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
22 import jalview.schemes.*;
\r
24 import jalview.gui.*;
\r
32 import java.util.jar.*;
\r
34 import javax.swing.*;
\r
36 import org.exolab.castor.xml.*;
\r
38 import jalview.schemabinding.version2.*;
\r
47 * @version $Revision$
\r
49 public class Jalview2XML
\r
51 // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
\r
52 public void SaveState(File statefile)
\r
54 long creation = System.currentTimeMillis();
\r
55 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
\r
64 FileOutputStream fos = new FileOutputStream(statefile);
\r
65 JarOutputStream jout = new JarOutputStream(fos);
\r
67 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
\r
68 ////////////////////////////////////////////////////
\r
69 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
\r
72 Vector shortNames = new Vector();
\r
75 for (int i = frames.length - 1; i > -1; i--)
\r
77 if (frames[i] instanceof AlignFrame)
\r
79 AlignFrame af = (AlignFrame) frames[i];
\r
81 String shortName = af.getTitle();
\r
83 if (shortName.indexOf(File.separatorChar) > -1)
\r
85 shortName = shortName.substring(shortName.lastIndexOf(
\r
86 File.separatorChar) + 1);
\r
91 while (shortNames.contains(shortName))
\r
93 if (shortName.endsWith("_" + (count - 1)))
\r
95 shortName = shortName.substring(0,
\r
96 shortName.lastIndexOf("_"));
\r
99 shortName = shortName.concat("_" + count);
\r
103 shortNames.addElement(shortName);
\r
105 if (!shortName.endsWith(".xml"))
\r
107 shortName = shortName + ".xml";
\r
110 SaveState(af, creation, shortName, jout, out);
\r
117 catch (Exception ex)
\r
119 ex.printStackTrace();
\r
123 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
\r
124 public void SaveAlignment(AlignFrame af, String jarFile,
\r
129 FileOutputStream fos = new FileOutputStream(jarFile);
\r
130 JarOutputStream jout = new JarOutputStream(fos);
\r
132 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
\r
133 ////////////////////////////////////////////////////
\r
134 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
\r
137 SaveState(af, System.currentTimeMillis(), fileName, jout, out);
\r
141 catch (Exception ex)
\r
143 ex.printStackTrace();
\r
150 * @param af DOCUMENT ME!
\r
151 * @param timeStamp DOCUMENT ME!
\r
152 * @param fileName DOCUMENT ME!
\r
153 * @param jout DOCUMENT ME!
\r
154 * @param out DOCUMENT ME!
\r
156 public void SaveState(AlignFrame af, long timeStamp,
\r
157 String fileName, JarOutputStream jout, PrintWriter out)
\r
159 Vector seqids = new Vector();
\r
160 Vector userColours = new Vector();
\r
162 AlignViewport av = af.viewport;
\r
164 JalviewModel object = new JalviewModel();
\r
165 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
\r
167 object.setCreationDate(new java.util.Date(timeStamp));
\r
168 object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
\r
170 jalview.datamodel.AlignmentI jal = af.viewport.alignment;
\r
172 SequenceSet vamsasSet = new SequenceSet();
\r
173 Sequence vamsasSeq;
\r
174 JalviewModelSequence jms = new JalviewModelSequence();
\r
176 vamsasSet.setGapChar(jal.getGapCharacter() + "");
\r
183 for (int i = 0; i < jal.getHeight(); i++)
\r
185 seqids.add(jal.getSequenceAt(i));
\r
187 vamsasSeq = new Sequence();
\r
188 vamsasSeq.setId(id + "");
\r
189 vamsasSeq.setName(jal.getSequenceAt(i).getName());
\r
190 vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
\r
191 vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());
\r
194 jseq.setStart(jal.getSequenceAt(i).getStart());
\r
195 jseq.setEnd(jal.getSequenceAt(i).getEnd());
\r
197 jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
\r
201 if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)
\r
203 jalview.datamodel.SequenceFeature[] sf
\r
204 = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
\r
206 while(index < sf.length)
\r
208 Features features = new Features();
\r
210 features.setBegin(sf[index].getBegin());
\r
211 features.setEnd(sf[index].getEnd());
\r
212 features.setDescription(sf[index].getDescription());
\r
213 features.setStatus(sf[index].getStatus());
\r
