2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 import java.util.jar.*;
28 import org.exolab.castor.xml.*;
29 import jalview.schemabinding.version2.*;
30 import jalview.schemes.*;
31 import jalview.structure.StructureSelectionManager;
39 public class Jalview2XML
45 * This maintains a list of viewports, the key being the
46 * seqSetId. Important to set historyItem and redoList
49 Hashtable viewportsAdded;
51 Hashtable annotationIds = new Hashtable();
53 String uniqueSetSuffix = "";
55 * List of pdbfiles added to Jar
57 Vector pdbfiles = null;
59 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
60 public void SaveState(File statefile)
62 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
71 FileOutputStream fos = new FileOutputStream(statefile);
72 JarOutputStream jout = new JarOutputStream(fos);
74 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
75 ////////////////////////////////////////////////////
76 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
79 Vector shortNames = new Vector();
82 for (int i = frames.length - 1; i > -1; i--)
84 if (frames[i] instanceof AlignFrame)
86 AlignFrame af = (AlignFrame) frames[i];
88 String shortName = af.getTitle();
90 if (shortName.indexOf(File.separatorChar) > -1)
92 shortName = shortName.substring(shortName.lastIndexOf(
93 File.separatorChar) + 1);
98 while (shortNames.contains(shortName))
100 if (shortName.endsWith("_" + (count - 1)))
102 shortName = shortName.substring(0,
103 shortName.lastIndexOf("_"));
106 shortName = shortName.concat("_" + count);
110 shortNames.addElement(shortName);
112 if (!shortName.endsWith(".xml"))
114 shortName = shortName + ".xml";
117 int ap, apSize = af.alignPanels.size();
118 for (ap = 0; ap < apSize; ap++)
120 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.
124 apSize == 1 ? shortName : ap + shortName,
135 ex.printStackTrace();
139 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
140 public boolean SaveAlignment(AlignFrame af, String jarFile,
145 int ap, apSize = af.alignPanels.size();
146 FileOutputStream fos = new FileOutputStream(jarFile);
147 JarOutputStream jout = new JarOutputStream(fos);
148 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
150 for (ap = 0; ap < apSize; ap++)
152 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.elementAt(ap);
155 apSize == 1 ? fileName : fileName + ap,
165 ex.printStackTrace();
173 * @param af DOCUMENT ME!
174 * @param timeStamp DOCUMENT ME!
175 * @param fileName DOCUMENT ME!
176 * @param jout DOCUMENT ME!
177 * @param out DOCUMENT ME!
179 public JalviewModel SaveState(AlignmentPanel ap,
181 JarOutputStream jout,
184 if (seqRefIds == null)
186 seqRefIds = new Hashtable();
189 Vector userColours = new Vector();
191 AlignViewport av = ap.av;
193 JalviewModel object = new JalviewModel();
194 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
196 object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
197 object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
199 jalview.datamodel.AlignmentI jal = av.alignment;
201 if (av.hasHiddenRows)
203 jal = jal.getHiddenSequences().getFullAlignment();
206 SequenceSet vamsasSet = new SequenceSet();
208 JalviewModelSequence jms = new JalviewModelSequence();
210 vamsasSet.setGapChar(jal.getGapCharacter() + "");
212 if(jal.getProperties()!=null)
214 Enumeration en = jal.getProperties().keys();
215 while(en.hasMoreElements())
217 String key = en.nextElement().toString();
218 SequenceSetProperties ssp = new SequenceSetProperties();
220 ssp.setValue(jal.getProperties().get(key).toString());
221 vamsasSet.addSequenceSetProperties(ssp);
229 jalview.datamodel.SequenceI jds;
230 for (int i = 0; i < jal.getHeight(); i++)
232 jds = jal.getSequenceAt(i);
235 if (seqRefIds.get(id + "") != null)
241 vamsasSeq = new Sequence();
242 vamsasSeq.setId(id + "");
243 vamsasSeq.setName(jds.getName());
244 vamsasSeq.setSequence(jds.getSequenceAsString());
245 vamsasSeq.setDescription(jds.getDescription());
247 if (jds.getDatasetSequence().getDBRef() != null)
249 jalview.datamodel.DBRefEntry[] dbrefs =
250 jds.getDatasetSequence().getDBRef();
252 for (int d = 0; d < dbrefs.length; d++)
254 DBRef dbref = new DBRef();
255 dbref.setSource(dbrefs[d].getSource());
256 dbref.setVersion(dbrefs[d].getVersion());
257 dbref.setAccessionId(dbrefs[d].getAccessionId());
258 vamsasSeq.addDBRef(dbref);
262 vamsasSet.addSequence(vamsasSeq);
263 seqRefIds.put(id + "", jal.getSequenceAt(i));
267 jseq.setStart(jds.getStart());
268 jseq.setEnd(jds.getEnd());
269 jseq.setColour(av.getSequenceColour(jds).getRGB());
273 if (av.hasHiddenRows)
275 jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
277 if (av.hiddenRepSequences != null
278 && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
280 jalview.datamodel.SequenceI[] reps =
281 ( (jalview.datamodel.SequenceGroup)
282 av.hiddenRepSequences.get(
283 jal.getSequenceAt(i))).getSequencesInOrder(jal);
285 for (int h = 0; h < reps.length; h++)
287 if (reps[h] != jal.getSequenceAt(i))
289 jseq.addHiddenSequences(
290 jal.findIndex(reps[h])
297 if (jds.getDatasetSequence().getSequenceFeatures() != null)
299 jalview.datamodel.SequenceFeature[] sf
300 = jds.getDatasetSequence().getSequenceFeatures();
302 while (index < sf.length)
304 Features features = new Features();
306 features.setBegin(sf[index].getBegin());
307 features.setEnd(sf[index].getEnd());
308 features.setDescription(sf[index].getDescription());
309 features.setType(sf[index].getType());
310 features.setFeatureGroup(sf[index].getFeatureGroup());
311 features.setScore(sf[index].getScore());
312 if (sf[index].links != null)
314 for (int l = 0; l < sf[index].links.size(); l++)
316 OtherData keyValue = new OtherData();
317 keyValue.setKey("LINK_" + l);
318 keyValue.setValue(sf[index].links.elementAt(l).toString());
319 features.addOtherData(keyValue);
322 if (sf[index].otherDetails != null)
325 Enumeration keys = sf[index].otherDetails.keys();
326 while (keys.hasMoreElements())
328 key = keys.nextElement().toString();
329 OtherData keyValue = new OtherData();
330 keyValue.setKey(key);
332 sf[index].otherDetails.get(key).toString());
333 features.addOtherData(keyValue);
337 jseq.addFeatures(features);
342 if (jds.getDatasetSequence().getPDBId() != null)
344 Enumeration en = jds.getDatasetSequence().getPDBId().elements();
345 while (en.hasMoreElements())
347 Pdbids pdb = new Pdbids();
348 jalview.datamodel.PDBEntry entry
349 = (jalview.datamodel.PDBEntry) en.nextElement();
351 pdb.setId(entry.getId());
352 pdb.setType(entry.getType());
355 //This must have been loaded, is it still visible?
