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() + "");
216 jalview.datamodel.SequenceI jds;
217 for (int i = 0; i < jal.getHeight(); i++)
219 jds = jal.getSequenceAt(i);
222 if (seqRefIds.get(id + "") != null)
228 vamsasSeq = new Sequence();
229 vamsasSeq.setId(id + "");
230 vamsasSeq.setName(jds.getName());
231 vamsasSeq.setSequence(jds.getSequenceAsString());
232 vamsasSeq.setDescription(jds.getDescription());
234 if (jds.getDatasetSequence().getDBRef() != null)
236 jalview.datamodel.DBRefEntry[] dbrefs =
237 jds.getDatasetSequence().getDBRef();
239 for (int d = 0; d < dbrefs.length; d++)
241 DBRef dbref = new DBRef();
242 dbref.setSource(dbrefs[d].getSource());
243 dbref.setVersion(dbrefs[d].getVersion());
244 dbref.setAccessionId(dbrefs[d].getAccessionId());
245 vamsasSeq.addDBRef(dbref);
249 vamsasSet.addSequence(vamsasSeq);
250 seqRefIds.put(id + "", jal.getSequenceAt(i));
254 jseq.setStart(jds.getStart());
255 jseq.setEnd(jds.getEnd());
256 jseq.setColour(av.getSequenceColour(jds).getRGB());
260 if (av.hasHiddenRows)
262 jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
264 if (av.hiddenRepSequences != null
265 && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
267 jalview.datamodel.SequenceI[] reps =
268 ( (jalview.datamodel.SequenceGroup)
269 av.hiddenRepSequences.get(
270 jal.getSequenceAt(i))).getSequencesInOrder(jal);
272 for (int h = 0; h < reps.length; h++)
274 if (reps[h] != jal.getSequenceAt(i))
276 jseq.addHiddenSequences(
277 jal.findIndex(reps[h])
284 if (jds.getDatasetSequence().getSequenceFeatures() != null)
286 jalview.datamodel.SequenceFeature[] sf
287 = jds.getDatasetSequence().getSequenceFeatures();
289 while (index < sf.length)
291 Features features = new Features();
293 features.setBegin(sf[index].getBegin());
294 features.setEnd(sf[index].getEnd());
295 features.setDescription(sf[index].getDescription());
296 features.setType(sf[index].getType());
297 features.setFeatureGroup(sf[index].getFeatureGroup());
298 features.setScore(sf[index].getScore());
299 if (sf[index].links != null)
301 for (int l = 0; l < sf[index].links.size(); l++)
303 OtherData keyValue = new OtherData();
304 keyValue.setKey("LINK_" + l);
305 keyValue.setValue(sf[index].links.elementAt(l).toString());
306 features.addOtherData(keyValue);
309 if (sf[index].otherDetails != null)
312 Enumeration keys = sf[index].otherDetails.keys();
313 while (keys.hasMoreElements())
315 key = keys.nextElement().toString();
316 OtherData keyValue = new OtherData();
317 keyValue.setKey(key);
319 sf[index].otherDetails.get(key).toString());
320 features.addOtherData(keyValue);
324 jseq.addFeatures(features);
329 if (jds.getDatasetSequence().getPDBId() != null)
331 Enumeration en = jds.getDatasetSequence().getPDBId().elements();
332 while (en.hasMoreElements())
334 Pdbids pdb = new Pdbids();
335 jalview.datamodel.PDBEntry entry
336 = (jalview.datamodel.PDBEntry) en.nextElement();
338 pdb.setId(entry.getId());
339 pdb.setType(entry.getType());
342 //This must have been loaded, is it still visible?