214 features.setType(sf[index].getType());
\r
215 features.setFeatureGroup(sf[index].getFeatureGroup());
\r
216 jseq.addFeatures(features);
\r
221 if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)
\r
223 Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();
\r
224 while(en.hasMoreElements())
\r
226 Pdbids pdb = new Pdbids();
\r
227 jalview.datamodel.PDBEntry entry
\r
228 = (jalview.datamodel.PDBEntry)en.nextElement();
\r
230 pdb.setId(entry.getId());
\r
231 pdb.setType(entry.getType());
\r
233 if(entry.getProperty()!=null)
\r
235 PdbentryItem item = new PdbentryItem();
\r
236 Hashtable properties = entry.getProperty();
\r
237 Enumeration en2 = properties.keys();
\r
238 while(en2.hasMoreElements())
\r
240 Property prop = new Property();
\r
241 String key = en2.nextElement().toString();
\r
243 prop.setValue( properties.get(key).toString() );
\r
244 item.addProperty(prop);
\r
246 pdb.addPdbentryItem(item);
\r
249 jseq.addPdbids(pdb);
\r
254 vamsasSet.addSequence(vamsasSeq);
\r
259 ///////////////////////////////////
\r
260 if (af.viewport.currentTree != null)
\r
262 // FIND ANY ASSOCIATED TREES
\r
263 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
\r
264 if (Desktop.desktop != null)
\r
266 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
\r
268 for (int t = 0; t < frames.length; t++)
\r
270 if (frames[t] instanceof TreePanel)
\r
272 TreePanel tp = (TreePanel) frames[t];
\r
274 if (tp.treeCanvas.av.alignment == jal)
\r
276 Tree tree = new Tree();
\r
277 tree.setTitle(tp.getTitle());
\r
278 tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));
\r
279 tree.setNewick(tp.getTree().toString());
\r
280 tree.setThreshold(tp.treeCanvas.threshold);
\r
282 tree.setFitToWindow(tp.fitToWindow.getState());
\r
283 tree.setFontName(tp.getTreeFont().getName());
\r
284 tree.setFontSize(tp.getTreeFont().getSize());
\r
285 tree.setFontStyle(tp.getTreeFont().getStyle());
\r
286 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
\r
288 tree.setShowBootstrap(tp.bootstrapMenu.getState());
\r
289 tree.setShowDistances(tp.distanceMenu.getState());
\r
291 tree.setHeight(tp.getHeight());
\r
292 tree.setWidth(tp.getWidth());
\r
293 tree.setXpos(tp.getX());
\r
294 tree.setYpos(tp.getY());
\r
304 if (jal.getAlignmentAnnotation() != null)
\r
306 jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
\r
308 for (int i = 0; i < aa.length; i++)
\r
310 if (aa[i].label.equals("Quality") ||
\r
311 aa[i].label.equals("Conservation") ||
\r
312 aa[i].label.equals("Consensus"))
\r
317 Annotation an = new Annotation();
\r
318 an.setDescription(aa[i].description);
\r
322 an.setGraphType(aa[i].graph);
\r
323 if(aa[i].getThreshold()!=null)
\r
325 ThresholdLine line = new ThresholdLine();
\r
326 line.setLabel(aa[i].getThreshold().label);
\r
327 line.setValue(aa[i].getThreshold().value);
\r
328 line.setColour(aa[i].getThreshold().colour.getRGB());
\r
329 an.setThresholdLine(line);
\r
333 an.setGraph(false);
\r
335 an.setLabel(aa[i].label);
\r
337 AnnotationElement ae;
\r
339 for (int a = 0; a < aa[i].annotations.length; a++)
\r
341 if ((aa[i] == null) || (aa[i].annotations[a] == null))
\r
346 ae = new AnnotationElement();
\r
347 ae.setDescription(aa[i].annotations[a].description);
\r
348 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
\r
349 ae.setValue(aa[i].annotations[a].value);
\r
351 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
\r
353 an.addAnnotationElement(ae);
\r
356 vamsasSet.addAnnotation(an);
\r
361 if (jal.getGroups() != null)
\r
363 JGroup[] groups = new JGroup[jal.getGroups().size()];
\r
365 for (int i = 0; i < groups.length; i++)
\r
367 groups[i] = new JGroup();
\r
369 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
\r
371 groups[i].setStart(sg.getStartRes());
\r
372 groups[i].setEnd(sg.getEndRes());
\r
373 groups[i].setName(sg.getName());
\r
376 if (sg.cs.conservationApplied())
\r
378 groups[i].setConsThreshold(sg.cs.getConservationInc());
\r
380 if (sg.cs instanceof jalview.schemes.UserColourScheme)
\r
382 groups[i].setColour(SetUserColourScheme(sg.cs,
\r
388 groups[i].setColour(ColourSchemeProperty.getColourName(sg.