356 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
357 for (int f = frames.length - 1; f > -1; f--)
359 if (frames[f] instanceof AppJmol)
361 jmol = (AppJmol) frames[f];
362 if (!jmol.pdbentry.getId().equals(entry.getId()))
366 StructureState state = new StructureState();
367 state.setVisible(true);
368 state.setXpos(jmol.getX());
369 state.setYpos(jmol.getY());
370 state.setWidth(jmol.getWidth());
371 state.setHeight(jmol.getHeight());
373 String statestring = jmol.viewer.getStateInfo();
376 state.setContent(statestring.replaceAll("\n", ""));
378 for (int s = 0; s < jmol.sequence.length; s++)
380 if (jal.findIndex(jmol.sequence[s]) > -1)
382 pdb.addStructureState(state);
389 if (entry.getFile() != null)
391 pdb.setFile(entry.getFile());
392 if (pdbfiles == null)
394 pdbfiles = new Vector();
397 if (!pdbfiles.contains(entry.getId()))
399 pdbfiles.addElement(entry.getId());
402 File file = new File(entry.getFile());
403 if (file.exists() && jout != null)
405 byte[] data = new byte[ (int) file.length()];
406 jout.putNextEntry(new JarEntry(entry.getId()));
407 DataInputStream dis = new DataInputStream(new
408 FileInputStream(file));
411 DataOutputStream dout = new DataOutputStream(jout);
412 dout.write(data, 0, data.length);
418 ex.printStackTrace();
424 if (entry.getProperty() != null)
426 PdbentryItem item = new PdbentryItem();
427 Hashtable properties = entry.getProperty();
428 Enumeration en2 = properties.keys();
429 while (en2.hasMoreElements())
431 Property prop = new Property();
432 String key = en2.nextElement().toString();
434 prop.setValue(properties.get(key).toString());
435 item.addProperty(prop);
437 pdb.addPdbentryItem(item);
447 if (av.hasHiddenRows)
453 ///////////////////////////////////
454 if (av.currentTree != null)
456 // FIND ANY ASSOCIATED TREES
457 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
458 if (Desktop.desktop != null)
460 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
462 for (int t = 0; t < frames.length; t++)
464 if (frames[t] instanceof TreePanel)
466 TreePanel tp = (TreePanel) frames[t];
468 if (tp.treeCanvas.av.alignment == jal)
470 Tree tree = new Tree();
471 tree.setTitle(tp.getTitle());
472 tree.setCurrentTree( (av.currentTree == tp.getTree()));
473 tree.setNewick(tp.getTree().toString());
474 tree.setThreshold(tp.treeCanvas.threshold);
476 tree.setFitToWindow(tp.fitToWindow.getState());
477 tree.setFontName(tp.getTreeFont().getName());
478 tree.setFontSize(tp.getTreeFont().getSize());
479 tree.setFontStyle(tp.getTreeFont().getStyle());
480 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
482 tree.setShowBootstrap(tp.bootstrapMenu.getState());
483 tree.setShowDistances(tp.distanceMenu.getState());
485 tree.setHeight(tp.getHeight());
486 tree.setWidth(tp.getWidth());
487 tree.setXpos(tp.getX());
488 tree.setYpos(tp.getY());
498 if (jal.getAlignmentAnnotation() != null)
500 jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
502 for (int i = 0; i < aa.length; i++)
504 Annotation an = new Annotation();
506 if (aa[i].annotationId != null)
508 annotationIds.put(aa[i].annotationId, aa[i]);
511 an.setId(aa[i].annotationId);
513 if (aa[i] == av.quality ||
514 aa[i] == av.conservation ||
515 aa[i] == av.consensus)
517 an.setLabel(aa[i].label);
519 vamsasSet.addAnnotation(an);
523 an.setVisible(aa[i].visible);
525 an.setDescription(aa[i].description);
527 if (aa[i].sequenceRef != null)
529 an.setSequenceRef(aa[i].sequenceRef.getName());
535 an.setGraphType(aa[i].graph);
536 an.setGraphGroup(aa[i].graphGroup);
537 if (aa[i].getThreshold() != null)
539 ThresholdLine line = new ThresholdLine();
540 line.setLabel(aa[i].getThreshold().label);
541 line.setValue(aa[i].getThreshold().value);
542 line.setColour(aa[i].getThreshold().colour.getRGB());
543 an.setThresholdLine(line);
551 an.setLabel(aa[i].label);
552 if (aa[i].hasScore())
554 an.setScore(aa[i].getScore());
556 AnnotationElement ae;
557 if (aa[i].annotations!=null)
559 an.setScoreOnly(false);
560 for (int a = 0; a < aa[i].annotations.length; a++)
562 if ((aa[i] == null) || (aa[i].annotations[a] == null))
567 ae = new AnnotationElement();
568 if (aa[i].annotations[a].description != null)
569 ae.setDescription(aa[i].annotations[a].description);
570 if(aa[i].annotations[a].displayCharacter!=null)
571 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
573 if (!Float.isNaN(aa[i].annotations[a].value))
574 ae.setValue(aa[i].annotations[a].value);
577 if (aa[i].annotations[a].secondaryStructure != ' '
578 && aa[i].annotations[a].secondaryStructure != '\0')
579 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
582 if (aa[i].annotations[a].colour!=null
583 && aa[i].annotations[a].colour != java.awt.Color.black)
585 ae.setColour(aa[i].annotations[a].colour.getRGB());
588 an.addAnnotationElement(ae);
591 an.setScoreOnly(true);
593 vamsasSet.addAnnotation(an);
598 if (jal.getGroups() != null)
