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.setDescription(aa[i].description);
525 if (aa[i].sequenceRef != null)
527 an.setSequenceRef(aa[i].sequenceRef.getName());
533 an.setGraphType(aa[i].graph);
534 an.setGraphGroup(aa[i].graphGroup);
535 if (aa[i].getThreshold() != null)
537 ThresholdLine line = new ThresholdLine();
538 line.setLabel(aa[i].getThreshold().label);
539 line.setValue(aa[i].getThreshold().value);
540 line.setColour(aa[i].getThreshold().colour.getRGB());
541 an.setThresholdLine(line);
549 an.setLabel(aa[i].label);
550 if (aa[i].hasScore())
552 an.setScore(aa[i].getScore());
554 AnnotationElement ae;
555 if (aa[i].annotations!=null)
557 an.setScoreOnly(false);
558 for (int a = 0; a < aa[i].annotations.length; a++)
560 if ((aa[i] == null) || (aa[i].annotations[a] == null))
565 ae = new AnnotationElement();
566 if (aa[i].annotations[a].description != null)
567 ae.setDescription(aa[i].annotations[a].description);
568 if(aa[i].annotations[a].displayCharacter!=null)
569 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
571 if (!Float.isNaN(aa[i].annotations[a].value))
572 ae.setValue(aa[i].annotations[a].value);
575 if (aa[i].annotations[a].secondaryStructure != ' '
576 && aa[i].annotations[a].secondaryStructure != '\0')
577 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
580 if (aa[i].annotations[a].colour!=null
581 && aa[i].annotations[a].colour != java.awt.Color.black)
583 ae.setColour(aa[i].annotations[a].colour.getRGB());
586 an.addAnnotationElement(ae);
589 an.setScoreOnly(true);
591 vamsasSet.addAnnotation(an);
596 if (jal.getGroups() != null)
598 JGroup[] groups = new JGroup[jal.getGroups().size()];
600 for (int i = 0; i < groups.length; i++)
602 groups[i] = new JGroup();
604 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup)
607 groups[i].setStart(sg.getStartRes());
608 groups[i].setEnd(sg.getEndRes());
609 groups[i].setName(sg.getName());
612 if (sg.cs.conservationApplied())
614 groups[i].setConsThreshold(sg.cs.getConservationInc());
616 if (sg.cs instanceof jalview.schemes.UserColourScheme)
618 groups[i].setColour(SetUserColourScheme(sg.cs,
624 groups[i].setColour(ColourSchemeProperty.getColourName(sg.
628 else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
631 ColourSchemeProperty.getColourName(
632 ( (jalview.schemes.AnnotationColourGradient) sg.cs).
635 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
637 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
642 groups[i].setColour(ColourSchemeProperty.getColourName(
646 groups[i].setPidThreshold(sg.cs.getThreshold());
649 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
650 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
651 groups[i].setDisplayText(sg.getDisplayText());
652 groups[i].setColourText(sg.getColourText());
653 groups[i].setTextCol1(sg.textColour.getRGB());
654 groups[i].setTextCol2(sg.textColour2.getRGB());
655 groups[i].setTextColThreshold(sg.thresholdTextColour);
657 for (int s = 0; s < sg.getSize(); s++)
659 jalview.datamodel.Sequence seq =
660 (jalview.datamodel.Sequence) sg.getSequenceAt(s);
661 groups[i].addSeq(seq.hashCode());
665 jms.setJGroup(groups);
668 ///////////SAVE VIEWPORT
669 Viewport view = new Viewport();
670 view.setTitle(ap.alignFrame.getTitle());
671 view.setSequenceSetId(av.getSequenceSetId());
672 view.setViewName(av.viewName);
673 view.setGatheredViews(av.gatherViewsHere);
677 if (ap.av.explodedPosition != null)
679 view.setXpos(av.explodedPosition.x);
680 view.setYpos(av.explodedPosition.y);
681 view.setWidth(av.explodedPosition.width);
682 view.setHeight(av.explodedPosition.height);
686 view.setXpos(ap.alignFrame.getBounds().x);
687 view.setYpos(ap.alignFrame.getBounds().y);
688 view.setWidth(ap.alignFrame.getBounds().width);
689 view.setHeight(ap.alignFrame.getBounds().height);
692 view.setStartRes(av.startRes);
693 view.setStartSeq(av.startSeq);
695 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
697 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
700 else if (av.getGlobalColourScheme() instanceof jalview.schemes.
