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.*;
30 import uk.ac.vamsas.objects.utils.MapList;
31 import jalview.datamodel.Alignment;
32 import jalview.datamodel.AlignmentI;
33 import jalview.datamodel.SequenceI;
34 import jalview.schemabinding.version2.*;
35 import jalview.schemes.*;
36 import jalview.structure.StructureSelectionManager;
39 * Write out the current jalview desktop state
40 * as a Jalview XML stream.
42 * Note: the vamsas objects referred to here are primitive
43 * versions of the VAMSAS project schema elements - they are
44 * not the same and most likely never will be :)
49 public class Jalview2XML
52 * create/return unique hash string for sq
54 * @return new or existing unique string for sq
56 String seqHash(SequenceI sq)
62 if (seqsToIds.containsKey(sq))
64 return (String) seqsToIds.get(sq);
66 // create sequential key
67 String key = "sq"+(seqsToIds.size()+1);
68 seqsToIds.put(sq, key);
81 seqsToIds = new IdentityHashMap();
85 seqRefIds = new Hashtable();
88 java.util.IdentityHashMap seqsToIds = null; // SequenceI->key resolution
89 java.util.Hashtable seqRefIds = null; // key->SequenceI resolution
91 Vector frefedSequence = null;
92 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
96 public Jalview2XML(boolean raiseGUI)
98 this.raiseGUI = raiseGUI;
101 public void resolveFrefedSequences()
103 if (frefedSequence.size() > 0)
105 int r = 0, rSize = frefedSequence.size();
108 Object[] ref = (Object[]) frefedSequence.elementAt(r);
111 String sref = (String) ref[0];
112 if (seqRefIds.containsKey(sref))
114 if (ref[1] instanceof jalview.datamodel.Mapping)
116 SequenceI seq = (SequenceI) seqRefIds.get(sref);
117 while (seq.getDatasetSequence() != null)
119 seq = seq.getDatasetSequence();
121 ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
126 .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
127 + ref[1].getClass() + " type objects.");
129 frefedSequence.remove(r);
139 frefedSequence.remove(r);
147 * This maintains a list of viewports, the key being the
148 * seqSetId. Important to set historyItem and redoList
151 Hashtable viewportsAdded;
153 Hashtable annotationIds = new Hashtable();
155 String uniqueSetSuffix = "";
158 * List of pdbfiles added to Jar
160 Vector pdbfiles = null;
162 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
163 public void SaveState(File statefile)
165 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
174 FileOutputStream fos = new FileOutputStream(statefile);
175 JarOutputStream jout = new JarOutputStream(fos);
177 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
178 ////////////////////////////////////////////////////
179 //NOTE ALSO new PrintWriter must be used for each new JarEntry
180 PrintWriter out = null;
182 Vector shortNames = new Vector();
185 for (int i = frames.length - 1; i > -1; i--)
187 if (frames[i] instanceof AlignFrame)
189 AlignFrame af = (AlignFrame) frames[i];
191 String shortName = af.getTitle();
193 if (shortName.indexOf(File.separatorChar) > -1)
195 shortName = shortName.substring(shortName
196 .lastIndexOf(File.separatorChar) + 1);
201 while (shortNames.contains(shortName))
203 if (shortName.endsWith("_" + (count - 1)))
205 shortName = shortName
206 .substring(0, shortName.lastIndexOf("_"));
209 shortName = shortName.concat("_" + count);
213 shortNames.addElement(shortName);
215 if (!shortName.endsWith(".xml"))
217 shortName = shortName + ".xml";
220 int ap, apSize = af.alignPanels.size();
221 for (ap = 0; ap < apSize; ap++)
223 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
225 String fileName = apSize == 1 ? shortName : ap + shortName;
226 if (!fileName.endsWith(".xml"))
228 fileName = fileName + ".xml";
231 JarEntry entry = new JarEntry(fileName);
232 jout.putNextEntry(entry);
233 out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8"));
234 SaveState(apanel, fileName,
239 try { out.flush(); } catch (Exception foo) {};
241 try { jout.flush(); } catch (Exception foo) {};
243 } catch (Exception ex)
245 //TODO: inform user of the problem - they need to know if their data was not saved !
246 ex.printStackTrace();
250 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
251 public boolean SaveAlignment(AlignFrame af, String jarFile,
256 int ap, apSize = af.alignPanels.size();
257 FileOutputStream fos = new FileOutputStream(jarFile);
258 JarOutputStream jout = new JarOutputStream(fos);
259 for (ap = 0; ap < apSize; ap++)
261 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
263 String jfileName = apSize == 1 ? fileName : fileName + ap;
264 if (!jfileName.endsWith(".xml"))
266 jfileName = jfileName + ".xml";
268 JarEntry entry = new JarEntry(jfileName);
269 jout.putNextEntry(entry);
270 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
272 SaveState(apanel, jfileName, jout, out);
273 try { out.flush(); } catch (Exception foo) {};
277 try { jout.flush(); } catch (Exception foo) {};
280 } catch (Exception ex)
282 ex.printStackTrace();
290 * @param af DOCUMENT ME!
291 * @param timeStamp DOCUMENT ME!
292 * @param fileName DOCUMENT ME!
293 * @param jout DOCUMENT ME!
294 * @param out DOCUMENT ME!
296 public JalviewModel SaveState(AlignmentPanel ap, String fileName,
297 JarOutputStream jout, PrintWriter out)
301 Vector userColours = new Vector();
303 AlignViewport av = ap.av;
305 JalviewModel object = new JalviewModel();
306 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
308 object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
309 object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
311 jalview.datamodel.AlignmentI jal = av.alignment;
313 if (av.hasHiddenRows)
315 jal = jal.getHiddenSequences().getFullAlignment();
318 SequenceSet vamsasSet = new SequenceSet();
320 JalviewModelSequence jms = new JalviewModelSequence();
322 vamsasSet.setGapChar(jal.getGapCharacter() + "");
324 if (jal.getDataset() != null)
326 // dataset id is the dataset's hashcode
327 vamsasSet.setDatasetId(jal.getDataset().hashCode() + "");
329 if (jal.getProperties() != null)
331 Enumeration en = jal.getProperties().keys();
332 while (en.hasMoreElements())
334 String key = en.nextElement().toString();
335 SequenceSetProperties ssp = new SequenceSetProperties();
337 ssp.setValue(jal.getProperties().get(key).toString());
338 vamsasSet.addSequenceSetProperties(ssp);
346 jalview.datamodel.SequenceI jds;
347 for (int i = 0; i < jal.getHeight(); i++)
349 jds = jal.getSequenceAt(i);
352 if (seqRefIds.get(id) != null)
354 // This happens for two reasons: 1. multiple views are being serialised. 2. the hashCode has collided with another sequence's code. This DOES HAPPEN! (PF00072.15.stk does this)
355 // JBPNote: Uncomment to debug writing out of files that do not read back in due to ArrayOutOfBoundExceptions.