600 JGroup[] groups = new JGroup[jal.getGroups().size()];
602 for (int i = 0; i < groups.length; i++)
604 groups[i] = new JGroup();
606 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup)
609 groups[i].setStart(sg.getStartRes());
610 groups[i].setEnd(sg.getEndRes());
611 groups[i].setName(sg.getName());
614 if (sg.cs.conservationApplied())
616 groups[i].setConsThreshold(sg.cs.getConservationInc());
618 if (sg.cs instanceof jalview.schemes.UserColourScheme)
620 groups[i].setColour(SetUserColourScheme(sg.cs,
626 groups[i].setColour(ColourSchemeProperty.getColourName(sg.
630 else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
633 ColourSchemeProperty.getColourName(
634 ( (jalview.schemes.AnnotationColourGradient) sg.cs).
637 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
639 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
644 groups[i].setColour(ColourSchemeProperty.getColourName(
648 groups[i].setPidThreshold(sg.cs.getThreshold());
651 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
652 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
653 groups[i].setDisplayText(sg.getDisplayText());
654 groups[i].setColourText(sg.getColourText());
655 groups[i].setTextCol1(sg.textColour.getRGB());
656 groups[i].setTextCol2(sg.textColour2.getRGB());
657 groups[i].setTextColThreshold(sg.thresholdTextColour);
659 for (int s = 0; s < sg.getSize(); s++)
661 jalview.datamodel.Sequence seq =
662 (jalview.datamodel.Sequence) sg.getSequenceAt(s);
663 groups[i].addSeq(seq.hashCode());
667 jms.setJGroup(groups);
670 ///////////SAVE VIEWPORT
671 Viewport view = new Viewport();
672 view.setTitle(ap.alignFrame.getTitle());
673 view.setSequenceSetId(av.getSequenceSetId());
674 view.setViewName(av.viewName);
675 view.setGatheredViews(av.gatherViewsHere);
679 if (ap.av.explodedPosition != null)
681 view.setXpos(av.explodedPosition.x);
682 view.setYpos(av.explodedPosition.y);
683 view.setWidth(av.explodedPosition.width);
684 view.setHeight(av.explodedPosition.height);
688 view.setXpos(ap.alignFrame.getBounds().x);
689 view.setYpos(ap.alignFrame.getBounds().y);
690 view.setWidth(ap.alignFrame.getBounds().width);
691 view.setHeight(ap.alignFrame.getBounds().height);
694 view.setStartRes(av.startRes);
695 view.setStartSeq(av.startSeq);
697 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
699 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
702 else if (av.getGlobalColourScheme() instanceof jalview.schemes.
703 AnnotationColourGradient)
705 jalview.schemes.AnnotationColourGradient acg
706 = (jalview.schemes.AnnotationColourGradient) av.getGlobalColourScheme();
708 AnnotationColours ac = new AnnotationColours();
709 ac.setAboveThreshold(acg.getAboveThreshold());
710 ac.setThreshold(acg.getAnnotationThreshold());
711 ac.setAnnotation(acg.getAnnotation());
712 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
714 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
719 ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
722 ac.setMaxColour(acg.getMaxColour().getRGB());
723 ac.setMinColour(acg.getMinColour().getRGB());
724 view.setAnnotationColours(ac);
725 view.setBgColour("AnnotationColourGradient");
729 view.setBgColour(ColourSchemeProperty.getColourName(
730 av.getGlobalColourScheme()));
733 ColourSchemeI cs = av.getGlobalColourScheme();
737 if (cs.conservationApplied())
739 view.setConsThreshold(cs.getConservationInc());
740 if (cs instanceof jalview.schemes.UserColourScheme)
742 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
746 if (cs instanceof ResidueColourScheme)
748 view.setPidThreshold(cs.getThreshold());
752 view.setConservationSelected(av.getConservationSelected());
753 view.setPidSelected(av.getAbovePIDThreshold());
754 view.setFontName(av.font.getName());
755 view.setFontSize(av.font.getSize());
756 view.setFontStyle(av.font.getStyle());
757 view.setRenderGaps(av.renderGaps);
758 view.setShowAnnotation(av.getShowAnnotation());
759 view.setShowBoxes(av.getShowBoxes());
760 view.setShowColourText(av.getColourText());
761 view.setShowFullId(av.getShowJVSuffix());
762 view.setRightAlignIds(av.rightAlignIds);
763 view.setShowSequenceFeatures(av.showSequenceFeatures);
764 view.setShowText(av.getShowText());
765 view.setWrapAlignment(av.getWrapAlignment());
766 view.setTextCol1(av.textColour.getRGB());
767 view.setTextCol2(av.textColour2.getRGB());
768 view.setTextColThreshold(av.thresholdTextColour);
770 if (av.featuresDisplayed != null)
772 jalview.schemabinding.version2.FeatureSettings fs
773 = new jalview.schemabinding.version2.FeatureSettings();
775 String[] renderOrder =
776 ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
778 Vector settingsAdded = new Vector();
779 for (int ro = 0; ro < renderOrder.length; ro++)
781 Setting setting = new Setting();
782 setting.setType(renderOrder[ro]);
784 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).
