2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
3 * Copyright (C) 2008 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 as a Jalview XML stream.
41 * Note: the vamsas objects referred to here are primitive versions of the
42 * VAMSAS project schema elements - they are not the same and most likely never
48 public class Jalview2XML
51 * create/return unique hash string for sq
54 * @return new or existing unique string for sq
56 String seqHash(SequenceI sq)
58 if (seqsToIds == null)
62 if (seqsToIds.containsKey(sq))
64 return (String) seqsToIds.get(sq);
68 // create sequential key
69 String key = "sq" + (seqsToIds.size() + 1);
70 seqsToIds.put(sq, key);
83 if (seqsToIds == null)
85 seqsToIds = new IdentityHashMap();
87 if (seqRefIds == null)
89 seqRefIds = new Hashtable();
93 java.util.IdentityHashMap seqsToIds = null; // SequenceI->key resolution
95 java.util.Hashtable seqRefIds = null; // key->SequenceI resolution
97 Vector frefedSequence = null;
99 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
105 public Jalview2XML(boolean raiseGUI)
107 this.raiseGUI = raiseGUI;
110 public void resolveFrefedSequences()
112 if (frefedSequence.size() > 0)
114 int r = 0, rSize = frefedSequence.size();
117 Object[] ref = (Object[]) frefedSequence.elementAt(r);
120 String sref = (String) ref[0];
121 if (seqRefIds.containsKey(sref))
123 if (ref[1] instanceof jalview.datamodel.Mapping)
125 SequenceI seq = (SequenceI) seqRefIds.get(sref);
126 while (seq.getDatasetSequence() != null)
128 seq = seq.getDatasetSequence();
130 ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
134 if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame)
136 SequenceI seq = (SequenceI) seqRefIds.get(sref);
137 while (seq.getDatasetSequence() != null)
139 seq = seq.getDatasetSequence();
142 && ref[2] instanceof jalview.datamodel.Mapping)
144 jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2];
145 ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap(
146 seq, mp.getTo(), mp.getMap());
151 .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving "
152 + ref[2].getClass() + " type objects.");
158 .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
159 + ref[1].getClass() + " type objects.");
161 frefedSequence.remove(r);
168 .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string "
170 + " with objecttype "
171 + ref[1].getClass());
177 frefedSequence.remove(r);
185 * This maintains a list of viewports, the key being the seqSetId. Important
186 * to set historyItem and redoList for multiple views
188 Hashtable viewportsAdded;
190 Hashtable annotationIds = new Hashtable();
192 String uniqueSetSuffix = "";
195 * List of pdbfiles added to Jar
197 Vector pdbfiles = null;
199 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
200 public void SaveState(File statefile)
202 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
211 FileOutputStream fos = new FileOutputStream(statefile);
212 JarOutputStream jout = new JarOutputStream(fos);
214 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
215 // //////////////////////////////////////////////////
216 // NOTE ALSO new PrintWriter must be used for each new JarEntry
217 PrintWriter out = null;
219 Vector shortNames = new Vector();
222 for (int i = frames.length - 1; i > -1; i--)
224 if (frames[i] instanceof AlignFrame)
226 AlignFrame af = (AlignFrame) frames[i];
228 String shortName = af.getTitle();
230 if (shortName.indexOf(File.separatorChar) > -1)
232 shortName = shortName.substring(shortName
233 .lastIndexOf(File.separatorChar) + 1);
238 while (shortNames.contains(shortName))
240 if (shortName.endsWith("_" + (count - 1)))
242 shortName = shortName
243 .substring(0, shortName.lastIndexOf("_"));
246 shortName = shortName.concat("_" + count);
250 shortNames.addElement(shortName);
252 if (!shortName.endsWith(".xml"))
254 shortName = shortName + ".xml";
257 int ap, apSize = af.alignPanels.size();
258 for (ap = 0; ap < apSize; ap++)
260 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
262 String fileName = apSize == 1 ? shortName : ap + shortName;
263 if (!fileName.endsWith(".xml"))
265 fileName = fileName + ".xml";
268 SaveState(apanel, fileName, jout);
275 } catch (Exception foo)
280 } catch (Exception ex)
282 // TODO: inform user of the problem - they need to know if their data was
284 ex.printStackTrace();
288 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
289 public boolean SaveAlignment(AlignFrame af, String jarFile,
294 int ap, apSize = af.alignPanels.size();
295 FileOutputStream fos = new FileOutputStream(jarFile);
296 JarOutputStream jout = new JarOutputStream(fos);
297 for (ap = 0; ap < apSize; ap++)
299 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
301 String jfileName = apSize == 1 ? fileName : fileName + ap;
302 if (!jfileName.endsWith(".xml"))
304 jfileName = jfileName + ".xml";
306 SaveState(apanel, jfileName, jout);
312 } catch (Exception foo)
318 } catch (Exception ex)
320 ex.printStackTrace();
326 * create a JalviewModel from an algnment view and marshall it to a
330 * panel to create jalview model for
332 * name of alignment panel written to output stream
338 public JalviewModel SaveState(AlignmentPanel ap, String fileName,
339 JarOutputStream jout)
343 Vector userColours = new Vector();
345 AlignViewport av = ap.av;
347 JalviewModel object = new JalviewModel();
348 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
350 object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
351 object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
353 jalview.datamodel.AlignmentI jal = av.alignment;
355 if (av.hasHiddenRows)
357 jal = jal.getHiddenSequences().getFullAlignment();
360 SequenceSet vamsasSet = new SequenceSet();
362 JalviewModelSequence jms = new JalviewModelSequence();
364 vamsasSet.setGapChar(jal.getGapCharacter() + "");
366 if (jal.getDataset() != null)
368 // dataset id is the dataset's hashcode
369 vamsasSet.setDatasetId(jal.getDataset().hashCode() + "");
371 if (jal.getProperties() != null)
373 Enumeration en = jal.getProperties().keys();
374 while (en.hasMoreElements())
376 String key = en.nextElement().toString();
377 SequenceSetProperties ssp = new SequenceSetProperties();
379 ssp.setValue(jal.getProperties().get(key).toString());
380 vamsasSet.addSequenceSetProperties(ssp);
388 jalview.datamodel.SequenceI jds;
389 for (int i = 0; i < jal.getHeight(); i++)
391 jds = jal.getSequenceAt(i);
394 if (seqRefIds.get(id) != null)
396 // This happens for two reasons: 1. multiple views are being serialised.