343 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
344 for (int f = frames.length - 1; f > -1; f--)
346 if (frames[f] instanceof AppJMol)
348 jmol = (AppJMol) frames[f];
349 if (!jmol.pdbentry.getId().equals(entry.getId()))
352 StructureState state = new StructureState();
353 state.setVisible(true);
354 state.setXpos(jmol.getX());
355 state.setYpos(jmol.getY());
356 state.setWidth(jmol.getWidth());
357 state.setHeight(jmol.getHeight());
359 state.setContent(jmol.viewer.getStateInfo().replaceAll("\n", ""));
361 for (int s = 0; s < jmol.sequence.length; s++)
363 if (jal.findIndex(jmol.sequence[s]) > -1)
365 pdb.addStructureState(state);
372 if (entry.getFile() != null)
374 pdb.setFile(entry.getFile());
375 if (pdbfiles == null)
377 pdbfiles = new Vector();
380 if (!pdbfiles.contains(entry.getId()))
382 pdbfiles.addElement(entry.getId());
385 File file = new File(entry.getFile());
386 if (file.exists() && jout != null)
388 byte[] data = new byte[ (int) file.length()];
389 jout.putNextEntry(new JarEntry(entry.getId()));
390 DataInputStream dis = new DataInputStream(new
391 FileInputStream(file));
394 DataOutputStream dout = new DataOutputStream(jout);
395 dout.write(data, 0, data.length);
401 ex.printStackTrace();
407 if (entry.getProperty() != null)
409 PdbentryItem item = new PdbentryItem();
410 Hashtable properties = entry.getProperty();
411 Enumeration en2 = properties.keys();
412 while (en2.hasMoreElements())
414 Property prop = new Property();
415 String key = en2.nextElement().toString();
417 prop.setValue(properties.get(key).toString());
418 item.addProperty(prop);
420 pdb.addPdbentryItem(item);
430 if (av.hasHiddenRows)
436 ///////////////////////////////////
437 if (av.currentTree != null)
439 // FIND ANY ASSOCIATED TREES
440 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
441 if (Desktop.desktop != null)
443 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
445 for (int t = 0; t < frames.length; t++)
447 if (frames[t] instanceof TreePanel)
449 TreePanel tp = (TreePanel) frames[t];
451 if (tp.treeCanvas.av.alignment == jal)
453 Tree tree = new Tree();
454 tree.setTitle(tp.getTitle());
455 tree.setCurrentTree( (av.currentTree == tp.getTree()));
456 tree.setNewick(tp.getTree().toString());
457 tree.setThreshold(tp.treeCanvas.threshold);
459 tree.setFitToWindow(tp.fitToWindow.getState());
460 tree.setFontName(tp.getTreeFont().getName());
461 tree.setFontSize(tp.getTreeFont().getSize());
462 tree.setFontStyle(tp.getTreeFont().getStyle());
463 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
465 tree.setShowBootstrap(tp.bootstrapMenu.getState());
466 tree.setShowDistances(tp.distanceMenu.getState());
468 tree.setHeight(tp.getHeight());
469 tree.setWidth(tp.getWidth());
470 tree.setXpos(tp.getX());
471 tree.setYpos(tp.getY());
481 if (jal.getAlignmentAnnotation() != null)
483 jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
485 for (int i = 0; i < aa.length; i++)
487 Annotation an = new Annotation();
489 if (aa[i].annotationId != null)
491 annotationIds.put(aa[i].annotationId, aa[i]);
494 an.setId(aa[i].annotationId);
496 if (aa[i] == av.quality ||
497 aa[i] == av.conservation ||
498 aa[i] == av.consensus)
500 an.setLabel(aa[i].label);
502 vamsasSet.addAnnotation(an);
506 an.setDescription(aa[i].description);
508 if (aa[i].sequenceRef != null)
510 an.setSequenceRef(aa[i].sequenceRef.getName());
516 an.setGraphType(aa[i].graph);
517 an.setGraphGroup(aa[i].graphGroup);
518 if (aa[i].getThreshold() != null)
520 ThresholdLine line = new ThresholdLine();
521 line.setLabel(aa[i].getThreshold().label);
522 line.setValue(aa[i].getThreshold().value);
523 line.setColour(aa[i].getThreshold().colour.getRGB());
524 an.setThresholdLine(line);
532 an.setLabel(aa[i].label);
533 if (aa[i].hasScore())
535 an.setScore(aa[i].getScore());
537 AnnotationElement ae;
538 if (aa[i].annotations!=null)
540 an.setScoreOnly(false);
541 for (int a = 0; a < aa[i].annotations.length; a++)
543 if ((aa[i] == null) || (aa[i].annotations[a] == null))
548 ae = new AnnotationElement();
549 ae.setDescription(aa[i].annotations[a].description);
550 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
551 ae.setValue(aa[i].annotations[a].value);
554 .setSecondaryStructure(aa[i].annotations[a].secondaryStructure
557 if (aa[i].annotations[a].colour != java.awt.Color.black)
559 ae.setColour(aa[i].annotations[a].colour.getRGB());
562 an.addAnnotationElement(ae);
565 an.setScoreOnly(true);
567 vamsasSet.addAnnotation(an);
572 if (jal.getGroups() != null)
574 JGroup[] groups = new JGroup[jal.getGroups().size()];
576 for (int i = 0; i < groups.length; i++)
578 groups[i] = new JGroup();
580 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup)
583 groups[i].setStart(sg.getStartRes());
584 groups[i].setEnd(sg.getEndRes());
585 groups[i].setName(sg.getName());
588 if (sg.cs.conservationApplied())
590 groups[i].setConsThreshold(sg.cs.getConservationInc());
592 if (sg.cs instanceof jalview.schemes.UserColourScheme)
594 groups[i].setColour(SetUserColourScheme(sg.cs,
600 groups[i].setColour(ColourSchemeProperty.getColourName(sg.
604 else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
607 ColourSchemeProperty.getColourName(
608 ( (jalview.schemes.AnnotationColourGradient) sg.cs).