356 //System.err.println("vamsasSeq backref: "+id+"");
357 //System.err.println(jds.getName()+" "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
358 //System.err.println("Hashcode: "+seqHash(jds));
359 //SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
360 //System.err.println(rsq.getName()+" "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
361 //System.err.println("Hashcode: "+seqHash(rsq));
365 vamsasSeq = createVamsasSequence(id, jds);
366 vamsasSet.addSequence(vamsasSeq);
367 seqRefIds.put(id, jds);
371 jseq.setStart(jds.getStart());
372 jseq.setEnd(jds.getEnd());
373 jseq.setColour(av.getSequenceColour(jds).getRGB());
375 jseq.setId(id); // jseq id should be a string not a number
377 if (av.hasHiddenRows)
379 jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
381 if (av.hiddenRepSequences != null
382 && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
384 jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences
385 .get(jal.getSequenceAt(i))).getSequencesInOrder(jal);
387 for (int h = 0; h < reps.length; h++)
389 if (reps[h] != jal.getSequenceAt(i))
391 jseq.addHiddenSequences(jal.findIndex(reps[h]));
397 if (jds.getDatasetSequence().getSequenceFeatures() != null)
399 jalview.datamodel.SequenceFeature[] sf = jds.getDatasetSequence()
400 .getSequenceFeatures();
402 while (index < sf.length)
404 Features features = new Features();
406 features.setBegin(sf[index].getBegin());
407 features.setEnd(sf[index].getEnd());
408 features.setDescription(sf[index].getDescription());
409 features.setType(sf[index].getType());
410 features.setFeatureGroup(sf[index].getFeatureGroup());
411 features.setScore(sf[index].getScore());
412 if (sf[index].links != null)
414 for (int l = 0; l < sf[index].links.size(); l++)
416 OtherData keyValue = new OtherData();
417 keyValue.setKey("LINK_" + l);
418 keyValue.setValue(sf[index].links.elementAt(l).toString());
419 features.addOtherData(keyValue);
422 if (sf[index].otherDetails != null)
425 Enumeration keys = sf[index].otherDetails.keys();
426 while (keys.hasMoreElements())
428 key = keys.nextElement().toString();
429 OtherData keyValue = new OtherData();
430 keyValue.setKey(key);
431 keyValue.setValue(sf[index].otherDetails.get(key).toString());
432 features.addOtherData(keyValue);
436 jseq.addFeatures(features);
441 if (jds.getDatasetSequence().getPDBId() != null)
443 Enumeration en = jds.getDatasetSequence().getPDBId().elements();
444 while (en.hasMoreElements())
446 Pdbids pdb = new Pdbids();
447 jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
450 pdb.setId(entry.getId());
451 pdb.setType(entry.getType());
454 //This must have been loaded, is it still visible?
455 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
456 for (int f = frames.length - 1; f > -1; f--)
458 if (frames[f] instanceof AppJmol)
460 jmol = (AppJmol) frames[f];
461 if (!jmol.pdbentry.getId().equals(entry.getId()))
464 StructureState state = new StructureState();
465 state.setVisible(true);
466 state.setXpos(jmol.getX());
467 state.setYpos(jmol.getY());
468 state.setWidth(jmol.getWidth());
469 state.setHeight(jmol.getHeight());
471 String statestring = jmol.viewer.getStateInfo();
474 state.setContent(statestring.replaceAll("\n", ""));
476 for (int s = 0; s < jmol.sequence.length; s++)
478 if (jal.findIndex(jmol.sequence[s]) > -1)
480 pdb.addStructureState(state);
486 if (entry.getFile() != null)
488 pdb.setFile(entry.getFile());
489 if (pdbfiles == null)
491 pdbfiles = new Vector();
494 if (!pdbfiles.contains(entry.getId()))
496 pdbfiles.addElement(entry.getId());
499 File file = new File(entry.getFile());
500 if (file.exists() && jout != null)
502 byte[] data = new byte[(int) file.length()];
503 jout.putNextEntry(new JarEntry(entry.getId()));
504 DataInputStream dis = new DataInputStream(
505 new FileInputStream(file));
508 DataOutputStream dout = new DataOutputStream(jout);
509 dout.write(data, 0, data.length);
513 } catch (Exception ex)
515 ex.printStackTrace();
521 if (entry.getProperty() != null)
523 PdbentryItem item = new PdbentryItem();
524 Hashtable properties = entry.getProperty();
525 Enumeration en2 = properties.keys();
526 while (en2.hasMoreElements())
528 Property prop = new Property();
529 String key = en2.nextElement().toString();
531 prop.setValue(properties.get(key).toString());
532 item.addProperty(prop);
534 pdb.addPdbentryItem(item);
544 if (av.hasHiddenRows)
549 if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
551 jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
552 for (int i = 0; i < jac.length; i++)
554 AlcodonFrame alc = new AlcodonFrame();
555 vamsasSet.addAlcodonFrame(alc);
556 for (int p = 0; p < jac[i].aaWidth; p++)
558 Alcodon cmap = new Alcodon();
559 cmap.setPos1(jac[i].codons[p][0]);
560 cmap.setPos2(jac[i].codons[p][1]);
561 cmap.setPos3(jac[i].codons[p][2]);
562 alc.addAlcodon(cmap);
564 if (jac[i].getProtMappings() != null
565 && jac[i].getProtMappings().length > 0)
567 SequenceI[] dnas = jac[i].getdnaSeqs();
568 jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings();
569 for (int m = 0; m < pmaps.length; m++)
571 AlcodMap alcmap = new AlcodMap();
572 alcmap.setDnasq("" + dnas[m].hashCode());
573 alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
575 alc.addAlcodMap(alcmap);
582 ///////////////////////////////////
583 if (av.currentTree != null)
585 // FIND ANY ASSOCIATED TREES
586 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
587 if (Desktop.desktop != null)
589 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
591 for (int t = 0; t < frames.length; t++)
593 if (frames[t] instanceof TreePanel)
595 TreePanel tp = (TreePanel) frames[t];
597 if (tp.treeCanvas.av.alignment == jal)
599 Tree tree = new Tree();
600 tree.setTitle(tp.getTitle());
601 tree.setCurrentTree((av.currentTree == tp.getTree()));
602 tree.setNewick(tp.getTree().toString());
603 tree.setThreshold(tp.treeCanvas.threshold);
605 tree.setFitToWindow(tp.fitToWindow.getState());
606 tree.setFontName(tp.getTreeFont().getName());
607 tree.setFontSize(tp.getTreeFont().getSize());
608 tree.setFontStyle(tp.getTreeFont().getStyle());
609 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
611 tree.setShowBootstrap(tp.bootstrapMenu.getState());
612 tree.setShowDistances(tp.distanceMenu.getState());
614 tree.setHeight(tp.getHeight());
615 tree.setWidth(tp.getWidth());
616 tree.setXpos(tp.getX());
617 tree.setYpos(tp.getY());
627 if (jal.getAlignmentAnnotation() != null)
629 jalview.datamodel.AlignmentAnnotation[] aa = jal
630 .getAlignmentAnnotation();
632 for (int i = 0; i < aa.length; i++)
634 Annotation an = new Annotation();
636 if (aa[i].annotationId != null)
638 annotationIds.put(aa[i].annotationId, aa[i]);
641 an.setId(aa[i].annotationId);
643 if (aa[i] == av.quality || aa[i] == av.conservation
644 || aa[i] == av.consensus)
646 an.setLabel(aa[i].label);
648 vamsasSet.addAnnotation(an);
652 an.setVisible(aa[i].visible);
654 an.setDescription(aa[i].description);
656 if (aa[i].sequenceRef != null)
