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);
534 AnnotationElement ae;
536 for (int a = 0; a < aa[i].annotations.length; a++)
538 if ( (aa[i] == null) || (aa[i].annotations[a] == null))
543 ae = new AnnotationElement();
544 ae.setDescription(aa[i].annotations[a].description);
545 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
546 ae.setValue(aa[i].annotations[a].value);
548 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
551 if (aa[i].annotations[a].colour != java.awt.Color.black)
553 ae.setColour(aa[i].annotations[a].colour.getRGB());
556 an.addAnnotationElement(ae);
559 vamsasSet.addAnnotation(an);
564 if (jal.getGroups() != null)
566 JGroup[] groups = new JGroup[jal.getGroups().size()];
568 for (int i = 0; i < groups.length; i++)
570 groups[i] = new JGroup();
572 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup)
575 groups[i].setStart(sg.getStartRes());
576 groups[i].setEnd(sg.getEndRes());
577 groups[i].setName(sg.getName());
580 if (sg.cs.conservationApplied())
582 groups[i].setConsThreshold(sg.cs.getConservationInc());
584 if (sg.cs instanceof jalview.schemes.UserColourScheme)
586 groups[i].setColour(SetUserColourScheme(sg.cs,
592 groups[i].setColour(ColourSchemeProperty.getColourName(sg.
596 else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
599 ColourSchemeProperty.getColourName(
600 ( (jalview.schemes.AnnotationColourGradient) sg.cs).
603 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
605 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
610 groups[i].setColour(ColourSchemeProperty.getColourName(
614 groups[i].setPidThreshold(sg.cs.getThreshold());
617 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
618 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
619 groups[i].setDisplayText(sg.getDisplayText());
620 groups[i].setColourText(sg.getColourText());
621 groups[i].setTextCol1(sg.textColour.getRGB());
622 groups[i].setTextCol2(sg.textColour2.getRGB());
623 groups[i].setTextColThreshold(sg.thresholdTextColour);
625 for (int s = 0; s < sg.getSize(); s++)
627 jalview.datamodel.Sequence seq =
628 (jalview.datamodel.Sequence) sg.getSequenceAt(s);
629 groups[i].addSeq(seq.hashCode());
633 jms.setJGroup(groups);
636 ///////////SAVE VIEWPORT
637 Viewport view = new Viewport();
638 view.setTitle(ap.alignFrame.getTitle());
639 view.setSequenceSetId(av.getSequenceSetId());
640 view.setViewName(av.viewName);
641 view.setGatheredViews(av.gatherViewsHere);
645 if (ap.av.explodedPosition != null)
647 view.setXpos(av.explodedPosition.x);
648 view.setYpos(av.explodedPosition.y);
649 view.setWidth(av.explodedPosition.width);
650 view.setHeight(av.explodedPosition.height);
654 view.setXpos(ap.alignFrame.getBounds().x);
655 view.setYpos(ap.alignFrame.getBounds().y);
656 view.setWidth(ap.alignFrame.getBounds().width);
657 view.setHeight(ap.alignFrame.getBounds().height);
660 view.setStartRes(av.startRes);
661 view.setStartSeq(av.startSeq);
663 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
665 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
668 else if (av.getGlobalColourScheme() instanceof jalview.schemes.
