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);
125 if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame)
127 SequenceI seq = (SequenceI) seqRefIds.get(sref);
128 while (seq.getDatasetSequence() != null)
130 seq = seq.getDatasetSequence();
133 && ref[2] instanceof jalview.datamodel.Mapping)
135 jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2];
136 ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap(
137 seq, mp.getTo(), mp.getMap());
142 .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving "
143 + ref[2].getClass() + " type objects.");
149 .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
150 + ref[1].getClass() + " type objects.");
152 frefedSequence.remove(r);
158 System.err.println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string "+ref[0]+" with objecttype "+ref[1].getClass());
164 frefedSequence.remove(r);
172 * This maintains a list of viewports, the key being the
173 * seqSetId. Important to set historyItem and redoList
176 Hashtable viewportsAdded;
178 Hashtable annotationIds = new Hashtable();
180 String uniqueSetSuffix = "";
183 * List of pdbfiles added to Jar
185 Vector pdbfiles = null;
187 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
188 public void SaveState(File statefile)
190 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
199 FileOutputStream fos = new FileOutputStream(statefile);
200 JarOutputStream jout = new JarOutputStream(fos);
202 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
203 ////////////////////////////////////////////////////
204 //NOTE ALSO new PrintWriter must be used for each new JarEntry
205 PrintWriter out = null;
207 Vector shortNames = new Vector();
210 for (int i = frames.length - 1; i > -1; i--)
212 if (frames[i] instanceof AlignFrame)
214 AlignFrame af = (AlignFrame) frames[i];
216 String shortName = af.getTitle();
218 if (shortName.indexOf(File.separatorChar) > -1)
220 shortName = shortName.substring(shortName
221 .lastIndexOf(File.separatorChar) + 1);
226 while (shortNames.contains(shortName))
228 if (shortName.endsWith("_" + (count - 1)))
230 shortName = shortName
231 .substring(0, shortName.lastIndexOf("_"));
234 shortName = shortName.concat("_" + count);
238 shortNames.addElement(shortName);
240 if (!shortName.endsWith(".xml"))
242 shortName = shortName + ".xml";
245 int ap, apSize = af.alignPanels.size();
246 for (ap = 0; ap < apSize; ap++)
248 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
250 String fileName = apSize == 1 ? shortName : ap + shortName;
251 if (!fileName.endsWith(".xml"))
253 fileName = fileName + ".xml";
256 SaveState(apanel, fileName, jout);
260 try { jout.flush(); } catch (Exception foo) {};
262 } catch (Exception ex)
264 //TODO: inform user of the problem - they need to know if their data was not saved !
265 ex.printStackTrace();
269 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
270 public boolean SaveAlignment(AlignFrame af, String jarFile,
275 int ap, apSize = af.alignPanels.size();
276 FileOutputStream fos = new FileOutputStream(jarFile);
277 JarOutputStream jout = new JarOutputStream(fos);
278 for (ap = 0; ap < apSize; ap++)
280 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
282 String jfileName = apSize == 1 ? fileName : fileName + ap;
283 if (!jfileName.endsWith(".xml"))
285 jfileName = jfileName + ".xml";
287 SaveState(apanel, jfileName, jout);
290 try { jout.flush(); } catch (Exception foo) {};
293 } catch (Exception ex)
295 ex.printStackTrace();
301 * create a JalviewModel from an algnment view and marshall it
302 * to a JarOutputStream
304 * @param ap panel to create jalview model for
305 * @param fileName name of alignment panel written to output stream
306 * @param jout jar output stream
307 * @param out jar entry name
309 public JalviewModel SaveState(AlignmentPanel ap, String fileName,
310 JarOutputStream jout)
314 Vector userColours = new Vector();
316 AlignViewport av = ap.av;
318 JalviewModel object = new JalviewModel();
319 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
321 object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
322 object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
324 jalview.datamodel.AlignmentI jal = av.alignment;
326 if (av.hasHiddenRows)
328 jal = jal.getHiddenSequences().getFullAlignment();
331 SequenceSet vamsasSet = new SequenceSet();
333 JalviewModelSequence jms = new JalviewModelSequence();
335 vamsasSet.setGapChar(jal.getGapCharacter() + "");
337 if (jal.getDataset() != null)
339 // dataset id is the dataset's hashcode
340 vamsasSet.setDatasetId(jal.getDataset().hashCode() + "");
342 if (jal.getProperties() != null)
344 Enumeration en = jal.getProperties().keys();
345 while (en.hasMoreElements())
347 String key = en.nextElement().toString();
348 SequenceSetProperties ssp = new SequenceSetProperties();
350 ssp.setValue(jal.getProperties().get(key).toString());
351 vamsasSet.addSequenceSetProperties(ssp);
359 jalview.datamodel.SequenceI jds;
360 for (int i = 0; i < jal.getHeight(); i++)
362 jds = jal.getSequenceAt(i);
365 if (seqRefIds.get(id) != null)
367 // 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)
368 // JBPNote: Uncomment to debug writing out of files that do not read back in due to ArrayOutOfBoundExceptions.
369 //System.err.println("vamsasSeq backref: "+id+"");
370 //System.err.println(jds.getName()+" "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
371 //System.err.println("Hashcode: "+seqHash(jds));
372 //SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
373 //System.err.println(rsq.getName()+" "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
374 //System.err.println("Hashcode: "+seqHash(rsq));
378 vamsasSeq = createVamsasSequence(id, jds);
379 vamsasSet.addSequence(vamsasSeq);
380 seqRefIds.put(id, jds);
384 jseq.setStart(jds.getStart());
385 jseq.setEnd(jds.getEnd());
386 jseq.setColour(av.getSequenceColour(jds).getRGB());
388 jseq.setId(id); // jseq id should be a string not a number
390 if (av.hasHiddenRows)
392 jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
394 if (av.hiddenRepSequences != null
395 && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
397 jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences
398 .get(jal.getSequenceAt(i))).getSequencesInOrder(jal);
400 for (int h = 0; h < reps.length; h++)
402 if (reps[h] != jal.getSequenceAt(i))
404 jseq.addHiddenSequences(jal.findIndex(reps[h]));
410 if (jds.getDatasetSequence().getSequenceFeatures() != null)
412 jalview.datamodel.SequenceFeature[] sf = jds.getDatasetSequence()
413 .getSequenceFeatures();
415 while (index < sf.length)
417 Features features = new Features();
419 features.setBegin(sf[index].getBegin());
420 features.setEnd(sf[index].getEnd());
421 features.setDescription(sf[index].getDescription());
422 features.setType(sf[index].getType());
423 features.setFeatureGroup(sf[index].getFeatureGroup());
424 features.setScore(sf[index].getScore());
425 if (sf[index].links != null)
427 for (int l = 0; l < sf[index].links.size(); l++)
429 OtherData keyValue = new OtherData();
430 keyValue.setKey("LINK_" + l);
431 keyValue.setValue(sf[index].links.elementAt(l).toString());
432 features.addOtherData(keyValue);
435 if (sf[index].otherDetails != null)
438 Enumeration keys = sf[index].otherDetails.keys();
439 while (keys.hasMoreElements())
441 key = keys.nextElement().toString();
442 OtherData keyValue = new OtherData();
443 keyValue.setKey(key);
444 keyValue.setValue(sf[index].otherDetails.get(key).toString());
445 features.addOtherData(keyValue);
449 jseq.addFeatures(features);
454 if (jds.getDatasetSequence().getPDBId() != null)
456 Enumeration en = jds.getDatasetSequence().getPDBId().elements();
457 while (en.hasMoreElements())
459 Pdbids pdb = new Pdbids();
460 jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
463 pdb.setId(entry.getId());
464 pdb.setType(entry.getType());
467 //This must have been loaded, is it still visible?