397 // 2. the hashCode has collided with another sequence's code. This DOES
398 // HAPPEN! (PF00072.15.stk does this)
399 // JBPNote: Uncomment to debug writing out of files that do not read
400 // back in due to ArrayOutOfBoundExceptions.
401 // System.err.println("vamsasSeq backref: "+id+"");
402 // System.err.println(jds.getName()+"
403 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
404 // System.err.println("Hashcode: "+seqHash(jds));
405 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
406 // System.err.println(rsq.getName()+"
407 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
408 // System.err.println("Hashcode: "+seqHash(rsq));
412 vamsasSeq = createVamsasSequence(id, jds);
413 vamsasSet.addSequence(vamsasSeq);
414 seqRefIds.put(id, jds);
418 jseq.setStart(jds.getStart());
419 jseq.setEnd(jds.getEnd());
420 jseq.setColour(av.getSequenceColour(jds).getRGB());
422 jseq.setId(id); // jseq id should be a string not a number
424 if (av.hasHiddenRows)
426 jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
428 if (av.hiddenRepSequences != null
429 && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
431 jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences
432 .get(jal.getSequenceAt(i))).getSequencesInOrder(jal);
434 for (int h = 0; h < reps.length; h++)
436 if (reps[h] != jal.getSequenceAt(i))
438 jseq.addHiddenSequences(jal.findIndex(reps[h]));
444 if (jds.getDatasetSequence().getSequenceFeatures() != null)
446 jalview.datamodel.SequenceFeature[] sf = jds.getDatasetSequence()
447 .getSequenceFeatures();
449 while (index < sf.length)
451 Features features = new Features();
453 features.setBegin(sf[index].getBegin());
454 features.setEnd(sf[index].getEnd());
455 features.setDescription(sf[index].getDescription());
456 features.setType(sf[index].getType());
457 features.setFeatureGroup(sf[index].getFeatureGroup());
458 features.setScore(sf[index].getScore());
459 if (sf[index].links != null)
461 for (int l = 0; l < sf[index].links.size(); l++)
463 OtherData keyValue = new OtherData();
464 keyValue.setKey("LINK_" + l);
465 keyValue.setValue(sf[index].links.elementAt(l).toString());
466 features.addOtherData(keyValue);
469 if (sf[index].otherDetails != null)
472 Enumeration keys = sf[index].otherDetails.keys();
473 while (keys.hasMoreElements())
475 key = keys.nextElement().toString();
476 OtherData keyValue = new OtherData();
477 keyValue.setKey(key);
478 keyValue.setValue(sf[index].otherDetails.get(key).toString());
479 features.addOtherData(keyValue);
483 jseq.addFeatures(features);
488 if (jds.getDatasetSequence().getPDBId() != null)
490 Enumeration en = jds.getDatasetSequence().getPDBId().elements();
491 while (en.hasMoreElements())
493 Pdbids pdb = new Pdbids();
494 jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
497 pdb.setId(entry.getId());
498 pdb.setType(entry.getType());
501 // This must have been loaded, is it still visible?
502 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
503 for (int f = frames.length - 1; f > -1; f--)
505 if (frames[f] instanceof AppJmol)
507 jmol = (AppJmol) frames[f];
508 if (!jmol.pdbentry.getId().equals(entry.getId()))
511 StructureState state = new StructureState();
512 state.setVisible(true);
513 state.setXpos(jmol.getX());
514 state.setYpos(jmol.getY());
515 state.setWidth(jmol.getWidth());
516 state.setHeight(jmol.getHeight());
518 String statestring = jmol.viewer.getStateInfo();
521 state.setContent(statestring.replaceAll("\n", ""));
523 for (int s = 0; s < jmol.sequence.length; s++)
525 if (jal.findIndex(jmol.sequence[s]) > -1)
527 pdb.addStructureState(state);
533 if (entry.getFile() != null)
535 pdb.setFile(entry.getFile());
536 if (pdbfiles == null)
538 pdbfiles = new Vector();
541 if (!pdbfiles.contains(entry.getId()))
543 pdbfiles.addElement(entry.getId());
546 File file = new File(entry.getFile());
547 if (file.exists() && jout != null)
549 byte[] data = new byte[(int) file.length()];
550 jout.putNextEntry(new JarEntry(entry.getId()));
551 DataInputStream dis = new DataInputStream(
552 new FileInputStream(file));
555 DataOutputStream dout = new DataOutputStream(jout);
556 dout.write(data, 0, data.length);
560 } catch (Exception ex)
562 ex.printStackTrace();
568 if (entry.getProperty() != null)
570 PdbentryItem item = new PdbentryItem();
571 Hashtable properties = entry.getProperty();
572 Enumeration en2 = properties.keys();
573 while (en2.hasMoreElements())
575 Property prop = new Property();
576 String key = en2.nextElement().toString();
578 prop.setValue(properties.get(key).toString());
579 item.addProperty(prop);
581 pdb.addPdbentryItem(item);
591 if (av.hasHiddenRows)
596 if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
598 jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
599 for (int i = 0; i < jac.length; i++)
601 AlcodonFrame alc = new AlcodonFrame();
602 vamsasSet.addAlcodonFrame(alc);
603 for (int p = 0; p < jac[i].aaWidth; p++)
605 Alcodon cmap = new Alcodon();
606 cmap.setPos1(jac[i].codons[p][0]);
607 cmap.setPos2(jac[i].codons[p][1]);
608 cmap.setPos3(jac[i].codons[p][2]);
609 alc.addAlcodon(cmap);
611 if (jac[i].getProtMappings() != null
612 && jac[i].getProtMappings().length > 0)
614 SequenceI[] dnas = jac[i].getdnaSeqs();