669 AnnotationColourGradient)
671 jalview.schemes.AnnotationColourGradient acg
672 = (jalview.schemes.AnnotationColourGradient) av.getGlobalColourScheme();
674 AnnotationColours ac = new AnnotationColours();
675 ac.setAboveThreshold(acg.getAboveThreshold());
676 ac.setThreshold(acg.getAnnotationThreshold());
677 ac.setAnnotation(acg.getAnnotation());
678 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
680 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
685 ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
688 ac.setMaxColour(acg.getMaxColour().getRGB());
689 ac.setMinColour(acg.getMinColour().getRGB());
690 view.setAnnotationColours(ac);
691 view.setBgColour("AnnotationColourGradient");
695 view.setBgColour(ColourSchemeProperty.getColourName(
696 av.getGlobalColourScheme()));
699 ColourSchemeI cs = av.getGlobalColourScheme();
703 if (cs.conservationApplied())
705 view.setConsThreshold(cs.getConservationInc());
706 if (cs instanceof jalview.schemes.UserColourScheme)
708 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
712 if (cs instanceof ResidueColourScheme)
714 view.setPidThreshold(cs.getThreshold());
718 view.setConservationSelected(av.getConservationSelected());
719 view.setPidSelected(av.getAbovePIDThreshold());
720 view.setFontName(av.font.getName());
721 view.setFontSize(av.font.getSize());
722 view.setFontStyle(av.font.getStyle());
723 view.setRenderGaps(av.renderGaps);
724 view.setShowAnnotation(av.getShowAnnotation());
725 view.setShowBoxes(av.getShowBoxes());
726 view.setShowColourText(av.getColourText());
727 view.setShowFullId(av.getShowJVSuffix());
728 view.setRightAlignIds(av.rightAlignIds);
729 view.setShowSequenceFeatures(av.showSequenceFeatures);
730 view.setShowText(av.getShowText());
731 view.setWrapAlignment(av.getWrapAlignment());
732 view.setTextCol1(av.textColour.getRGB());
733 view.setTextCol2(av.textColour2.getRGB());
734 view.setTextColThreshold(av.thresholdTextColour);
736 if (av.featuresDisplayed != null)
738 jalview.schemabinding.version2.FeatureSettings fs
739 = new jalview.schemabinding.version2.FeatureSettings();
741 String[] renderOrder =
742 ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
744 Vector settingsAdded = new Vector();
745 for (int ro = 0; ro < renderOrder.length; ro++)
747 Setting setting = new Setting();
748 setting.setType(renderOrder[ro]);
750 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).
755 av.featuresDisplayed.containsKey(renderOrder[ro])
757 float rorder=ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(renderOrder[ro]);
759 setting.setOrder(rorder);
761 fs.addSetting(setting);
762 settingsAdded.addElement(renderOrder[ro]);
765 //Make sure we save none displayed feature settings
767 ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
768 while (en.hasMoreElements())
770 String key = en.nextElement().toString();
771 if (settingsAdded.contains(key))
776 Setting setting = new Setting();
777 setting.setType(key);
779 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
782 setting.setDisplay(false);
783 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(key);
786 setting.setOrder(rorder);
788 fs.addSetting(setting);
789 settingsAdded.addElement(key);
791 en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
792 Vector groupsAdded=new Vector();
793 while (en.hasMoreElements())
795 String grp = en.nextElement().toString();
796 if (groupsAdded.contains(grp))
800 Group g = new Group();
802 g.setDisplay(((Boolean)ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.get(grp)).booleanValue());
804 groupsAdded.addElement(grp);
806 jms.setFeatureSettings(fs);
810 if (av.hasHiddenColumns)
812 for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
814 int[] region = (int[]) av.getColumnSelection().getHiddenColumns().
816 HiddenColumns hc = new HiddenColumns();
817 hc.setStart(region[0]);
818 hc.setEnd(region[1]);
819 view.addHiddenColumns(hc);
823 jms.addViewport(view);
825 object.setJalviewModelSequence(jms);
826 object.getVamsasModel().addSequenceSet(vamsasSet);
830 //We may not want to right the object to disk,
831 //eg we can copy the alignViewport to a new view object
832 //using save and then load
835 if (!fileName.endsWith(".xml"))
837 fileName = fileName + ".xml";
840 JarEntry entry = new JarEntry(fileName);
841 jout.putNextEntry(entry);
847 ex.printStackTrace();
853 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
854 Vector userColours, JalviewModelSequence jms)
857 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)
860 if (!userColours.contains(ucs))
862 userColours.add(ucs);
864 java.awt.Color[] colours = ucs.getColours();
865 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.
866 version2.UserColours();
867 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.
868 schemabinding.version2.UserColourScheme();
870 for (int i = 0; i < colours.length; i++)
872 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.