468 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
469 for (int f = frames.length - 1; f > -1; f--)
471 if (frames[f] instanceof AppJmol)
473 jmol = (AppJmol) frames[f];
474 if (!jmol.pdbentry.getId().equals(entry.getId()))
477 StructureState state = new StructureState();
478 state.setVisible(true);
479 state.setXpos(jmol.getX());
480 state.setYpos(jmol.getY());
481 state.setWidth(jmol.getWidth());
482 state.setHeight(jmol.getHeight());
484 String statestring = jmol.viewer.getStateInfo();
487 state.setContent(statestring.replaceAll("\n", ""));
489 for (int s = 0; s < jmol.sequence.length; s++)
491 if (jal.findIndex(jmol.sequence[s]) > -1)
493 pdb.addStructureState(state);
499 if (entry.getFile() != null)
501 pdb.setFile(entry.getFile());
502 if (pdbfiles == null)
504 pdbfiles = new Vector();
507 if (!pdbfiles.contains(entry.getId()))
509 pdbfiles.addElement(entry.getId());
512 File file = new File(entry.getFile());
513 if (file.exists() && jout != null)
515 byte[] data = new byte[(int) file.length()];
516 jout.putNextEntry(new JarEntry(entry.getId()));
517 DataInputStream dis = new DataInputStream(
518 new FileInputStream(file));
521 DataOutputStream dout = new DataOutputStream(jout);
522 dout.write(data, 0, data.length);
526 } catch (Exception ex)
528 ex.printStackTrace();
534 if (entry.getProperty() != null)
536 PdbentryItem item = new PdbentryItem();
537 Hashtable properties = entry.getProperty();
538 Enumeration en2 = properties.keys();
539 while (en2.hasMoreElements())
541 Property prop = new Property();
542 String key = en2.nextElement().toString();
544 prop.setValue(properties.get(key).toString());
545 item.addProperty(prop);
547 pdb.addPdbentryItem(item);
557 if (av.hasHiddenRows)
562 if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
564 jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
565 for (int i = 0; i < jac.length; i++)
567 AlcodonFrame alc = new AlcodonFrame();
568 vamsasSet.addAlcodonFrame(alc);
569 for (int p = 0; p < jac[i].aaWidth; p++)
571 Alcodon cmap = new Alcodon();
572 cmap.setPos1(jac[i].codons[p][0]);
573 cmap.setPos2(jac[i].codons[p][1]);
574 cmap.setPos3(jac[i].codons[p][2]);
575 alc.addAlcodon(cmap);
577 if (jac[i].getProtMappings() != null
578 && jac[i].getProtMappings().length > 0)
580 SequenceI[] dnas = jac[i].getdnaSeqs();
581 jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings();
582 for (int m = 0; m < pmaps.length; m++)
584 AlcodMap alcmap = new AlcodMap();
585 alcmap.setDnasq("" + dnas[m].hashCode());
586 alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
588 alc.addAlcodMap(alcmap);
595 ///////////////////////////////////
596 if (av.currentTree != null)
598 // FIND ANY ASSOCIATED TREES
599 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
600 if (Desktop.desktop != null)
602 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
604 for (int t = 0; t < frames.length; t++)
606 if (frames[t] instanceof TreePanel)
608 TreePanel tp = (TreePanel) frames[t];
610 if (tp.treeCanvas.av.alignment == jal)
612 Tree tree = new Tree();
613 tree.setTitle(tp.getTitle());
614 tree.setCurrentTree((av.currentTree == tp.getTree()));
615 tree.setNewick(tp.getTree().toString());
616 tree.setThreshold(tp.treeCanvas.threshold);
618 tree.setFitToWindow(tp.fitToWindow.getState());
619 tree.setFontName(tp.getTreeFont().getName());
620 tree.setFontSize(tp.getTreeFont().getSize());
621 tree.setFontStyle(tp.getTreeFont().getStyle());
622 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
624 tree.setShowBootstrap(tp.bootstrapMenu.getState());
625 tree.setShowDistances(tp.distanceMenu.getState());
627 tree.setHeight(tp.getHeight());
628 tree.setWidth(tp.getWidth());
629 tree.setXpos(tp.getX());
630 tree.setYpos(tp.getY());
640 if (jal.getAlignmentAnnotation() != null)
642 jalview.datamodel.AlignmentAnnotation[] aa = jal
643 .getAlignmentAnnotation();
645 for (int i = 0; i < aa.length; i++)
647 Annotation an = new Annotation();
649 if (aa[i].annotationId != null)
651 annotationIds.put(aa[i].annotationId, aa[i]);
654 an.setId(aa[i].annotationId);
656 if (aa[i] == av.quality || aa[i] == av.conservation
657 || aa[i] == av.consensus)
659 an.setLabel(aa[i].label);
661 vamsasSet.addAnnotation(an);
665 an.setVisible(aa[i].visible);
667 an.setDescription(aa[i].description);
669 if (aa[i].sequenceRef != null)
671 an.setSequenceRef(aa[i].sequenceRef.getName());
677 an.setGraphType(aa[i].graph);
678 an.setGraphGroup(aa[i].graphGroup);
679 if (aa[i].getThreshold() != null)
681 ThresholdLine line = new ThresholdLine();
682 line.setLabel(aa[i].getThreshold().label);
683 line.setValue(aa[i].getThreshold().value);
684 line.setColour(aa[i].getThreshold().colour.getRGB());
685 an.setThresholdLine(line);
693 an.setLabel(aa[i].label);
694 if (aa[i].hasScore())
696 an.setScore(aa[i].getScore());
698 AnnotationElement ae;
699 if (aa[i].annotations != null)
701 an.setScoreOnly(false);
702 for (int a = 0; a < aa[i].annotations.length; a++)
704 if ((aa[i] == null) || (aa[i].annotations[a] == null))
709 ae = new AnnotationElement();
710 if (aa[i].annotations[a].description != null)
711 ae.setDescription(aa[i].annotations[a].description);
712 if (aa[i].annotations[a].displayCharacter != null)
713 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
715 if (!Float.isNaN(aa[i].annotations[a].value))
716 ae.setValue(aa[i].annotations[a].value);
719 if (aa[i].annotations[a].secondaryStructure != ' '
720 && aa[i].annotations[a].secondaryStructure != '\0')
722 .setSecondaryStructure(aa[i].annotations[a].secondaryStructure
725 if (aa[i].annotations[a].colour != null
726 && aa[i].annotations[a].colour != java.awt.Color.black)
728 ae.setColour(aa[i].annotations[a].colour.getRGB());
731 an.addAnnotationElement(ae);
736 an.setScoreOnly(true);
738 vamsasSet.addAnnotation(an);
743 if (jal.getGroups() != null)
745 JGroup[] groups = new JGroup[jal.getGroups().size()];
747 for (int i = 0; i < groups.length; i++)
749 groups[i] = new JGroup();
751 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal
752 .getGroups().elementAt(i);
753 groups[i].setStart(sg.getStartRes());
754 groups[i].setEnd(sg.getEndRes());
755 groups[i].setName(sg.getName());
758 if (sg.cs.conservationApplied())
760 groups[i].setConsThreshold(sg.cs.getConservationInc());
762 if (sg.cs instanceof jalview.schemes.UserColourScheme)
764 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