658 an.setSequenceRef(aa[i].sequenceRef.getName());
664 an.setGraphType(aa[i].graph);
665 an.setGraphGroup(aa[i].graphGroup);
666 if (aa[i].getThreshold() != null)
668 ThresholdLine line = new ThresholdLine();
669 line.setLabel(aa[i].getThreshold().label);
670 line.setValue(aa[i].getThreshold().value);
671 line.setColour(aa[i].getThreshold().colour.getRGB());
672 an.setThresholdLine(line);
680 an.setLabel(aa[i].label);
681 if (aa[i].hasScore())
683 an.setScore(aa[i].getScore());
685 AnnotationElement ae;
686 if (aa[i].annotations != null)
688 an.setScoreOnly(false);
689 for (int a = 0; a < aa[i].annotations.length; a++)
691 if ((aa[i] == null) || (aa[i].annotations[a] == null))
696 ae = new AnnotationElement();
697 if (aa[i].annotations[a].description != null)
698 ae.setDescription(aa[i].annotations[a].description);
699 if (aa[i].annotations[a].displayCharacter != null)
700 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
702 if (!Float.isNaN(aa[i].annotations[a].value))
703 ae.setValue(aa[i].annotations[a].value);
706 if (aa[i].annotations[a].secondaryStructure != ' '
707 && aa[i].annotations[a].secondaryStructure != '\0')
709 .setSecondaryStructure(aa[i].annotations[a].secondaryStructure
712 if (aa[i].annotations[a].colour != null
713 && aa[i].annotations[a].colour != java.awt.Color.black)
715 ae.setColour(aa[i].annotations[a].colour.getRGB());
718 an.addAnnotationElement(ae);
723 an.setScoreOnly(true);
725 vamsasSet.addAnnotation(an);
730 if (jal.getGroups() != null)
732 JGroup[] groups = new JGroup[jal.getGroups().size()];
734 for (int i = 0; i < groups.length; i++)
736 groups[i] = new JGroup();
738 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal
739 .getGroups().elementAt(i);
740 groups[i].setStart(sg.getStartRes());
741 groups[i].setEnd(sg.getEndRes());
742 groups[i].setName(sg.getName());
745 if (sg.cs.conservationApplied())
747 groups[i].setConsThreshold(sg.cs.getConservationInc());
749 if (sg.cs instanceof jalview.schemes.UserColourScheme)
751 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
757 .setColour(ColourSchemeProperty.getColourName(sg.cs));
760 else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
763 .setColour(ColourSchemeProperty
764 .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
767 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
770 .setColour(SetUserColourScheme(sg.cs, userColours, jms));
774 groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
777 groups[i].setPidThreshold(sg.cs.getThreshold());
780 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
781 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
782 groups[i].setDisplayText(sg.getDisplayText());
783 groups[i].setColourText(sg.getColourText());
784 groups[i].setTextCol1(sg.textColour.getRGB());
785 groups[i].setTextCol2(sg.textColour2.getRGB());
786 groups[i].setTextColThreshold(sg.thresholdTextColour);
788 for (int s = 0; s < sg.getSize(); s++)
790 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
792 groups[i].addSeq(seqHash(seq));
796 jms.setJGroup(groups);
799 ///////////SAVE VIEWPORT
800 Viewport view = new Viewport();
801 view.setTitle(ap.alignFrame.getTitle());
802 view.setSequenceSetId(av.getSequenceSetId());
803 view.setViewName(av.viewName);
804 view.setGatheredViews(av.gatherViewsHere);
806 if (ap.av.explodedPosition != null)
808 view.setXpos(av.explodedPosition.x);
809 view.setYpos(av.explodedPosition.y);
810 view.setWidth(av.explodedPosition.width);
811 view.setHeight(av.explodedPosition.height);
815 view.setXpos(ap.alignFrame.getBounds().x);
816 view.setYpos(ap.alignFrame.getBounds().y);
817 view.setWidth(ap.alignFrame.getBounds().width);
818 view.setHeight(ap.alignFrame.getBounds().height);
821 view.setStartRes(av.startRes);
822 view.setStartSeq(av.startSeq);
824 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
826 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
829 else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
831 jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
832 .getGlobalColourScheme();
834 AnnotationColours ac = new AnnotationColours();
835 ac.setAboveThreshold(acg.getAboveThreshold());
836 ac.setThreshold(acg.getAnnotationThreshold());
837 ac.setAnnotation(acg.getAnnotation());
838 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
840 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
845 ac.setColourScheme(ColourSchemeProperty.getColourName(acg
849 ac.setMaxColour(acg.getMaxColour().getRGB());
850 ac.setMinColour(acg.getMinColour().getRGB());
851 view.setAnnotationColours(ac);
852 view.setBgColour("AnnotationColourGradient");
856 view.setBgColour(ColourSchemeProperty.getColourName(av
857 .getGlobalColourScheme()));
860 ColourSchemeI cs = av.getGlobalColourScheme();
864 if (cs.conservationApplied())
866 view.setConsThreshold(cs.getConservationInc());
867 if (cs instanceof jalview.schemes.UserColourScheme)
869 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
873 if (cs instanceof ResidueColourScheme)
875 view.setPidThreshold(cs.getThreshold());
879 view.setConservationSelected(av.getConservationSelected());
880 view.setPidSelected(av.getAbovePIDThreshold());
881 view.setFontName(av.font.getName());
882 view.setFontSize(av.font.getSize());
883 view.setFontStyle(av.font.getStyle());
884 view.setRenderGaps(av.renderGaps);
885 view.setShowAnnotation(av.getShowAnnotation());
886 view.setShowBoxes(av.getShowBoxes());
887 view.setShowColourText(av.getColourText());
888 view.setShowFullId(av.getShowJVSuffix());
889 view.setRightAlignIds(av.rightAlignIds);
890 view.setShowSequenceFeatures(av.showSequenceFeatures);
891 view.setShowText(av.getShowText());
892 view.setWrapAlignment(av.getWrapAlignment());
893 view.setTextCol1(av.textColour.getRGB());
894 view.setTextCol2(av.textColour2.getRGB());
895 view.setTextColThreshold(av.thresholdTextColour);
897 if (av.featuresDisplayed != null)
899 jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
901 String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
903 Vector settingsAdded = new Vector();
904 for (int ro = 0; ro < renderOrder.length; ro++)
906 Setting setting = new Setting();
907 setting.setType(renderOrder[ro]);
908 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
909 .getColour(renderOrder[ro]).getRGB());
911 setting.setDisplay(av.featuresDisplayed
912 .containsKey(renderOrder[ro]));
913 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
917 setting.setOrder(rorder);
919 fs.addSetting(setting);
920 settingsAdded.addElement(renderOrder[ro]);
923 //Make sure we save none displayed feature settings
924 Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
926 while (en.hasMoreElements())
928 String key = en.nextElement().toString();
929 if (settingsAdded.contains(key))
934 Setting setting = new Setting();
935 setting.setType(key);
936 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
937 .getColour(key).getRGB());
939 setting.setDisplay(false);
940 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