611 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
613 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
618 groups[i].setColour(ColourSchemeProperty.getColourName(
622 groups[i].setPidThreshold(sg.cs.getThreshold());
625 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
626 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
627 groups[i].setDisplayText(sg.getDisplayText());
628 groups[i].setColourText(sg.getColourText());
629 groups[i].setTextCol1(sg.textColour.getRGB());
630 groups[i].setTextCol2(sg.textColour2.getRGB());
631 groups[i].setTextColThreshold(sg.thresholdTextColour);
633 for (int s = 0; s < sg.getSize(); s++)
635 jalview.datamodel.Sequence seq =
636 (jalview.datamodel.Sequence) sg.getSequenceAt(s);
637 groups[i].addSeq(seq.hashCode());
641 jms.setJGroup(groups);
644 ///////////SAVE VIEWPORT
645 Viewport view = new Viewport();
646 view.setTitle(ap.alignFrame.getTitle());
647 view.setSequenceSetId(av.getSequenceSetId());
648 view.setViewName(av.viewName);
649 view.setGatheredViews(av.gatherViewsHere);
653 if (ap.av.explodedPosition != null)
655 view.setXpos(av.explodedPosition.x);
656 view.setYpos(av.explodedPosition.y);
657 view.setWidth(av.explodedPosition.width);
658 view.setHeight(av.explodedPosition.height);
662 view.setXpos(ap.alignFrame.getBounds().x);
663 view.setYpos(ap.alignFrame.getBounds().y);
664 view.setWidth(ap.alignFrame.getBounds().width);
665 view.setHeight(ap.alignFrame.getBounds().height);
668 view.setStartRes(av.startRes);
669 view.setStartSeq(av.startSeq);
671 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
673 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
676 else if (av.getGlobalColourScheme() instanceof jalview.schemes.
677 AnnotationColourGradient)
679 jalview.schemes.AnnotationColourGradient acg
680 = (jalview.schemes.AnnotationColourGradient) av.getGlobalColourScheme();
682 AnnotationColours ac = new AnnotationColours();
683 ac.setAboveThreshold(acg.getAboveThreshold());
684 ac.setThreshold(acg.getAnnotationThreshold());
685 ac.setAnnotation(acg.getAnnotation());
686 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
688 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
693 ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
696 ac.setMaxColour(acg.getMaxColour().getRGB());
697 ac.setMinColour(acg.getMinColour().getRGB());
698 view.setAnnotationColours(ac);
699 view.setBgColour("AnnotationColourGradient");
703 view.setBgColour(ColourSchemeProperty.getColourName(
704 av.getGlobalColourScheme()));
707 ColourSchemeI cs = av.getGlobalColourScheme();
711 if (cs.conservationApplied())
713 view.setConsThreshold(cs.getConservationInc());
714 if (cs instanceof jalview.schemes.UserColourScheme)
716 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
720 if (cs instanceof ResidueColourScheme)
722 view.setPidThreshold(cs.getThreshold());
726 view.setConservationSelected(av.getConservationSelected());
727 view.setPidSelected(av.getAbovePIDThreshold());
728 view.setFontName(av.font.getName());
729 view.setFontSize(av.font.getSize());
730 view.setFontStyle(av.font.getStyle());
731 view.setRenderGaps(av.renderGaps);
732 view.setShowAnnotation(av.getShowAnnotation());
733 view.setShowBoxes(av.getShowBoxes());
734 view.setShowColourText(av.getColourText());
735 view.setShowFullId(av.getShowJVSuffix());
736 view.setRightAlignIds(av.rightAlignIds);
737 view.setShowSequenceFeatures(av.showSequenceFeatures);
738 view.setShowText(av.getShowText());
739 view.setWrapAlignment(av.getWrapAlignment());
740 view.setTextCol1(av.textColour.getRGB());
741 view.setTextCol2(av.textColour2.getRGB());
742 view.setTextColThreshold(av.thresholdTextColour);
744 if (av.featuresDisplayed != null)
746 jalview.schemabinding.version2.FeatureSettings fs
747 = new jalview.schemabinding.version2.FeatureSettings();
749 String[] renderOrder =
750 ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
752 Vector settingsAdded = new Vector();
753 for (int ro = 0; ro < renderOrder.length; ro++)
755 Setting setting = new Setting();
756 setting.setType(renderOrder[ro]);
758 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).
763 av.featuresDisplayed.containsKey(renderOrder[ro])
765 float rorder=ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(renderOrder[ro]);
767 setting.setOrder(rorder);
769 fs.addSetting(setting);
770 settingsAdded.addElement(renderOrder[ro]);
773 //Make sure we save none displayed feature settings
775 ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
776 while (en.hasMoreElements())
778 String key = en.nextElement().toString();
779 if (settingsAdded.contains(key))
784 Setting setting = new Setting();
785 setting.setType(key);
787 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
790 setting.setDisplay(false);
791 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(key);
794 setting.setOrder(rorder);
796 fs.addSetting(setting);
797 settingsAdded.addElement(key);
799 en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
800 Vector groupsAdded=new Vector();
801 while (en.hasMoreElements())
803 String grp = en.nextElement().toString();
804 if (groupsAdded.contains(grp))
808 Group g = new Group();
810 g.setDisplay(((Boolean)ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.get(grp)).booleanValue());
812 groupsAdded.addElement(grp);
814 jms.setFeatureSettings(fs);
818 if (av.hasHiddenColumns)
820 for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
822 int[] region = (int[]) av.getColumnSelection().getHiddenColumns().