770 .setColour(ColourSchemeProperty.getColourName(sg.cs));
773 else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
776 .setColour(ColourSchemeProperty
777 .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
780 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
783 .setColour(SetUserColourScheme(sg.cs, userColours, jms));
787 groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
790 groups[i].setPidThreshold(sg.cs.getThreshold());
793 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
794 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
795 groups[i].setDisplayText(sg.getDisplayText());
796 groups[i].setColourText(sg.getColourText());
797 groups[i].setTextCol1(sg.textColour.getRGB());
798 groups[i].setTextCol2(sg.textColour2.getRGB());
799 groups[i].setTextColThreshold(sg.thresholdTextColour);
801 for (int s = 0; s < sg.getSize(); s++)
803 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
805 groups[i].addSeq(seqHash(seq));
809 jms.setJGroup(groups);
812 ///////////SAVE VIEWPORT
813 Viewport view = new Viewport();
814 view.setTitle(ap.alignFrame.getTitle());
815 view.setSequenceSetId(av.getSequenceSetId());
816 view.setViewName(av.viewName);
817 view.setGatheredViews(av.gatherViewsHere);
819 if (ap.av.explodedPosition != null)
821 view.setXpos(av.explodedPosition.x);
822 view.setYpos(av.explodedPosition.y);
823 view.setWidth(av.explodedPosition.width);
824 view.setHeight(av.explodedPosition.height);
828 view.setXpos(ap.alignFrame.getBounds().x);
829 view.setYpos(ap.alignFrame.getBounds().y);
830 view.setWidth(ap.alignFrame.getBounds().width);
831 view.setHeight(ap.alignFrame.getBounds().height);
834 view.setStartRes(av.startRes);
835 view.setStartSeq(av.startSeq);
837 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
839 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
842 else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
844 jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
845 .getGlobalColourScheme();
847 AnnotationColours ac = new AnnotationColours();
848 ac.setAboveThreshold(acg.getAboveThreshold());
849 ac.setThreshold(acg.getAnnotationThreshold());
850 ac.setAnnotation(acg.getAnnotation());
851 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
853 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
858 ac.setColourScheme(ColourSchemeProperty.getColourName(acg
862 ac.setMaxColour(acg.getMaxColour().getRGB());
863 ac.setMinColour(acg.getMinColour().getRGB());
864 view.setAnnotationColours(ac);
865 view.setBgColour("AnnotationColourGradient");
869 view.setBgColour(ColourSchemeProperty.getColourName(av
870 .getGlobalColourScheme()));
873 ColourSchemeI cs = av.getGlobalColourScheme();
877 if (cs.conservationApplied())
879 view.setConsThreshold(cs.getConservationInc());
880 if (cs instanceof jalview.schemes.UserColourScheme)
882 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
886 if (cs instanceof ResidueColourScheme)
888 view.setPidThreshold(cs.getThreshold());
892 view.setConservationSelected(av.getConservationSelected());
893 view.setPidSelected(av.getAbovePIDThreshold());
894 view.setFontName(av.font.getName());
895 view.setFontSize(av.font.getSize());
896 view.setFontStyle(av.font.getStyle());
897 view.setRenderGaps(av.renderGaps);
898 view.setShowAnnotation(av.getShowAnnotation());
899 view.setShowBoxes(av.getShowBoxes());
900 view.setShowColourText(av.getColourText());
901 view.setShowFullId(av.getShowJVSuffix());
902 view.setRightAlignIds(av.rightAlignIds);
903 view.setShowSequenceFeatures(av.showSequenceFeatures);
904 view.setShowText(av.getShowText());
905 view.setWrapAlignment(av.getWrapAlignment());
906 view.setTextCol1(av.textColour.getRGB());
907 view.setTextCol2(av.textColour2.getRGB());
908 view.setTextColThreshold(av.thresholdTextColour);
910 if (av.featuresDisplayed != null)
912 jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
914 String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
916 Vector settingsAdded = new Vector();
917 for (int ro = 0; ro < renderOrder.length; ro++)
919 Setting setting = new Setting();
920 setting.setType(renderOrder[ro]);
921 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
922 .getColour(renderOrder[ro]).getRGB());
924 setting.setDisplay(av.featuresDisplayed
925 .containsKey(renderOrder[ro]));
926 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
930 setting.setOrder(rorder);
932 fs.addSetting(setting);
933 settingsAdded.addElement(renderOrder[ro]);
936 //Make sure we save none displayed feature settings
937 Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
939 while (en.hasMoreElements())
941 String key = en.nextElement().toString();
942 if (settingsAdded.contains(key))
947 Setting setting = new Setting();
948 setting.setType(key);
949 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
950 .getColour(key).getRGB());
952 setting.setDisplay(false);
953 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
957 setting.setOrder(rorder);
959 fs.addSetting(setting);
960 settingsAdded.addElement(key);
962 en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
963 Vector groupsAdded = new Vector();
964 while (en.hasMoreElements())
966 String grp = en.nextElement().toString();
967 if (groupsAdded.contains(grp))
971 Group g = new Group();
974 .setDisplay(((Boolean) ap.seqPanel.seqCanvas
975 .getFeatureRenderer().featureGroups.get(grp))
978 groupsAdded.addElement(grp);
980 jms.setFeatureSettings(fs);
984 if (av.hasHiddenColumns)
986 for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
988 int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
990 HiddenColumns hc = new HiddenColumns();
991 hc.setStart(region[0]);
992 hc.setEnd(region[1]);
993 view.addHiddenColumns(hc);
997 jms.addViewport(view);
999 object.setJalviewModelSequence(jms);
1000 object.getVamsasModel().addSequenceSet(vamsasSet);
1002 if (jout!=null && fileName!=null)
1004 //We may not want to write the object to disk,
1005 //eg we can copy the alignViewport to a new view object
1006 //using save and then load
1009 JarEntry entry = new JarEntry(fileName);
1010 jout.putNextEntry(entry);
1011 PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
1013 org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(pout);
1014 marshaller.marshal(object);
1017 } catch (Exception ex)
1019 // TODO: raise error in GUI if marshalling failed.
