfer(false); - cap.setText(output); - java.awt.Frame frame = new java.awt.Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100); - } - - protected void fontSize_actionPerformed(ActionEvent e) - { - /* if( treeCanvas==null ) - return; - - String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1); - - Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop, - "Select font size", - "Font size", - JOptionPane.QUESTION_MESSAGE, - null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"} - ,"Font Size - "+size); - if(selection!=null) - { - fontSize.setText("Font Size - " + selection); - - int i = Integer.parseInt(selection.toString()); - treeCanvas.setFontSize(i); - } - scrollPane.setViewportView(treeCanvas); - */ - } - - protected void distanceMenu_actionPerformed(ActionEvent e) - { - treeCanvas.setShowDistances(distanceMenu.getState()); - } - - protected void bootstrapMenu_actionPerformed(ActionEvent e) - { - treeCanvas.setShowBootstrap(bootstrapMenu.getState()); - } - - protected void placeholdersMenu_actionPerformed(ActionEvent e) - { - treeCanvas.setMarkPlaceholders(placeholdersMenu.getState()); - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 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 jalview.analysis.NJTree; +import jalview.api.analysis.ScoreModelI; +import jalview.api.analysis.ViewBasedAnalysisI; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.SequenceI; +import jalview.io.NewickFile; +import jalview.schemes.ResidueProperties; +import jalview.util.MessageManager; + +import java.awt.BorderLayout; +import java.awt.CheckboxMenuItem; +import java.awt.Color; +import java.awt.Menu; +import java.awt.MenuBar; +import java.awt.MenuItem; +import java.awt.ScrollPane; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; + +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()); + } + ScoreModelI sm = ResidueProperties.getScoreModel(pwtype); + if (sm instanceof ViewBasedAnalysisI) + { + try + { + sm = sm.getClass().newInstance(); + ((ViewBasedAnalysisI) sm) + .configureFromAlignmentView(treeCanvas.ap); + } catch (Exception q) + { + System.err.println("Couldn't create a scoremodel instance for " + + sm.getName()); + q.printStackTrace(); + } + tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end); + } + else + { + tree = new NJTree(seqs, seqStrings, type, pwtype, null, 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); + } + +}