824 HiddenColumns hc = new HiddenColumns();
825 hc.setStart(region[0]);
826 hc.setEnd(region[1]);
827 view.addHiddenColumns(hc);
831 jms.addViewport(view);
833 object.setJalviewModelSequence(jms);
834 object.getVamsasModel().addSequenceSet(vamsasSet);
838 //We may not want to right the object to disk,
839 //eg we can copy the alignViewport to a new view object
840 //using save and then load
843 if (!fileName.endsWith(".xml"))
845 fileName = fileName + ".xml";
848 JarEntry entry = new JarEntry(fileName);
849 jout.putNextEntry(entry);
855 ex.printStackTrace();
861 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
862 Vector userColours, JalviewModelSequence jms)
865 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)
868 if (!userColours.contains(ucs))
870 userColours.add(ucs);
872 java.awt.Color[] colours = ucs.getColours();
873 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.
874 version2.UserColours();
875 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.
876 schemabinding.version2.UserColourScheme();
878 for (int i = 0; i < colours.length; i++)
880 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.
882 col.setName(ResidueProperties.aa[i]);
883 col.setRGB(jalview.util.Format.getHexString(colours[i]));
884 jbucs.addColour(col);
886 if (ucs.getLowerCaseColours() != null)
888 colours = ucs.getLowerCaseColours();
889 for (int i = 0; i < colours.length; i++)
891 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.
893 col.setName(ResidueProperties.aa[i].toLowerCase());
894 col.setRGB(jalview.util.Format.getHexString(colours[i]));
895 jbucs.addColour(col);
899 id = "ucs" + userColours.indexOf(ucs);
901 uc.setUserColourScheme(jbucs);
902 jms.addUserColours(uc);
908 jalview.schemes.UserColourScheme GetUserColourScheme(
909 JalviewModelSequence jms, String id)
911 UserColours[] uc = jms.getUserColours();
912 UserColours colours = null;
914 for (int i = 0; i < uc.length; i++)
916 if (uc[i].getId().equals(id))
924 java.awt.Color[] newColours = new java.awt.Color[24];
926 for (int i = 0; i < 24; i++)
928 newColours[i] = new java.awt.Color(Integer.parseInt(
929 colours.getUserColourScheme().getColour(i).getRGB(), 16));
932 jalview.schemes.UserColourScheme ucs =
933 new jalview.schemes.UserColourScheme(newColours);
935 if (colours.getUserColourScheme().getColourCount() > 24)
937 newColours = new java.awt.Color[23];
938 for (int i = 0; i < 23; i++)
940 newColours[i] = new java.awt.Color(Integer.parseInt(
941 colours.getUserColourScheme().getColour(i + 24).getRGB(), 16));
943 ucs.setLowerCaseColours(newColours);
952 * @param file DOCUMENT ME!
954 public AlignFrame LoadJalviewAlign(final String file)
956 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
958 jalview.gui.AlignFrame af = null;
960 seqRefIds = new Hashtable();
961 viewportsAdded = new Hashtable();
963 Hashtable gatherToThisFrame = new Hashtable();
967 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
970 if (file.startsWith("http://"))
975 JarInputStream jin = null;
976 JarEntry jarentry = null;
983 jin = new JarInputStream(url.openStream());
987 jin = new JarInputStream(new FileInputStream(file));
990 for (int i = 0; i < entryCount; i++)
992 jarentry = jin.getNextJarEntry();
995 if (jarentry != null && jarentry.getName().endsWith(".xml"))
997 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
998 JalviewModel object = new JalviewModel();
1000 Unmarshaller unmar = new Unmarshaller(object);
1001 unmar.setValidation(false);
1002 object = (JalviewModel) unmar.unmarshal(in);
1004 af = LoadFromObject(object, file, true);
1005 if (af.viewport.gatherViewsHere)
1007 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
1011 else if (jarentry != null)
1013 //Some other file here.
1017 while (jarentry != null);
1019 catch (java.net.UnknownHostException ex)
1021 ex.printStackTrace();
1022 System.err.println("Couldn't locate Jalview XML file : " +
1025 javax.swing.SwingUtilities.invokeLater(new Runnable()
1029 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1030 "Couldn't locate " + file,
1032 JOptionPane.WARNING_MESSAGE);
1036 catch (Exception ex)
1038 //Is Version 1 Jar file?