944 setting.setOrder(rorder);
946 fs.addSetting(setting);
947 settingsAdded.addElement(key);
949 en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
950 Vector groupsAdded = new Vector();
951 while (en.hasMoreElements())
953 String grp = en.nextElement().toString();
954 if (groupsAdded.contains(grp))
958 Group g = new Group();
961 .setDisplay(((Boolean) ap.seqPanel.seqCanvas
962 .getFeatureRenderer().featureGroups.get(grp))
965 groupsAdded.addElement(grp);
967 jms.setFeatureSettings(fs);
971 if (av.hasHiddenColumns)
973 for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
975 int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
977 HiddenColumns hc = new HiddenColumns();
978 hc.setStart(region[0]);
979 hc.setEnd(region[1]);
980 view.addHiddenColumns(hc);
984 jms.addViewport(view);
986 object.setJalviewModelSequence(jms);
987 object.getVamsasModel().addSequenceSet(vamsasSet);
991 //We may not want to write the object to disk,
992 //eg we can copy the alignViewport to a new view object
993 //using save and then load
996 org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(out);
997 marshaller.marshal(object);
999 } catch (Exception ex)
1001 ex.printStackTrace();
1007 private Sequence createVamsasSequence(String id, SequenceI jds)
1009 return createVamsasSequence(true, id, jds, null);
1012 private Sequence createVamsasSequence(boolean recurse, String id,
1013 SequenceI jds, SequenceI parentseq)
1015 Sequence vamsasSeq = new Sequence();
1016 vamsasSeq.setId(id);
1017 vamsasSeq.setName(jds.getName());
1018 vamsasSeq.setSequence(jds.getSequenceAsString());
1019 vamsasSeq.setDescription(jds.getDescription());
1020 jalview.datamodel.DBRefEntry[] dbrefs = null;
1021 if (jds.getDatasetSequence() != null)
1023 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
1024 if (jds.getDatasetSequence().getDBRef() != null)
1026 dbrefs = jds.getDatasetSequence().getDBRef();
1031 vamsasSeq.setDsseqid(id); // so we can tell which sequences really are dataset sequences only
1032 dbrefs = jds.getDBRef();
1036 for (int d = 0; d < dbrefs.length; d++)
1038 DBRef dbref = new DBRef();
1039 dbref.setSource(dbrefs[d].getSource());
1040 dbref.setVersion(dbrefs[d].getVersion());
1041 dbref.setAccessionId(dbrefs[d].getAccessionId());
1042 if (dbrefs[d].hasMap())
1044 Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
1046 dbref.setMapping(mp);
1048 vamsasSeq.addDBRef(dbref);
1054 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
1055 SequenceI parentseq, SequenceI jds, boolean recurse)
1058 if (jmp.getMap() != null)
1062 jalview.util.MapList mlst = jmp.getMap();
1063 int r[] = mlst.getFromRanges();
1064 for (int s = 0; s < r.length; s += 2)
1066 MapListFrom mfrom = new MapListFrom();
1067 mfrom.setStart(r[s]);
1068 mfrom.setEnd(r[s + 1]);
1069 mp.addMapListFrom(mfrom);
1071 r = mlst.getToRanges();
1072 for (int s = 0; s < r.length; s += 2)
1074 MapListTo mto = new MapListTo();
1076 mto.setEnd(r[s + 1]);
1077 mp.addMapListTo(mto);
1079 mp.setMapFromUnit(mlst.getFromRatio());
1080 mp.setMapToUnit(mlst.getToRatio());
1081 if (jmp.getTo() != null)
1083 MappingChoice mpc = new MappingChoice();
1085 && (parentseq != jmp.getTo() || parentseq
1086 .getDatasetSequence() != jmp.getTo()))
1088 mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo())
1089 , jmp.getTo(), jds));
1094 SequenceI ps = null;
1095 if (parentseq != jmp.getTo()
1096 && parentseq.getDatasetSequence() != jmp.getTo())
1098 // chaining dbref rather than a handshaking one
1099 jmpid = seqHash(ps = jmp.getTo());
1103 jmpid = seqHash(ps = parentseq);
1105 mpc.setDseqFor(jmpid);
1106 if (!seqRefIds.containsKey(mpc.getDseqFor()))
1108 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
1109 seqRefIds.put(mpc.getDseqFor(), ps);
1113 jalview.bin.Cache.log.debug("reusing DseqFor ID");
1116 mp.setMappingChoice(mpc);
1122 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
1123 Vector userColours, JalviewModelSequence jms)
1126 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
1128 if (!userColours.contains(ucs))
1130 userColours.add(ucs);
1132 java.awt.Color[] colours = ucs.getColours();
1133 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
1134 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
1136 for (int i = 0; i < colours.length; i++)
1138 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1139 col.setName(ResidueProperties.aa[i]);
1140 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1141 jbucs.addColour(col);
1143 if (ucs.getLowerCaseColours() != null)
1145 colours = ucs.getLowerCaseColours();
1146 for (int i = 0; i < colours.length; i++)
1148 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1149 col.setName(ResidueProperties.aa[i].toLowerCase());
1150 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1151 jbucs.addColour(col);
1155 id = "ucs" + userColours.indexOf(ucs);
1157 uc.setUserColourScheme(jbucs);
1158 jms.addUserColours(uc);
1164 jalview.schemes.UserColourScheme GetUserColourScheme(
1165 JalviewModelSequence jms, String id)
1167 UserColours[] uc = jms.getUserColours();
1168 UserColours colours = null;
1170 for (int i = 0; i < uc.length; i++)
1172 if (uc[i].getId().equals(id))
1180 java.awt.Color[] newColours = new java.awt.Color[24];
1182 for (int i = 0; i < 24; i++)
1184 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1185 .getUserColourScheme().getColour(i).getRGB(), 16));
1188 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
1191 if (colours.getUserColourScheme().getColourCount() > 24)
1193 newColours = new java.awt.Color[23];
1194 for (int i = 0; i < 23; i++)
1196 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1197 .getUserColourScheme().getColour(i + 24).getRGB(), 16));
1199 ucs.setLowerCaseColours(newColours);
1208 * @param file DOCUMENT ME!
1210 public AlignFrame LoadJalviewAlign(final String file)
1212 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
1214 jalview.gui.AlignFrame af = null;
1216 seqRefIds = new Hashtable();
1217 viewportsAdded = new Hashtable();
1218 frefedSequence = new Vector();
1219 Hashtable gatherToThisFrame = new Hashtable();
1221 String errorMessage = null;
1225 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
1228 if (file.startsWith("http://"))
1230 url = new URL(file);
1233 JarInputStream jin = null;
1234 JarEntry jarentry = null;
1241 jin = new JarInputStream(url.openStream());
1245 jin = new JarInputStream(new FileInputStream(file));
1248 for (int i = 0; i < entryCount; i++)
1250 jarentry = jin.getNextJarEntry();
1253 if (jarentry != null && jarentry.getName().endsWith(".xml"))
1255 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
1256 JalviewModel object = new JalviewModel();
1258 Unmarshaller unmar = new Unmarshaller(object);
1259 unmar.setValidation(false);
1260 object = (JalviewModel) unmar.unmarshal(in);
1262 af = LoadFromObject(object, file, true);
1263 if (af.viewport.gatherViewsHere)
1265 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
1269 else if (jarentry != null)
1271 //Some other file here.