701 AnnotationColourGradient)
703 jalview.schemes.AnnotationColourGradient acg
704 = (jalview.schemes.AnnotationColourGradient) av.getGlobalColourScheme();
706 AnnotationColours ac = new AnnotationColours();
707 ac.setAboveThreshold(acg.getAboveThreshold());
708 ac.setThreshold(acg.getAnnotationThreshold());
709 ac.setAnnotation(acg.getAnnotation());
710 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
712 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
717 ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
720 ac.setMaxColour(acg.getMaxColour().getRGB());
721 ac.setMinColour(acg.getMinColour().getRGB());
722 view.setAnnotationColours(ac);
723 view.setBgColour("AnnotationColourGradient");
727 view.setBgColour(ColourSchemeProperty.getColourName(
728 av.getGlobalColourScheme()));
731 ColourSchemeI cs = av.getGlobalColourScheme();
735 if (cs.conservationApplied())
737 view.setConsThreshold(cs.getConservationInc());
738 if (cs instanceof jalview.schemes.UserColourScheme)
740 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
744 if (cs instanceof ResidueColourScheme)
746 view.setPidThreshold(cs.getThreshold());
750 view.setConservationSelected(av.getConservationSelected());
751 view.setPidSelected(av.getAbovePIDThreshold());
752 view.setFontName(av.font.getName());
753 view.setFontSize(av.font.getSize());
754 view.setFontStyle(av.font.getStyle());
755 view.setRenderGaps(av.renderGaps);
756 view.setShowAnnotation(av.getShowAnnotation());
757 view.setShowBoxes(av.getShowBoxes());
758 view.setShowColourText(av.getColourText());
759 view.setShowFullId(av.getShowJVSuffix());
760 view.setRightAlignIds(av.rightAlignIds);
761 view.setShowSequenceFeatures(av.showSequenceFeatures);
762 view.setShowText(av.getShowText());
763 view.setWrapAlignment(av.getWrapAlignment());
764 view.setTextCol1(av.textColour.getRGB());
765 view.setTextCol2(av.textColour2.getRGB());
766 view.setTextColThreshold(av.thresholdTextColour);
768 if (av.featuresDisplayed != null)
770 jalview.schemabinding.version2.FeatureSettings fs
771 = new jalview.schemabinding.version2.FeatureSettings();
773 String[] renderOrder =
774 ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
776 Vector settingsAdded = new Vector();
777 for (int ro = 0; ro < renderOrder.length; ro++)
779 Setting setting = new Setting();
780 setting.setType(renderOrder[ro]);
782 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).
787 av.featuresDisplayed.containsKey(renderOrder[ro])
789 float rorder=ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(renderOrder[ro]);
791 setting.setOrder(rorder);
793 fs.addSetting(setting);
794 settingsAdded.addElement(renderOrder[ro]);
797 //Make sure we save none displayed feature settings
799 ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
800 while (en.hasMoreElements())
802 String key = en.nextElement().toString();
803 if (settingsAdded.contains(key))
808 Setting setting = new Setting();
809 setting.setType(key);
811 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
814 setting.setDisplay(false);
815 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(key);
818 setting.setOrder(rorder);
820 fs.addSetting(setting);
821 settingsAdded.addElement(key);
823 en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
824 Vector groupsAdded=new Vector();
825 while (en.hasMoreElements())
827 String grp = en.nextElement().toString();
828 if (groupsAdded.contains(grp))
832 Group g = new Group();
834 g.setDisplay(((Boolean)ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.get(grp)).booleanValue());
836 groupsAdded.addElement(grp);
838 jms.setFeatureSettings(fs);
842 if (av.hasHiddenColumns)
844 for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
846 int[] region = (int[]) av.getColumnSelection().getHiddenColumns().