874 col.setName(ResidueProperties.aa[i]);
875 col.setRGB(jalview.util.Format.getHexString(colours[i]));
876 jbucs.addColour(col);
878 if (ucs.getLowerCaseColours() != null)
880 colours = ucs.getLowerCaseColours();
881 for (int i = 0; i < colours.length; i++)
883 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.
885 col.setName(ResidueProperties.aa[i].toLowerCase());
886 col.setRGB(jalview.util.Format.getHexString(colours[i]));
887 jbucs.addColour(col);
891 id = "ucs" + userColours.indexOf(ucs);
893 uc.setUserColourScheme(jbucs);
894 jms.addUserColours(uc);
900 jalview.schemes.UserColourScheme GetUserColourScheme(
901 JalviewModelSequence jms, String id)
903 UserColours[] uc = jms.getUserColours();
904 UserColours colours = null;
906 for (int i = 0; i < uc.length; i++)
908 if (uc[i].getId().equals(id))
916 java.awt.Color[] newColours = new java.awt.Color[24];
918 for (int i = 0; i < 24; i++)
920 newColours[i] = new java.awt.Color(Integer.parseInt(
921 colours.getUserColourScheme().getColour(i).getRGB(), 16));
924 jalview.schemes.UserColourScheme ucs =
925 new jalview.schemes.UserColourScheme(newColours);
927 if (colours.getUserColourScheme().getColourCount() > 24)
929 newColours = new java.awt.Color[23];
930 for (int i = 0; i < 23; i++)
932 newColours[i] = new java.awt.Color(Integer.parseInt(
933 colours.getUserColourScheme().getColour(i + 24).getRGB(), 16));
935 ucs.setLowerCaseColours(newColours);
944 * @param file DOCUMENT ME!
946 public AlignFrame LoadJalviewAlign(final String file)
948 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
950 jalview.gui.AlignFrame af = null;
952 seqRefIds = new Hashtable();
953 viewportsAdded = new Hashtable();
955 Hashtable gatherToThisFrame = new Hashtable();
959 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
962 if (file.startsWith("http://"))
967 JarInputStream jin = null;
968 JarEntry jarentry = null;
975 jin = new JarInputStream(url.openStream());
979 jin = new JarInputStream(new FileInputStream(file));
982 for (int i = 0; i < entryCount; i++)
984 jarentry = jin.getNextJarEntry();
987 if (jarentry != null && jarentry.getName().endsWith(".xml"))
989 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
990 JalviewModel object = new JalviewModel();
992 Unmarshaller unmar = new Unmarshaller(object);
993 unmar.setValidation(false);
994 object = (JalviewModel) unmar.unmarshal(in);
996 af = LoadFromObject(object, file, true);
997 if (af.viewport.gatherViewsHere)
999 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
1003 else if (jarentry != null)
1005 //Some other file here.
1009 while (jarentry != null);
1011 catch (java.net.UnknownHostException ex)
1013 ex.printStackTrace();
1014 System.err.println("Couldn't locate Jalview XML file : " +
1017 javax.swing.SwingUtilities.invokeLater(new Runnable()
1021 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1022 "Couldn't locate " + file,
1024 JOptionPane.WARNING_MESSAGE);
1028 catch (Exception ex)
1030 //Is Version 1 Jar file?