789 av.featuresDisplayed.containsKey(renderOrder[ro])
791 float rorder=ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(renderOrder[ro]);
793 setting.setOrder(rorder);
795 fs.addSetting(setting);
796 settingsAdded.addElement(renderOrder[ro]);
799 //Make sure we save none displayed feature settings
801 ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
802 while (en.hasMoreElements())
804 String key = en.nextElement().toString();
805 if (settingsAdded.contains(key))
810 Setting setting = new Setting();
811 setting.setType(key);
813 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
816 setting.setDisplay(false);
817 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(key);
820 setting.setOrder(rorder);
822 fs.addSetting(setting);
823 settingsAdded.addElement(key);
825 en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
826 Vector groupsAdded=new Vector();
827 while (en.hasMoreElements())
829 String grp = en.nextElement().toString();
830 if (groupsAdded.contains(grp))
834 Group g = new Group();
836 g.setDisplay(((Boolean)ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.get(grp)).booleanValue());
838 groupsAdded.addElement(grp);
840 jms.setFeatureSettings(fs);
844 if (av.hasHiddenColumns)
846 for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
848 int[] region = (int[]) av.getColumnSelection().getHiddenColumns().
850 HiddenColumns hc = new HiddenColumns();
851 hc.setStart(region[0]);
852 hc.setEnd(region[1]);
853 view.addHiddenColumns(hc);
857 jms.addViewport(view);
859 object.setJalviewModelSequence(jms);
860 object.getVamsasModel().addSequenceSet(vamsasSet);
864 //We may not want to right the object to disk,
865 //eg we can copy the alignViewport to a new view object
866 //using save and then load
869 if (!fileName.endsWith(".xml"))
871 fileName = fileName + ".xml";
874 JarEntry entry = new JarEntry(fileName);
875 jout.putNextEntry(entry);
881 ex.printStackTrace();
887 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
888 Vector userColours, JalviewModelSequence jms)
891 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)
894 if (!userColours.contains(ucs))
896 userColours.add(ucs);
898 java.awt.Color[] colours = ucs.getColours();
899 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.
900 version2.UserColours();
901 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.
902 schemabinding.version2.UserColourScheme();
904 for (int i = 0; i < colours.length; i++)
906 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.
908 col.setName(ResidueProperties.aa[i]);
909 col.setRGB(jalview.util.Format.getHexString(colours[i]));
910 jbucs.addColour(col);
912 if (ucs.getLowerCaseColours() != null)
914 colours = ucs.getLowerCaseColours();
915 for (int i = 0; i < colours.length; i++)
917 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.
919 col.setName(ResidueProperties.aa[i].toLowerCase());
920 col.setRGB(jalview.util.Format.getHexString(colours[i]));
921 jbucs.addColour(col);
925 id = "ucs" + userColours.indexOf(ucs);
927 uc.setUserColourScheme(jbucs);
928 jms.addUserColours(uc);
934 jalview.schemes.UserColourScheme GetUserColourScheme(
935 JalviewModelSequence jms, String id)
937 UserColours[] uc = jms.getUserColours();
938 UserColours colours = null;
940 for (int i = 0; i < uc.length; i++)
942 if (uc[i].getId().equals(id))
950 java.awt.Color[] newColours = new java.awt.Color[24];
952 for (int i = 0; i < 24; i++)
954 newColours[i] = new java.awt.Color(Integer.parseInt(
955 colours.getUserColourScheme().getColour(i).getRGB(), 16));
958 jalview.schemes.UserColourScheme ucs =
959 new jalview.schemes.UserColourScheme(newColours);
961 if (colours.getUserColourScheme().getColourCount() > 24)
963 newColours = new java.awt.Color[23];
964 for (int i = 0; i < 23; i++)
966 newColours[i] = new java.awt.Color(Integer.parseInt(
967 colours.getUserColourScheme().getColour(i + 24).getRGB(), 16));
969 ucs.setLowerCaseColours(newColours);
978 * @param file DOCUMENT ME!
980 public AlignFrame LoadJalviewAlign(final String file)
982 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
984 jalview.gui.AlignFrame af = null;
986 seqRefIds = new Hashtable();
987 viewportsAdded = new Hashtable();
989 Hashtable gatherToThisFrame = new Hashtable();
991 String errorMessage = null;
995 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
998 if (file.startsWith("http://"))
1000 url = new URL(file);
1003 JarInputStream jin = null;
1004 JarEntry jarentry = null;
1011 jin = new JarInputStream(url.openStream());
1015 jin = new JarInputStream(new FileInputStream(file));
1018 for (int i = 0; i < entryCount; i++)
1020 jarentry = jin.getNextJarEntry();
1023 if (jarentry != null && jarentry.getName().endsWith(".xml"))
1025 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
1026 JalviewModel object = new JalviewModel();
1028 Unmarshaller unmar = new Unmarshaller(object);
1029 unmar.setValidation(false);
1030 object = (JalviewModel) unmar.unmarshal(in);
1032 af = LoadFromObject(object, file, true);
1033 if (af.viewport.gatherViewsHere)
1035 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
1039 else if (jarentry != null)
1041 //Some other file here.