848 HiddenColumns hc = new HiddenColumns();
849 hc.setStart(region[0]);
850 hc.setEnd(region[1]);
851 view.addHiddenColumns(hc);
855 jms.addViewport(view);
857 object.setJalviewModelSequence(jms);
858 object.getVamsasModel().addSequenceSet(vamsasSet);
862 //We may not want to right the object to disk,
863 //eg we can copy the alignViewport to a new view object
864 //using save and then load
867 if (!fileName.endsWith(".xml"))
869 fileName = fileName + ".xml";
872 JarEntry entry = new JarEntry(fileName);
873 jout.putNextEntry(entry);
879 ex.printStackTrace();
885 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
886 Vector userColours, JalviewModelSequence jms)
889 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)
892 if (!userColours.contains(ucs))
894 userColours.add(ucs);
896 java.awt.Color[] colours = ucs.getColours();
897 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.
898 version2.UserColours();
899 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.
900 schemabinding.version2.UserColourScheme();
902 for (int i = 0; i < colours.length; i++)
904 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.
906 col.setName(ResidueProperties.aa[i]);
907 col.setRGB(jalview.util.Format.getHexString(colours[i]));
908 jbucs.addColour(col);
910 if (ucs.getLowerCaseColours() != null)
912 colours = ucs.getLowerCaseColours();
913 for (int i = 0; i < colours.length; i++)
915 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.
917 col.setName(ResidueProperties.aa[i].toLowerCase());
918 col.setRGB(jalview.util.Format.getHexString(colours[i]));
919 jbucs.addColour(col);
923 id = "ucs" + userColours.indexOf(ucs);
925 uc.setUserColourScheme(jbucs);
926 jms.addUserColours(uc);
932 jalview.schemes.UserColourScheme GetUserColourScheme(
933 JalviewModelSequence jms, String id)
935 UserColours[] uc = jms.getUserColours();
936 UserColours colours = null;
938 for (int i = 0; i < uc.length; i++)
940 if (uc[i].getId().equals(id))
948 java.awt.Color[] newColours = new java.awt.Color[24];
950 for (int i = 0; i < 24; i++)
952 newColours[i] = new java.awt.Color(Integer.parseInt(
953 colours.getUserColourScheme().getColour(i).getRGB(), 16));
956 jalview.schemes.UserColourScheme ucs =
957 new jalview.schemes.UserColourScheme(newColours);
959 if (colours.getUserColourScheme().getColourCount() > 24)
961 newColours = new java.awt.Color[23];
962 for (int i = 0; i < 23; i++)
964 newColours[i] = new java.awt.Color(Integer.parseInt(
965 colours.getUserColourScheme().getColour(i + 24).getRGB(), 16));
967 ucs.setLowerCaseColours(newColours);
976 * @param file DOCUMENT ME!
978 public AlignFrame LoadJalviewAlign(final String file)
980 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
982 jalview.gui.AlignFrame af = null;
984 seqRefIds = new Hashtable();
985 viewportsAdded = new Hashtable();
987 Hashtable gatherToThisFrame = new Hashtable();
991 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
994 if (file.startsWith("http://"))
999 JarInputStream jin = null;
1000 JarEntry jarentry = null;
1007 jin = new JarInputStream(url.openStream());
1011 jin = new JarInputStream(new FileInputStream(file));
1014 for (int i = 0; i < entryCount; i++)
1016 jarentry = jin.getNextJarEntry();
1019 if (jarentry != null && jarentry.getName().endsWith(".xml"))
1021 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
1022 JalviewModel object = new JalviewModel();
1024 Unmarshaller unmar = new Unmarshaller(object);
1025 unmar.setValidation(false);
1026 object = (JalviewModel) unmar.unmarshal(in);
1028 af = LoadFromObject(object, file, true);
1029 if (af.viewport.gatherViewsHere)
1031 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
1035 else if (jarentry != null)
1037 //Some other file here.
1041 while (jarentry != null);
1043 catch (java.net.UnknownHostException ex)
1045 ex.printStackTrace();
1046 System.err.println("Couldn't locate Jalview XML file : " +
1049 javax.swing.SwingUtilities.invokeLater(new Runnable()
1053 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1054 "Couldn't locate " + file,
1056 JOptionPane.WARNING_MESSAGE);
1060 catch (Exception ex)
1062 //Is Version 1 Jar file?