1020 ex.printStackTrace();
1026 private Sequence createVamsasSequence(String id, SequenceI jds)
1028 return createVamsasSequence(true, id, jds, null);
1031 private Sequence createVamsasSequence(boolean recurse, String id,
1032 SequenceI jds, SequenceI parentseq)
1034 Sequence vamsasSeq = new Sequence();
1035 vamsasSeq.setId(id);
1036 vamsasSeq.setName(jds.getName());
1037 vamsasSeq.setSequence(jds.getSequenceAsString());
1038 vamsasSeq.setDescription(jds.getDescription());
1039 jalview.datamodel.DBRefEntry[] dbrefs = null;
1040 if (jds.getDatasetSequence() != null)
1042 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
1043 if (jds.getDatasetSequence().getDBRef() != null)
1045 dbrefs = jds.getDatasetSequence().getDBRef();
1050 vamsasSeq.setDsseqid(id); // so we can tell which sequences really are dataset sequences only
1051 dbrefs = jds.getDBRef();
1055 for (int d = 0; d < dbrefs.length; d++)
1057 DBRef dbref = new DBRef();
1058 dbref.setSource(dbrefs[d].getSource());
1059 dbref.setVersion(dbrefs[d].getVersion());
1060 dbref.setAccessionId(dbrefs[d].getAccessionId());
1061 if (dbrefs[d].hasMap())
1063 Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
1065 dbref.setMapping(mp);
1067 vamsasSeq.addDBRef(dbref);
1073 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
1074 SequenceI parentseq, SequenceI jds, boolean recurse)
1077 if (jmp.getMap() != null)
1081 jalview.util.MapList mlst = jmp.getMap();
1082 int r[] = mlst.getFromRanges();
1083 for (int s = 0; s < r.length; s += 2)
1085 MapListFrom mfrom = new MapListFrom();
1086 mfrom.setStart(r[s]);
1087 mfrom.setEnd(r[s + 1]);
1088 mp.addMapListFrom(mfrom);
1090 r = mlst.getToRanges();
1091 for (int s = 0; s < r.length; s += 2)
1093 MapListTo mto = new MapListTo();
1095 mto.setEnd(r[s + 1]);
1096 mp.addMapListTo(mto);
1098 mp.setMapFromUnit(mlst.getFromRatio());
1099 mp.setMapToUnit(mlst.getToRatio());
1100 if (jmp.getTo() != null)
1102 MappingChoice mpc = new MappingChoice();
1104 && (parentseq != jmp.getTo() || parentseq
1105 .getDatasetSequence() != jmp.getTo()))
1107 mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo())
1108 , jmp.getTo(), jds));
1113 SequenceI ps = null;
1114 if (parentseq != jmp.getTo()
1115 && parentseq.getDatasetSequence() != jmp.getTo())
1117 // chaining dbref rather than a handshaking one
1118 jmpid = seqHash(ps = jmp.getTo());
1122 jmpid = seqHash(ps = parentseq);
1124 mpc.setDseqFor(jmpid);
1125 if (!seqRefIds.containsKey(mpc.getDseqFor()))
1127 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
1128 seqRefIds.put(mpc.getDseqFor(), ps);
1132 jalview.bin.Cache.log.debug("reusing DseqFor ID");
1135 mp.setMappingChoice(mpc);
1141 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
1142 Vector userColours, JalviewModelSequence jms)
1145 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
1147 if (!userColours.contains(ucs))
1149 userColours.add(ucs);
1151 java.awt.Color[] colours = ucs.getColours();
1152 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
1153 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
1155 for (int i = 0; i < colours.length; i++)
1157 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1158 col.setName(ResidueProperties.aa[i]);
1159 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1160 jbucs.addColour(col);
1162 if (ucs.getLowerCaseColours() != null)
1164 colours = ucs.getLowerCaseColours();
1165 for (int i = 0; i < colours.length; i++)
1167 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1168 col.setName(ResidueProperties.aa[i].toLowerCase());
1169 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1170 jbucs.addColour(col);
1174 id = "ucs" + userColours.indexOf(ucs);
1176 uc.setUserColourScheme(jbucs);
1177 jms.addUserColours(uc);
1183 jalview.schemes.UserColourScheme GetUserColourScheme(
1184 JalviewModelSequence jms, String id)
1186 UserColours[] uc = jms.getUserColours();
1187 UserColours colours = null;
1189 for (int i = 0; i < uc.length; i++)
1191 if (uc[i].getId().equals(id))
1199 java.awt.Color[] newColours = new java.awt.Color[24];
1201 for (int i = 0; i < 24; i++)
1203 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1204 .getUserColourScheme().getColour(i).getRGB(), 16));
1207 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
1210 if (colours.getUserColourScheme().getColourCount() > 24)
1212 newColours = new java.awt.Color[23];
1213 for (int i = 0; i < 23; i++)
1215 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1216 .getUserColourScheme().getColour(i + 24).getRGB(), 16));
1218 ucs.setLowerCaseColours(newColours);
1227 * @param file DOCUMENT ME!
1229 public AlignFrame LoadJalviewAlign(final String file)
1231 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
1233 jalview.gui.AlignFrame af = null;
1235 seqRefIds = new Hashtable();
1236 viewportsAdded = new Hashtable();
1237 frefedSequence = new Vector();
1238 Hashtable gatherToThisFrame = new Hashtable();
1240 String errorMessage = null;
1244 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
1247 if (file.startsWith("http://"))
1249 url = new URL(file);
1252 JarInputStream jin = null;
1253 JarEntry jarentry = null;
1260 jin = new JarInputStream(url.openStream());
1264 jin = new JarInputStream(new FileInputStream(file));
1267 for (int i = 0; i < entryCount; i++)
1269 jarentry = jin.getNextJarEntry();
1272 if (jarentry != null && jarentry.getName().endsWith(".xml"))
1274 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
1275 JalviewModel object = new JalviewModel();
1277 Unmarshaller unmar = new Unmarshaller(object);
1278 unmar.setValidation(false);
1279 object = (JalviewModel) unmar.unmarshal(in);
1281 af = LoadFromObject(object, file, true);
1282 if (af.viewport.gatherViewsHere)
1284 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
1288 else if (jarentry != null)
1290 //Some other file here.
1293 } while (jarentry != null);
1294 resolveFrefedSequences();
1295 } catch (java.io.FileNotFoundException ex)
1297 ex.printStackTrace();
1298 errorMessage = "Couldn't locate Jalview XML file : " + file;
1299 System.err.println("Exception whilst loading jalview XML file : "
1301 } catch (java.net.UnknownHostException ex)
1303 ex.printStackTrace();
1304 errorMessage = "Couldn't locate Jalview XML file : " + file;
1305 System.err.println("Exception whilst loading jalview XML file : "
1307 } catch (Exception ex)
1309 System.err.println("Parsing as Jalview Version 2 file failed.");
1310 ex.printStackTrace(System.err);
1312 //Is Version 1 Jar file?