1039 af = new Jalview2XML_V1().LoadJalviewAlign(file);
1043 System.out.println("Successfully loaded archive file");
1046 ex.printStackTrace();
1048 System.err.println("Exception whilst loading jalview XML file : " +
1050 javax.swing.SwingUtilities.invokeLater(new Runnable()
1055 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1056 "Error loading " + file,
1057 "Error loading Jalview file",
1058 JOptionPane.WARNING_MESSAGE);
1063 if (Desktop.instance != null)
1065 Desktop.instance.stopLoading();
1068 Enumeration en = gatherToThisFrame.elements();
1069 while(en.hasMoreElements())
1071 Desktop.instance.gatherViews(
1072 (AlignFrame) en.nextElement());
1078 Hashtable alreadyLoadedPDB;
1079 String loadPDBFile(String file, String pdbId)
1081 if (alreadyLoadedPDB == null)
1082 alreadyLoadedPDB = new Hashtable();
1084 if (alreadyLoadedPDB.containsKey(pdbId))
1085 return alreadyLoadedPDB.get(pdbId).toString();
1089 JarInputStream jin = null;
1091 if (file.startsWith("http://"))
1093 jin = new JarInputStream(new URL(file).openStream());
1097 jin = new JarInputStream(new FileInputStream(file));
1100 JarEntry entry = null;
1103 entry = jin.getNextJarEntry();
1105 while (!entry.getName().equals(pdbId));
1107 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1108 File outFile = File.createTempFile("jalview_pdb", ".txt");
1109 outFile.deleteOnExit();
1110 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1113 while ( (data = in.readLine()) != null)
1119 alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
1120 return outFile.getAbsolutePath();
1123 catch (Exception ex)
1125 ex.printStackTrace();
1131 AlignFrame LoadFromObject(JalviewModel object,
1133 boolean loadTreesAndStructures)
1135 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1136 Sequence[] vamsasSeq = vamsasSet.getSequence();
1138 JalviewModelSequence jms = object.getJalviewModelSequence();
1140 Viewport view = jms.getViewport(0);
1142 //////////////////////////////////
1145 Vector hiddenSeqs = null;
1146 jalview.datamodel.Sequence jseq;
1148 ArrayList tmpseqs = new ArrayList();
1150 boolean multipleView = false;
1152 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1153 for (int i = 0; i < JSEQ.length; i++)
1155 String seqId = JSEQ[i].getId() + "";
1157 if (seqRefIds.get(seqId) != null)
1159 tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1160 multipleView = true;
1164 jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
1165 vamsasSeq[i].getSequence());
1166 jseq.setDescription(vamsasSeq[i].getDescription());
1167 jseq.setStart(JSEQ[i].getStart());
1168 jseq.setEnd(JSEQ[i].getEnd());
1169 seqRefIds.put(vamsasSeq[i].getId(), jseq);
1173 if (JSEQ[i].getHidden())
1175 if (hiddenSeqs == null)
1177 hiddenSeqs = new Vector();
1180 hiddenSeqs.addElement(
1181 (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1186 ///SequenceFeatures are added to the DatasetSequence,
1187 // so we must create the dataset before loading features
1188 /////////////////////////////////
1191 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
1194 tmpseqs.toArray(orderedSeqs);
1196 jalview.datamodel.Alignment al =
1197 new jalview.datamodel.Alignment(orderedSeqs);
1199 al.setDataset(null);
1200 /////////////////////////////////
1203 Hashtable pdbloaded = new Hashtable();
1207 for (int i = 0; i < vamsasSeq.length; i++)
1209 if (JSEQ[i].getFeaturesCount() > 0)
1211 Features[] features = JSEQ[i].getFeatures();
1212 for (int f = 0; f < features.length; f++)
1214 jalview.datamodel.SequenceFeature sf
1215 = new jalview.datamodel.SequenceFeature(features[f].getType(),
1216 features[f].getDescription(), features[f].getStatus(),
1217 features[f].getBegin(), features[f].getEnd(),
1218 features[f].getFeatureGroup());
1220 sf.setScore(features[f].getScore());
1221 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1223 OtherData keyValue = features[f].getOtherData(od);
1224 if (keyValue.getKey().startsWith("LINK"))
1226 sf.addLink(keyValue.getValue());
1230 sf.setValue(keyValue.getKey(), keyValue.getValue());
1235 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1239 if (JSEQ[i].getPdbidsCount() > 0)
1241 Pdbids[] ids = JSEQ[i].getPdbids();
1242 for (int p = 0; p < ids.length; p++)
1244 jalview.datamodel.PDBEntry entry = new jalview.datamodel.
1246 entry.setId(ids[p].getId());
1247 entry.setType(ids[p].getType());
1248 if (ids[p].getFile() != null)
1250 if (!pdbloaded.containsKey(ids[p].getFile()))
1252 entry.setFile(loadPDBFile(file, ids[p].getId()));
1256 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1260 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1263 if (vamsasSeq[i].getDBRefCount() > 0)
1265 for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
1267 jalview.datamodel.DBRefEntry entry =
1268 new jalview.datamodel.DBRefEntry(
1269 vamsasSeq[i].getDBRef(d).getSource(),
1270 vamsasSeq[i].getDBRef(d).getVersion(),
1271 vamsasSeq[i].getDBRef(d).getAccessionId()
1273 al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1280 /////////////////////////////////
1281 //////////////////////////////////
1283 boolean hideQuality = true,
1284 hideConservation = true,
1285 hideConsensus = true;
1287 if (vamsasSet.getAnnotationCount() > 0)
1289 Annotation[] an = vamsasSet.getAnnotation();
1291 for (int i = 0; i < an.length; i++)
1293 if (an[i].getLabel().equals("Quality"))
1295 hideQuality = false;
1298 else if (an[i].getLabel().equals("Conservation"))
1300 hideConservation = false;
1303 else if (an[i].getLabel().equals("Consensus"))
1305 hideConsensus = false;
1309 if (an[i].getId() != null
1310 && annotationIds.containsKey(an[i].getId()))
1313 (jalview.datamodel.AlignmentAnnotation) annotationIds.get(an[i].