1045 while (jarentry != null);
1047 catch(java.io.FileNotFoundException ex)
1049 ex.printStackTrace();
1050 errorMessage = "Couldn't locate Jalview XML file : "+file;
1051 System.err.println("Exception whilst loading jalview XML file : " +
1054 catch (java.net.UnknownHostException ex)
1056 ex.printStackTrace();
1057 errorMessage = "Couldn't locate Jalview XML file : " +file;
1058 System.err.println("Exception whilst loading jalview XML file : " +
1061 catch (Exception ex)
1063 //Is Version 1 Jar file?
1064 af = new Jalview2XML_V1().LoadJalviewAlign(file);
1068 System.out.println("Successfully loaded archive file");
1071 ex.printStackTrace();
1073 System.err.println("Exception whilst loading jalview XML file : " +
1077 if (Desktop.instance != null)
1079 Desktop.instance.stopLoading();
1082 Enumeration en = gatherToThisFrame.elements();
1083 while(en.hasMoreElements())
1085 Desktop.instance.gatherViews(
1086 (AlignFrame) en.nextElement());
1089 if(errorMessage!=null)
1091 final String finalErrorMessage = errorMessage;
1092 javax.swing.SwingUtilities.invokeLater(new Runnable()
1096 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1098 "Error loading Jalview file",
1099 JOptionPane.WARNING_MESSAGE);
1107 Hashtable alreadyLoadedPDB;
1108 String loadPDBFile(String file, String pdbId)
1110 if (alreadyLoadedPDB == null)
1111 alreadyLoadedPDB = new Hashtable();
1113 if (alreadyLoadedPDB.containsKey(pdbId))
1114 return alreadyLoadedPDB.get(pdbId).toString();
1118 JarInputStream jin = null;
1120 if (file.startsWith("http://"))
1122 jin = new JarInputStream(new URL(file).openStream());
1126 jin = new JarInputStream(new FileInputStream(file));
1129 JarEntry entry = null;
1132 entry = jin.getNextJarEntry();
1134 while (!entry.getName().equals(pdbId));
1136 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1137 File outFile = File.createTempFile("jalview_pdb", ".txt");
1138 outFile.deleteOnExit();
1139 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1142 while ( (data = in.readLine()) != null)
1148 alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
1149 return outFile.getAbsolutePath();
1152 catch (Exception ex)
1154 ex.printStackTrace();
1160 AlignFrame LoadFromObject(JalviewModel object,
1162 boolean loadTreesAndStructures)
1164 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1165 Sequence[] vamsasSeq = vamsasSet.getSequence();
1167 JalviewModelSequence jms = object.getJalviewModelSequence();
1169 Viewport view = jms.getViewport(0);
1171 //////////////////////////////////
1174 Vector hiddenSeqs = null;
1175 jalview.datamodel.Sequence jseq;
1177 ArrayList tmpseqs = new ArrayList();
1179 boolean multipleView = false;
1181 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1182 for (int i = 0; i < JSEQ.length; i++)
1184 String seqId = JSEQ[i].getId() + "";
1186 if (seqRefIds.get(seqId) != null)
1188 tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1189 multipleView = true;
1193 jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
1194 vamsasSeq[i].getSequence());
1195 jseq.setDescription(vamsasSeq[i].getDescription());
1196 jseq.setStart(JSEQ[i].getStart());
1197 jseq.setEnd(JSEQ[i].getEnd());
1198 seqRefIds.put(vamsasSeq[i].getId(), jseq);
1202 if (JSEQ[i].getHidden())
1204 if (hiddenSeqs == null)
1206 hiddenSeqs = new Vector();
1209 hiddenSeqs.addElement(
1210 (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1215 ///SequenceFeatures are added to the DatasetSequence,
1216 // so we must create the dataset before loading features
1217 /////////////////////////////////
1220 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
1223 tmpseqs.toArray(orderedSeqs);
1225 jalview.datamodel.Alignment al =
1226 new jalview.datamodel.Alignment(orderedSeqs);
1228 for(int i=0; i<vamsasSet.getSequenceSetPropertiesCount(); i++ )
1230 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
1231 al.setProperty(ssp.getKey(), ssp.getValue());
1235 al.setDataset(null);
1236 /////////////////////////////////
1239 Hashtable pdbloaded = new Hashtable();
1243 for (int i = 0; i < vamsasSeq.length; i++)
1245 if (JSEQ[i].getFeaturesCount() > 0)
1247 Features[] features = JSEQ[i].getFeatures();
1248 for (int f = 0; f < features.length; f++)
1250 jalview.datamodel.SequenceFeature sf
1251 = new jalview.datamodel.SequenceFeature(features[f].getType(),
1252 features[f].getDescription(), features[f].getStatus(),
1253 features[f].getBegin(), features[f].getEnd(),
1254 features[f].getFeatureGroup());
1256 sf.setScore(features[f].getScore());
1257 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1259 OtherData keyValue = features[f].getOtherData(od);
1260 if (keyValue.getKey().startsWith("LINK"))
1262 sf.addLink(keyValue.getValue());
1266 sf.setValue(keyValue.getKey(), keyValue.getValue());
1271 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1275 if (JSEQ[i].getPdbidsCount() > 0)
1277 Pdbids[] ids = JSEQ[i].getPdbids();
1278 for (int p = 0; p < ids.length; p++)
1280 jalview.datamodel.PDBEntry entry = new jalview.datamodel.