1314 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(file);
1315 } catch (Exception ex2) {
1316 System.err.println("Exception whilst loading as jalviewXMLV1:");
1317 ex2.printStackTrace();
1321 if (Desktop.instance != null)
1323 Desktop.instance.stopLoading();
1327 System.out.println("Successfully loaded archive file");
1330 ex.printStackTrace();
1332 System.err.println("Exception whilst loading jalview XML file : "
1336 if (Desktop.instance != null)
1338 Desktop.instance.stopLoading();
1341 Enumeration en = gatherToThisFrame.elements();
1342 while (en.hasMoreElements())
1344 Desktop.instance.gatherViews((AlignFrame) en.nextElement());
1347 if (errorMessage != null)
1349 final String finalErrorMessage = errorMessage;
1352 javax.swing.SwingUtilities.invokeLater(new Runnable()
1356 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1357 finalErrorMessage, "Error loading Jalview file",
1358 JOptionPane.WARNING_MESSAGE);
1362 System.err.println("Problem loading Jalview file: "+errorMessage);
1369 Hashtable alreadyLoadedPDB;
1371 String loadPDBFile(String file, String pdbId)
1373 if (alreadyLoadedPDB == null)
1374 alreadyLoadedPDB = new Hashtable();
1376 if (alreadyLoadedPDB.containsKey(pdbId))
1377 return alreadyLoadedPDB.get(pdbId).toString();
1381 JarInputStream jin = null;
1383 if (file.startsWith("http://"))
1385 jin = new JarInputStream(new URL(file).openStream());
1389 jin = new JarInputStream(new FileInputStream(file));
1392 JarEntry entry = null;
1395 entry = jin.getNextJarEntry();
1396 } while (!entry.getName().equals(pdbId));
1398 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1399 File outFile = File.createTempFile("jalview_pdb", ".txt");
1400 outFile.deleteOnExit();
1401 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1404 while ((data = in.readLine()) != null)
1408 try { out.flush(); } catch (Exception foo) {};
1411 alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
1412 return outFile.getAbsolutePath();
1414 } catch (Exception ex)
1416 ex.printStackTrace();
1422 AlignFrame LoadFromObject(JalviewModel object, String file,
1423 boolean loadTreesAndStructures)
1425 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1426 Sequence[] vamsasSeq = vamsasSet.getSequence();
1428 JalviewModelSequence jms = object.getJalviewModelSequence();
1430 Viewport view = jms.getViewport(0);
1432 //////////////////////////////////
1435 Vector hiddenSeqs = null;
1436 jalview.datamodel.Sequence jseq;
1438 ArrayList tmpseqs = new ArrayList();
1440 boolean multipleView = false;
1442 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1443 int vi=0; // counter in vamsasSeq array
1444 for (int i = 0; i < JSEQ.length; i++)
1446 String seqId = JSEQ[i].getId() + "";
1448 if (seqRefIds.get(seqId) != null)
1450 tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId));
1451 multipleView = true;
1455 jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
1456 vamsasSeq[vi].getSequence());
1457 jseq.setDescription(vamsasSeq[vi].getDescription());
1458 jseq.setStart(JSEQ[i].getStart());
1459 jseq.setEnd(JSEQ[i].getEnd());
1460 jseq.setVamsasId(uniqueSetSuffix + seqId);
1461 seqRefIds.put(vamsasSeq[vi].getId()+"", jseq);
1466 if (JSEQ[i].getHidden())
1468 if (hiddenSeqs == null)
1470 hiddenSeqs = new Vector();
1473 hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
1480 // Create the alignment object from the sequence set
1481 /////////////////////////////////
1482 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
1485 tmpseqs.toArray(orderedSeqs);
1487 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
1490 /// Add the alignment properties
1491 for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
1493 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
1494 al.setProperty(ssp.getKey(), ssp.getValue());
1498 // SequenceFeatures are added to the DatasetSequence,
1499 // so we must create or recover the dataset before loading features
1500 /////////////////////////////////
1501 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
1503 // older jalview projects do not have a dataset id.
1504 al.setDataset(null);
1508 recoverDatasetFor(vamsasSet, al);
1510 /////////////////////////////////
1512 Hashtable pdbloaded = new Hashtable();
1515 for (int i = 0; i < vamsasSeq.length; i++)
1517 if (JSEQ[i].getFeaturesCount() > 0)
1519 Features[] features = JSEQ[i].getFeatures();
1520 for (int f = 0; f < features.length; f++)
1522 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
1523 features[f].getType(), features[f].getDescription(),
1524 features[f].getStatus(), features[f].getBegin(),
1525 features[f].getEnd(), features[f].getFeatureGroup());
1527 sf.setScore(features[f].getScore());
1528 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1530 OtherData keyValue = features[f].getOtherData(od);
1531 if (keyValue.getKey().startsWith("LINK"))
1533 sf.addLink(keyValue.getValue());
1537 sf.setValue(keyValue.getKey(), keyValue.getValue());
1542 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1545 if (vamsasSeq[i].getDBRefCount() > 0)
1547 addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
1549 if (JSEQ[i].getPdbidsCount() > 0)
1551 Pdbids[] ids = JSEQ[i].getPdbids();
1552 for (int p = 0; p < ids.length; p++)
1554 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
1555 entry.setId(ids[p].getId());
1556 entry.setType(ids[p].getType());
1557 if (ids[p].getFile() != null)
1559 if (!pdbloaded.containsKey(ids[p].getFile()))
1561 entry.setFile(loadPDBFile(file, ids[p].getId()));
1565 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1569 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1575 /////////////////////////////////
1576 // LOAD SEQUENCE MAPPINGS
1577 if (vamsasSet.getAlcodonFrameCount() > 0)
1579 AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
1580 for (int i = 0; i < alc.length; i++)
1582 jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
1583 alc[i].getAlcodonCount());
1584 if (alc[i].getAlcodonCount() > 0)
1586 Alcodon[] alcods = alc[i].getAlcodon();
1587 for (int p = 0; p < cf.codons.length; p++)
1589 cf.codons[p] = new int[3];
1590 cf.codons[p][0] = (int) alcods[p].getPos1();
1591 cf.codons[p][1] = (int) alcods[p].getPos2();
1592 cf.codons[p][2] = (int) alcods[p].getPos3();
1595 if (alc[i].getAlcodMapCount() > 0)
1597 AlcodMap[] maps = alc[i].getAlcodMap();
1598 for (int m = 0; m < maps.length; m++)
1600 SequenceI dnaseq = (SequenceI) seqRefIds
1601 .get(maps[m].getDnasq());
1603 jalview.datamodel.Mapping mapping = null;
1604 // attach to dna sequence reference.