1031 af = new Jalview2XML_V1().LoadJalviewAlign(file);
1035 System.out.println("Successfully loaded archive file");
1038 ex.printStackTrace();
1040 System.err.println("Exception whilst loading jalview XML file : " +
1042 javax.swing.SwingUtilities.invokeLater(new Runnable()
1047 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1048 "Error loading " + file,
1049 "Error loading Jalview file",
1050 JOptionPane.WARNING_MESSAGE);
1055 if (Desktop.instance != null)
1057 Desktop.instance.stopLoading();
1060 Enumeration en = gatherToThisFrame.elements();
1061 while(en.hasMoreElements())
1063 Desktop.instance.gatherViews(
1064 (AlignFrame) en.nextElement());
1070 Hashtable alreadyLoadedPDB;
1071 String loadPDBFile(String file, String pdbId)
1073 if (alreadyLoadedPDB == null)
1074 alreadyLoadedPDB = new Hashtable();
1076 if (alreadyLoadedPDB.containsKey(pdbId))
1077 return alreadyLoadedPDB.get(pdbId).toString();
1081 JarInputStream jin = null;
1083 if (file.startsWith("http://"))
1085 jin = new JarInputStream(new URL(file).openStream());
1089 jin = new JarInputStream(new FileInputStream(file));
1092 JarEntry entry = null;
1095 entry = jin.getNextJarEntry();
1097 while (!entry.getName().equals(pdbId));
1099 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1100 File outFile = File.createTempFile("jalview_pdb", ".txt");
1101 outFile.deleteOnExit();
1102 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1105 while ( (data = in.readLine()) != null)
1111 alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
1112 return outFile.getAbsolutePath();
1115 catch (Exception ex)
1117 ex.printStackTrace();
1123 AlignFrame LoadFromObject(JalviewModel object,
1125 boolean loadTreesAndStructures)
1127 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1128 Sequence[] vamsasSeq = vamsasSet.getSequence();
1130 JalviewModelSequence jms = object.getJalviewModelSequence();
1132 Viewport view = jms.getViewport(0);
1134 //////////////////////////////////
1137 Vector hiddenSeqs = null;
1138 jalview.datamodel.Sequence jseq;
1140 ArrayList tmpseqs = new ArrayList();
1142 boolean multipleView = false;
1144 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1145 for (int i = 0; i < JSEQ.length; i++)
1147 String seqId = JSEQ[i].getId() + "";
1149 if (seqRefIds.get(seqId) != null)
1151 tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1152 multipleView = true;
1156 jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
1157 vamsasSeq[i].getSequence());
1158 jseq.setDescription(vamsasSeq[i].getDescription());
1159 jseq.setStart(JSEQ[i].getStart());
1160 jseq.setEnd(JSEQ[i].getEnd());
1161 seqRefIds.put(vamsasSeq[i].getId(), jseq);
1165 if (JSEQ[i].getHidden())
1167 if (hiddenSeqs == null)
1169 hiddenSeqs = new Vector();
1172 hiddenSeqs.addElement(
1173 (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1178 ///SequenceFeatures are added to the DatasetSequence,
1179 // so we must create the dataset before loading features
1180 /////////////////////////////////
1183 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
1186 tmpseqs.toArray(orderedSeqs);
1188 jalview.datamodel.Alignment al =
1189 new jalview.datamodel.Alignment(orderedSeqs);
1191 al.setDataset(null);
1192 /////////////////////////////////
1195 Hashtable pdbloaded = new Hashtable();
1199 for (int i = 0; i < vamsasSeq.length; i++)
1201 if (JSEQ[i].getFeaturesCount() > 0)
1203 Features[] features = JSEQ[i].getFeatures();
1204 for (int f = 0; f < features.length; f++)
1206 jalview.datamodel.SequenceFeature sf
1207 = new jalview.datamodel.SequenceFeature(features[f].getType(),
1208 features[f].getDescription(), features[f].getStatus(),
1209 features[f].getBegin(), features[f].getEnd(),
1210 features[f].getFeatureGroup());
1212 sf.setScore(features[f].getScore());
1213 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1215 OtherData keyValue = features[f].getOtherData(od);
1216 if (keyValue.getKey().startsWith("LINK"))
1218 sf.addLink(keyValue.getValue());
1222 sf.setValue(keyValue.getKey(), keyValue.getValue());
1227 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1231 if (JSEQ[i].getPdbidsCount() > 0)
1233 Pdbids[] ids = JSEQ[i].getPdbids();
1234 for (int p = 0; p < ids.length; p++)
1236 jalview.datamodel.PDBEntry entry = new jalview.datamodel.