1282 entry.setId(ids[p].getId());
1283 entry.setType(ids[p].getType());
1284 if (ids[p].getFile() != null)
1286 if (!pdbloaded.containsKey(ids[p].getFile()))
1288 entry.setFile(loadPDBFile(file, ids[p].getId()));
1292 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1296 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1299 if (vamsasSeq[i].getDBRefCount() > 0)
1301 for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
1303 jalview.datamodel.DBRefEntry entry =
1304 new jalview.datamodel.DBRefEntry(
1305 vamsasSeq[i].getDBRef(d).getSource(),
1306 vamsasSeq[i].getDBRef(d).getVersion(),
1307 vamsasSeq[i].getDBRef(d).getAccessionId()
1309 al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1316 /////////////////////////////////
1317 //////////////////////////////////
1319 boolean hideQuality = true,
1320 hideConservation = true,
1321 hideConsensus = true;
1323 if (vamsasSet.getAnnotationCount() > 0)
1325 Annotation[] an = vamsasSet.getAnnotation();
1327 for (int i = 0; i < an.length; i++)
1329 if (an[i].getLabel().equals("Quality"))
1331 hideQuality = false;
1334 else if (an[i].getLabel().equals("Conservation"))
1336 hideConservation = false;
1339 else if (an[i].getLabel().equals("Consensus"))
1341 hideConsensus = false;
1345 if (an[i].getId() != null
1346 && annotationIds.containsKey(an[i].getId()))
1348 jalview.datamodel.AlignmentAnnotation jda =
1349 (jalview.datamodel.AlignmentAnnotation) annotationIds.get(an[i].
1351 if (an[i].hasVisible())
1352 jda.visible = an[i].getVisible();
1354 al.addAnnotation(jda);
1359 AnnotationElement[] ae = an[i].getAnnotationElement();
1360 jalview.datamodel.Annotation[] anot = null;
1362 if (!an[i].getScoreOnly())
1364 anot = new jalview.datamodel.Annotation[
1367 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
1369 if(ae[aa].getPosition()>=anot.length)
1372 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
1374 ae[aa].getDisplayCharacter(),
1375 ae[aa].getDescription(),
1376 (ae[aa].getSecondaryStructure()==null || ae[aa].getSecondaryStructure().length() == 0) ? ' ' :
1377 ae[aa].getSecondaryStructure().charAt(0),
1383 anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa].
1387 jalview.datamodel.AlignmentAnnotation jaa = null;
1389 if (an[i].getGraph())
1391 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1392 an[i].getDescription(), anot, 0, 0,
1393 an[i].getGraphType());
1395 jaa.graphGroup = an[i].getGraphGroup();
1397 if (an[i].getThresholdLine() != null)
1399 jaa.setThreshold(new jalview.datamodel.GraphLine(
1400 an[i].getThresholdLine().getValue(),
1401 an[i].getThresholdLine().getLabel(),
1402 new java.awt.Color(an[i].getThresholdLine().getColour()))
1410 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1411 an[i].getDescription(), anot);
1414 if (an[i].getId() != null)
1416 annotationIds.put(an[i].getId(), jaa);
1417 jaa.annotationId = an[i].getId();
1420 if (an[i].getSequenceRef() != null)
1422 if (al.findName(an[i].getSequenceRef()) != null)
1424 jaa.createSequenceMapping(
1425 al.findName(an[i].getSequenceRef()), 1, true
1427 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1430 if (an[i].hasScore())
1432 jaa.setScore(an[i].getScore());
1435 if(an[i].hasVisible())
1436 jaa.visible = an[i].getVisible();
1438 al.addAnnotation(jaa);
1442 /////////////////////////
1444 if (jms.getJGroupCount() > 0)
1446 JGroup[] groups = jms.getJGroup();
1448 for (int i = 0; i < groups.length; i++)
1450 ColourSchemeI cs = null;
1452 if (groups[i].getColour() != null)
1454 if (groups[i].getColour().startsWith("ucs"))
1456 cs = GetUserColourScheme(jms, groups[i].getColour());
1460 cs = ColourSchemeProperty.getColour(al,
1461 groups[i].getColour());
1466 cs.setThreshold(groups[i].getPidThreshold(), true);
1470 Vector seqs = new Vector();
1472 for (int s = 0; s < groups[i].getSeqCount(); s++)
1474 String seqId = groups[i].getSeq(s) + "";
1475 jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI)
1476 seqRefIds.get(seqId);
1480 seqs.addElement(ts);
1484 if (seqs.size() < 1)
1489 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.