1605 if (maps[m].getMapping() != null)
1607 mapping = addMapping(maps[m]
1612 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
1615 frefedSequence.add(new Object[] { maps[m].getDnasq(), cf, mapping});
1619 al.addCodonFrame(cf);
1624 //////////////////////////////////
1626 boolean hideQuality = true, hideConservation = true, hideConsensus = true;
1628 if (vamsasSet.getAnnotationCount() > 0)
1630 Annotation[] an = vamsasSet.getAnnotation();
1632 for (int i = 0; i < an.length; i++)
1634 if (an[i].getLabel().equals("Quality"))
1636 hideQuality = false;
1639 else if (an[i].getLabel().equals("Conservation"))
1641 hideConservation = false;
1644 else if (an[i].getLabel().equals("Consensus"))
1646 hideConsensus = false;
1650 if (an[i].getId() != null
1651 && annotationIds.containsKey(an[i].getId()))
1653 jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
1654 .get(an[i].getId());
1655 if (an[i].hasVisible())
1656 jda.visible = an[i].getVisible();
1658 al.addAnnotation(jda);
1663 AnnotationElement[] ae = an[i].getAnnotationElement();
1664 jalview.datamodel.Annotation[] anot = null;
1666 if (!an[i].getScoreOnly())
1668 anot = new jalview.datamodel.Annotation[al.getWidth()];
1670 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
1672 if (ae[aa].getPosition() >= anot.length)
1675 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
1677 ae[aa].getDisplayCharacter(), ae[aa].getDescription(), (ae[aa]
1678 .getSecondaryStructure() == null || ae[aa]
1679 .getSecondaryStructure().length() == 0) ? ' ' : ae[aa]
1680 .getSecondaryStructure().charAt(0), ae[aa].getValue()
1683 // JBPNote: Consider verifying dataflow for IO of secondary structure annotation read from Stockholm files
1684 // this was added to try to ensure that
1685 //if (anot[ae[aa].getPosition()].secondaryStructure>' ')
1687 // anot[ae[aa].getPosition()].displayCharacter = "";
1689 anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]
1693 jalview.datamodel.AlignmentAnnotation jaa = null;
1695 if (an[i].getGraph())
1697 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1698 an[i].getDescription(), anot, 0, 0, an[i].getGraphType());
1700 jaa.graphGroup = an[i].getGraphGroup();
1702 if (an[i].getThresholdLine() != null)
1704 jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
1705 .getThresholdLine().getValue(), an[i]
1706 .getThresholdLine().getLabel(), new java.awt.Color(
1707 an[i].getThresholdLine().getColour())));
1714 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1715 an[i].getDescription(), anot);
1718 if (an[i].getId() != null)
1720 annotationIds.put(an[i].getId(), jaa);
1721 jaa.annotationId = an[i].getId();
1724 if (an[i].getSequenceRef() != null)
1726 if (al.findName(an[i].getSequenceRef()) != null)
1728 jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
1730 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1733 if (an[i].hasScore())
1735 jaa.setScore(an[i].getScore());
1738 if (an[i].hasVisible())
1739 jaa.visible = an[i].getVisible();
1741 al.addAnnotation(jaa);
1745 /////////////////////////
1747 if (jms.getJGroupCount() > 0)
1749 JGroup[] groups = jms.getJGroup();
1751 for (int i = 0; i < groups.length; i++)
1753 ColourSchemeI cs = null;
1755 if (groups[i].getColour() != null)
1757 if (groups[i].getColour().startsWith("ucs"))
1759 cs = GetUserColourScheme(jms, groups[i].getColour());
1763 cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
1768 cs.setThreshold(groups[i].getPidThreshold(), true);
1772 Vector seqs = new Vector();
1774 for (int s = 0; s < groups[i].getSeqCount(); s++)
1776 String seqId = groups[i].getSeq(s) + "";
1777 jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds
1782 seqs.addElement(ts);
1786 if (seqs.size() < 1)
1791 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
1792 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1793 groups[i].getDisplayText(), groups[i].getColourText(),
1794 groups[i].getStart(), groups[i].getEnd());
1797 .setOutlineColour(new java.awt.Color(groups[i]
1798 .getOutlineColour()));
1800 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
1801 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
1802 sg.thresholdTextColour = groups[i].getTextColThreshold();
1804 if (groups[i].getConsThreshold() != 0)
1806 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
1807 "All", ResidueProperties.propHash, 3, sg
1808 .getSequences(null), 0, sg.getWidth() - 1);
1810 c.verdict(false, 25);
1811 sg.cs.setConservation(c);
1818 /////////////////////////////////
1821 AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
1823 af.setFileName(file, "Jalview");
1825 for (int i = 0; i < JSEQ.length; i++)
1827 af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
1828 new java.awt.Color(JSEQ[i].getColour()));
1831 //If we just load in the same jar file again, the sequenceSetId
1832 //will be the same, and we end up with multiple references
1833 //to the same sequenceSet. We must modify this id on load
1834 //so that each load of the file gives a unique id
1835 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
1837 af.viewport.gatherViewsHere = view.getGatheredViews();
1839 if (view.getSequenceSetId() != null)
1841 jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
1842 .get(uniqueSeqSetId);
1844 af.viewport.sequenceSetID = uniqueSeqSetId;
1848 af.viewport.historyList = av.historyList;
1849 af.viewport.redoList = av.redoList;
1853 viewportsAdded.put(uniqueSeqSetId, af.viewport);
1856 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1858 if (hiddenSeqs != null)
1860 for (int s = 0; s < JSEQ.length; s++)
1862 jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
1864 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
1866 hidden.addSequence(al
1867 .getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
1869 af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
1872 jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
1875 for (int s = 0; s < hiddenSeqs.size(); s++)
1877 hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
1880 af.viewport.hideSequence(hseqs);
1884 if ((hideConsensus || hideQuality || hideConservation)
1885 && al.getAlignmentAnnotation() != null)
1887 int hSize = al.getAlignmentAnnotation().length;
1888 for (int h = 0; h < hSize; h++)
1890 if ((hideConsensus && al.getAlignmentAnnotation()[h].label
1891 .equals("Consensus"))
1892 || (hideQuality && al.getAlignmentAnnotation()[h].label
1894 || (hideConservation && al.getAlignmentAnnotation()[h].label
1895 .equals("Conservation")))
1897 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1902 af.alignPanel.adjustAnnotationHeight();
1905 if (view.getViewName() != null)
1907 af.viewport.viewName = view.getViewName();
1908 af.setInitialTabVisible();
1910 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
1913 af.viewport.setShowAnnotation(view.getShowAnnotation());
1914 af.viewport.setAbovePIDThreshold(view.getPidSelected());
1916 af.viewport.setColourText(view.getShowColourText());
1918 af.viewport.setConservationSelected(view.getConservationSelected());
1919 af.viewport.setShowJVSuffix(view.getShowFullId());
1920 af.viewport.rightAlignIds = view.getRightAlignIds();
1921 af.viewport.setFont(new java.awt.Font(view.getFontName(), view
1922 .getFontStyle(), view.getFontSize()));
1923 af.alignPanel.fontChanged();
1924 af.viewport.setRenderGaps(view.getRenderGaps());
1925 af.viewport.setWrapAlignment(view.getWrapAlignment());
1926 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1927 af.viewport.setShowAnnotation(view.getShowAnnotation());
1928 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1930 af.viewport.setShowBoxes(view.getShowBoxes());
1932 af.viewport.setShowText(view.getShowText());
1934 af.viewport.textColour = new java.awt.Color(view.getTextCol1());
1935 af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
1936 af.viewport.thresholdTextColour = view.getTextColThreshold();
1938 af.viewport.setStartRes(view.getStartRes());
1939 af.viewport.setStartSeq(view.getStartSeq());
1941 ColourSchemeI cs = null;
1943 if (view.getBgColour() != null)
1945 if (view.getBgColour().startsWith("ucs"))
1947 cs = GetUserColourScheme(jms, view.getBgColour());
1949 else if (view.getBgColour().startsWith("Annotation"))
1951 //int find annotation
1952 for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1954 if (af.viewport.alignment.getAlignmentAnnotation()[i].label
1955 .equals(view.getAnnotationColours().getAnnotation()))
1957 if (af.viewport.alignment.getAlignmentAnnotation()[i]
1958 .getThreshold() == null)
1960 af.viewport.alignment.getAlignmentAnnotation()[i]
1961 .setThreshold(new jalview.datamodel.GraphLine(view
1962 .getAnnotationColours().getThreshold(),
1963 "Threshold", java.awt.Color.black)
1968 if (view.getAnnotationColours().getColourScheme()
1971 cs = new AnnotationColourGradient(af.viewport.alignment
1972 .getAlignmentAnnotation()[i], new java.awt.Color(view
1973 .getAnnotationColours().getMinColour()),
1974 new java.awt.Color(view.getAnnotationColours()
1975 .getMaxColour()), view.getAnnotationColours()
1976 .getAboveThreshold());
1978 else if (view.getAnnotationColours().getColourScheme()
1981 cs = new AnnotationColourGradient(af.viewport.alignment
1982 .getAlignmentAnnotation()[i], GetUserColourScheme(
1983 jms, view.getAnnotationColours().getColourScheme()),
1984 view.getAnnotationColours().getAboveThreshold());
1988 cs = new AnnotationColourGradient(af.viewport.alignment
1989 .getAlignmentAnnotation()[i], ColourSchemeProperty
1990 .getColour(al, view.getAnnotationColours()
1991 .getColourScheme()), view
1992 .getAnnotationColours().getAboveThreshold());
1995 // Also use these settings for all the groups
1996 if (al.getGroups() != null)
1998 for (int g = 0; g < al.getGroups().size(); g++)
2000 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
2001 .getGroups().elementAt(g);
2008 /* if (view.getAnnotationColours().getColourScheme().equals("None"))
2010 sg.cs = new AnnotationColourGradient(
2011 af.viewport.alignment.getAlignmentAnnotation()[i],
2012 new java.awt.Color(view.getAnnotationColours().