\r
392 else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)
\r
394 groups[i].setColour(
\r
395 ColourSchemeProperty.getColourName(
\r
396 ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));
\r
398 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
\r
400 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
\r
405 groups[i].setColour(ColourSchemeProperty.getColourName(
\r
409 groups[i].setPidThreshold(sg.cs.getThreshold());
\r
412 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
\r
413 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
\r
414 groups[i].setDisplayText(sg.getDisplayText());
\r
415 groups[i].setColourText(sg.getColourText());
\r
417 for (int s = 0; s < sg.getSize(); s++)
\r
419 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);
\r
420 int index = seqids.indexOf(seq);
\r
421 groups[i].addSeq(index);
\r
425 jms.setJGroup(groups);
\r
429 ///////////SAVE VIEWPORT
\r
430 Viewport view = new Viewport();
\r
431 view.setTitle(af.getTitle());
\r
432 view.setXpos(af.getX());
\r
433 view.setYpos(af.getY());
\r
434 view.setWidth(af.getWidth());
\r
435 view.setHeight(af.getHeight());
\r
436 view.setStartRes(av.startRes);
\r
437 view.setStartSeq(av.startSeq);
\r
439 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
\r
441 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
\r
442 userColours, jms));
\r
444 else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
\r
446 jalview.schemes.AnnotationColourGradient acg
\r
447 = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();
\r
449 AnnotationColours ac = new AnnotationColours();
\r
450 ac.setAboveThreshold(acg.getAboveThreshold());
\r
451 ac.setThreshold(acg.getAnnotationThreshold());
\r
452 ac.setAnnotation(acg.getAnnotation());
\r
453 if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
\r
454 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
\r
455 userColours, jms));
\r
457 ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
\r
459 ac.setMaxColour(acg.getMaxColour().getRGB());
\r
460 ac.setMinColour(acg.getMinColour().getRGB());
\r
461 view.setAnnotationColours(ac);
\r
462 view.setBgColour("AnnotationColourGradient");
\r
466 view.setBgColour(ColourSchemeProperty.getColourName(
\r
467 av.getGlobalColourScheme()));
\r
470 ColourSchemeI cs = av.getGlobalColourScheme();
\r
474 if (cs.conservationApplied())
\r
476 view.setConsThreshold(cs.getConservationInc());
\r
477 if (cs instanceof jalview.schemes.UserColourScheme)
\r
478 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
\r
481 if (cs instanceof ResidueColourScheme)
\r
483 view.setPidThreshold(cs.getThreshold());
\r
487 view.setConservationSelected(av.getConservationSelected());
\r
488 view.setPidSelected(av.getAbovePIDThreshold());
\r
489 view.setFontName(av.font.getName());
\r
490 view.setFontSize(av.font.getSize());
\r
491 view.setFontStyle(av.font.getStyle());
\r
492 view.setRenderGaps(av.renderGaps);
\r
493 view.setShowAnnotation(av.getShowAnnotation());
\r
494 view.setShowBoxes(av.getShowBoxes());
\r
495 view.setShowColourText(av.getColourText());
\r
496 view.setShowConservation(av.showConservation);
\r
497 view.setShowFullId(av.getShowJVSuffix());
\r
498 view.setShowIdentity(av.showIdentity);
\r
499 view.setShowQuality(av.showQuality);
\r
500 view.setShowSequenceFeatures(av.showSequenceFeatures);
\r
501 view.setShowText(av.getShowText());
\r
502 view.setWrapAlignment(av.getWrapAlignment());
\r
504 if(av.featuresDisplayed!=null)
\r
506 jalview.schemabinding.version2.FeatureSettings fs
\r
507 = new jalview.schemabinding.version2.FeatureSettings();