1491 groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1492 groups[i].getDisplayText(), groups[i].getColourText(),
1493 groups[i].getStart(), groups[i].getEnd());
1495 sg.setOutlineColour(new java.awt.Color(
1496 groups[i].getOutlineColour()));
1498 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
1499 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
1500 sg.thresholdTextColour = groups[i].getTextColThreshold();
1502 if (groups[i].getConsThreshold() != 0)
1504 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
1506 ResidueProperties.propHash, 3, sg.getSequences(null), 0,
1509 c.verdict(false, 25);
1510 sg.cs.setConservation(c);
1517 /////////////////////////////////
1520 AlignFrame af = new AlignFrame(al,
1524 af.setFileName(file, "Jalview");
1526 for (int i = 0; i < JSEQ.length; i++)
1528 af.viewport.setSequenceColour(
1529 af.viewport.alignment.getSequenceAt(i),
1531 JSEQ[i].getColour()));
1534 //If we just load in the same jar file again, the sequenceSetId
1535 //will be the same, and we end up with multiple references
1536 //to the same sequenceSet. We must modify this id on load
1537 //so that each load of the file gives a unique id
1538 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
1540 af.viewport.gatherViewsHere = view.getGatheredViews();
1542 if (view.getSequenceSetId() != null)
1544 jalview.gui.AlignViewport av =
1545 (jalview.gui.AlignViewport)
1546 viewportsAdded.get(uniqueSeqSetId);
1548 af.viewport.sequenceSetID = uniqueSeqSetId;
1552 af.viewport.historyList = av.historyList;
1553 af.viewport.redoList = av.redoList;
1557 viewportsAdded.put(uniqueSeqSetId, af.viewport);
1560 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1562 if (hiddenSeqs != null)
1564 for (int s = 0; s < JSEQ.length; s++)
1566 jalview.datamodel.SequenceGroup hidden =
1567 new jalview.datamodel.SequenceGroup();
1569 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
1572 al.getSequenceAt(JSEQ[s].getHiddenSequences(r))
1576 af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
1579 jalview.datamodel.SequenceI[] hseqs = new
1580 jalview.datamodel.SequenceI[hiddenSeqs.size()];
1582 for (int s = 0; s < hiddenSeqs.size(); s++)
1584 hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
1587 af.viewport.hideSequence(hseqs);
1591 if ( (hideConsensus || hideQuality || hideConservation)
1592 && al.getAlignmentAnnotation() != null)
1594 int hSize = al.getAlignmentAnnotation().length;
1595 for (int h = 0; h < hSize; h++)
1599 al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1602 al.getAlignmentAnnotation()[h].label.equals("Quality"))
1604 (hideConservation &&
1605 al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1607 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1612 af.alignPanel.adjustAnnotationHeight();
1615 if (view.getViewName() != null)
1617 af.viewport.viewName = view.getViewName();
1618 af.setInitialTabVisible();
1620 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1623 af.viewport.setShowAnnotation(view.getShowAnnotation());
1624 af.viewport.setAbovePIDThreshold(view.getPidSelected());
1626 af.viewport.setColourText(view.getShowColourText());
1628 af.viewport.setConservationSelected(view.getConservationSelected());
1629 af.viewport.setShowJVSuffix(view.getShowFullId());
1630 af.viewport.rightAlignIds = view.getRightAlignIds();
1631 af.viewport.setFont(new java.awt.Font(view.getFontName(),
1632 view.getFontStyle(), view.getFontSize()));
1633 af.alignPanel.fontChanged();
1634 af.viewport.setRenderGaps(view.getRenderGaps());
1635 af.viewport.setWrapAlignment(view.getWrapAlignment());
1636 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1637 af.viewport.setShowAnnotation(view.getShowAnnotation());
1638 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1640 af.viewport.setShowBoxes(view.getShowBoxes());
1642 af.viewport.setShowText(view.getShowText());
1644 af.viewport.textColour = new java.awt.Color(view.getTextCol1());
1645 af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
1646 af.viewport.thresholdTextColour = view.getTextColThreshold();
1648 af.viewport.setStartRes(view.getStartRes());
1649 af.viewport.setStartSeq(view.getStartSeq());
1651 ColourSchemeI cs = null;
1653 if (view.getBgColour() != null)
1655 if (view.getBgColour().startsWith("ucs"))
1657 cs = GetUserColourScheme(jms, view.getBgColour());
1659 else if (view.getBgColour().startsWith("Annotation"))
1661 //int find annotation
1663 i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1665 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1666 equals(view.getAnnotationColours().getAnnotation()))
1668 if (af.viewport.alignment.getAlignmentAnnotation()[i].
1669 getThreshold() == null)
1671 af.viewport.alignment.getAlignmentAnnotation()[i].
1673 new jalview.datamodel.GraphLine(
1674 view.getAnnotationColours().getThreshold(),
1675 "Threshold", java.awt.Color.black)
1680 if (view.getAnnotationColours().getColourScheme().equals(
1683 cs = new AnnotationColourGradient(
1684 af.viewport.alignment.getAlignmentAnnotation()[i],
1685 new java.awt.Color(view.getAnnotationColours().
1687 new java.awt.Color(view.getAnnotationColours().
1689 view.getAnnotationColours().getAboveThreshold());
1691 else if (view.getAnnotationColours().getColourScheme().
1694 cs = new AnnotationColourGradient(
1695 af.viewport.alignment.getAlignmentAnnotation()[i],
1696 GetUserColourScheme(jms, view.getAnnotationColours().
1698 view.getAnnotationColours().getAboveThreshold()
1703 cs = new AnnotationColourGradient(
1704 af.viewport.alignment.getAlignmentAnnotation()[i],
1705 ColourSchemeProperty.getColour(al,
1706 view.getAnnotationColours().
1708 view.getAnnotationColours().getAboveThreshold()
1712 // Also use these settings for all the groups
1713 if (al.getGroups() != null)
1715 for (int g = 0; g < al.getGroups().size(); g++)
1717 jalview.datamodel.SequenceGroup sg
1718 = (jalview.datamodel.SequenceGroup) al.getGroups().
1726 /* if (view.getAnnotationColours().getColourScheme().equals("None"))
1728 sg.cs = new AnnotationColourGradient(
1729 af.viewport.alignment.getAlignmentAnnotation()[i],
1730 new java.awt.Color(view.getAnnotationColours().
1732 new java.awt.Color(view.getAnnotationColours().
1734 view.getAnnotationColours().getAboveThreshold());
1738 sg.cs = new AnnotationColourGradient(
1739 af.viewport.alignment.getAlignmentAnnotation()[i],
1741 view.getAnnotationColours().getAboveThreshold()
1755 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1760 cs.setThreshold(view.getPidThreshold(), true);
1761 cs.setConsensus(af.viewport.hconsensus);
1765 af.viewport.setGlobalColourScheme(cs);
1766 af.viewport.setColourAppliesToAllGroups(false);
1768 if (view.getConservationSelected() && cs != null)
1770 cs.setConservationInc(view.getConsThreshold());
1773 af.changeColour(cs);
1775 af.viewport.setColourAppliesToAllGroups(true);
1777 if (view.getShowSequenceFeatures())
1779 af.viewport.showSequenceFeatures = true;
1782 if (jms.getFeatureSettings() != null)
1784 af.viewport.featuresDisplayed = new Hashtable();
1785 String[] renderOrder = new String[jms.getFeatureSettings().
1787 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
1789 Setting setting = jms.getFeatureSettings().getSetting(fs);
1791 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.