2014 new java.awt.Color(view.getAnnotationColours().
2016 view.getAnnotationColours().getAboveThreshold());
2020 sg.cs = new AnnotationColourGradient(
2021 af.viewport.alignment.getAlignmentAnnotation()[i],
2022 sg.cs, view.getAnnotationColours()
2023 .getAboveThreshold());
2036 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
2041 cs.setThreshold(view.getPidThreshold(), true);
2042 cs.setConsensus(af.viewport.hconsensus);
2046 af.viewport.setGlobalColourScheme(cs);
2047 af.viewport.setColourAppliesToAllGroups(false);
2049 if (view.getConservationSelected() && cs != null)
2051 cs.setConservationInc(view.getConsThreshold());
2054 af.changeColour(cs);
2056 af.viewport.setColourAppliesToAllGroups(true);
2058 if (view.getShowSequenceFeatures())
2060 af.viewport.showSequenceFeatures = true;
2063 if (jms.getFeatureSettings() != null)
2065 af.viewport.featuresDisplayed = new Hashtable();
2066 String[] renderOrder = new String[jms.getFeatureSettings()
2067 .getSettingCount()];
2068 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
2070 Setting setting = jms.getFeatureSettings().getSetting(fs);
2072 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
2073 setting.getType(), new java.awt.Color(setting.getColour()));
2074 renderOrder[fs] = setting.getType();
2075 if (setting.hasOrder())
2076 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2077 setting.getType(), setting.getOrder());
2079 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2081 fs / jms.getFeatureSettings().getSettingCount());
2082 if (setting.getDisplay())
2084 af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
2085 setting.getColour()));
2088 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
2090 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
2091 for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
2093 Group grp = jms.getFeatureSettings().getGroup(gs);
2094 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
2098 if (view.getHiddenColumnsCount() > 0)
2100 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
2102 af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
2103 .getHiddenColumns(c).getEnd() //+1
2108 af.setMenusFromViewport(af.viewport);
2110 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
2114 ///////////////////////////////////////
2115 if (loadTreesAndStructures && jms.getTreeCount() > 0)
2119 for (int t = 0; t < jms.getTreeCount(); t++)
2122 Tree tree = jms.getTree(t);
2124 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(tree
2125 .getNewick()), tree.getTitle(), tree.getWidth(), tree
2126 .getHeight(), tree.getXpos(), tree.getYpos());
2128 tp.fitToWindow.setState(tree.getFitToWindow());
2129 tp.fitToWindow_actionPerformed(null);
2131 if (tree.getFontName() != null)
2133 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
2134 .getFontStyle(), tree.getFontSize()));
2138 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
2139 .getFontStyle(), tree.getFontSize()));
2142 tp.showPlaceholders(tree.getMarkUnlinked());
2143 tp.showBootstrap(tree.getShowBootstrap());
2144 tp.showDistances(tree.getShowDistances());
2146 tp.treeCanvas.threshold = tree.getThreshold();
2148 if (tree.getCurrentTree())
2150 af.viewport.setCurrentTree(tp.getTree());
2154 } catch (Exception ex)
2156 ex.printStackTrace();
2161 if (loadTreesAndStructures)
2163 for (int i = 0; i < JSEQ.length; i++)
2165 if (JSEQ[i].getPdbidsCount() > 0)
2167 Pdbids[] ids = JSEQ[i].getPdbids();
2168 for (int p = 0; p < ids.length; p++)
2170 for (int s = 0; s < ids[p].getStructureStateCount(); s++)
2172 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
2174 jpdb.setFile(loadPDBFile(ids[p].getFile(), ids[p].getId()));
2175 jpdb.setId(ids[p].getId());
2177 int x = ids[p].getStructureState(s).getXpos();
2178 int y = ids[p].getStructureState(s).getYpos();
2179 int width = ids[p].getStructureState(s).getWidth();
2180 int height = ids[p].getStructureState(s).getHeight();
2182 java.awt.Component comp = null;
2184 JInternalFrame[] frames = null;
2187 frames = Desktop.desktop.getAllFrames();
2189 catch (ArrayIndexOutOfBoundsException e)
2191 // occasional No such child exceptions are thrown here...
2195 } catch (Exception f) {};
2197 } while (frames==null);
2198 for (int f = 0; f < frames.length; f++)
2200 if (frames[f] instanceof AppJmol)
2202 if (frames[f].getX() == x && frames[f].getY() == y
2203 && frames[f].getHeight() == height
2204 && frames[f].getWidth() == width)
2212 Desktop.desktop.getComponentAt(x, y);
2214 String pdbFile = loadPDBFile(file, ids[p].getId());
2216 jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
2217 { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId()
2222 String state = ids[p].getStructureState(s).getContent();
2224 StringBuffer newFileLoc = new StringBuffer(state.substring(
2225 0, state.indexOf("\"", state.indexOf("load")) + 1));
2227 newFileLoc.append(jpdb.getFile());
2228 newFileLoc.append(state.substring(state.indexOf("\"", state
2229 .indexOf("load \"") + 6)));
2231 new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel,
2232 newFileLoc.toString(), new java.awt.Rectangle(x, y,
2236 else if (comp != null)
2238 StructureSelectionManager.getStructureSelectionManager()
2239 .setMapping(seq, null, pdbFile,
2240 jalview.io.AppletFormatAdapter.FILE);
2242 ((AppJmol) comp).addSequence(seq);
2253 private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
2255 jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
2256 Vector dseqs = null;
2259 // create a list of new dataset sequences
2260 dseqs = new Vector();
2262 for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
2264 Sequence vamsasSeq = vamsasSet.getSequence(i);
2265 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
2267 // create a new dataset
2270 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
2271 dseqs.copyInto(dsseqs);
2272 ds = new jalview.datamodel.Alignment(dsseqs);
2273 addDatasetRef(vamsasSet.getDatasetId(), ds);
2275 // set the dataset for the newly imported alignment.