1238 entry.setId(ids[p].getId());
1239 entry.setType(ids[p].getType());
1240 if (ids[p].getFile() != null)
1242 if (!pdbloaded.containsKey(ids[p].getFile()))
1244 entry.setFile(loadPDBFile(file, ids[p].getId()));
1248 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1252 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1255 if (vamsasSeq[i].getDBRefCount() > 0)
1257 for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
1259 jalview.datamodel.DBRefEntry entry =
1260 new jalview.datamodel.DBRefEntry(
1261 vamsasSeq[i].getDBRef(d).getSource(),
1262 vamsasSeq[i].getDBRef(d).getVersion(),
1263 vamsasSeq[i].getDBRef(d).getAccessionId()
1265 al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1272 /////////////////////////////////
1273 //////////////////////////////////
1275 boolean hideQuality = true,
1276 hideConservation = true,
1277 hideConsensus = true;
1279 if (vamsasSet.getAnnotationCount() > 0)
1281 Annotation[] an = vamsasSet.getAnnotation();
1283 for (int i = 0; i < an.length; i++)
1285 if (an[i].getLabel().equals("Quality"))
1287 hideQuality = false;
1290 else if (an[i].getLabel().equals("Conservation"))
1292 hideConservation = false;
1295 else if (an[i].getLabel().equals("Consensus"))
1297 hideConsensus = false;
1301 if (an[i].getId() != null
1302 && annotationIds.containsKey(an[i].getId()))
1305 (jalview.datamodel.AlignmentAnnotation) annotationIds.get(an[i].
1312 AnnotationElement[] ae = an[i].getAnnotationElement();
1313 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[
1316 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
1318 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].
1319 getDisplayCharacter(),
1320 ae[aa].getDescription(),
1321 ae[aa].getSecondaryStructure().length() == 0 ? ' ' :
1322 ae[aa].getSecondaryStructure().charAt(0),
1324 anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa].
1328 jalview.datamodel.AlignmentAnnotation jaa = null;
1330 if (an[i].getGraph())
1332 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1333 an[i].getDescription(), anot, 0, 0,
1334 an[i].getGraphType());
1336 jaa.graphGroup = an[i].getGraphGroup();
1338 if (an[i].getThresholdLine() != null)
1340 jaa.setThreshold(new jalview.datamodel.GraphLine(
1341 an[i].getThresholdLine().getValue(),
1342 an[i].getThresholdLine().getLabel(),
1343 new java.awt.Color(an[i].getThresholdLine().getColour()))
1351 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1352 an[i].getDescription(), anot);
1355 if (an[i].getId() != null)
1357 annotationIds.put(an[i].getId(), jaa);
1358 jaa.annotationId = an[i].getId();
1361 if (an[i].getSequenceRef() != null)
1363 jaa.createSequenceMapping(
1364 al.findName(an[i].getSequenceRef()), 1, true
1366 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1369 al.addAnnotation(jaa);
1373 /////////////////////////
1375 if (jms.getJGroupCount() > 0)
1377 JGroup[] groups = jms.getJGroup();
1379 for (int i = 0; i < groups.length; i++)
1381 ColourSchemeI cs = null;
1383 if (groups[i].getColour() != null)
1385 if (groups[i].getColour().startsWith("ucs"))
1387 cs = GetUserColourScheme(jms, groups[i].getColour());
1391 cs = ColourSchemeProperty.getColour(al,
1392 groups[i].getColour());
1397 cs.setThreshold(groups[i].getPidThreshold(), true);
1401 Vector seqs = new Vector();
1403 for (int s = 0; s < groups[i].getSeqCount(); s++)
1405 String seqId = groups[i].getSeq(s) + "";
1406 jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI)
1407 seqRefIds.get(seqId);
1411 seqs.addElement(ts);
1415 if (seqs.size() < 1)
1420 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.