615 jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings();
616 for (int m = 0; m < pmaps.length; m++)
618 AlcodMap alcmap = new AlcodMap();
619 alcmap.setDnasq("" + seqHash(dnas[m]));
620 alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
622 alc.addAlcodMap(alcmap);
629 // /////////////////////////////////
630 if (av.currentTree != null)
632 // FIND ANY ASSOCIATED TREES
633 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
634 if (Desktop.desktop != null)
636 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
638 for (int t = 0; t < frames.length; t++)
640 if (frames[t] instanceof TreePanel)
642 TreePanel tp = (TreePanel) frames[t];
644 if (tp.treeCanvas.av.alignment == jal)
646 Tree tree = new Tree();
647 tree.setTitle(tp.getTitle());
648 tree.setCurrentTree((av.currentTree == tp.getTree()));
649 tree.setNewick(tp.getTree().toString());
650 tree.setThreshold(tp.treeCanvas.threshold);
652 tree.setFitToWindow(tp.fitToWindow.getState());
653 tree.setFontName(tp.getTreeFont().getName());
654 tree.setFontSize(tp.getTreeFont().getSize());
655 tree.setFontStyle(tp.getTreeFont().getStyle());
656 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
658 tree.setShowBootstrap(tp.bootstrapMenu.getState());
659 tree.setShowDistances(tp.distanceMenu.getState());
661 tree.setHeight(tp.getHeight());
662 tree.setWidth(tp.getWidth());
663 tree.setXpos(tp.getX());
664 tree.setYpos(tp.getY());
674 if (jal.getAlignmentAnnotation() != null)
676 jalview.datamodel.AlignmentAnnotation[] aa = jal
677 .getAlignmentAnnotation();
679 for (int i = 0; i < aa.length; i++)
681 Annotation an = new Annotation();
683 if (aa[i].annotationId != null)
685 annotationIds.put(aa[i].annotationId, aa[i]);
688 an.setId(aa[i].annotationId);
690 if (aa[i] == av.quality || aa[i] == av.conservation
691 || aa[i] == av.consensus)
693 an.setLabel(aa[i].label);
695 vamsasSet.addAnnotation(an);
699 an.setVisible(aa[i].visible);
701 an.setDescription(aa[i].description);
703 if (aa[i].sequenceRef != null)
705 an.setSequenceRef(aa[i].sequenceRef.getName());
711 an.setGraphType(aa[i].graph);
712 an.setGraphGroup(aa[i].graphGroup);
713 if (aa[i].getThreshold() != null)
715 ThresholdLine line = new ThresholdLine();
716 line.setLabel(aa[i].getThreshold().label);
717 line.setValue(aa[i].getThreshold().value);
718 line.setColour(aa[i].getThreshold().colour.getRGB());
719 an.setThresholdLine(line);
727 an.setLabel(aa[i].label);
728 if (aa[i].hasScore())
730 an.setScore(aa[i].getScore());
732 AnnotationElement ae;
733 if (aa[i].annotations != null)
735 an.setScoreOnly(false);
736 for (int a = 0; a < aa[i].annotations.length; a++)
738 if ((aa[i] == null) || (aa[i].annotations[a] == null))
743 ae = new AnnotationElement();
744 if (aa[i].annotations[a].description != null)
745 ae.setDescription(aa[i].annotations[a].description);
746 if (aa[i].annotations[a].displayCharacter != null)
747 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
749 if (!Float.isNaN(aa[i].annotations[a].value))
750 ae.setValue(aa[i].annotations[a].value);
753 if (aa[i].annotations[a].secondaryStructure != ' '
754 && aa[i].annotations[a].secondaryStructure != '\0')
756 .setSecondaryStructure(aa[i].annotations[a].secondaryStructure
759 if (aa[i].annotations[a].colour != null
760 && aa[i].annotations[a].colour != java.awt.Color.black)
762 ae.setColour(aa[i].annotations[a].colour.getRGB());
765 an.addAnnotationElement(ae);
770 an.setScoreOnly(true);
772 vamsasSet.addAnnotation(an);
777 if (jal.getGroups() != null)
779 JGroup[] groups = new JGroup[jal.getGroups().size()];
781 for (int i = 0; i < groups.length; i++)
783 groups[i] = new JGroup();
785 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal
786 .getGroups().elementAt(i);
787 groups[i].setStart(sg.getStartRes());
788 groups[i].setEnd(sg.getEndRes());
789 groups[i].setName(sg.getName());
792 if (sg.cs.conservationApplied())
794 groups[i].setConsThreshold(sg.cs.getConservationInc());
796 if (sg.cs instanceof jalview.schemes.UserColourScheme)
798 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
804 .setColour(ColourSchemeProperty.getColourName(sg.cs));
807 else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
810 .setColour(ColourSchemeProperty
811 .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
814 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
817 .setColour(SetUserColourScheme(sg.cs, userColours, jms));
821 groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
824 groups[i].setPidThreshold(sg.cs.getThreshold());
827 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
828 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
829 groups[i].setDisplayText(sg.getDisplayText());
830 groups[i].setColourText(sg.getColourText());
831 groups[i].setTextCol1(sg.textColour.getRGB());
832 groups[i].setTextCol2(sg.textColour2.getRGB());
833 groups[i].setTextColThreshold(sg.thresholdTextColour);
835 for (int s = 0; s < sg.getSize(); s++)
837 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
839 groups[i].addSeq(seqHash(seq));
843 jms.setJGroup(groups);
846 // /////////SAVE VIEWPORT
847 Viewport view = new Viewport();
848 view.setTitle(ap.alignFrame.getTitle());
849 view.setSequenceSetId(av.getSequenceSetId());