2276 if (al.getDataset() == null)
2285 * @param vamsasSeq sequence definition to create/merge dataset sequence for
2286 * @param ds dataset alignment
2287 * @param dseqs vector to add new dataset sequence to
2289 private void ensureJalviewDatasetSequence(Sequence vamsasSeq, AlignmentI ds, Vector dseqs)
2291 // JBP TODO: Check this is called for AlCodonFrames to support recovery of xRef Codon Maps
2292 jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds.get(vamsasSeq.getId());
2293 jalview.datamodel.SequenceI dsq = null;
2294 if (sq!=null && sq.getDatasetSequence()!=null)
2296 dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
2299 String sqid = vamsasSeq.getDsseqid();
2302 // need to create or add a new dataset sequence reference to this sequence
2305 dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
2310 // make a new dataset sequence
2311 dsq = sq.createDatasetSequence();
2314 // make up a new dataset reference for this sequence
2315 sqid = seqHash(dsq);
2317 dsq.setVamsasId(uniqueSetSuffix + sqid);
2318 seqRefIds.put(sqid, dsq);
2323 dseqs.addElement(dsq);
2328 ds.addSequence(dsq);
2332 { // make this dataset sequence sq's dataset sequence
2333 sq.setDatasetSequence(dsq);
2337 // TODO: refactor this as a merge dataset sequence function
2338 // now check that sq (the dataset sequence) sequence really is the union of all references to it
2339 //boolean pre = sq.getStart() < dsq.getStart();
2340 //boolean post = sq.getEnd() > dsq.getEnd();
2344 StringBuffer sb = new StringBuffer();
2345 String newres = jalview.analysis.AlignSeq.extractGaps(
2346 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
2347 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString()) && newres.length()>dsq.getLength())
2349 // Update with the longer sequence.
2355 .substring(0, dsq.getStart() - sq.getStart()));
2356 dsq.setStart(sq.getStart());
2360 sb.append(newres.substring(newres.length() - sq.getEnd()
2362 dsq.setEnd(sq.getEnd());
2365 dsq.setSequence(sb.toString());
2367 //TODO: merges will never happen if we 'know' we have the real dataset sequence - this should be detected when id==dssid
2369 .println("DEBUG Notice: Merged dataset sequence"); // ("
2370 // + (pre ? "prepended" : "") + " "
2371 //+ (post ? "appended" : ""));
2376 java.util.Hashtable datasetIds = null;
2378 private Alignment getDatasetFor(String datasetId)
2380 if (datasetIds == null)
2382 datasetIds = new Hashtable();
2385 if (datasetIds.containsKey(datasetId))
2387 return (Alignment) datasetIds.get(datasetId);
2392 private void addDatasetRef(String datasetId, Alignment dataset)
2394 if (datasetIds == null)
2396 datasetIds = new Hashtable();
2398 datasetIds.put(datasetId, dataset);
2401 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
2403 for (int d = 0; d < sequence.getDBRefCount(); d++)
2405 DBRef dr = sequence.getDBRef(d);
2406 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
2407 sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
2408 .getVersion(), sequence.getDBRef(d).getAccessionId());
2409 if (dr.getMapping() != null)
2411 entry.setMap(addMapping(dr.getMapping()));
2413 datasetSequence.addDBRef(entry);
2417 private jalview.datamodel.Mapping addMapping(Mapping m)
2419 SequenceI dsto = null;
2420 // Mapping m = dr.getMapping();
2421 int fr[] = new int[m.getMapListFromCount() * 2];
2422 Enumeration f = m.enumerateMapListFrom();
2423 for (int _i = 0; f.hasMoreElements(); _i += 2)
2425 MapListFrom mf = (MapListFrom) f.nextElement();
2426 fr[_i] = mf.getStart();
2427 fr[_i + 1] = mf.getEnd();
2429 int fto[] = new int[m.getMapListToCount() * 2];
2430 f = m.enumerateMapListTo();
2431 for (int _i = 0; f.hasMoreElements(); _i += 2)
2433 MapListTo mf = (MapListTo) f.nextElement();
2434 fto[_i] = mf.getStart();
2435 fto[_i + 1] = mf.getEnd();
2437 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
2438 fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
2439 if (m.getMappingChoice() != null)
2441 MappingChoice mc = m.getMappingChoice();
2442 if (mc.getDseqFor() != null)
2444 if (seqRefIds.containsKey(mc.getDseqFor()))
2449 jmap.setTo((SequenceI) seqRefIds.get(mc.getDseqFor()));
2453 frefedSequence.add(new Object[]
2454 { mc.getDseqFor(), jmap });
2460 * local sequence definition
2462 Sequence ms = mc.getSequence();
2463 jalview.datamodel.Sequence djs=null;
2464 String sqid = ms.getDsseqid();
2465 if (sqid!=null && sqid.length()>0)
2468 * recover dataset sequence
2470 djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
2472 System.err.println("Warning - making up dataset sequence id for DbRef sequence map reference");
2473 sqid = ((Object)ms).toString(); // make up a new hascode for undefined dataset sequence hash (unlikely to happen)
2478 * make a new dataset sequence and add it to refIds hash
2480 djs = new jalview.datamodel.Sequence(ms
2481 .getName(), ms.getSequence());
2482 djs.setStart(jmap.getMap().getToLowest());
2483 djs.setEnd(jmap.getMap().getToHighest());
2484 djs.setVamsasId(uniqueSetSuffix + sqid);
2486 seqRefIds.put(sqid, djs);
2489 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
2498 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
2499 boolean keepSeqRefs)
2501 jalview.schemabinding.version2.JalviewModel jm =
2502 SaveState(ap, null, null);
2507 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
2511 uniqueSetSuffix = "";
2514 viewportsAdded = new Hashtable();
2516 AlignFrame af = LoadFromObject(jm, null, false);
2517 af.alignPanels.clear();
2518 af.closeMenuItem_actionPerformed(true);
2520 /* if(ap.av.alignment.getAlignmentAnnotation()!=null)
2522 for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length; i++)
2524 if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated)
2526 af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
2527 ap.av.alignment.getAlignmentAnnotation()[i];
2532 return af.alignPanel;
2535 * @see java.lang.Object#finalize()
2537 protected void finalize() throws Throwable
2539 // really make sure we have no buried refs left.
2541 this.seqRefIds = null;
2542 this.seqsToIds = null;