\r
509 String [] renderOrder =
\r
510 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
\r
511 for(int ro=0; ro<renderOrder.length; ro++)
\r
513 Setting setting = new Setting();
\r
514 setting.setType(renderOrder[ro]);
\r
516 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
\r
519 setting.setDisplay(
\r
520 av.featuresDisplayed.containsKey(renderOrder[ro])
\r
523 fs.addSetting(setting);
\r
526 jms.setFeatureSettings(fs);
\r
530 jms.addViewport(view);
\r
533 object.setJalviewModelSequence(jms);
\r
534 object.getVamsasModel().addSequenceSet(vamsasSet);
\r
538 if (!fileName.endsWith(".xml"))
\r
540 fileName = fileName + ".xml";
\r
543 JarEntry entry = new JarEntry(fileName);
\r
544 jout.putNextEntry(entry);
\r
546 object.marshal(out);
\r
548 catch (Exception ex)
\r
550 ex.printStackTrace();
\r
554 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
\r
555 Vector userColours, JalviewModelSequence jms)
\r
558 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
\r
560 if (!userColours.contains(ucs))
\r
562 userColours.add(ucs);
\r
564 java.awt.Color[] colours = ucs.getColours();
\r
565 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
\r
566 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
\r
568 for (int i = 0; i < colours.length; i++)
\r
570 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
\r
571 col.setRGB(jalview.util.Format.getHexString(colours[i]));
\r
572 jbucs.addColour(col);
\r
575 id = "ucs" + userColours.indexOf(ucs);
\r
577 uc.setUserColourScheme(jbucs);
\r
578 jms.addUserColours(uc);
\r
584 jalview.schemes.UserColourScheme GetUserColourScheme(
\r
585 JalviewModelSequence jms, String id)
\r
587 UserColours[] uc = jms.getUserColours();
\r
588 UserColours colours = null;
\r
590 for (int i = 0; i < uc.length; i++)
\r
592 if (uc[i].getId().equals(id))
\r
600 int csize = colours.getUserColourScheme().getColourCount();
\r
601 java.awt.Color[] newColours = new java.awt.Color[csize];
\r
603 for (int i = 0; i < csize; i++)
\r
605 newColours[i] = new java.awt.Color(Integer.parseInt(
\r
606 colours.getUserColourScheme().getColour(i).getRGB(), 16));
\r
609 return new jalview.schemes.UserColourScheme(newColours);
\r
615 * @param file DOCUMENT ME!
\r
617 public AlignFrame LoadJalviewAlign(String file)
\r
620 jalview.gui.AlignFrame af = null;
\r
624 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
\r
627 if (file.startsWith("http://"))
\r
629 url = new URL(file);
\r
632 JarInputStream jin = null;
\r
633 JarEntry jarentry = null;
\r
634 int entryCount = 1;
\r
640 jin = new JarInputStream(url.openStream());
\r
644 jin = new JarInputStream(new FileInputStream(file));
\r
647 for (int i = 0; i < entryCount; i++)
\r
649 jarentry = jin.getNextJarEntry();
\r
654 class NoDescIDResolver implements IDResolver
\r
656 public Object resolve(String idref)
\r
658 System.out.println(idref+" used");
\r
664 if (jarentry != null)
\r
666 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
\r
667 JalviewModel object = new JalviewModel();
\r
669 Unmarshaller unmar = new Unmarshaller(object);
\r
670 unmar.setValidation(false);
\r
671 object = (JalviewModel) unmar.unmarshal( in );
\r
673 af = LoadFromObject(object);
\r
677 while (jarentry != null);
\r
679 catch(java.net.UnknownHostException ex)
\r
681 ex.printStackTrace();
\r
682 System.err.println("Couldn't locate Jalview XML file : " +
\r
684 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
685 "Couldn't locate " + file,
\r
687 JOptionPane.WARNING_MESSAGE);
\r
690 catch (Exception ex)
\r
692 //Is Version 1 Jar file?