1063 af = new Jalview2XML_V1().LoadJalviewAlign(file);
1067 System.out.println("Successfully loaded archive file");
1070 ex.printStackTrace();
1072 System.err.println("Exception whilst loading jalview XML file : " +
1074 javax.swing.SwingUtilities.invokeLater(new Runnable()
1079 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1080 "Error loading " + file,
1081 "Error loading Jalview file",
1082 JOptionPane.WARNING_MESSAGE);
1087 if (Desktop.instance != null)
1089 Desktop.instance.stopLoading();
1092 Enumeration en = gatherToThisFrame.elements();
1093 while(en.hasMoreElements())
1095 Desktop.instance.gatherViews(
1096 (AlignFrame) en.nextElement());
1102 Hashtable alreadyLoadedPDB;
1103 String loadPDBFile(String file, String pdbId)
1105 if (alreadyLoadedPDB == null)
1106 alreadyLoadedPDB = new Hashtable();
1108 if (alreadyLoadedPDB.containsKey(pdbId))
1109 return alreadyLoadedPDB.get(pdbId).toString();
1113 JarInputStream jin = null;
1115 if (file.startsWith("http://"))
1117 jin = new JarInputStream(new URL(file).openStream());
1121 jin = new JarInputStream(new FileInputStream(file));
1124 JarEntry entry = null;
1127 entry = jin.getNextJarEntry();
1129 while (!entry.getName().equals(pdbId));
1131 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1132 File outFile = File.createTempFile("jalview_pdb", ".txt");
1133 outFile.deleteOnExit();
1134 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1137 while ( (data = in.readLine()) != null)
1143 alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
1144 return outFile.getAbsolutePath();
1147 catch (Exception ex)
1149 ex.printStackTrace();
1155 AlignFrame LoadFromObject(JalviewModel object,
1157 boolean loadTreesAndStructures)
1159 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1160 Sequence[] vamsasSeq = vamsasSet.getSequence();
1162 JalviewModelSequence jms = object.getJalviewModelSequence();
1164 Viewport view = jms.getViewport(0);
1166 //////////////////////////////////
1169 Vector hiddenSeqs = null;
1170 jalview.datamodel.Sequence jseq;
1172 ArrayList tmpseqs = new ArrayList();
1174 boolean multipleView = false;
1176 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1177 for (int i = 0; i < JSEQ.length; i++)
1179 String seqId = JSEQ[i].getId() + "";
1181 if (seqRefIds.get(seqId) != null)
1183 tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1184 multipleView = true;
1188 jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
1189 vamsasSeq[i].getSequence());
1190 jseq.setDescription(vamsasSeq[i].getDescription());
1191 jseq.setStart(JSEQ[i].getStart());
1192 jseq.setEnd(JSEQ[i].getEnd());
1193 seqRefIds.put(vamsasSeq[i].getId(), jseq);
1197 if (JSEQ[i].getHidden())
1199 if (hiddenSeqs == null)
1201 hiddenSeqs = new Vector();
1204 hiddenSeqs.addElement(
1205 (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1210 ///SequenceFeatures are added to the DatasetSequence,
1211 // so we must create the dataset before loading features
1212 /////////////////////////////////
1215 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
1218 tmpseqs.toArray(orderedSeqs);
1220 jalview.datamodel.Alignment al =
1221 new jalview.datamodel.Alignment(orderedSeqs);
1223 for(int i=0; i<vamsasSet.getSequenceSetPropertiesCount(); i++ )
1225 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
1226 al.setProperty(ssp.getKey(), ssp.getValue());
1230 al.setDataset(null);
1231 /////////////////////////////////
1234 Hashtable pdbloaded = new Hashtable();
1238 for (int i = 0; i < vamsasSeq.length; i++)
1240 if (JSEQ[i].getFeaturesCount() > 0)
1242 Features[] features = JSEQ[i].getFeatures();
1243 for (int f = 0; f < features.length; f++)
1245 jalview.datamodel.SequenceFeature sf
1246 = new jalview.datamodel.SequenceFeature(features[f].getType(),
1247 features[f].getDescription(), features[f].getStatus(),
1248 features[f].getBegin(), features[f].getEnd(),
1249 features[f].getFeatureGroup());
1251 sf.setScore(features[f].getScore());
1252 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1254 OtherData keyValue = features[f].getOtherData(od);
1255 if (keyValue.getKey().startsWith("LINK"))
1257 sf.addLink(keyValue.getValue());
1261 sf.setValue(keyValue.getKey(), keyValue.getValue());
1266 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1270 if (JSEQ[i].getPdbidsCount() > 0)
1272 Pdbids[] ids = JSEQ[i].getPdbids();
1273 for (int p = 0; p < ids.length; p++)
1275 jalview.datamodel.PDBEntry entry = new jalview.datamodel.