1320 AnnotationElement[] ae = an[i].getAnnotationElement();
1321 jalview.datamodel.Annotation[] anot = null;
1322 if (!an[i].getScoreOnly())
1324 anot = new jalview.datamodel.Annotation[
1327 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
1329 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].
1330 getDisplayCharacter(),
1331 ae[aa].getDescription(),
1332 ae[aa].getSecondaryStructure().length() == 0 ? ' ' :
1333 ae[aa].getSecondaryStructure().charAt(0),
1335 anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa].
1339 jalview.datamodel.AlignmentAnnotation jaa = null;
1341 if (an[i].getGraph())
1343 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1344 an[i].getDescription(), anot, 0, 0,
1345 an[i].getGraphType());
1347 jaa.graphGroup = an[i].getGraphGroup();
1349 if (an[i].getThresholdLine() != null)
1351 jaa.setThreshold(new jalview.datamodel.GraphLine(
1352 an[i].getThresholdLine().getValue(),
1353 an[i].getThresholdLine().getLabel(),
1354 new java.awt.Color(an[i].getThresholdLine().getColour()))
1362 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1363 an[i].getDescription(), anot);
1366 if (an[i].getId() != null)
1368 annotationIds.put(an[i].getId(), jaa);
1369 jaa.annotationId = an[i].getId();
1372 if (an[i].getSequenceRef() != null)
1374 jaa.createSequenceMapping(
1375 al.findName(an[i].getSequenceRef()), 1, true
1377 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1379 if (an[i].hasScore())
1381 jaa.setScore(an[i].getScore());
1383 al.addAnnotation(jaa);
1387 /////////////////////////
1389 if (jms.getJGroupCount() > 0)
1391 JGroup[] groups = jms.getJGroup();
1393 for (int i = 0; i < groups.length; i++)
1395 ColourSchemeI cs = null;
1397 if (groups[i].getColour() != null)
1399 if (groups[i].getColour().startsWith("ucs"))
1401 cs = GetUserColourScheme(jms, groups[i].getColour());
1405 cs = ColourSchemeProperty.getColour(al,
1406 groups[i].getColour());
1411 cs.setThreshold(groups[i].getPidThreshold(), true);
1415 Vector seqs = new Vector();
1417 for (int s = 0; s < groups[i].getSeqCount(); s++)
1419 String seqId = groups[i].getSeq(s) + "";
1420 jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI)
1421 seqRefIds.get(seqId);
1425 seqs.addElement(ts);
1429 if (seqs.size() < 1)
1434 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.
1436 groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1437 groups[i].getDisplayText(), groups[i].getColourText(),
1438 groups[i].getStart(), groups[i].getEnd());
1440 sg.setOutlineColour(new java.awt.Color(
1441 groups[i].getOutlineColour()));
1443 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
1444 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
1445 sg.thresholdTextColour = groups[i].getTextColThreshold();
1447 if (groups[i].getConsThreshold() != 0)
1449 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
1451 ResidueProperties.propHash, 3, sg.getSequences(null), 0,
1454 c.verdict(false, 25);
1455 sg.cs.setConservation(c);
1462 /////////////////////////////////
1465 AlignFrame af = new AlignFrame(al,
1469 af.setFileName(file, "Jalview");
1471 for (int i = 0; i < JSEQ.length; i++)
1473 af.viewport.setSequenceColour(
1474 af.viewport.alignment.getSequenceAt(i),
1476 JSEQ[i].getColour()));
1479 //If we just load in the same jar file again, the sequenceSetId
1480 //will be the same, and we end up with multiple references
1481 //to the same sequenceSet. We must modify this id on load
1482 //so that each load of the file gives a unique id
1483 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
1485 af.viewport.gatherViewsHere = view.getGatheredViews();
1487 if (view.getSequenceSetId() != null)
1489 jalview.gui.AlignViewport av =
1490 (jalview.gui.AlignViewport)
1491 viewportsAdded.get(uniqueSeqSetId);
1493 af.viewport.sequenceSetID = uniqueSeqSetId;
1497 af.viewport.historyList = av.historyList;
1498 af.viewport.redoList = av.redoList;
1502 viewportsAdded.put(uniqueSeqSetId, af.viewport);
1505 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1507 if (hiddenSeqs != null)
1509 for (int s = 0; s < JSEQ.length; s++)
1511 jalview.datamodel.SequenceGroup hidden =
1512 new jalview.datamodel.SequenceGroup();
1514 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
1517 al.getSequenceAt(JSEQ[s].getHiddenSequences(r))
1521 af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
1524 jalview.datamodel.SequenceI[] hseqs = new
1525 jalview.datamodel.SequenceI[hiddenSeqs.size()];
1527 for (int s = 0; s < hiddenSeqs.size(); s++)
1529 hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
1532 af.viewport.hideSequence(hseqs);
1536 if ( (hideConsensus || hideQuality || hideConservation)
1537 && al.getAlignmentAnnotation() != null)
1539 int hSize = al.getAlignmentAnnotation().length;
1540 for (int h = 0; h < hSize; h++)
