2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
19 package jalview.gui;
\r
21 import jalview.io.*;
\r
23 import jalview.schemes.*;
\r
30 import java.util.jar.*;
\r
32 import javax.swing.*;
\r
34 import jalview.binding.*;
\r
41 * @version $Revision$
\r
43 public class Jalview2XML
\r
45 // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
\r
46 public static void SaveState(File statefile)
\r
48 long creation = System.currentTimeMillis();
\r
49 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
\r
58 FileOutputStream fos = new FileOutputStream(statefile);
\r
59 JarOutputStream jout = new JarOutputStream(fos);
\r
61 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
\r
62 ////////////////////////////////////////////////////
\r
63 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
\r
66 Vector shortNames = new Vector();
\r
69 for (int i = frames.length - 1; i > -1; i--)
\r
71 if (frames[i] instanceof AlignFrame)
\r
73 AlignFrame af = (AlignFrame) frames[i];
\r
75 String shortName = af.getTitle();
\r
77 if (shortName.indexOf(File.separatorChar) > -1)
\r
79 shortName = shortName.substring(shortName.lastIndexOf(
\r
80 File.separatorChar) + 1);
\r
85 while (shortNames.contains(shortName))
\r
87 if (shortName.endsWith("_" + (count - 1)))
\r
89 shortName = shortName.substring(0,
\r
90 shortName.lastIndexOf("_"));
\r
93 shortName = shortName.concat("_" + count);
\r
97 shortNames.addElement(shortName);
\r
99 if (!shortName.endsWith(".xml"))
\r
101 shortName = shortName + ".xml";
\r
104 SaveState(af, creation, shortName, jout, out);
\r
111 catch (Exception ex)
\r
113 ex.printStackTrace();
\r
117 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
\r
118 public static void SaveAlignment(AlignFrame af, String jarFile,
\r
123 FileOutputStream fos = new FileOutputStream(jarFile);
\r
124 JarOutputStream jout = new JarOutputStream(fos);
\r
126 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
\r
127 ////////////////////////////////////////////////////
\r
128 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
\r
131 SaveState(af, System.currentTimeMillis(), fileName, jout, out);
\r
135 catch (Exception ex)
\r
137 ex.printStackTrace();
\r
144 * @param af DOCUMENT ME!
\r
145 * @param timeStamp DOCUMENT ME!
\r
146 * @param fileName DOCUMENT ME!
\r
147 * @param jout DOCUMENT ME!
\r
148 * @param out DOCUMENT ME!
\r
150 public static void SaveState(AlignFrame af, long timeStamp,
\r
151 String fileName, JarOutputStream jout, PrintWriter out)
\r
153 Vector seqids = new Vector();
\r
154 Vector userColours = new Vector();
\r
156 AlignViewport av = af.viewport;
\r
158 JalviewModel object = new JalviewModel();
\r
159 object.setVamsasModel(new jalview.binding.VamsasModel());
\r
161 object.setCreationDate(new java.util.Date(timeStamp));
\r
162 object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
\r
164 jalview.datamodel.AlignmentI jal = af.viewport.alignment;
\r
166 SequenceSet vamsasSet = new SequenceSet();
\r
167 Sequence vamsasSeq;
\r
168 JalviewModelSequence jms = new JalviewModelSequence();
\r
170 vamsasSet.setGapChar(jal.getGapCharacter() + "");
\r
177 for (int i = 0; i < jal.getHeight(); i++)
\r
179 seqids.add(jal.getSequenceAt(i));
\r
181 vamsasSeq = new Sequence();
\r
182 vamsasSeq.setId(id + "");
\r
183 vamsasSeq.setName(jal.getSequenceAt(i).getName());
\r
184 vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
\r
187 jseq.setStart(jal.getSequenceAt(i).getStart());
\r
188 jseq.setEnd(jal.getSequenceAt(i).getEnd());
\r
190 jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