1422 groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1423 groups[i].getDisplayText(), groups[i].getColourText(),
1424 groups[i].getStart(), groups[i].getEnd());
1426 sg.setOutlineColour(new java.awt.Color(
1427 groups[i].getOutlineColour()));
1429 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
1430 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
1431 sg.thresholdTextColour = groups[i].getTextColThreshold();
1433 if (groups[i].getConsThreshold() != 0)
1435 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
1437 ResidueProperties.propHash, 3, sg.getSequences(null), 0,
1440 c.verdict(false, 25);
1441 sg.cs.setConservation(c);
1448 /////////////////////////////////
1451 AlignFrame af = new AlignFrame(al,
1455 af.setFileName(file, "Jalview");
1457 for (int i = 0; i < JSEQ.length; i++)
1459 af.viewport.setSequenceColour(
1460 af.viewport.alignment.getSequenceAt(i),
1462 JSEQ[i].getColour()));
1465 //If we just load in the same jar file again, the sequenceSetId
1466 //will be the same, and we end up with multiple references
1467 //to the same sequenceSet. We must modify this id on load
1468 //so that each load of the file gives a unique id
1469 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
1471 af.viewport.gatherViewsHere = view.getGatheredViews();
1473 if (view.getSequenceSetId() != null)
1475 jalview.gui.AlignViewport av =
1476 (jalview.gui.AlignViewport)
1477 viewportsAdded.get(uniqueSeqSetId);
1479 af.viewport.sequenceSetID = uniqueSeqSetId;
1483 af.viewport.historyList = av.historyList;
1484 af.viewport.redoList = av.redoList;
1488 viewportsAdded.put(uniqueSeqSetId, af.viewport);
1491 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1493 if (hiddenSeqs != null)
1495 for (int s = 0; s < JSEQ.length; s++)
1497 jalview.datamodel.SequenceGroup hidden =
1498 new jalview.datamodel.SequenceGroup();
1500 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
1503 al.getSequenceAt(JSEQ[s].getHiddenSequences(r))
1507 af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
1510 jalview.datamodel.SequenceI[] hseqs = new
1511 jalview.datamodel.SequenceI[hiddenSeqs.size()];
1513 for (int s = 0; s < hiddenSeqs.size(); s++)
1515 hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
1518 af.viewport.hideSequence(hseqs);
1522 if ( (hideConsensus || hideQuality || hideConservation)
1523 && al.getAlignmentAnnotation() != null)
1525 int hSize = al.getAlignmentAnnotation().length;
1526 for (int h = 0; h < hSize; h++)
1530 al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1533 al.getAlignmentAnnotation()[h].label.equals("Quality"))
1535 (hideConservation &&
1536 al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1538 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1543 af.alignPanel.adjustAnnotationHeight();
1546 if (view.getViewName() != null)
1548 af.viewport.viewName = view.getViewName();
1549 af.setInitialTabVisible();
1551 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1554 af.viewport.setShowAnnotation(view.getShowAnnotation());
1555 af.viewport.setAbovePIDThreshold(view.getPidSelected());
1557 af.viewport.setColourText(view.getShowColourText());
1559 af.viewport.setConservationSelected(view.getConservationSelected());
1560 af.viewport.setShowJVSuffix(view.getShowFullId());
1561 af.viewport.rightAlignIds = view.getRightAlignIds();
1562 af.viewport.setFont(new java.awt.Font(view.getFontName(),
1563 view.getFontStyle(), view.getFontSize()));
1564 af.alignPanel.fontChanged();
1565 af.viewport.setRenderGaps(view.getRenderGaps());
1566 af.viewport.setWrapAlignment(view.getWrapAlignment());
1567 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1568 af.viewport.setShowAnnotation(view.getShowAnnotation());
1569 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1571 af.viewport.setShowBoxes(view.getShowBoxes());
1573 af.viewport.setShowText(view.getShowText());
1575 af.viewport.textColour = new java.awt.Color(view.getTextCol1());
1576 af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
1577 af.viewport.thresholdTextColour = view.getTextColThreshold();
1579 af.viewport.setStartRes(view.getStartRes());
1580 af.viewport.setStartSeq(view.getStartSeq());
1582 ColourSchemeI cs = null;
1584 if (view.getBgColour() != null)
1586 if (view.getBgColour().startsWith("ucs"))
1588 cs = GetUserColourScheme(jms, view.getBgColour());
1590 else if (view.getBgColour().startsWith("Annotation"))
1592 //int find annotation
1594 i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1596 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1597 equals(view.getAnnotationColours().getAnnotation()))
1599 if (af.viewport.alignment.getAlignmentAnnotation()[i].