1793 new java.awt.Color(setting.getColour()));
1794 renderOrder[fs] = setting.getType();
1795 if (setting.hasOrder())
1796 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(setting.getType(), setting.getOrder());
1798 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(setting.getType(), fs/jms.getFeatureSettings().getSettingCount());
1799 if (setting.getDisplay())
1801 af.viewport.featuresDisplayed.put(
1802 setting.getType(), new Integer(setting.getColour()));
1805 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder =
1808 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable=new Hashtable();
1809 for (int gs=0;gs<jms.getFeatureSettings().getGroupCount(); gs++)
1811 Group grp = jms.getFeatureSettings().getGroup(gs);
1812 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
1816 if (view.getHiddenColumnsCount() > 0)
1818 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1820 af.viewport.hideColumns(
1821 view.getHiddenColumns(c).getStart(),
1822 view.getHiddenColumns(c).getEnd() //+1
1827 af.setMenusFromViewport(af.viewport);
1829 Desktop.addInternalFrame(af, view.getTitle(),
1830 view.getWidth(), view.getHeight());
1833 ///////////////////////////////////////
1834 if (loadTreesAndStructures && jms.getTreeCount() > 0)
1838 for (int t = 0; t < jms.getTreeCount(); t++)
1841 Tree tree = jms.getTree(t);
1843 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1844 tree.getNewick()), tree.getTitle(),
1845 tree.getWidth(), tree.getHeight(),
1846 tree.getXpos(), tree.getYpos());
1848 tp.fitToWindow.setState(tree.getFitToWindow());
1849 tp.fitToWindow_actionPerformed(null);
1851 if (tree.getFontName() != null)
1853 tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1854 tree.getFontStyle(),
1855 tree.getFontSize()));
1859 tp.setTreeFont(new java.awt.Font(view.getFontName(),
1860 view.getFontStyle(),
1861 tree.getFontSize()));
1864 tp.showPlaceholders(tree.getMarkUnlinked());
1865 tp.showBootstrap(tree.getShowBootstrap());
1866 tp.showDistances(tree.getShowDistances());
1868 tp.treeCanvas.threshold = tree.getThreshold();
1870 if (tree.getCurrentTree())
1872 af.viewport.setCurrentTree(tp.getTree());
1877 catch (Exception ex)
1879 ex.printStackTrace();
1884 if(loadTreesAndStructures)
1886 for (int i = 0; i < JSEQ.length; i++)
1888 if (JSEQ[i].getPdbidsCount() > 0)
1890 Pdbids[] ids = JSEQ[i].getPdbids();
1891 for (int p = 0; p < ids.length; p++)
1893 for (int s = 0; s < ids[p].getStructureStateCount(); s++)
1895 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
1897 jpdb.setFile(loadPDBFile(ids[p].getFile(), ids[p].getId()));
1898 jpdb.setId(ids[p].getId());
1900 int x = ids[p].getStructureState(s).getXpos();
1901 int y = ids[p].getStructureState(s).getYpos();
1902 int width = ids[p].getStructureState(s).getWidth();
1903 int height = ids[p].getStructureState(s).getHeight();
1905 java.awt.Component comp = null;
1907 JInternalFrame [] frames = Desktop.desktop.getAllFrames();
1908 for(int f=0; f<frames.length; f++)
1910 if(frames[f] instanceof AppJmol)
1912 if (frames[f].getX() == x && frames[f].getY() == y
1913 && frames[f].getHeight() == height
1914 && frames[f].getWidth() == width)
1923 Desktop.desktop.getComponentAt(x, y);
1925 String pdbFile = loadPDBFile(file, ids[p].getId());
1927 jalview.datamodel.SequenceI[] seq = new jalview.datamodel.
1930 (jalview.datamodel.SequenceI)
1931 seqRefIds.get(JSEQ[i].getId()+"")};
1936 String state = ids[p].getStructureState(s).getContent();
1938 StringBuffer newFileLoc = new StringBuffer(state.substring(0,
1939 state.indexOf("\"", state.indexOf("load")) + 1));
1941 newFileLoc.append(jpdb.getFile());
1942 newFileLoc.append(state.substring(
1943 state.indexOf("\"", state.indexOf("load \"") + 6)));
1945 new AppJmol(pdbFile,
1949 newFileLoc.toString(),
1950 new java.awt.Rectangle(x, y, width, height));
1955 StructureSelectionManager.getStructureSelectionManager()
1956 .setMapping(seq, null, pdbFile,
1957 jalview.io.AppletFormatAdapter.FILE);
1959 ( (AppJmol) comp).addSequence(seq);
1970 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
1971 boolean keepSeqRefs)
1973 jalview.schemabinding.version2.JalviewModel jm
1974 = SaveState(ap, null, null, null);
1979 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
1983 uniqueSetSuffix = "";
1986 viewportsAdded = new Hashtable();
1988 AlignFrame af = LoadFromObject(jm, null, false);
1989 af.alignPanels.clear();
1990 af.closeMenuItem_actionPerformed(true);
1992 /* if(ap.av.alignment.getAlignmentAnnotation()!=null)
1994 for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length; i++)
1996 if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated)
1998 af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
1999 ap.av.alignment.getAlignmentAnnotation()[i];
2004 return af.alignPanel;