1544 al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1547 al.getAlignmentAnnotation()[h].label.equals("Quality"))
1549 (hideConservation &&
1550 al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1552 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1557 af.alignPanel.adjustAnnotationHeight();
1560 if (view.getViewName() != null)
1562 af.viewport.viewName = view.getViewName();
1563 af.setInitialTabVisible();
1565 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1568 af.viewport.setShowAnnotation(view.getShowAnnotation());
1569 af.viewport.setAbovePIDThreshold(view.getPidSelected());
1571 af.viewport.setColourText(view.getShowColourText());
1573 af.viewport.setConservationSelected(view.getConservationSelected());
1574 af.viewport.setShowJVSuffix(view.getShowFullId());
1575 af.viewport.rightAlignIds = view.getRightAlignIds();
1576 af.viewport.setFont(new java.awt.Font(view.getFontName(),
1577 view.getFontStyle(), view.getFontSize()));
1578 af.alignPanel.fontChanged();
1579 af.viewport.setRenderGaps(view.getRenderGaps());
1580 af.viewport.setWrapAlignment(view.getWrapAlignment());
1581 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1582 af.viewport.setShowAnnotation(view.getShowAnnotation());
1583 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1585 af.viewport.setShowBoxes(view.getShowBoxes());
1587 af.viewport.setShowText(view.getShowText());
1589 af.viewport.textColour = new java.awt.Color(view.getTextCol1());
1590 af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
1591 af.viewport.thresholdTextColour = view.getTextColThreshold();
1593 af.viewport.setStartRes(view.getStartRes());
1594 af.viewport.setStartSeq(view.getStartSeq());
1596 ColourSchemeI cs = null;
1598 if (view.getBgColour() != null)
1600 if (view.getBgColour().startsWith("ucs"))
1602 cs = GetUserColourScheme(jms, view.getBgColour());
1604 else if (view.getBgColour().startsWith("Annotation"))
1606 //int find annotation
1608 i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1610 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1611 equals(view.getAnnotationColours().getAnnotation()))
1613 if (af.viewport.alignment.getAlignmentAnnotation()[i].
1614 getThreshold() == null)
1616 af.viewport.alignment.getAlignmentAnnotation()[i].
1618 new jalview.datamodel.GraphLine(
1619 view.getAnnotationColours().getThreshold(),
1620 "Threshold", java.awt.Color.black)
1625 if (view.getAnnotationColours().getColourScheme().equals(
1628 cs = new AnnotationColourGradient(
1629 af.viewport.alignment.getAlignmentAnnotation()[i],
1630 new java.awt.Color(view.getAnnotationColours().
1632 new java.awt.Color(view.getAnnotationColours().
1634 view.getAnnotationColours().getAboveThreshold());
1636 else if (view.getAnnotationColours().getColourScheme().
1639 cs = new AnnotationColourGradient(
1640 af.viewport.alignment.getAlignmentAnnotation()[i],
1641 GetUserColourScheme(jms, view.getAnnotationColours().
1643 view.getAnnotationColours().getAboveThreshold()
1648 cs = new AnnotationColourGradient(
1649 af.viewport.alignment.getAlignmentAnnotation()[i],
1650 ColourSchemeProperty.getColour(al,
1651 view.getAnnotationColours().
1653 view.getAnnotationColours().getAboveThreshold()
1657 // Also use these settings for all the groups
1658 if (al.getGroups() != null)
1660 for (int g = 0; g < al.getGroups().size(); g++)
1662 jalview.datamodel.SequenceGroup sg
1663 = (jalview.datamodel.SequenceGroup) al.getGroups().
1671 /* if (view.getAnnotationColours().getColourScheme().equals("None"))
1673 sg.cs = new AnnotationColourGradient(
1674 af.viewport.alignment.getAlignmentAnnotation()[i],
1675 new java.awt.Color(view.getAnnotationColours().
1677 new java.awt.Color(view.getAnnotationColours().
1679 view.getAnnotationColours().getAboveThreshold());
1683 sg.cs = new AnnotationColourGradient(
1684 af.viewport.alignment.getAlignmentAnnotation()[i],
1686 view.getAnnotationColours().getAboveThreshold()
1700 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1705 cs.setThreshold(view.getPidThreshold(), true);
1706 cs.setConsensus(af.viewport.hconsensus);
1710 af.viewport.setGlobalColourScheme(cs);
1711 af.viewport.setColourAppliesToAllGroups(false);
1713 if (view.getConservationSelected() && cs != null)
1715 cs.setConservationInc(view.getConsThreshold());
1718 af.changeColour(cs);
1720 af.viewport.setColourAppliesToAllGroups(true);
1722 if (view.getShowSequenceFeatures())
1724 af.viewport.showSequenceFeatures = true;
1727 if (jms.getFeatureSettings() != null)
1729 af.viewport.featuresDisplayed = new Hashtable();
1730 String[] renderOrder = new String[jms.getFeatureSettings().
1732 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
1734 Setting setting = jms.getFeatureSettings().getSetting(fs);
1736 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.