1277 entry.setId(ids[p].getId());
1278 entry.setType(ids[p].getType());
1279 if (ids[p].getFile() != null)
1281 if (!pdbloaded.containsKey(ids[p].getFile()))
1283 entry.setFile(loadPDBFile(file, ids[p].getId()));
1287 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1291 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1294 if (vamsasSeq[i].getDBRefCount() > 0)
1296 for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
1298 jalview.datamodel.DBRefEntry entry =
1299 new jalview.datamodel.DBRefEntry(
1300 vamsasSeq[i].getDBRef(d).getSource(),
1301 vamsasSeq[i].getDBRef(d).getVersion(),
1302 vamsasSeq[i].getDBRef(d).getAccessionId()
1304 al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1311 /////////////////////////////////
1312 //////////////////////////////////
1314 boolean hideQuality = true,
1315 hideConservation = true,
1316 hideConsensus = true;
1318 if (vamsasSet.getAnnotationCount() > 0)
1320 Annotation[] an = vamsasSet.getAnnotation();
1322 for (int i = 0; i < an.length; i++)
1324 if (an[i].getLabel().equals("Quality"))
1326 hideQuality = false;
1329 else if (an[i].getLabel().equals("Conservation"))
1331 hideConservation = false;
1334 else if (an[i].getLabel().equals("Consensus"))
1336 hideConsensus = false;
1340 if (an[i].getId() != null
1341 && annotationIds.containsKey(an[i].getId()))
1344 (jalview.datamodel.AlignmentAnnotation) annotationIds.get(an[i].
1351 AnnotationElement[] ae = an[i].getAnnotationElement();
1352 jalview.datamodel.Annotation[] anot = null;
1354 if (!an[i].getScoreOnly())
1356 anot = new jalview.datamodel.Annotation[
1359 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
1361 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
1363 ae[aa].getDisplayCharacter(),
1364 ae[aa].getDescription(),
1365 (ae[aa].getSecondaryStructure()==null || ae[aa].getSecondaryStructure().length() == 0) ? ' ' :
1366 ae[aa].getSecondaryStructure().charAt(0),
1372 anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa].
1376 jalview.datamodel.AlignmentAnnotation jaa = null;
1378 if (an[i].getGraph())
1380 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1381 an[i].getDescription(), anot, 0, 0,
1382 an[i].getGraphType());
1384 jaa.graphGroup = an[i].getGraphGroup();
1386 if (an[i].getThresholdLine() != null)
1388 jaa.setThreshold(new jalview.datamodel.GraphLine(
1389 an[i].getThresholdLine().getValue(),
1390 an[i].getThresholdLine().getLabel(),
1391 new java.awt.Color(an[i].getThresholdLine().getColour()))
1399 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1400 an[i].getDescription(), anot);
1403 if (an[i].getId() != null)
1405 annotationIds.put(an[i].getId(), jaa);
1406 jaa.annotationId = an[i].getId();
1409 if (an[i].getSequenceRef() != null)
1411 jaa.createSequenceMapping(
1412 al.findName(an[i].getSequenceRef()), 1, true
1414 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1416 if (an[i].hasScore())
1418 jaa.setScore(an[i].getScore());
1420 al.addAnnotation(jaa);
1424 /////////////////////////
1426 if (jms.getJGroupCount() > 0)
1428 JGroup[] groups = jms.getJGroup();
1430 for (int i = 0; i < groups.length; i++)
1432 ColourSchemeI cs = null;
1434 if (groups[i].getColour() != null)
1436 if (groups[i].getColour().startsWith("ucs"))
1438 cs = GetUserColourScheme(jms, groups[i].getColour());
1442 cs = ColourSchemeProperty.getColour(al,
1443 groups[i].getColour());
1448 cs.setThreshold(groups[i].getPidThreshold(), true);
1452 Vector seqs = new Vector();
1454 for (int s = 0; s < groups[i].getSeqCount(); s++)
1456 String seqId = groups[i].getSeq(s) + "";
1457 jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI)
1458 seqRefIds.get(seqId);
1462 seqs.addElement(ts);
1466 if (seqs.size() < 1)
1471 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.