\r
195 vamsasSet.addSequence(vamsasSeq);
\r
200 ///////////////////////////////////
\r
201 if (af.viewport.currentTree != null)
\r
203 // FIND ANY ASSOCIATED TREES
\r
204 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
\r
205 if (Desktop.desktop != null)
\r
207 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
\r
209 for (int t = 0; t < frames.length; t++)
\r
211 if (frames[t] instanceof TreePanel)
\r
213 TreePanel tp = (TreePanel) frames[t];
\r
215 if (tp.treeCanvas.av.alignment == jal)
\r
217 Tree tree = new Tree();
\r
218 tree.setTitle(tp.getTitle());
\r
219 tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));
\r
220 tree.setNewick(tp.getTree().toString());
\r
221 tree.setThreshold(tp.treeCanvas.threshold);
\r
223 tree.setFitToWindow(tp.fitToWindow.getState());
\r
224 tree.setFontName(tp.getTreeFont().getName());
\r
225 tree.setFontSize(tp.getTreeFont().getSize());
\r
226 tree.setFontStyle(tp.getTreeFont().getStyle());
\r
227 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
\r
229 tree.setShowBootstrap(tp.bootstrapMenu.getState());
\r
230 tree.setShowDistances(tp.distanceMenu.getState());
\r
232 tree.setHeight(tp.getHeight());
\r
233 tree.setWidth(tp.getWidth());
\r
234 tree.setXpos(tp.getX());
\r
235 tree.setYpos(tp.getY());
\r
245 if (jal.getAlignmentAnnotation() != null)
\r
247 jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
\r
249 for (int i = 0; i < aa.length; i++)
\r
251 if (aa[i].label.equals("Quality") ||
\r
252 aa[i].label.equals("Conservation") ||
\r
253 aa[i].label.equals("Consensus"))
\r
258 Annotation an = new Annotation();
\r
259 an.setDescription(aa[i].description);
\r
260 an.setGraph(aa[i].isGraph);
\r
261 an.setLabel(aa[i].label);
\r
263 AnnotationElement ae;
\r
265 for (int a = 0; a < aa[i].annotations.length; a++)
\r
267 if ((aa[i] == null) || (aa[i].annotations[a] == null))
\r
272 ae = new AnnotationElement();
\r
273 ae.setDescription(aa[i].annotations[a].description);
\r
274 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
\r
275 ae.setValue(aa[i].annotations[a].value);
\r
277 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
\r
279 an.addAnnotationElement(ae);
\r
282 vamsasSet.addAnnotation(an);
\r
287 if (jal.getGroups() != null)
\r
289 JGroup[] groups = new JGroup[jal.getGroups().size()];
\r
291 for (int i = 0; i < groups.length; i++)
\r
293 groups[i] = new JGroup();
\r
295 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
\r
297 groups[i].setStart(sg.getStartRes());
\r
298 groups[i].setEnd(sg.getEndRes());
\r
299 groups[i].setName(sg.getName());
\r
302 if (sg.cs.conservationApplied())
\r
304 groups[i].setConsThreshold(sg.cs.getConservationInc());
\r
306 if (sg.cs instanceof jalview.schemes.UserColourScheme)
\r
308 groups[i].setColour(SetUserColourScheme(sg.cs,
\r
314 groups[i].setColour(ColourSchemeProperty.getColourName(sg.
\r
318 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
\r
320 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
\r
325 groups[i].setColour(ColourSchemeProperty.getColourName(
\r
329 groups[i].setPidThreshold(sg.cs.getThreshold());
\r
332 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
\r
333 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
\r
334 groups[i].setDisplayText(sg.getDisplayText());
\r
335 groups[i].setColourText(sg.getColourText());
\r
337 for (int s = 0; s < sg.getSize(); s++)
\r
339 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);
\r
340 int index = seqids.indexOf(seq);
\r
341 groups[i].addSeq(index);
\r
345 jms.setJGroup(groups);
\r