1274 } while (jarentry != null);
1275 resolveFrefedSequences();
1276 } catch (java.io.FileNotFoundException ex)
1278 ex.printStackTrace();
1279 errorMessage = "Couldn't locate Jalview XML file : " + file;
1280 System.err.println("Exception whilst loading jalview XML file : "
1282 } catch (java.net.UnknownHostException ex)
1284 ex.printStackTrace();
1285 errorMessage = "Couldn't locate Jalview XML file : " + file;
1286 System.err.println("Exception whilst loading jalview XML file : "
1288 } catch (Exception ex)
1290 //Is Version 1 Jar file?
1292 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(file);
1293 } catch (Exception ex2) {
1294 System.err.println("Exception whilst loading as jalviewXMLV1:");
1295 ex2.printStackTrace();
1299 if (Desktop.instance != null)
1301 Desktop.instance.stopLoading();
1305 System.out.println("Successfully loaded archive file");
1308 ex.printStackTrace();
1310 System.err.println("Exception whilst loading jalview XML file : "
1314 if (Desktop.instance != null)
1316 Desktop.instance.stopLoading();
1319 Enumeration en = gatherToThisFrame.elements();
1320 while (en.hasMoreElements())
1322 Desktop.instance.gatherViews((AlignFrame) en.nextElement());
1325 if (errorMessage != null)
1327 final String finalErrorMessage = errorMessage;
1330 javax.swing.SwingUtilities.invokeLater(new Runnable()
1334 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1335 finalErrorMessage, "Error loading Jalview file",
1336 JOptionPane.WARNING_MESSAGE);
1340 System.err.println("Problem loading Jalview file: "+errorMessage);
1347 Hashtable alreadyLoadedPDB;
1349 String loadPDBFile(String file, String pdbId)
1351 if (alreadyLoadedPDB == null)
1352 alreadyLoadedPDB = new Hashtable();
1354 if (alreadyLoadedPDB.containsKey(pdbId))
1355 return alreadyLoadedPDB.get(pdbId).toString();
1359 JarInputStream jin = null;
1361 if (file.startsWith("http://"))
1363 jin = new JarInputStream(new URL(file).openStream());
1367 jin = new JarInputStream(new FileInputStream(file));
1370 JarEntry entry = null;
1373 entry = jin.getNextJarEntry();
1374 } while (!entry.getName().equals(pdbId));
1376 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1377 File outFile = File.createTempFile("jalview_pdb", ".txt");
1378 outFile.deleteOnExit();
1379 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1382 while ((data = in.readLine()) != null)
1386 try { out.flush(); } catch (Exception foo) {};
1389 alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
1390 return outFile.getAbsolutePath();
1392 } catch (Exception ex)
1394 ex.printStackTrace();
1400 AlignFrame LoadFromObject(JalviewModel object, String file,
1401 boolean loadTreesAndStructures)
1403 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1404 Sequence[] vamsasSeq = vamsasSet.getSequence();
1406 JalviewModelSequence jms = object.getJalviewModelSequence();
1408 Viewport view = jms.getViewport(0);
1410 //////////////////////////////////
1413 Vector hiddenSeqs = null;
1414 jalview.datamodel.Sequence jseq;
1416 ArrayList tmpseqs = new ArrayList();
1418 boolean multipleView = false;
1420 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1421 int vi=0; // counter in vamsasSeq array
1422 for (int i = 0; i < JSEQ.length; i++)
1424 String seqId = JSEQ[i].getId() + "";
1426 if (seqRefIds.get(seqId) != null)
1428 tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId));
1429 multipleView = true;
1433 jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
1434 vamsasSeq[vi].getSequence());
1435 jseq.setDescription(vamsasSeq[vi].getDescription());
1436 jseq.setStart(JSEQ[i].getStart());
1437 jseq.setEnd(JSEQ[i].getEnd());
1438 jseq.setVamsasId(uniqueSetSuffix + seqId);
1439 seqRefIds.put(vamsasSeq[vi].getId()+"", jseq);
1444 if (JSEQ[i].getHidden())
1446 if (hiddenSeqs == null)
1448 hiddenSeqs = new Vector();
1451 hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
1458 // Create the alignment object from the sequence set
1459 /////////////////////////////////
1460 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
1463 tmpseqs.toArray(orderedSeqs);
1465 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
1468 /// Add the alignment properties
1469 for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
1471 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
1472 al.setProperty(ssp.getKey(), ssp.getValue());
1476 // SequenceFeatures are added to the DatasetSequence,
1477 // so we must create or recover the dataset before loading features
1478 /////////////////////////////////
1479 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
1481 // older jalview projects do not have a dataset id.
1482 al.setDataset(null);
1486 recoverDatasetFor(vamsasSet, al);
1488 /////////////////////////////////
1490 Hashtable pdbloaded = new Hashtable();
1493 for (int i = 0; i < vamsasSeq.length; i++)
1495 if (JSEQ[i].getFeaturesCount() > 0)
1497 Features[] features = JSEQ[i].getFeatures();
1498 for (int f = 0; f < features.length; f++)
1500 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
1501 features[f].getType(), features[f].getDescription(),
1502 features[f].getStatus(), features[f].getBegin(),
1503 features[f].getEnd(), features[f].getFeatureGroup());
1505 sf.setScore(features[f].getScore());
1506 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1508 OtherData keyValue = features[f].getOtherData(od);
1509 if (keyValue.getKey().startsWith("LINK"))
1511 sf.addLink(keyValue.getValue());
1515 sf.setValue(keyValue.getKey(), keyValue.getValue());
1520 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1523 if (vamsasSeq[i].getDBRefCount() > 0)
1525 addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
1527 if (JSEQ[i].getPdbidsCount() > 0)
1529 Pdbids[] ids = JSEQ[i].getPdbids();
1530 for (int p = 0; p < ids.length; p++)
1532 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
1533 entry.setId(ids[p].getId());
1534 entry.setType(ids[p].getType());
1535 if (ids[p].getFile() != null)
1537 if (!pdbloaded.containsKey(ids[p].getFile()))
1539 entry.setFile(loadPDBFile(file, ids[p].getId()));
1543 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1547 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1553 /////////////////////////////////
1554 // LOAD SEQUENCE MAPPINGS
1555 if (vamsasSet.getAlcodonFrameCount() > 0)
1557 AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
1558 for (int i = 0; i < alc.length; i++)
1560 jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
1561 alc[i].getAlcodonCount());
1562 if (alc[i].getAlcodonCount() > 0)
1564 Alcodon[] alcods = alc[i].getAlcodon();
1565 for (int p = 0; p < cf.codons.length; p++)
1567 cf.codons[p] = new int[3];
1568 cf.codons[p][0] = (int) alcods[p].getPos1();
1569 cf.codons[p][1] = (int) alcods[p].getPos2();
1570 cf.codons[p][2] = (int) alcods[p].getPos3();
1573 if (alc[i].getAlcodMapCount() > 0)
1575 AlcodMap[] maps = alc[i].getAlcodMap();
1576 for (int m = 0; m < maps.length; m++)
1578 SequenceI dnaseq = (SequenceI) seqRefIds
1579 .get(maps[m].getDnasq());
1581 // attach to dna sequence reference.