1473 groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1474 groups[i].getDisplayText(), groups[i].getColourText(),
1475 groups[i].getStart(), groups[i].getEnd());
1477 sg.setOutlineColour(new java.awt.Color(
1478 groups[i].getOutlineColour()));
1480 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
1481 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
1482 sg.thresholdTextColour = groups[i].getTextColThreshold();
1484 if (groups[i].getConsThreshold() != 0)
1486 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
1488 ResidueProperties.propHash, 3, sg.getSequences(null), 0,
1491 c.verdict(false, 25);
1492 sg.cs.setConservation(c);
1499 /////////////////////////////////
1502 AlignFrame af = new AlignFrame(al,
1506 af.setFileName(file, "Jalview");
1508 for (int i = 0; i < JSEQ.length; i++)
1510 af.viewport.setSequenceColour(
1511 af.viewport.alignment.getSequenceAt(i),
1513 JSEQ[i].getColour()));
1516 //If we just load in the same jar file again, the sequenceSetId
1517 //will be the same, and we end up with multiple references
1518 //to the same sequenceSet. We must modify this id on load
1519 //so that each load of the file gives a unique id
1520 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
1522 af.viewport.gatherViewsHere = view.getGatheredViews();
1524 if (view.getSequenceSetId() != null)
1526 jalview.gui.AlignViewport av =
1527 (jalview.gui.AlignViewport)
1528 viewportsAdded.get(uniqueSeqSetId);
1530 af.viewport.sequenceSetID = uniqueSeqSetId;
1534 af.viewport.historyList = av.historyList;
1535 af.viewport.redoList = av.redoList;
1539 viewportsAdded.put(uniqueSeqSetId, af.viewport);
1542 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1544 if (hiddenSeqs != null)
1546 for (int s = 0; s < JSEQ.length; s++)
1548 jalview.datamodel.SequenceGroup hidden =
1549 new jalview.datamodel.SequenceGroup();
1551 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
1554 al.getSequenceAt(JSEQ[s].getHiddenSequences(r))
1558 af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
1561 jalview.datamodel.SequenceI[] hseqs = new
1562 jalview.datamodel.SequenceI[hiddenSeqs.size()];
1564 for (int s = 0; s < hiddenSeqs.size(); s++)
1566 hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
1569 af.viewport.hideSequence(hseqs);
1573 if ( (hideConsensus || hideQuality || hideConservation)
1574 && al.getAlignmentAnnotation() != null)
1576 int hSize = al.getAlignmentAnnotation().length;
1577 for (int h = 0; h < hSize; h++)
1581 al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1584 al.getAlignmentAnnotation()[h].label.equals("Quality"))
1586 (hideConservation &&
1587 al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1589 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1594 af.alignPanel.adjustAnnotationHeight();
1597 if (view.getViewName() != null)
1599 af.viewport.viewName = view.getViewName();
1600 af.setInitialTabVisible();
1602 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1605 af.viewport.setShowAnnotation(view.getShowAnnotation());
1606 af.viewport.setAbovePIDThreshold(view.getPidSelected());
1608 af.viewport.setColourText(view.getShowColourText());
1610 af.viewport.setConservationSelected(view.getConservationSelected());
1611 af.viewport.setShowJVSuffix(view.getShowFullId());
1612 af.viewport.rightAlignIds = view.getRightAlignIds();
1613 af.viewport.setFont(new java.awt.Font(view.getFontName(),
1614 view.getFontStyle(), view.getFontSize()));
1615 af.alignPanel.fontChanged();
1616 af.viewport.setRenderGaps(view.getRenderGaps());
1617 af.viewport.setWrapAlignment(view.getWrapAlignment());
1618 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1619 af.viewport.setShowAnnotation(view.getShowAnnotation());
1620 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1622 af.viewport.setShowBoxes(view.getShowBoxes());
1624 af.viewport.setShowText(view.getShowText());
1626 af.viewport.textColour = new java.awt.Color(view.getTextCol1());
1627 af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
1628 af.viewport.thresholdTextColour = view.getTextColThreshold();
1630 af.viewport.setStartRes(view.getStartRes());
1631 af.viewport.setStartSeq(view.getStartSeq());
1633 ColourSchemeI cs = null;
1635 if (view.getBgColour() != null)
1637 if (view.getBgColour().startsWith("ucs"))
1639 cs = GetUserColourScheme(jms, view.getBgColour());
1641 else if (view.getBgColour().startsWith("Annotation"))
1643 //int find annotation
1645 i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1647 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1648 equals(view.getAnnotationColours().getAnnotation()))
1650 if (af.viewport.alignment.getAlignmentAnnotation()[i].