850 view.setViewName(av.viewName);
851 view.setGatheredViews(av.gatherViewsHere);
853 if (ap.av.explodedPosition != null)
855 view.setXpos(av.explodedPosition.x);
856 view.setYpos(av.explodedPosition.y);
857 view.setWidth(av.explodedPosition.width);
858 view.setHeight(av.explodedPosition.height);
862 view.setXpos(ap.alignFrame.getBounds().x);
863 view.setYpos(ap.alignFrame.getBounds().y);
864 view.setWidth(ap.alignFrame.getBounds().width);
865 view.setHeight(ap.alignFrame.getBounds().height);
868 view.setStartRes(av.startRes);
869 view.setStartSeq(av.startSeq);
871 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
873 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
876 else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
878 jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
879 .getGlobalColourScheme();
881 AnnotationColours ac = new AnnotationColours();
882 ac.setAboveThreshold(acg.getAboveThreshold());
883 ac.setThreshold(acg.getAnnotationThreshold());
884 ac.setAnnotation(acg.getAnnotation());
885 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
887 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
892 ac.setColourScheme(ColourSchemeProperty.getColourName(acg
896 ac.setMaxColour(acg.getMaxColour().getRGB());
897 ac.setMinColour(acg.getMinColour().getRGB());
898 view.setAnnotationColours(ac);
899 view.setBgColour("AnnotationColourGradient");
903 view.setBgColour(ColourSchemeProperty.getColourName(av
904 .getGlobalColourScheme()));
907 ColourSchemeI cs = av.getGlobalColourScheme();
911 if (cs.conservationApplied())
913 view.setConsThreshold(cs.getConservationInc());
914 if (cs instanceof jalview.schemes.UserColourScheme)
916 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
920 if (cs instanceof ResidueColourScheme)
922 view.setPidThreshold(cs.getThreshold());
926 view.setConservationSelected(av.getConservationSelected());
927 view.setPidSelected(av.getAbovePIDThreshold());
928 view.setFontName(av.font.getName());
929 view.setFontSize(av.font.getSize());
930 view.setFontStyle(av.font.getStyle());
931 view.setRenderGaps(av.renderGaps);
932 view.setShowAnnotation(av.getShowAnnotation());
933 view.setShowBoxes(av.getShowBoxes());
934 view.setShowColourText(av.getColourText());
935 view.setShowFullId(av.getShowJVSuffix());
936 view.setRightAlignIds(av.rightAlignIds);
937 view.setShowSequenceFeatures(av.showSequenceFeatures);
938 view.setShowText(av.getShowText());
939 view.setWrapAlignment(av.getWrapAlignment());
940 view.setTextCol1(av.textColour.getRGB());
941 view.setTextCol2(av.textColour2.getRGB());
942 view.setTextColThreshold(av.thresholdTextColour);
944 if (av.featuresDisplayed != null)
946 jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
948 String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
950 Vector settingsAdded = new Vector();
951 for (int ro = 0; ro < renderOrder.length; ro++)
953 Setting setting = new Setting();
954 setting.setType(renderOrder[ro]);
955 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
956 .getColour(renderOrder[ro]).getRGB());
958 setting.setDisplay(av.featuresDisplayed
959 .containsKey(renderOrder[ro]));
960 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
964 setting.setOrder(rorder);
966 fs.addSetting(setting);
967 settingsAdded.addElement(renderOrder[ro]);
970 // Make sure we save none displayed feature settings
971 Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
973 while (en.hasMoreElements())
975 String key = en.nextElement().toString();
976 if (settingsAdded.contains(key))
981 Setting setting = new Setting();
982 setting.setType(key);
983 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
984 .getColour(key).getRGB());
986 setting.setDisplay(false);
987 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
991 setting.setOrder(rorder);
993 fs.addSetting(setting);
994 settingsAdded.addElement(key);
996 en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
997 Vector groupsAdded = new Vector();
998 while (en.hasMoreElements())
1000 String grp = en.nextElement().toString();
1001 if (groupsAdded.contains(grp))
1005 Group g = new Group();
1008 .setDisplay(((Boolean) ap.seqPanel.seqCanvas
1009 .getFeatureRenderer().featureGroups.get(grp))
1012 groupsAdded.addElement(grp);
1014 jms.setFeatureSettings(fs);
1018 if (av.hasHiddenColumns)
1020 for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
1022 int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
1024 HiddenColumns hc = new HiddenColumns();
1025 hc.setStart(region[0]);
1026 hc.setEnd(region[1]);
1027 view.addHiddenColumns(hc);
1031 jms.addViewport(view);
1033 object.setJalviewModelSequence(jms);
1034 object.getVamsasModel().addSequenceSet(vamsasSet);
1036 if (jout != null && fileName != null)
1038 // We may not want to write the object to disk,
1039 // eg we can copy the alignViewport to a new view object
1040 // using save and then load
1043 JarEntry entry = new JarEntry(fileName);
1044 jout.putNextEntry(entry);
1045 PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
1047 org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(
1049 marshaller.marshal(object);
1052 } catch (Exception ex)
1054 // TODO: raise error in GUI if marshalling failed.