1584 if (maps[m].getMapping() != null)
1586 jalview.datamodel.Mapping mapping = addMapping(maps[m]
1588 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
1593 al.addCodonFrame(cf);
1598 //////////////////////////////////
1600 boolean hideQuality = true, hideConservation = true, hideConsensus = true;
1602 if (vamsasSet.getAnnotationCount() > 0)
1604 Annotation[] an = vamsasSet.getAnnotation();
1606 for (int i = 0; i < an.length; i++)
1608 if (an[i].getLabel().equals("Quality"))
1610 hideQuality = false;
1613 else if (an[i].getLabel().equals("Conservation"))
1615 hideConservation = false;
1618 else if (an[i].getLabel().equals("Consensus"))
1620 hideConsensus = false;
1624 if (an[i].getId() != null
1625 && annotationIds.containsKey(an[i].getId()))
1627 jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
1628 .get(an[i].getId());
1629 if (an[i].hasVisible())
1630 jda.visible = an[i].getVisible();
1632 al.addAnnotation(jda);
1637 AnnotationElement[] ae = an[i].getAnnotationElement();
1638 jalview.datamodel.Annotation[] anot = null;
1640 if (!an[i].getScoreOnly())
1642 anot = new jalview.datamodel.Annotation[al.getWidth()];
1644 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
1646 if (ae[aa].getPosition() >= anot.length)
1649 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
1651 ae[aa].getDisplayCharacter(), ae[aa].getDescription(), (ae[aa]
1652 .getSecondaryStructure() == null || ae[aa]
1653 .getSecondaryStructure().length() == 0) ? ' ' : ae[aa]
1654 .getSecondaryStructure().charAt(0), ae[aa].getValue()
1657 // JBPNote: Consider verifying dataflow for IO of secondary structure annotation read from Stockholm files
1658 // this was added to try to ensure that
1659 //if (anot[ae[aa].getPosition()].secondaryStructure>' ')
1661 // anot[ae[aa].getPosition()].displayCharacter = "";
1663 anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]
1667 jalview.datamodel.AlignmentAnnotation jaa = null;
1669 if (an[i].getGraph())
1671 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1672 an[i].getDescription(), anot, 0, 0, an[i].getGraphType());
1674 jaa.graphGroup = an[i].getGraphGroup();
1676 if (an[i].getThresholdLine() != null)
1678 jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
1679 .getThresholdLine().getValue(), an[i]
1680 .getThresholdLine().getLabel(), new java.awt.Color(
1681 an[i].getThresholdLine().getColour())));
1688 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1689 an[i].getDescription(), anot);
1692 if (an[i].getId() != null)
1694 annotationIds.put(an[i].getId(), jaa);
1695 jaa.annotationId = an[i].getId();
1698 if (an[i].getSequenceRef() != null)
1700 if (al.findName(an[i].getSequenceRef()) != null)
1702 jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
1704 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1707 if (an[i].hasScore())
1709 jaa.setScore(an[i].getScore());
1712 if (an[i].hasVisible())
1713 jaa.visible = an[i].getVisible();
1715 al.addAnnotation(jaa);
1719 /////////////////////////
1721 if (jms.getJGroupCount() > 0)
1723 JGroup[] groups = jms.getJGroup();
1725 for (int i = 0; i < groups.length; i++)
1727 ColourSchemeI cs = null;
1729 if (groups[i].getColour() != null)
1731 if (groups[i].getColour().startsWith("ucs"))
1733 cs = GetUserColourScheme(jms, groups[i].getColour());
1737 cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
1742 cs.setThreshold(groups[i].getPidThreshold(), true);
1746 Vector seqs = new Vector();
1748 for (int s = 0; s < groups[i].getSeqCount(); s++)
1750 String seqId = groups[i].getSeq(s) + "";
1751 jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds
1756 seqs.addElement(ts);
1760 if (seqs.size() < 1)
1765 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
1766 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1767 groups[i].getDisplayText(), groups[i].getColourText(),
1768 groups[i].getStart(), groups[i].getEnd());
1771 .setOutlineColour(new java.awt.Color(groups[i]
1772 .getOutlineColour()));
1774 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
1775 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
1776 sg.thresholdTextColour = groups[i].getTextColThreshold();
1778 if (groups[i].getConsThreshold() != 0)
1780 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
1781 "All", ResidueProperties.propHash, 3, sg
1782 .getSequences(null), 0, sg.getWidth() - 1);
1784 c.verdict(false, 25);
1785 sg.cs.setConservation(c);
1792 /////////////////////////////////
1795 AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
1797 af.setFileName(file, "Jalview");
1799 for (int i = 0; i < JSEQ.length; i++)
1801 af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
1802 new java.awt.Color(JSEQ[i].getColour()));
1805 //If we just load in the same jar file again, the sequenceSetId
1806 //will be the same, and we end up with multiple references
1807 //to the same sequenceSet. We must modify this id on load
1808 //so that each load of the file gives a unique id
1809 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
1811 af.viewport.gatherViewsHere = view.getGatheredViews();
1813 if (view.getSequenceSetId() != null)
1815 jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
1816 .get(uniqueSeqSetId);
1818 af.viewport.sequenceSetID = uniqueSeqSetId;
1822 af.viewport.historyList = av.historyList;
1823 af.viewport.redoList = av.redoList;
1827 viewportsAdded.put(uniqueSeqSetId, af.viewport);
1830 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1832 if (hiddenSeqs != null)
1834 for (int s = 0; s < JSEQ.length; s++)
1836 jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
1838 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
1840 hidden.addSequence(al
1841 .getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
1843 af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
1846 jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
1849 for (int s = 0; s < hiddenSeqs.size(); s++)
1851 hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
1854 af.viewport.hideSequence(hseqs);
1858 if ((hideConsensus || hideQuality || hideConservation)
1859 && al.getAlignmentAnnotation() != null)
1861 int hSize = al.getAlignmentAnnotation().length;
1862 for (int h = 0; h < hSize; h++)
1864 if ((hideConsensus && al.getAlignmentAnnotation()[h].label
1865 .equals("Consensus"))
1866 || (hideQuality && al.getAlignmentAnnotation()[h].label
1868 || (hideConservation && al.getAlignmentAnnotation()[h].label
1869 .equals("Conservation")))
1871 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1876 af.alignPanel.adjustAnnotationHeight();
1879 if (view.getViewName() != null)
1881 af.viewport.viewName = view.getViewName();
1882 af.setInitialTabVisible();
1884 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
1887 af.viewport.setShowAnnotation(view.getShowAnnotation());
1888 af.viewport.setAbovePIDThreshold(view.getPidSelected());
1890 af.viewport.setColourText(view.getShowColourText());
1892 af.viewport.setConservationSelected(view.getConservationSelected());
1893 af.viewport.setShowJVSuffix(view.getShowFullId());
1894 af.viewport.rightAlignIds = view.getRightAlignIds();