1600 getThreshold() == null)
1602 af.viewport.alignment.getAlignmentAnnotation()[i].
1604 new jalview.datamodel.GraphLine(
1605 view.getAnnotationColours().getThreshold(),
1606 "Threshold", java.awt.Color.black)
1611 if (view.getAnnotationColours().getColourScheme().equals(
1614 cs = new AnnotationColourGradient(
1615 af.viewport.alignment.getAlignmentAnnotation()[i],
1616 new java.awt.Color(view.getAnnotationColours().
1618 new java.awt.Color(view.getAnnotationColours().
1620 view.getAnnotationColours().getAboveThreshold());
1622 else if (view.getAnnotationColours().getColourScheme().
1625 cs = new AnnotationColourGradient(
1626 af.viewport.alignment.getAlignmentAnnotation()[i],
1627 GetUserColourScheme(jms, view.getAnnotationColours().
1629 view.getAnnotationColours().getAboveThreshold()
1634 cs = new AnnotationColourGradient(
1635 af.viewport.alignment.getAlignmentAnnotation()[i],
1636 ColourSchemeProperty.getColour(al,
1637 view.getAnnotationColours().
1639 view.getAnnotationColours().getAboveThreshold()
1643 // Also use these settings for all the groups
1644 if (al.getGroups() != null)
1646 for (int g = 0; g < al.getGroups().size(); g++)
1648 jalview.datamodel.SequenceGroup sg
1649 = (jalview.datamodel.SequenceGroup) al.getGroups().
1657 /* if (view.getAnnotationColours().getColourScheme().equals("None"))
1659 sg.cs = new AnnotationColourGradient(
1660 af.viewport.alignment.getAlignmentAnnotation()[i],
1661 new java.awt.Color(view.getAnnotationColours().
1663 new java.awt.Color(view.getAnnotationColours().
1665 view.getAnnotationColours().getAboveThreshold());
1669 sg.cs = new AnnotationColourGradient(
1670 af.viewport.alignment.getAlignmentAnnotation()[i],
1672 view.getAnnotationColours().getAboveThreshold()
1686 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1691 cs.setThreshold(view.getPidThreshold(), true);
1692 cs.setConsensus(af.viewport.hconsensus);
1696 af.viewport.setGlobalColourScheme(cs);
1697 af.viewport.setColourAppliesToAllGroups(false);
1699 if (view.getConservationSelected() && cs != null)
1701 cs.setConservationInc(view.getConsThreshold());
1704 af.changeColour(cs);
1706 af.viewport.setColourAppliesToAllGroups(true);
1708 if (view.getShowSequenceFeatures())
1710 af.viewport.showSequenceFeatures = true;
1713 if (jms.getFeatureSettings() != null)
1715 af.viewport.featuresDisplayed = new Hashtable();
1716 String[] renderOrder = new String[jms.getFeatureSettings().
1718 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
1720 Setting setting = jms.getFeatureSettings().getSetting(fs);
1722 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.