\r
693 af = new Jalview2XML_V1().LoadJalviewAlign(file);
\r
697 System.out.println("Successfuly loaded archive file");
\r
700 ex.printStackTrace();
\r
701 System.err.println("Exception whilst loading jalview XML file : " +
\r
703 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
704 "Error loading " + file,
\r
705 "Error loading Jalview file",
\r
706 JOptionPane.WARNING_MESSAGE);
\r
713 AlignFrame LoadFromObject(JalviewModel object)
\r
715 Vector seqids = new Vector();
\r
716 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
\r
717 Sequence[] vamsasSeq = vamsasSet.getSequence();
\r
719 JalviewModelSequence jms = object.getJalviewModelSequence();
\r
721 //////////////////////////////////
\r
723 jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
\r
724 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
\r
725 for (int i = 0; i < vamsasSeq.length; i++)
\r
727 jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
\r
728 vamsasSeq[i].getSequence());
\r
729 jseqs[i].setDescription( vamsasSeq[i].getDescription() );
\r
731 jseqs[i].setStart(JSEQ[i].getStart());
\r
732 jseqs[i].setEnd(JSEQ[i].getEnd());
\r
733 jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
\r
734 seqids.add(jseqs[i]);
\r
737 ///SequenceFeatures are added to the DatasetSequence,
\r
738 // so we must create the dataset before loading features
\r
739 /////////////////////////////////
\r
740 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
\r
741 al.setDataset(null);
\r
742 /////////////////////////////////
\r
744 for (int i = 0; i < vamsasSeq.length; i++)
\r
746 if (JSEQ[i].getFeaturesCount() > 0)
\r
748 Features[] features = JSEQ[i].getFeatures();
\r
749 for (int f = 0; f < features.length; f++)
\r
751 jalview.datamodel.SequenceFeature sf
\r
752 = new jalview.datamodel.SequenceFeature(features[f].getType(),
\r
753 features[f].getDescription(), features[f].getStatus(),
\r
754 features[f].getBegin(), features[f].getEnd(),
\r
755 features[f].getFeatureGroup());
\r
757 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
\r
760 if (JSEQ[i].getPdbidsCount() > 0)
\r
762 Pdbids[] ids = JSEQ[i].getPdbids();
\r
763 for (int p = 0; p < ids.length; p++)
\r
765 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
\r
766 entry.setId(ids[p].getId());
\r
767 entry.setType(ids[p].getType());
\r
768 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
\r
774 /////////////////////////////////
\r
775 //////////////////////////////////
\r
777 if (vamsasSet.getAnnotation() != null)
\r
779 Annotation[] an = vamsasSet.getAnnotation();
\r
781 for (int i = 0; i < an.length; i++)
\r
783 AnnotationElement[] ae = an[i].getAnnotationElement();
\r
784 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
\r
786 for (int aa = 0; aa < ae.length; aa++)
\r
788 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
\r
789 ae[aa].getDescription(),
\r
790 ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
\r
791 ae[aa].getValue());
\r
794 jalview.datamodel.AlignmentAnnotation jaa = null;
\r
796 if (an[i].getGraph())
\r
798 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
\r
799 an[i].getDescription(), anot, 0, 0,
\r
800 an[i].getGraphType());
\r
802 if (an[i].getThresholdLine() != null)
\r
804 jaa.setThreshold(new jalview.datamodel.GraphLine(
\r
805 an[i].getThresholdLine().getValue(),
\r
806 an[i].getThresholdLine().getLabel(),
\r
807 new java.awt.Color(an[i].getThresholdLine().getColour()))
\r
815 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
\r
816 an[i].getDescription(), anot);
\r
819 al.addAnnotation(jaa);
\r
824 /////////////////////////////////
\r
826 Viewport[] views = jms.getViewport();
\r
827 Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
\r
829 AlignFrame af = new AlignFrame(al);
\r
832 // af.changeColour() );
\r
833 /////////////////////////
\r
835 if (jms.getJGroupCount() > 0)
\r
837 JGroup[] groups = jms.getJGroup();
\r
839 for (int i = 0; i < groups.length; i++)
\r
841 ColourSchemeI cs = null;
\r
843 if (groups[i].getColour() != null)