1895 af.viewport.setFont(new java.awt.Font(view.getFontName(), view
1896 .getFontStyle(), view.getFontSize()));
1897 af.alignPanel.fontChanged();
1898 af.viewport.setRenderGaps(view.getRenderGaps());
1899 af.viewport.setWrapAlignment(view.getWrapAlignment());
1900 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1901 af.viewport.setShowAnnotation(view.getShowAnnotation());
1902 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1904 af.viewport.setShowBoxes(view.getShowBoxes());
1906 af.viewport.setShowText(view.getShowText());
1908 af.viewport.textColour = new java.awt.Color(view.getTextCol1());
1909 af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
1910 af.viewport.thresholdTextColour = view.getTextColThreshold();
1912 af.viewport.setStartRes(view.getStartRes());
1913 af.viewport.setStartSeq(view.getStartSeq());
1915 ColourSchemeI cs = null;
1917 if (view.getBgColour() != null)
1919 if (view.getBgColour().startsWith("ucs"))
1921 cs = GetUserColourScheme(jms, view.getBgColour());
1923 else if (view.getBgColour().startsWith("Annotation"))
1925 //int find annotation
1926 for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1928 if (af.viewport.alignment.getAlignmentAnnotation()[i].label
1929 .equals(view.getAnnotationColours().getAnnotation()))
1931 if (af.viewport.alignment.getAlignmentAnnotation()[i]
1932 .getThreshold() == null)
1934 af.viewport.alignment.getAlignmentAnnotation()[i]
1935 .setThreshold(new jalview.datamodel.GraphLine(view
1936 .getAnnotationColours().getThreshold(),
1937 "Threshold", java.awt.Color.black)
1942 if (view.getAnnotationColours().getColourScheme()
1945 cs = new AnnotationColourGradient(af.viewport.alignment
1946 .getAlignmentAnnotation()[i], new java.awt.Color(view
1947 .getAnnotationColours().getMinColour()),
1948 new java.awt.Color(view.getAnnotationColours()
1949 .getMaxColour()), view.getAnnotationColours()
1950 .getAboveThreshold());
1952 else if (view.getAnnotationColours().getColourScheme()
1955 cs = new AnnotationColourGradient(af.viewport.alignment
1956 .getAlignmentAnnotation()[i], GetUserColourScheme(
1957 jms, view.getAnnotationColours().getColourScheme()),
1958 view.getAnnotationColours().getAboveThreshold());
1962 cs = new AnnotationColourGradient(af.viewport.alignment
1963 .getAlignmentAnnotation()[i], ColourSchemeProperty
1964 .getColour(al, view.getAnnotationColours()
1965 .getColourScheme()), view
1966 .getAnnotationColours().getAboveThreshold());
1969 // Also use these settings for all the groups
1970 if (al.getGroups() != null)
1972 for (int g = 0; g < al.getGroups().size(); g++)
1974 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
1975 .getGroups().elementAt(g);
1982 /* if (view.getAnnotationColours().getColourScheme().equals("None"))
1984 sg.cs = new AnnotationColourGradient(
1985 af.viewport.alignment.getAlignmentAnnotation()[i],
1986 new java.awt.Color(view.getAnnotationColours().
1988 new java.awt.Color(view.getAnnotationColours().
1990 view.getAnnotationColours().getAboveThreshold());
1994 sg.cs = new AnnotationColourGradient(
1995 af.viewport.alignment.getAlignmentAnnotation()[i],
1996 sg.cs, view.getAnnotationColours()
1997 .getAboveThreshold());
2010 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
2015 cs.setThreshold(view.getPidThreshold(), true);
2016 cs.setConsensus(af.viewport.hconsensus);
2020 af.viewport.setGlobalColourScheme(cs);
2021 af.viewport.setColourAppliesToAllGroups(false);
2023 if (view.getConservationSelected() && cs != null)
2025 cs.setConservationInc(view.getConsThreshold());
2028 af.changeColour(cs);
2030 af.viewport.setColourAppliesToAllGroups(true);
2032 if (view.getShowSequenceFeatures())
2034 af.viewport.showSequenceFeatures = true;
2037 if (jms.getFeatureSettings() != null)
2039 af.viewport.featuresDisplayed = new Hashtable();
2040 String[] renderOrder = new String[jms.getFeatureSettings()
2041 .getSettingCount()];
2042 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
2044 Setting setting = jms.getFeatureSettings().getSetting(fs);
2046 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
2047 setting.getType(), new java.awt.Color(setting.getColour()));
2048 renderOrder[fs] = setting.getType();
2049 if (setting.hasOrder())
2050 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2051 setting.getType(), setting.getOrder());
2053 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2055 fs / jms.getFeatureSettings().getSettingCount());
2056 if (setting.getDisplay())
2058 af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
2059 setting.getColour()));
2062 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
2064 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
2065 for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
2067 Group grp = jms.getFeatureSettings().getGroup(gs);
2068 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
2072 if (view.getHiddenColumnsCount() > 0)
2074 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
2076 af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
2077 .getHiddenColumns(c).getEnd() //+1
2082 af.setMenusFromViewport(af.viewport);
2084 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
2088 ///////////////////////////////////////
2089 if (loadTreesAndStructures && jms.getTreeCount() > 0)
2093 for (int t = 0; t < jms.getTreeCount(); t++)
2096 Tree tree = jms.getTree(t);
2098 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(tree
2099 .getNewick()), tree.getTitle(), tree.getWidth(), tree
2100 .getHeight(), tree.getXpos(), tree.getYpos());
2102 tp.fitToWindow.setState(tree.getFitToWindow());
2103 tp.fitToWindow_actionPerformed(null);
2105 if (tree.getFontName() != null)
2107 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
2108 .getFontStyle(), tree.getFontSize()));
2112 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
2113 .getFontStyle(), tree.getFontSize()));
2116 tp.showPlaceholders(tree.getMarkUnlinked());
2117 tp.showBootstrap(tree.getShowBootstrap());
2118 tp.showDistances(tree.getShowDistances());
2120 tp.treeCanvas.threshold = tree.getThreshold();
2122 if (tree.getCurrentTree())
2124 af.viewport.setCurrentTree(tp.getTree());
2128 } catch (Exception ex)
2130 ex.printStackTrace();
2135 if (loadTreesAndStructures)
2137 for (int i = 0; i < JSEQ.length; i++)
2139 if (JSEQ[i].getPdbidsCount() > 0)
2141 Pdbids[] ids = JSEQ[i].getPdbids();
2142 for (int p = 0; p < ids.length; p++)
2144 for (int s = 0; s < ids[p].getStructureStateCount(); s++)
2146 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
2148 jpdb.setFile(loadPDBFile(ids[p].getFile(), ids[p].getId()));
2149 jpdb.setId(ids[p].getId());
2151 int x = ids[p].getStructureState(s).getXpos();
2152 int y = ids[p].getStructureState(s).getYpos();
2153 int width = ids[p].getStructureState(s).getWidth();
2154 int height = ids[p].getStructureState(s).getHeight();
2156 java.awt.Component comp = null;
2158 JInternalFrame[] frames = null;
2161 frames = Desktop.desktop.getAllFrames();
2163 catch (ArrayIndexOutOfBoundsException e)
2165 // occasional No such child exceptions are thrown here...