348 ///////////SAVE VIEWPORT
\r
349 Viewport view = new Viewport();
\r
350 view.setTitle(af.getTitle());
\r
351 view.setXpos(af.getX());
\r
352 view.setYpos(af.getY());
\r
353 view.setWidth(af.getWidth());
\r
354 view.setHeight(af.getHeight());
\r
355 view.setStartRes(av.startRes);
\r
356 view.setStartSeq(av.startSeq);
\r
358 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
\r
360 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
\r
361 userColours, jms));
\r
365 view.setBgColour(ColourSchemeProperty.getColourName(
\r
366 av.getGlobalColourScheme()));
\r
369 ColourSchemeI cs = av.getGlobalColourScheme();
\r
373 if (cs.conservationApplied())
\r
375 view.setConsThreshold(cs.getConservationInc());
\r
376 if (cs instanceof jalview.schemes.UserColourScheme)
\r
377 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
\r
380 if (cs instanceof ResidueColourScheme)
\r
382 view.setPidThreshold(cs.getThreshold());
\r
386 view.setConservationSelected(av.getConservationSelected());
\r
387 view.setPidSelected(av.getAbovePIDThreshold());
\r
388 view.setFontName(av.font.getName());
\r
389 view.setFontSize(av.font.getSize());
\r
390 view.setFontStyle(av.font.getStyle());
\r
391 view.setRenderGaps(av.renderGaps);
\r
392 view.setShowAnnotation(av.getShowAnnotation());
\r
393 view.setShowBoxes(av.getShowBoxes());
\r
394 view.setShowColourText(av.getColourText());
\r
395 view.setShowConservation(av.showConservation);
\r
396 view.setShowFullId(av.getShowFullId());
\r
397 view.setShowIdentity(av.showIdentity);
\r
398 view.setShowQuality(av.showQuality);
\r
399 view.setShowSequenceFeatures(av.showSequenceFeatures);
\r
400 view.setShowText(av.getShowText());
\r
401 view.setWrapAlignment(av.getWrapAlignment());
\r
403 jms.addViewport(view);
\r
405 object.setJalviewModelSequence(jms);
\r
406 object.getVamsasModel().addSequenceSet(vamsasSet);
\r
410 if (!fileName.endsWith(".xml"))
\r
412 fileName = fileName + ".xml";
\r
415 JarEntry entry = new JarEntry(fileName);
\r
416 jout.putNextEntry(entry);
\r
418 object.marshal(out);
\r
420 catch (Exception ex)
\r
422 ex.printStackTrace();
\r
426 static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
\r
427 Vector userColours, JalviewModelSequence jms)
\r
430 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
\r
432 if (!userColours.contains(ucs))
\r
434 userColours.add(ucs);
\r
436 java.awt.Color[] colours = ucs.getColours();
\r
437 jalview.binding.UserColours uc = new jalview.binding.UserColours();
\r
438 jalview.binding.UserColourScheme jbucs = new jalview.binding.UserColourScheme();
\r
440 for (int i = 0; i < colours.length; i++)
\r
442 jalview.binding.Colour col = new jalview.binding.Colour();
\r
443 col.setRGB(jalview.util.Format.getHexString(colours[i]));
\r
444 jbucs.addColour(col);
\r
447 id = "ucs" + userColours.indexOf(ucs);
\r
449 uc.setUserColourScheme(jbucs);
\r
450 jms.addUserColours(uc);
\r
456 static jalview.schemes.UserColourScheme GetUserColourScheme(
\r
457 JalviewModelSequence jms, String id)
\r
459 UserColours[] uc = jms.getUserColours();
\r
460 UserColours colours = null;
\r
462 for (int i = 0; i < uc.length; i++)
\r
464 if (uc[i].getId().equals(id))
\r
472 int csize = colours.getUserColourScheme().getColourCount();
\r
473 java.awt.Color[] newColours = new java.awt.Color[csize];
\r
475 for (int i = 0; i < csize; i++)
\r
477 newColours[i] = new java.awt.Color(Integer.parseInt(
\r
478 colours.getUserColourScheme().getColour(i).getRGB(), 16));
\r
481 return new jalview.schemes.UserColourScheme(newColours);
\r
487 * @param file DOCUMENT ME!