\r
845 if (groups[i].getColour().startsWith("ucs"))
\r
847 cs = GetUserColourScheme(jms, groups[i].getColour());
\r
851 cs = ColourSchemeProperty.getColour(al,
\r
852 groups[i].getColour());
\r
856 cs.setThreshold(groups[i].getPidThreshold(), true);
\r
859 Vector seqs = new Vector();
\r
860 int[] ids = groups[i].getSeq();
\r
862 for (int s = 0; s < ids.length; s++)
\r
864 seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(
\r
868 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
\r
869 groups[i].getName(), cs, groups[i].getDisplayBoxes(),
\r
870 groups[i].getDisplayText(), groups[i].getColourText(),
\r
871 groups[i].getStart(), groups[i].getEnd());
\r
873 sg.setOutlineColour(new java.awt.Color(
\r
874 groups[i].getOutlineColour()));
\r
876 if (groups[i].getConsThreshold() != 0)
\r
878 jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
\r
879 ResidueProperties.propHash, 3, sg.sequences, 0,
\r
880 sg.getWidth() - 1);
\r
882 c.verdict(false, 25);
\r
883 sg.cs.setConservation(c);
\r
892 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
\r
894 af.viewport.setStartRes(view.getStartRes());
\r
895 af.viewport.setStartSeq(view.getStartSeq());
\r
896 af.viewport.setShowAnnotation(view.getShowAnnotation());
\r
897 af.viewport.showConservation = view.getShowConservation();
\r
898 af.viewport.showQuality = view.getShowQuality();
\r
899 af.viewport.showIdentity = view.getShowIdentity();
\r
900 af.viewport.setAbovePIDThreshold(view.getPidSelected());
\r
901 af.abovePIDThreshold.setSelected(view.getPidSelected());
\r
902 af.viewport.setColourText(view.getShowColourText());
\r
903 af.colourTextMenuItem.setSelected(view.getShowColourText());
\r
904 af.viewport.setConservationSelected(view.getConservationSelected());
\r
905 af.conservationMenuItem.setSelected(view.getConservationSelected());
\r
907 af.viewport.setShowJVSuffix(view.getShowFullId());
\r
908 af.seqLimits.setSelected(view.getShowFullId());
\r
910 af.viewport.setFont(new java.awt.Font(view.getFontName(),
\r
911 view.getFontStyle(), view.getFontSize()));
\r
912 af.alignPanel.fontChanged();
\r
914 af.viewport.setRenderGaps(view.getRenderGaps());
\r
915 af.renderGapsMenuItem.setSelected(view.getRenderGaps());
\r
917 af.viewport.setWrapAlignment(view.getWrapAlignment());
\r
918 af.wrapMenuItem.setSelected(view.getWrapAlignment());
\r
920 if (view.getWrapAlignment())
\r
922 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
\r
926 af.annotationPanelMenuItem.setState(view.getShowAnnotation());
\r
927 af.viewport.setShowAnnotation(view.getShowAnnotation());
\r
928 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
\r
931 af.viewport.setShowBoxes(view.getShowBoxes());
\r
932 af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
\r
933 af.viewport.setShowText(view.getShowText());
\r
934 af.viewTextMenuItem.setSelected(view.getShowText());
\r
936 ColourSchemeI cs = null;
\r
938 if (view.getBgColour() != null)
\r
940 if (view.getBgColour().startsWith("ucs"))
\r
942 cs = GetUserColourScheme(jms, view.getBgColour());
\r
944 else if(view.getBgColour().startsWith("Annotation"))
\r
946 //int find annotation
\r
947 for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
\r
949 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
\r
950 equals(view.getAnnotationColours().getAnnotation()))
\r
952 if (af.viewport.alignment.getAlignmentAnnotation()[i].
\r
953 getThreshold() == null)
\r
955 af.viewport.alignment.getAlignmentAnnotation()[i].
\r
957 new jalview.datamodel.GraphLine(
\r
958 view.getAnnotationColours().getThreshold(),
\r
959 "Threshold", java.awt.Color.black)
\r
965 if (view.getAnnotationColours().getColourScheme().equals(
\r
968 cs = new AnnotationColourGradient(
\r
969 af.viewport.alignment.getAlignmentAnnotation()[i],
\r
970 new java.awt.Color(view.getAnnotationColours().
\r
972 new java.awt.Color(view.getAnnotationColours().
\r
974 view.getAnnotationColours().getAboveThreshold());
\r
976 else if (view.getAnnotationColours().getColourScheme().