1055 ex.printStackTrace();
1061 private Sequence createVamsasSequence(String id, SequenceI jds)
1063 return createVamsasSequence(true, id, jds, null);
1066 private Sequence createVamsasSequence(boolean recurse, String id,
1067 SequenceI jds, SequenceI parentseq)
1069 Sequence vamsasSeq = new Sequence();
1070 vamsasSeq.setId(id);
1071 vamsasSeq.setName(jds.getName());
1072 vamsasSeq.setSequence(jds.getSequenceAsString());
1073 vamsasSeq.setDescription(jds.getDescription());
1074 jalview.datamodel.DBRefEntry[] dbrefs = null;
1075 if (jds.getDatasetSequence() != null)
1077 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
1078 if (jds.getDatasetSequence().getDBRef() != null)
1080 dbrefs = jds.getDatasetSequence().getDBRef();
1085 vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
1086 // dataset sequences only
1087 dbrefs = jds.getDBRef();
1091 for (int d = 0; d < dbrefs.length; d++)
1093 DBRef dbref = new DBRef();
1094 dbref.setSource(dbrefs[d].getSource());
1095 dbref.setVersion(dbrefs[d].getVersion());
1096 dbref.setAccessionId(dbrefs[d].getAccessionId());
1097 if (dbrefs[d].hasMap())
1099 Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
1101 dbref.setMapping(mp);
1103 vamsasSeq.addDBRef(dbref);
1109 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
1110 SequenceI parentseq, SequenceI jds, boolean recurse)
1113 if (jmp.getMap() != null)
1117 jalview.util.MapList mlst = jmp.getMap();
1118 int r[] = mlst.getFromRanges();
1119 for (int s = 0; s < r.length; s += 2)
1121 MapListFrom mfrom = new MapListFrom();
1122 mfrom.setStart(r[s]);
1123 mfrom.setEnd(r[s + 1]);
1124 mp.addMapListFrom(mfrom);
1126 r = mlst.getToRanges();
1127 for (int s = 0; s < r.length; s += 2)
1129 MapListTo mto = new MapListTo();
1131 mto.setEnd(r[s + 1]);
1132 mp.addMapListTo(mto);
1134 mp.setMapFromUnit(mlst.getFromRatio());
1135 mp.setMapToUnit(mlst.getToRatio());
1136 if (jmp.getTo() != null)
1138 MappingChoice mpc = new MappingChoice();
1140 && (parentseq != jmp.getTo() || parentseq
1141 .getDatasetSequence() != jmp.getTo()))
1143 mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
1149 SequenceI ps = null;
1150 if (parentseq != jmp.getTo()
1151 && parentseq.getDatasetSequence() != jmp.getTo())
1153 // chaining dbref rather than a handshaking one
1154 jmpid = seqHash(ps = jmp.getTo());
1158 jmpid = seqHash(ps = parentseq);
1160 mpc.setDseqFor(jmpid);
1161 if (!seqRefIds.containsKey(mpc.getDseqFor()))
1163 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
1164 seqRefIds.put(mpc.getDseqFor(), ps);
1168 jalview.bin.Cache.log.debug("reusing DseqFor ID");
1171 mp.setMappingChoice(mpc);
1177 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
1178 Vector userColours, JalviewModelSequence jms)
1181 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
1183 if (!userColours.contains(ucs))
1185 userColours.add(ucs);
1187 java.awt.Color[] colours = ucs.getColours();
1188 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
1189 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
1191 for (int i = 0; i < colours.length; i++)
1193 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1194 col.setName(ResidueProperties.aa[i]);
1195 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1196 jbucs.addColour(col);
1198 if (ucs.getLowerCaseColours() != null)
1200 colours = ucs.getLowerCaseColours();
1201 for (int i = 0; i < colours.length; i++)
1203 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1204 col.setName(ResidueProperties.aa[i].toLowerCase());
1205 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1206 jbucs.addColour(col);
1210 id = "ucs" + userColours.indexOf(ucs);
1212 uc.setUserColourScheme(jbucs);
1213 jms.addUserColours(uc);
1219 jalview.schemes.UserColourScheme GetUserColourScheme(
1220 JalviewModelSequence jms, String id)
1222 UserColours[] uc = jms.getUserColours();
1223 UserColours colours = null;
1225 for (int i = 0; i < uc.length; i++)
1227 if (uc[i].getId().equals(id))
1235 java.awt.Color[] newColours = new java.awt.Color[24];
1237 for (int i = 0; i < 24; i++)
1239 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1240 .getUserColourScheme().getColour(i).getRGB(), 16));
1243 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
1246 if (colours.getUserColourScheme().getColourCount() > 24)
1248 newColours = new java.awt.Color[23];
1249 for (int i = 0; i < 23; i++)
1251 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1252 .getUserColourScheme().getColour(i + 24).getRGB(), 16));
1254 ucs.setLowerCaseColours(newColours);
1266 public AlignFrame LoadJalviewAlign(final String file)
1268 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
1270 jalview.gui.AlignFrame af = null;
1272 seqRefIds = new Hashtable();
1273 viewportsAdded = new Hashtable();
1274 frefedSequence = new Vector();
1275 Hashtable gatherToThisFrame = new Hashtable();
1277 String errorMessage = null;
1281 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
1284 if (file.startsWith("http://"))
1286 url = new URL(file);
1289 JarInputStream jin = null;
1290 JarEntry jarentry = null;
1297 jin = new JarInputStream(url.openStream());
1301 jin = new JarInputStream(new FileInputStream(file));
1304 for (int i = 0; i < entryCount; i++)
1306 jarentry = jin.getNextJarEntry();
1309 if (jarentry != null && jarentry.getName().endsWith(".xml"))
1311 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
1312 JalviewModel object = new JalviewModel();
1314 Unmarshaller unmar = new Unmarshaller(object);
1315 unmar.setValidation(false);
1316 object = (JalviewModel) unmar.unmarshal(in);
1318 af = LoadFromObject(object, file, true);
1319 if (af.viewport.gatherViewsHere)
1321 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
1325 else if (jarentry != null)
1327 // Some other file here.