\r
489 public static AlignFrame LoadJalviewAlign(String file)
\r
491 JalviewModel object = new JalviewModel();
\r
492 jalview.gui.AlignFrame af = null;
\r
496 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
\r
499 if (file.startsWith("http://"))
\r
501 url = new URL(file);
\r
504 JarInputStream jin = null;
\r
505 JarEntry jarentry = null;
\r
506 int entryCount = 1;
\r
512 jin = new JarInputStream(url.openStream());
\r
516 jin = new JarInputStream(new FileInputStream(file));
\r
519 for (int i = 0; i < entryCount; i++)
\r
521 jarentry = jin.getNextJarEntry();
\r
524 if (jarentry != null)
\r
526 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
\r
527 object = (JalviewModel) object.unmarshal(in);
\r
528 af = LoadFromObject(object);
\r
532 while (jarentry != null);
\r
534 catch(java.net.UnknownHostException ex)
\r
536 ex.printStackTrace();
\r
537 System.err.println("Couldn't locate Jalview XML file : " +
\r
539 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
540 "Couldn't locate " + file,
\r
542 JOptionPane.WARNING_MESSAGE);
\r
545 catch (Exception ex)
\r
547 ex.printStackTrace();
\r
548 System.err.println("Exception whilst loading jalview XML file : " +
\r
550 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
551 "Error loading " + file,
\r
552 "Error loading Jalview file",
\r
553 JOptionPane.WARNING_MESSAGE);
\r
560 static AlignFrame LoadFromObject(JalviewModel object)
\r
562 Vector seqids = new Vector();
\r
563 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
\r
564 Sequence[] vamsasSeq = vamsasSet.getSequence();
\r
566 JalviewModelSequence jms = object.getJalviewModelSequence();
\r
568 //////////////////////////////////
\r
570 jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
\r
571 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
\r
573 for (int i = 0; i < vamsasSeq.length; i++)
\r
575 jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
\r
576 vamsasSeq[i].getSequence());
\r
578 jseqs[i].setStart(JSEQ[i].getStart());
\r
579 jseqs[i].setEnd(JSEQ[i].getEnd());
\r
580 jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
\r
581 seqids.add(jseqs[i]);
\r
584 /////////////////////////////////
\r
585 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
\r
587 /////////////////////////////////
\r
588 //////////////////////////////////
\r
590 if (vamsasSet.getAnnotation() != null)
\r
592 Annotation[] an = vamsasSet.getAnnotation();
\r
594 for (int i = 0; i < an.length; i++)
\r
596 AnnotationElement[] ae = an[i].getAnnotationElement();
\r
597 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
\r
599 for (int aa = 0; aa < ae.length; aa++)
\r
601 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
\r
602 ae[aa].getDescription(),
\r
603 ae[aa].getSecondaryStructure().charAt(0),
\r
604 ae[aa].getValue());
\r
607 jalview.datamodel.AlignmentAnnotation jaa = null;
\r
609 if (an[i].getGraph())
\r
611 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
\r
612 an[i].getDescription(), anot, 0, 0, 1);
\r
616 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
\r
617 an[i].getDescription(), anot);
\r
620 al.addAnnotation(jaa);
\r
624 /////////////////////////////////
\r
626 Viewport[] views = jms.getViewport();
\r
627 Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
\r
629 AlignFrame af = new AlignFrame(al);
\r
631 // af.changeColour() );
\r
632 /////////////////////////
\r
634 if (jms.getJGroupCount() > 0)
\r
636 JGroup[] groups = jms.getJGroup();
\r
638 for (int i = 0; i < groups.length; i++)
\r
640 ColourSchemeI cs = null;
\r
642 if (groups[i].getColour() != null)
\r
644 if (groups[i].getColour().startsWith("ucs"))
\r
646 cs = GetUserColourScheme(jms, groups[i].getColour());
\r
650 cs = ColourSchemeProperty.getColour(al,
\r
651 groups[i].getColour());
\r
654 cs.setThreshold(groups[i].getPidThreshold(), true);
\r
657 Vector seqs = new Vector();
\r
658 int[] ids = groups[i].getSeq();
\r
660 for (int s = 0; s < ids.length; s++)
\r
662 seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(
\r
666 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
\r
667 groups[i].getName(), cs, groups[i].getDisplayBoxes(),
\r
668 groups[i].getDisplayText(), groups[i].getColourText(),
\r
669 groups[i].getStart(), groups[i].getEnd());