\r
979 cs = new AnnotationColourGradient(
\r
980 af.viewport.alignment.getAlignmentAnnotation()[i],
\r
981 GetUserColourScheme(jms, view.getAnnotationColours().
\r
982 getColourScheme()),
\r
983 view.getAnnotationColours().getAboveThreshold()
\r
988 cs = new AnnotationColourGradient(
\r
989 af.viewport.alignment.getAlignmentAnnotation()[i],
\r
990 ColourSchemeProperty.getColour(al,
\r
991 view.getAnnotationColours().getColourScheme()),
\r
992 view.getAnnotationColours().getAboveThreshold()
\r
996 // Also use these settings for all the groups
\r
997 if (al.getGroups() != null)
\r
998 for (int g = 0; g < al.getGroups().size(); g++)
\r
1000 jalview.datamodel.SequenceGroup sg
\r
1001 = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
\r
1007 /* if (view.getAnnotationColours().getColourScheme().equals("None"))
\r
1009 sg.cs = new AnnotationColourGradient(
\r
1010 af.viewport.alignment.getAlignmentAnnotation()[i],
\r
1011 new java.awt.Color(view.getAnnotationColours().
\r
1013 new java.awt.Color(view.getAnnotationColours().
\r
1015 view.getAnnotationColours().getAboveThreshold());
\r
1019 sg.cs = new AnnotationColourGradient(
\r
1020 af.viewport.alignment.getAlignmentAnnotation()[i],
\r
1022 view.getAnnotationColours().getAboveThreshold()
\r
1036 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
\r
1041 cs.setThreshold(view.getPidThreshold(), true);
\r
1042 cs.setConsensus(af.viewport.vconsensus);
\r
1046 af.setColourSelected(view.getBgColour());
\r
1047 af.viewport.setGlobalColourScheme(cs);
\r
1048 af.viewport.setColourAppliesToAllGroups(false);
\r
1049 af.changeColour(cs);
\r
1050 if (view.getConservationSelected() && cs!=null)
\r
1052 cs.setConservationInc(view.getConsThreshold());
\r
1055 af.viewport.setColourAppliesToAllGroups(true);
\r
1057 if (view.getShowSequenceFeatures())
\r
1059 af.viewport.showSequenceFeatures = true;
\r
1060 af.showSeqFeatures.setSelected(true);
\r
1063 if(jms.getFeatureSettings()!=null)
\r
1065 af.viewport.featuresDisplayed = new Hashtable();
\r
1066 String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
\r
1067 for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
\r
1069 Setting setting = jms.getFeatureSettings().getSetting(fs);
\r
1071 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
\r
1072 new java.awt.Color(setting.getColour()));
\r
1074 renderOrder[fs] = setting.getType();
\r
1076 if(setting.getDisplay())
\r
1077 af.viewport.featuresDisplayed.put(
\r
1078 setting.getType(), new Integer(setting.getColour()));
\r
1080 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
\r
1084 Desktop.addInternalFrame(af, view.getTitle(),
\r
1085 view.getWidth(), view.getHeight());
\r
1088 ///////////////////////////////////////
\r
1089 if (jms.getTreeCount() > 0)
\r
1093 for (int t = 0; t < jms.getTreeCount(); t++)
\r
1096 Tree tree = jms.getTree(t);
\r
1098 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
\r
1099 tree.getNewick()), tree.getTitle(),
\r
1100 tree.getWidth(), tree.getHeight(),
\r
1101 tree.getXpos(), tree.getYpos());
\r
1103 tp.fitToWindow.setState(tree.getFitToWindow());
\r
1104 tp.fitToWindow_actionPerformed(null);
\r
1106 if(tree.getFontName()!=null)
\r
1107 tp.setTreeFont(new java.awt.Font(tree.getFontName(),
\r
1108 tree.getFontStyle(),
\r
1109 tree.getFontSize()));
\r
1111 tp.setTreeFont(new java.awt.Font(view.getFontName(),
\r
1112 view.getFontStyle(),
\r
1113 tree.getFontSize()));
\r
1115 tp.showPlaceholders(tree.getMarkUnlinked());
\r
1116 tp.showBootstrap(tree.getShowBootstrap());
\r
1117 tp.showDistances(tree.getShowDistances());
\r
1119 tp.treeCanvas.threshold = tree.getThreshold();
\r
1121 if (tree.getCurrentTree())
\r
1122 af.viewport.setCurrentTree(tp.getTree());
\r
1126 catch (Exception ex)
\r
1128 ex.printStackTrace();
\r