2169 } catch (Exception f) {};
2171 } while (frames==null);
2172 for (int f = 0; f < frames.length; f++)
2174 if (frames[f] instanceof AppJmol)
2176 if (frames[f].getX() == x && frames[f].getY() == y
2177 && frames[f].getHeight() == height
2178 && frames[f].getWidth() == width)
2186 Desktop.desktop.getComponentAt(x, y);
2188 String pdbFile = loadPDBFile(file, ids[p].getId());
2190 jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
2191 { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId()
2196 String state = ids[p].getStructureState(s).getContent();
2198 StringBuffer newFileLoc = new StringBuffer(state.substring(
2199 0, state.indexOf("\"", state.indexOf("load")) + 1));
2201 newFileLoc.append(jpdb.getFile());
2202 newFileLoc.append(state.substring(state.indexOf("\"", state
2203 .indexOf("load \"") + 6)));
2205 new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel,
2206 newFileLoc.toString(), new java.awt.Rectangle(x, y,
2210 else if (comp != null)
2212 StructureSelectionManager.getStructureSelectionManager()
2213 .setMapping(seq, null, pdbFile,
2214 jalview.io.AppletFormatAdapter.FILE);
2216 ((AppJmol) comp).addSequence(seq);
2227 private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
2229 jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
2230 Vector dseqs = null;
2233 // create a list of new dataset sequences
2234 dseqs = new Vector();
2236 for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
2238 Sequence vamsasSeq = vamsasSet.getSequence(i);
2239 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
2241 // create a new dataset
2244 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
2245 dseqs.copyInto(dsseqs);
2246 ds = new jalview.datamodel.Alignment(dsseqs);
2247 addDatasetRef(vamsasSet.getDatasetId(), ds);
2249 // set the dataset for the newly imported alignment.
2250 if (al.getDataset() == null)
2259 * @param vamsasSeq sequence definition to create/merge dataset sequence for
2260 * @param ds dataset alignment
2261 * @param dseqs vector to add new dataset sequence to
2263 private void ensureJalviewDatasetSequence(Sequence vamsasSeq, AlignmentI ds, Vector dseqs)
2265 jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds.get(vamsasSeq.getId());
2266 jalview.datamodel.SequenceI dsq = null;
2267 if (sq!=null && sq.getDatasetSequence()!=null)
2269 dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
2272 String sqid = vamsasSeq.getDsseqid();
2275 // need to create or add a new dataset sequence reference to this sequence
2278 dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
2283 // make a new dataset sequence
2284 dsq = sq.createDatasetSequence();
2287 // make up a new dataset reference for this sequence
2288 sqid = seqHash(dsq);
2290 dsq.setVamsasId(uniqueSetSuffix + sqid);
2291 seqRefIds.put(sqid, dsq);
2296 dseqs.addElement(dsq);
2301 ds.addSequence(dsq);
2305 { // make this dataset sequence sq's dataset sequence
2306 sq.setDatasetSequence(dsq);
2310 // TODO: refactor this as a merge dataset sequence function
2311 // now check that sq (the dataset sequence) sequence really is the union of all references to it
2312 //boolean pre = sq.getStart() < dsq.getStart();
2313 //boolean post = sq.getEnd() > dsq.getEnd();
2317 StringBuffer sb = new StringBuffer();
2318 String newres = jalview.analysis.AlignSeq.extractGaps(
2319 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
2320 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString()) && newres.length()>dsq.getLength())
2322 // Update with the longer sequence.
2328 .substring(0, dsq.getStart() - sq.getStart()));
2329 dsq.setStart(sq.getStart());
2333 sb.append(newres.substring(newres.length() - sq.getEnd()
2335 dsq.setEnd(sq.getEnd());
2338 dsq.setSequence(sb.toString());
2340 //TODO: merges will never happen if we 'know' we have the real dataset sequence - this should be detected when id==dssid
2342 .println("DEBUG Notice: Merged dataset sequence"); // ("
2343 // + (pre ? "prepended" : "") + " "
2344 //+ (post ? "appended" : ""));
2349 java.util.Hashtable datasetIds = null;
2351 private Alignment getDatasetFor(String datasetId)
2353 if (datasetIds == null)
2355 datasetIds = new Hashtable();
2358 if (datasetIds.containsKey(datasetId))
2360 return (Alignment) datasetIds.get(datasetId);
2365 private void addDatasetRef(String datasetId, Alignment dataset)
2367 if (datasetIds == null)
2369 datasetIds = new Hashtable();
2371 datasetIds.put(datasetId, dataset);
2374 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
2376 for (int d = 0; d < sequence.getDBRefCount(); d++)
2378 DBRef dr = sequence.getDBRef(d);
2379 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
2380 sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
2381 .getVersion(), sequence.getDBRef(d).getAccessionId());
2382 if (dr.getMapping() != null)
2384 entry.setMap(addMapping(dr.getMapping()));
2386 datasetSequence.addDBRef(entry);
2390 private jalview.datamodel.Mapping addMapping(Mapping m)
2392 SequenceI dsto = null;
2393 // Mapping m = dr.getMapping();
2394 int fr[] = new int[m.getMapListFromCount() * 2];
2395 Enumeration f = m.enumerateMapListFrom();
2396 for (int _i = 0; f.hasMoreElements(); _i += 2)
2398 MapListFrom mf = (MapListFrom) f.nextElement();
2399 fr[_i] = mf.getStart();
2400 fr[_i + 1] = mf.getEnd();
2402 int fto[] = new int[m.getMapListToCount() * 2];
2403 f = m.enumerateMapListTo();
2404 for (int _i = 0; f.hasMoreElements(); _i += 2)
2406 MapListTo mf = (MapListTo) f.nextElement();
2407 fto[_i] = mf.getStart();
2408 fto[_i + 1] = mf.getEnd();
2410 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
2411 fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
2412 if (m.getMappingChoice() != null)
2414 MappingChoice mc = m.getMappingChoice();
2415 if (mc.getDseqFor() != null)
2417 if (seqRefIds.containsKey(mc.getDseqFor()))
2422 jmap.setTo((SequenceI) seqRefIds.get(mc.getDseqFor()));
2426 frefedSequence.add(new Object[]
2427 { mc.getDseqFor(), jmap });
2433 * local sequence definition
2435 Sequence ms = mc.getSequence();
2436 jalview.datamodel.Sequence djs=null;
2437 String sqid = ms.getDsseqid();
2438 if (sqid!=null && sqid.length()>0)
2441 * recover dataset sequence
2443 djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
2445 System.err.println("Warning - making up dataset sequence id for DbRef sequence map reference");
2446 sqid = ((Object)ms).toString(); // make up a new hascode for undefined dataset sequence hash (unlikely to happen)
2451 * make a new dataset sequence and add it to refIds hash
2453 djs = new jalview.datamodel.Sequence(ms
2454 .getName(), ms.getSequence());
2455 djs.setStart(jmap.getMap().getToLowest());
2456 djs.setEnd(jmap.getMap().getToHighest());
2457 djs.setVamsasId(uniqueSetSuffix + sqid);
2459 seqRefIds.put(sqid, djs);
2462 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
2471 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
2472 boolean keepSeqRefs)
2474 jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
2480 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
2484 uniqueSetSuffix = "";
2487 viewportsAdded = new Hashtable();
2489 AlignFrame af = LoadFromObject(jm, null, false);
2490 af.alignPanels.clear();
2491 af.closeMenuItem_actionPerformed(true);
2493 /* if(ap.av.alignment.getAlignmentAnnotation()!=null)
2495 for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length; i++)
2497 if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated)
2499 af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
2500 ap.av.alignment.getAlignmentAnnotation()[i];
2505 return af.alignPanel;
2508 * @see java.lang.Object#finalize()
2510 protected void finalize() throws Throwable
2512 // really make sure we have no buried refs left.
2514 this.seqRefIds = null;
2515 this.seqsToIds = null;