1738 new java.awt.Color(setting.getColour()));
1739 renderOrder[fs] = setting.getType();
1740 if (setting.hasOrder())
1741 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(setting.getType(), setting.getOrder());
1743 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(setting.getType(), fs/jms.getFeatureSettings().getSettingCount());
1744 if (setting.getDisplay())
1746 af.viewport.featuresDisplayed.put(
1747 setting.getType(), new Integer(setting.getColour()));
1750 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder =
1753 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable=new Hashtable();
1754 for (int gs=0;gs<jms.getFeatureSettings().getGroupCount(); gs++)
1756 Group grp = jms.getFeatureSettings().getGroup(gs);
1757 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
1761 if (view.getHiddenColumnsCount() > 0)
1763 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1765 af.viewport.hideColumns(
1766 view.getHiddenColumns(c).getStart(),
1767 view.getHiddenColumns(c).getEnd() //+1
1772 af.setMenusFromViewport(af.viewport);
1774 Desktop.addInternalFrame(af, view.getTitle(),
1775 view.getWidth(), view.getHeight());
1778 ///////////////////////////////////////
1779 if (loadTreesAndStructures && jms.getTreeCount() > 0)
1783 for (int t = 0; t < jms.getTreeCount(); t++)
1786 Tree tree = jms.getTree(t);
1788 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1789 tree.getNewick()), tree.getTitle(),
1790 tree.getWidth(), tree.getHeight(),
1791 tree.getXpos(), tree.getYpos());
1793 tp.fitToWindow.setState(tree.getFitToWindow());
1794 tp.fitToWindow_actionPerformed(null);
1796 if (tree.getFontName() != null)
1798 tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1799 tree.getFontStyle(),
1800 tree.getFontSize()));
1804 tp.setTreeFont(new java.awt.Font(view.getFontName(),
1805 view.getFontStyle(),
1806 tree.getFontSize()));
1809 tp.showPlaceholders(tree.getMarkUnlinked());
1810 tp.showBootstrap(tree.getShowBootstrap());
1811 tp.showDistances(tree.getShowDistances());
1813 tp.treeCanvas.threshold = tree.getThreshold();
1815 if (tree.getCurrentTree())
1817 af.viewport.setCurrentTree(tp.getTree());
1822 catch (Exception ex)
1824 ex.printStackTrace();
1829 if(loadTreesAndStructures)
1831 for (int i = 0; i < JSEQ.length; i++)
1833 if (JSEQ[i].getPdbidsCount() > 0)
1835 Pdbids[] ids = JSEQ[i].getPdbids();
1836 for (int p = 0; p < ids.length; p++)
1838 for (int s = 0; s < ids[p].getStructureStateCount(); s++)
1840 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
1842 jpdb.setFile(loadPDBFile(ids[p].getFile(), ids[p].getId()));
1843 jpdb.setId(ids[p].getId());
1845 int x = ids[p].getStructureState(s).getXpos();
1846 int y = ids[p].getStructureState(s).getYpos();
1847 int width = ids[p].getStructureState(s).getWidth();
1848 int height = ids[p].getStructureState(s).getHeight();
1850 java.awt.Component comp = Desktop.desktop.getComponentAt(x, y);
1852 String pdbFile = loadPDBFile(file, ids[p].getId());
1854 jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
1856 al.getSequenceAt(i)};
1859 (comp.getWidth() != width && comp.getHeight() != height))
1861 String state = ids[p].getStructureState(s).getContent();
1863 StringBuffer newFileLoc = new StringBuffer(state.substring(0,
1864 state.indexOf("\"", state.indexOf("load")) + 1));
1866 newFileLoc.append(jpdb.getFile());
1867 newFileLoc.append(state.substring(
1868 state.indexOf("\"", state.indexOf("load \"") + 6)));
1870 new AppJMol(pdbFile,
1874 newFileLoc.toString(),
1875 new java.awt.Rectangle(x, y, width, height));
1880 StructureSelectionManager.getStructureSelectionManager()
1881 .setMapping(seq, pdbFile,
1882 jalview.io.AppletFormatAdapter.FILE);
1884 ( (AppJMol) comp).addSequence(seq);
1895 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
1896 boolean keepSeqRefs)
1898 jalview.schemabinding.version2.JalviewModel jm
1899 = SaveState(ap, null, null, null);
1904 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
1908 uniqueSetSuffix = "";
1911 viewportsAdded = new Hashtable();
1913 AlignFrame af = LoadFromObject(jm, null, false);
1914 af.alignPanels.clear();
1915 af.closeMenuItem_actionPerformed(true);
1917 /* if(ap.av.alignment.getAlignmentAnnotation()!=null)
1919 for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length; i++)
1921 if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated)
1923 af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
1924 ap.av.alignment.getAlignmentAnnotation()[i];
1929 return af.alignPanel;