1651 getThreshold() == null)
1653 af.viewport.alignment.getAlignmentAnnotation()[i].
1655 new jalview.datamodel.GraphLine(
1656 view.getAnnotationColours().getThreshold(),
1657 "Threshold", java.awt.Color.black)
1662 if (view.getAnnotationColours().getColourScheme().equals(
1665 cs = new AnnotationColourGradient(
1666 af.viewport.alignment.getAlignmentAnnotation()[i],
1667 new java.awt.Color(view.getAnnotationColours().
1669 new java.awt.Color(view.getAnnotationColours().
1671 view.getAnnotationColours().getAboveThreshold());
1673 else if (view.getAnnotationColours().getColourScheme().
1676 cs = new AnnotationColourGradient(
1677 af.viewport.alignment.getAlignmentAnnotation()[i],
1678 GetUserColourScheme(jms, view.getAnnotationColours().
1680 view.getAnnotationColours().getAboveThreshold()
1685 cs = new AnnotationColourGradient(
1686 af.viewport.alignment.getAlignmentAnnotation()[i],
1687 ColourSchemeProperty.getColour(al,
1688 view.getAnnotationColours().
1690 view.getAnnotationColours().getAboveThreshold()
1694 // Also use these settings for all the groups
1695 if (al.getGroups() != null)
1697 for (int g = 0; g < al.getGroups().size(); g++)
1699 jalview.datamodel.SequenceGroup sg
1700 = (jalview.datamodel.SequenceGroup) al.getGroups().
1708 /* if (view.getAnnotationColours().getColourScheme().equals("None"))
1710 sg.cs = new AnnotationColourGradient(
1711 af.viewport.alignment.getAlignmentAnnotation()[i],
1712 new java.awt.Color(view.getAnnotationColours().
1714 new java.awt.Color(view.getAnnotationColours().
1716 view.getAnnotationColours().getAboveThreshold());
1720 sg.cs = new AnnotationColourGradient(
1721 af.viewport.alignment.getAlignmentAnnotation()[i],
1723 view.getAnnotationColours().getAboveThreshold()
1737 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1742 cs.setThreshold(view.getPidThreshold(), true);
1743 cs.setConsensus(af.viewport.hconsensus);
1747 af.viewport.setGlobalColourScheme(cs);
1748 af.viewport.setColourAppliesToAllGroups(false);
1750 if (view.getConservationSelected() && cs != null)
1752 cs.setConservationInc(view.getConsThreshold());
1755 af.changeColour(cs);
1757 af.viewport.setColourAppliesToAllGroups(true);
1759 if (view.getShowSequenceFeatures())
1761 af.viewport.showSequenceFeatures = true;
1764 if (jms.getFeatureSettings() != null)
1766 af.viewport.featuresDisplayed = new Hashtable();
1767 String[] renderOrder = new String[jms.getFeatureSettings().
1769 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
1771 Setting setting = jms.getFeatureSettings().getSetting(fs);
1773 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.