1330 } while (jarentry != null);
1331 resolveFrefedSequences();
1332 } catch (java.io.FileNotFoundException ex)
1334 ex.printStackTrace();
1335 errorMessage = "Couldn't locate Jalview XML file : " + file;
1336 System.err.println("Exception whilst loading jalview XML file : "
1338 } catch (java.net.UnknownHostException ex)
1340 ex.printStackTrace();
1341 errorMessage = "Couldn't locate Jalview XML file : " + file;
1342 System.err.println("Exception whilst loading jalview XML file : "
1344 } catch (Exception ex)
1346 System.err.println("Parsing as Jalview Version 2 file failed.");
1347 ex.printStackTrace(System.err);
1349 // Is Version 1 Jar file?
1352 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(file);
1353 } catch (Exception ex2)
1355 System.err.println("Exception whilst loading as jalviewXMLV1:");
1356 ex2.printStackTrace();
1360 if (Desktop.instance != null)
1362 Desktop.instance.stopLoading();
1366 System.out.println("Successfully loaded archive file");
1369 ex.printStackTrace();
1371 System.err.println("Exception whilst loading jalview XML file : "
1375 if (Desktop.instance != null)
1377 Desktop.instance.stopLoading();
1380 Enumeration en = gatherToThisFrame.elements();
1381 while (en.hasMoreElements())
1383 Desktop.instance.gatherViews((AlignFrame) en.nextElement());
1386 if (errorMessage != null)
1388 final String finalErrorMessage = errorMessage;
1391 javax.swing.SwingUtilities.invokeLater(new Runnable()
1395 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1396 finalErrorMessage, "Error loading Jalview file",
1397 JOptionPane.WARNING_MESSAGE);
1403 System.err.println("Problem loading Jalview file: " + errorMessage);
1410 Hashtable alreadyLoadedPDB;
1412 String loadPDBFile(String file, String pdbId)
1414 if (alreadyLoadedPDB == null)
1415 alreadyLoadedPDB = new Hashtable();
1417 if (alreadyLoadedPDB.containsKey(pdbId))
1418 return alreadyLoadedPDB.get(pdbId).toString();
1422 JarInputStream jin = null;
1424 if (file.startsWith("http://"))
1426 jin = new JarInputStream(new URL(file).openStream());
1430 jin = new JarInputStream(new FileInputStream(file));
1433 JarEntry entry = null;
1436 entry = jin.getNextJarEntry();
1437 } while (!entry.getName().equals(pdbId));
1439 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1440 File outFile = File.createTempFile("jalview_pdb", ".txt");
1441 outFile.deleteOnExit();
1442 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1445 while ((data = in.readLine()) != null)
1452 } catch (Exception foo)
1458 alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
1459 return outFile.getAbsolutePath();
1461 } catch (Exception ex)
1463 ex.printStackTrace();
1469 AlignFrame LoadFromObject(JalviewModel object, String file,
1470 boolean loadTreesAndStructures)
1472 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1473 Sequence[] vamsasSeq = vamsasSet.getSequence();
1475 JalviewModelSequence jms = object.getJalviewModelSequence();
1477 Viewport view = jms.getViewport(0);
1479 // ////////////////////////////////
1482 Vector hiddenSeqs = null;
1483 jalview.datamodel.Sequence jseq;
1485 ArrayList tmpseqs = new ArrayList();
1487 boolean multipleView = false;
1489 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1490 int vi = 0; // counter in vamsasSeq array
1491 for (int i = 0; i < JSEQ.length; i++)
1493 String seqId = JSEQ[i].getId() + "";
1495 if (seqRefIds.get(seqId) != null)
1497 tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId));
1498 multipleView = true;
1502 jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
1503 vamsasSeq[vi].getSequence());
1504 jseq.setDescription(vamsasSeq[vi].getDescription());
1505 jseq.setStart(JSEQ[i].getStart());
1506 jseq.setEnd(JSEQ[i].getEnd());
1507 jseq.setVamsasId(uniqueSetSuffix + seqId);
1508 seqRefIds.put(vamsasSeq[vi].getId() + "", jseq);
1513 if (JSEQ[i].getHidden())
1515 if (hiddenSeqs == null)
1517 hiddenSeqs = new Vector();
1520 hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
1527 // Create the alignment object from the sequence set
1528 // ///////////////////////////////
1529 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
1532 tmpseqs.toArray(orderedSeqs);
1534 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
1537 // / Add the alignment properties
1538 for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
1540 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
1541 al.setProperty(ssp.getKey(), ssp.getValue());
1545 // SequenceFeatures are added to the DatasetSequence,
1546 // so we must create or recover the dataset before loading features
1547 // ///////////////////////////////
1548 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
1550 // older jalview projects do not have a dataset id.