1724 new java.awt.Color(setting.getColour()));
1725 renderOrder[fs] = setting.getType();
1726 if (setting.hasOrder())
1727 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(setting.getType(), setting.getOrder());
1729 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(setting.getType(), fs/jms.getFeatureSettings().getSettingCount());
1730 if (setting.getDisplay())
1732 af.viewport.featuresDisplayed.put(
1733 setting.getType(), new Integer(setting.getColour()));
1736 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder =
1739 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable=new Hashtable();
1740 for (int gs=0;gs<jms.getFeatureSettings().getGroupCount(); gs++)
1742 Group grp = jms.getFeatureSettings().getGroup(gs);
1743 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
1747 if (view.getHiddenColumnsCount() > 0)
1749 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1751 af.viewport.hideColumns(
1752 view.getHiddenColumns(c).getStart(),
1753 view.getHiddenColumns(c).getEnd() //+1
1758 af.setMenusFromViewport(af.viewport);
1760 Desktop.addInternalFrame(af, view.getTitle(),
1761 view.getWidth(), view.getHeight());
1764 ///////////////////////////////////////
1765 if (loadTreesAndStructures && jms.getTreeCount() > 0)
1769 for (int t = 0; t < jms.getTreeCount(); t++)
1772 Tree tree = jms.getTree(t);
1774 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1775 tree.getNewick()), tree.getTitle(),
1776 tree.getWidth(), tree.getHeight(),
1777 tree.getXpos(), tree.getYpos());
1779 tp.fitToWindow.setState(tree.getFitToWindow());
1780 tp.fitToWindow_actionPerformed(null);
1782 if (tree.getFontName() != null)
1784 tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1785 tree.getFontStyle(),
1786 tree.getFontSize()));
1790 tp.setTreeFont(new java.awt.Font(view.getFontName(),
1791 view.getFontStyle(),
1792 tree.getFontSize()));
1795 tp.showPlaceholders(tree.getMarkUnlinked());
1796 tp.showBootstrap(tree.getShowBootstrap());
1797 tp.showDistances(tree.getShowDistances());
1799 tp.treeCanvas.threshold = tree.getThreshold();
1801 if (tree.getCurrentTree())
1803 af.viewport.setCurrentTree(tp.getTree());
1808 catch (Exception ex)
1810 ex.printStackTrace();
1815 if(loadTreesAndStructures)
1817 for (int i = 0; i < JSEQ.length; i++)
1819 if (JSEQ[i].getPdbidsCount() > 0)
1821 Pdbids[] ids = JSEQ[i].getPdbids();
1822 for (int p = 0; p < ids.length; p++)
1824 for (int s = 0; s < ids[p].getStructureStateCount(); s++)
1826 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
1828 jpdb.setFile(loadPDBFile(ids[p].getFile(), ids[p].getId()));
1829 jpdb.setId(ids[p].getId());
1831 int x = ids[p].getStructureState(s).getXpos();
1832 int y = ids[p].getStructureState(s).getYpos();
1833 int width = ids[p].getStructureState(s).getWidth();
1834 int height = ids[p].getStructureState(s).getHeight();
1836 java.awt.Component comp = Desktop.desktop.getComponentAt(x, y);
1838 String pdbFile = loadPDBFile(file, ids[p].getId());
1840 jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
1842 al.getSequenceAt(i)};
1845 (comp.getWidth() != width && comp.getHeight() != height))
1847 String state = ids[p].getStructureState(s).getContent();
1849 StringBuffer newFileLoc = new StringBuffer(state.substring(0,
1850 state.indexOf("\"", state.indexOf("load")) + 1));
1852 newFileLoc.append(jpdb.getFile());
1853 newFileLoc.append(state.substring(
1854 state.indexOf("\"", state.indexOf("load \"") + 6)));
1856 new AppJMol(pdbFile,
1860 newFileLoc.toString(),
1861 new java.awt.Rectangle(x, y, width, height));
1866 StructureSelectionManager.getStructureSelectionManager()
1867 .setMapping(seq, pdbFile,
1868 jalview.io.AppletFormatAdapter.FILE);
1870 ( (AppJMol) comp).addSequence(seq);
1881 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
1882 boolean keepSeqRefs)
1884 jalview.schemabinding.version2.JalviewModel jm
1885 = SaveState(ap, null, null, null);
1890 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
1894 uniqueSetSuffix = "";
1897 viewportsAdded = new Hashtable();
1899 AlignFrame af = LoadFromObject(jm, null, false);
1900 af.alignPanels.clear();
1901 af.closeMenuItem_actionPerformed(true);
1903 /* if(ap.av.alignment.getAlignmentAnnotation()!=null)
1905 for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length; i++)
1907 if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated)
1909 af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
1910 ap.av.alignment.getAlignmentAnnotation()[i];
1915 return af.alignPanel;