1775 new java.awt.Color(setting.getColour()));
1776 renderOrder[fs] = setting.getType();
1777 if (setting.hasOrder())
1778 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(setting.getType(), setting.getOrder());
1780 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(setting.getType(), fs/jms.getFeatureSettings().getSettingCount());
1781 if (setting.getDisplay())
1783 af.viewport.featuresDisplayed.put(
1784 setting.getType(), new Integer(setting.getColour()));
1787 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder =
1790 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable=new Hashtable();
1791 for (int gs=0;gs<jms.getFeatureSettings().getGroupCount(); gs++)
1793 Group grp = jms.getFeatureSettings().getGroup(gs);
1794 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
1798 if (view.getHiddenColumnsCount() > 0)
1800 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1802 af.viewport.hideColumns(
1803 view.getHiddenColumns(c).getStart(),
1804 view.getHiddenColumns(c).getEnd() //+1
1809 af.setMenusFromViewport(af.viewport);
1811 Desktop.addInternalFrame(af, view.getTitle(),
1812 view.getWidth(), view.getHeight());
1815 ///////////////////////////////////////
1816 if (loadTreesAndStructures && jms.getTreeCount() > 0)
1820 for (int t = 0; t < jms.getTreeCount(); t++)
1823 Tree tree = jms.getTree(t);
1825 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1826 tree.getNewick()), tree.getTitle(),
1827 tree.getWidth(), tree.getHeight(),
1828 tree.getXpos(), tree.getYpos());
1830 tp.fitToWindow.setState(tree.getFitToWindow());
1831 tp.fitToWindow_actionPerformed(null);
1833 if (tree.getFontName() != null)
1835 tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1836 tree.getFontStyle(),
1837 tree.getFontSize()));
1841 tp.setTreeFont(new java.awt.Font(view.getFontName(),
1842 view.getFontStyle(),
1843 tree.getFontSize()));
1846 tp.showPlaceholders(tree.getMarkUnlinked());
1847 tp.showBootstrap(tree.getShowBootstrap());
1848 tp.showDistances(tree.getShowDistances());
1850 tp.treeCanvas.threshold = tree.getThreshold();
1852 if (tree.getCurrentTree())
1854 af.viewport.setCurrentTree(tp.getTree());
1859 catch (Exception ex)
1861 ex.printStackTrace();
1866 if(loadTreesAndStructures)
1868 for (int i = 0; i < JSEQ.length; i++)
1870 if (JSEQ[i].getPdbidsCount() > 0)
1872 Pdbids[] ids = JSEQ[i].getPdbids();
1873 for (int p = 0; p < ids.length; p++)
1875 for (int s = 0; s < ids[p].getStructureStateCount(); s++)
1877 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
1879 jpdb.setFile(loadPDBFile(ids[p].getFile(), ids[p].getId()));
1880 jpdb.setId(ids[p].getId());
1882 int x = ids[p].getStructureState(s).getXpos();
1883 int y = ids[p].getStructureState(s).getYpos();
1884 int width = ids[p].getStructureState(s).getWidth();
1885 int height = ids[p].getStructureState(s).getHeight();
1887 java.awt.Component comp = Desktop.desktop.getComponentAt(x, y);
1889 String pdbFile = loadPDBFile(file, ids[p].getId());
1891 jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
1893 al.getSequenceAt(i)};
1896 (comp.getWidth() != width && comp.getHeight() != height))
1898 String state = ids[p].getStructureState(s).getContent();
1900 StringBuffer newFileLoc = new StringBuffer(state.substring(0,
1901 state.indexOf("\"", state.indexOf("load")) + 1));
1903 newFileLoc.append(jpdb.getFile());
1904 newFileLoc.append(state.substring(
1905 state.indexOf("\"", state.indexOf("load \"") + 6)));
1907 new AppJMol(pdbFile,
1911 newFileLoc.toString(),
1912 new java.awt.Rectangle(x, y, width, height));
1917 StructureSelectionManager.getStructureSelectionManager()
1918 .setMapping(seq, null, pdbFile,
1919 jalview.io.AppletFormatAdapter.FILE);
1921 ( (AppJMol) comp).addSequence(seq);
1932 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
1933 boolean keepSeqRefs)
1935 jalview.schemabinding.version2.JalviewModel jm
1936 = SaveState(ap, null, null, null);
1941 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
1945 uniqueSetSuffix = "";
1948 viewportsAdded = new Hashtable();
1950 AlignFrame af = LoadFromObject(jm, null, false);
1951 af.alignPanels.clear();
1952 af.closeMenuItem_actionPerformed(true);
1954 /* if(ap.av.alignment.getAlignmentAnnotation()!=null)
1956 for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length; i++)
1958 if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated)
1960 af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
1961 ap.av.alignment.getAlignmentAnnotation()[i];
1966 return af.alignPanel;