X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=dc2b820b61f99ba130854a64ee1d54fd57c3a2bc;hb=e61219eaa31557203fa518aa03cba2cc651e1b84;hp=06f82694f6606f677d78cc5f665f1c57cf1e6f50;hpb=b6d133ff2200a05764410900ed01b75760860fcf;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 06f8269..dc2b820 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -1,554 +1,567 @@ -/* - * 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); - - // 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); - } - - public AlignmentI getAlignment() - { - return treeCanvas.av.getAlignment(); - } - - - void initTreePanel(AlignmentPanel ap, String type, String pwtype, - NewickFile newTree) - { - - 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); - 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(); - } - } -} +/* + * 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(); + } + } +}