\r
671 sg.setOutlineColour(new java.awt.Color(
\r
672 groups[i].getOutlineColour()));
\r
674 if (groups[i].getConsThreshold() != 0)
\r
676 jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
\r
677 ResidueProperties.propHash, 3, sg.sequences, 0,
\r
678 sg.getWidth() - 1);
\r
680 c.verdict(false, 25);
\r
681 sg.cs.setConservation(c);
\r
689 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
\r
691 af.viewport.setStartRes(view.getStartRes());
\r
692 af.viewport.setStartSeq(view.getStartSeq());
\r
693 af.viewport.showConservation = view.getShowConservation();
\r
694 af.viewport.showQuality = view.getShowQuality();
\r
695 af.viewport.showIdentity = view.getShowIdentity();
\r
696 af.viewport.setAbovePIDThreshold(view.getPidSelected());
\r
697 af.abovePIDThreshold.setSelected(view.getPidSelected());
\r
698 af.viewport.setColourText(view.getShowColourText());
\r
699 af.colourTextMenuItem.setSelected(view.getShowColourText());
\r
700 af.viewport.setConservationSelected(view.getConservationSelected());
\r
701 af.conservationMenuItem.setSelected(view.getConservationSelected());
\r
703 af.viewport.setShowFullId(view.getShowFullId());
\r
704 af.fullSeqId.setSelected(view.getShowFullId());
\r
706 af.viewport.setFont(new java.awt.Font(view.getFontName(),
\r
707 view.getFontStyle(), view.getFontSize()));
\r
708 af.alignPanel.fontChanged();
\r
710 af.viewport.setRenderGaps(view.getRenderGaps());
\r
711 af.renderGapsMenuItem.setSelected(view.getRenderGaps());
\r
713 af.viewport.setWrapAlignment(view.getWrapAlignment());
\r
714 af.wrapMenuItem.setSelected(view.getWrapAlignment());
\r
716 if (view.getWrapAlignment())
\r
718 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
\r
722 af.annotationPanelMenuItem.setState(view.getShowAnnotation());
\r
723 af.viewport.setShowAnnotation(view.getShowAnnotation());
\r
724 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
\r
727 af.viewport.setShowBoxes(view.getShowBoxes());
\r
728 af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
\r
729 af.viewport.setShowText(view.getShowText());
\r
730 af.viewTextMenuItem.setSelected(view.getShowText());
\r
732 ColourSchemeI cs = null;
\r
734 if (view.getBgColour() != null)
\r
736 if (view.getBgColour().startsWith("ucs"))
\r
738 cs = GetUserColourScheme(jms, view.getBgColour());
\r
742 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
\r
747 cs.setThreshold(view.getPidThreshold(), true);
\r
748 cs.setConsensus(af.viewport.vconsensus);
\r
752 af.setColourSelected(view.getBgColour());
\r
753 af.viewport.setGlobalColourScheme(cs);
\r
754 af.viewport.setColourAppliesToAllGroups(false);
\r
755 af.changeColour(cs);
\r
756 if (view.getConservationSelected() && cs!=null)
\r
758 cs.setConservationInc(view.getConsThreshold());
\r
761 af.viewport.setColourAppliesToAllGroups(true);
\r
763 if (view.getShowSequenceFeatures())
\r
765 af.viewport.showSequenceFeatures = true;
\r
766 af.sequenceFeatures.setSelected(true);
\r
767 new SequenceFeatureFetcher(al, af.alignPanel);
\r
768 al.featuresAdded = true;
\r
771 Desktop.addInternalFrame(af, view.getTitle(),
\r
772 view.getWidth(), view.getHeight());
\r
775 ///////////////////////////////////////
\r
776 if (jms.getTreeCount() > 0)
\r
780 for (int t = 0; t < jms.getTreeCount(); t++)
\r
783 Tree tree = jms.getTree(t);
\r
785 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
\r
786 tree.getNewick()), tree.getTitle(),
\r
787 tree.getWidth(), tree.getHeight(),
\r
788 tree.getXpos(), tree.getYpos());
\r
790 tp.fitToWindow.setState(tree.getFitToWindow());
\r
791 tp.fitToWindow_actionPerformed(null);
\r
793 if(tree.getFontName()!=null)
\r
794 tp.setTreeFont(new java.awt.Font(tree.getFontName(),
\r
795 tree.getFontStyle(),
\r
796 tree.getFontSize()));
\r
798 tp.setTreeFont(new java.awt.Font(view.getFontName(),
\r
799 view.getFontStyle(),
\r
800 tree.getFontSize()));
\r
802 tp.showPlaceholders(tree.getMarkUnlinked());
\r
803 tp.showBootstrap(tree.getShowBootstrap());
\r
804 tp.showDistances(tree.getShowDistances());
\r
806 tp.treeCanvas.threshold = tree.getThreshold();
\r
808 if (tree.getCurrentTree())
\r
809 af.viewport.setCurrentTree(tp.getTree());
\r
813 catch (Exception ex)
\r
815 ex.printStackTrace();
\r