1551 al.setDataset(null);
1555 recoverDatasetFor(vamsasSet, al);
1557 // ///////////////////////////////
1559 Hashtable pdbloaded = new Hashtable();
1562 for (int i = 0; i < vamsasSeq.length; i++)
1564 if (JSEQ[i].getFeaturesCount() > 0)
1566 Features[] features = JSEQ[i].getFeatures();
1567 for (int f = 0; f < features.length; f++)
1569 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
1570 features[f].getType(), features[f].getDescription(),
1571 features[f].getStatus(), features[f].getBegin(),
1572 features[f].getEnd(), features[f].getFeatureGroup());
1574 sf.setScore(features[f].getScore());
1575 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1577 OtherData keyValue = features[f].getOtherData(od);
1578 if (keyValue.getKey().startsWith("LINK"))
1580 sf.addLink(keyValue.getValue());
1584 sf.setValue(keyValue.getKey(), keyValue.getValue());
1589 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1592 if (vamsasSeq[i].getDBRefCount() > 0)
1594 addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
1596 if (JSEQ[i].getPdbidsCount() > 0)
1598 Pdbids[] ids = JSEQ[i].getPdbids();
1599 for (int p = 0; p < ids.length; p++)
1601 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
1602 entry.setId(ids[p].getId());
1603 entry.setType(ids[p].getType());
1604 if (ids[p].getFile() != null)
1606 if (!pdbloaded.containsKey(ids[p].getFile()))
1608 entry.setFile(loadPDBFile(file, ids[p].getId()));
1612 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1616 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1622 // ///////////////////////////////
1623 // LOAD SEQUENCE MAPPINGS
1624 if (vamsasSet.getAlcodonFrameCount() > 0)
1626 AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
1627 for (int i = 0; i < alc.length; i++)
1629 jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
1630 alc[i].getAlcodonCount());
1631 if (alc[i].getAlcodonCount() > 0)
1633 Alcodon[] alcods = alc[i].getAlcodon();
1634 for (int p = 0; p < cf.codons.length; p++)
1636 cf.codons[p] = new int[3];
1637 cf.codons[p][0] = (int) alcods[p].getPos1();
1638 cf.codons[p][1] = (int) alcods[p].getPos2();
1639 cf.codons[p][2] = (int) alcods[p].getPos3();
1642 if (alc[i].getAlcodMapCount() > 0)
1644 AlcodMap[] maps = alc[i].getAlcodMap();
1645 for (int m = 0; m < maps.length; m++)
1647 SequenceI dnaseq = (SequenceI) seqRefIds
1648 .get(maps[m].getDnasq());
1650 jalview.datamodel.Mapping mapping = null;
1651 // attach to dna sequence reference.
1652 if (maps[m].getMapping() != null)
1654 mapping = addMapping(maps[m].getMapping());
1658 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
1663 frefedSequence.add(new Object[]
1664 { maps[m].getDnasq(), cf, mapping });
1668 al.addCodonFrame(cf);
1673 // ////////////////////////////////
1675 boolean hideQuality = true, hideConservation = true, hideConsensus = true;
1677 if (vamsasSet.getAnnotationCount() > 0)
1679 Annotation[] an = vamsasSet.getAnnotation();
1681 for (int i = 0; i < an.length; i++)
1683 if (an[i].getLabel().equals("Quality"))
1685 hideQuality = false;
1688 else if (an[i].getLabel().equals("Conservation"))
1690 hideConservation = false;
1693 else if (an[i].getLabel().equals("Consensus"))
1695 hideConsensus = false;
1699 if (an[i].getId() != null
1700 && annotationIds.containsKey(an[i].getId()))
1702 jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
1703 .get(an[i].getId());
1704 if (an[i].hasVisible())
1705 jda.visible = an[i].getVisible();
1707 al.addAnnotation(jda);
1712 AnnotationElement[] ae = an[i].getAnnotationElement();
1713 jalview.datamodel.Annotation[] anot = null;
1715 if (!an[i].getScoreOnly())
1717 anot = new jalview.datamodel.Annotation[al.getWidth()];
1719 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
1721 if (ae[aa].getPosition() >= anot.length)
1724 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
1726 ae[aa].getDisplayCharacter(), ae[aa].getDescription(), (ae[aa]
1727 .getSecondaryStructure() == null || ae[aa]
1728 .getSecondaryStructure().length() == 0) ? ' ' : ae[aa]
1729 .getSecondaryStructure().charAt(0), ae[aa].getValue()
1732 // JBPNote: Consider verifying dataflow for IO of secondary
1733 // structure annotation read from Stockholm files
1734 // this was added to try to ensure that
1735 // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
1737 // anot[ae[aa].getPosition()].displayCharacter = "";
1739 anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]
1743 jalview.datamodel.AlignmentAnnotation jaa = null;
1745 if (an[i].getGraph())
1747 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1748 an[i].getDescription(), anot, 0, 0, an[i].getGraphType());
1750 jaa.graphGroup = an[i].getGraphGroup();
1752 if (an[i].getThresholdLine() != null)
1754 jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
1755 .getThresholdLine().getValue(), an[i]
1756 .getThresholdLine().getLabel(), new java.awt.Color(
1757 an[i].getThresholdLine().getColour())));
1764 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1765 an[i].getDescription(), anot);
1768 if (an[i].getId() != null)
1770 annotationIds.put(an[i].getId(), jaa);
1771 jaa.annotationId = an[i].getId();
1774 if (an[i].getSequenceRef() != null)
1776 if (al.findName(an[i].getSequenceRef()) != null)
1778 jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
1780 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1783 if (an[i].hasScore())
1785 jaa.setScore(an[i].getScore());
1788 if (an[i].hasVisible())
1789 jaa.visible = an[i].getVisible();
1791 al.addAnnotation(jaa);
1795 // ///////////////////////
1797 if (jms.getJGroupCount() > 0)
1799 JGroup[] groups = jms.getJGroup();
1801 for (int i = 0; i < groups.length; i++)
1803 ColourSchemeI cs = null;
1805 if (groups[i].getColour() != null)
1807 if (groups[i].getColour().startsWith("ucs"))
1809 cs = GetUserColourScheme(jms, groups[i].getColour());
1813 cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
1818 cs.setThreshold(groups[i].getPidThreshold(), true);
1822 Vector seqs = new Vector();
1824 for (int s = 0; s < groups[i].getSeqCount(); s++)
1826 String seqId = groups[i].getSeq(s) + "";
1827 jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds
1832 seqs.addElement(ts);
1836 if (seqs.size() < 1)
1841 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
1842 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1843 groups[i].getDisplayText(), groups[i].getColourText(),
1844 groups[i].getStart(), groups[i].getEnd());
1847 .setOutlineColour(new java.awt.Color(groups[i]
1848 .getOutlineColour()));
1850 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
1851 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
1852 sg.thresholdTextColour = groups[i].getTextColThreshold();
1854 if (groups[i].getConsThreshold() != 0)
1856 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
1857 "All", ResidueProperties.propHash, 3, sg
1858 .getSequences(null), 0, sg.getWidth() - 1);
1860 c.verdict(false, 25);
1861 sg.cs.setConservation(c);
1868 // ///////////////////////////////
1871 AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
1873 af.setFileName(file, "Jalview");
1875 for (int i = 0; i < JSEQ.length; i++)
1877 af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
1878 new java.awt.Color(JSEQ[i].getColour()));
1881 // If we just load in the same jar file again, the sequenceSetId
1882 // will be the same, and we end up with multiple references
1883 // to the same sequenceSet. We must modify this id on load
1884 // so that each load of the file gives a unique id
1885 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
1887 af.viewport.gatherViewsHere = view.getGatheredViews();
1889 if (view.getSequenceSetId() != null)
1891 jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
1892 .get(uniqueSeqSetId);
1894 af.viewport.sequenceSetID = uniqueSeqSetId;
1898 af.viewport.historyList = av.historyList;
1899 af.viewport.redoList = av.redoList;
1903 viewportsAdded.put(uniqueSeqSetId, af.viewport);
1906 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1908 if (hiddenSeqs != null)
1910 for (int s = 0; s < JSEQ.length; s++)
1912 jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
1914 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
1916 hidden.addSequence(al
1917 .getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
1919 af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
1922 jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
1925 for (int s = 0; s < hiddenSeqs.size(); s++)
1927 hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
1930 af.viewport.hideSequence(hseqs);
1934 if ((hideConsensus || hideQuality || hideConservation)
1935 && al.getAlignmentAnnotation() != null)
1937 int hSize = al.getAlignmentAnnotation().length;
1938 for (int h = 0; h < hSize; h++)
1940 if ((hideConsensus && al.getAlignmentAnnotation()[h].label
1941 .equals("Consensus"))
1942 || (hideQuality && al.getAlignmentAnnotation()[h].label
1944 || (hideConservation && al.getAlignmentAnnotation()[h].label
1945 .equals("Conservation")))
1947 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1952 af.alignPanel.adjustAnnotationHeight();
1955 if (view.getViewName() != null)
1957 af.viewport.viewName = view.getViewName();
1958 af.setInitialTabVisible();
1960 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
1963 af.viewport.setShowAnnotation(view.getShowAnnotation());
1964 af.viewport.setAbovePIDThreshold(view.getPidSelected());
1966 af.viewport.setColourText(view.getShowColourText());
1968 af.viewport.setConservationSelected(view.getConservationSelected());
1969 af.viewport.setShowJVSuffix(view.getShowFullId());
1970 af.viewport.rightAlignIds = view.getRightAlignIds();
1971 af.viewport.setFont(new java.awt.Font(view.getFontName(), view
1972 .getFontStyle(), view.getFontSize()));
1973 af.alignPanel.fontChanged();
1974 af.viewport.setRenderGaps(view.getRenderGaps());
1975 af.viewport.setWrapAlignment(view.getWrapAlignment());
1976 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1977 af.viewport.setShowAnnotation(view.getShowAnnotation());
1978 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1980 af.viewport.setShowBoxes(view.getShowBoxes());
1982 af.viewport.setShowText(view.getShowText());
1984 af.viewport.textColour = new java.awt.Color(view.getTextCol1());
1985 af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
1986 af.viewport.thresholdTextColour = view.getTextColThreshold();
1988 af.viewport.setStartRes(view.getStartRes());
1989 af.viewport.setStartSeq(view.getStartSeq());
1991 ColourSchemeI cs = null;
1993 if (view.getBgColour() != null)
1995 if (view.getBgColour().startsWith("ucs"))
1997 cs = GetUserColourScheme(jms, view.getBgColour());
1999 else if (view.getBgColour().startsWith("Annotation"))
2001 // int find annotation
2002 for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
2004 if (af.viewport.alignment.getAlignmentAnnotation()[i].label
2005 .equals(view.getAnnotationColours().getAnnotation()))
2007 if (af.viewport.alignment.getAlignmentAnnotation()[i]
2008 .getThreshold() == null)
2010 af.viewport.alignment.getAlignmentAnnotation()[i]
2011 .setThreshold(new jalview.datamodel.GraphLine(view
2012 .getAnnotationColours().getThreshold(),
2013 "Threshold", java.awt.Color.black)
2018 if (view.getAnnotationColours().getColourScheme()
2021 cs = new AnnotationColourGradient(af.viewport.alignment
2022 .getAlignmentAnnotation()[i], new java.awt.Color(view
2023 .getAnnotationColours().getMinColour()),
2024 new java.awt.Color(view.getAnnotationColours()
2025 .getMaxColour()), view.getAnnotationColours()
2026 .getAboveThreshold());
2028 else if (view.getAnnotationColours().getColourScheme()
2031 cs = new AnnotationColourGradient(af.viewport.alignment
2032 .getAlignmentAnnotation()[i], GetUserColourScheme(
2033 jms, view.getAnnotationColours().getColourScheme()),
2034 view.getAnnotationColours().getAboveThreshold());
2038 cs = new AnnotationColourGradient(af.viewport.alignment
2039 .getAlignmentAnnotation()[i], ColourSchemeProperty
2040 .getColour(al, view.getAnnotationColours()
2041 .getColourScheme()), view
2042 .getAnnotationColours().getAboveThreshold());
2045 // Also use these settings for all the groups
2046 if (al.getGroups() != null)
2048 for (int g = 0; g < al.getGroups().size(); g++)
2050 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
2051 .getGroups().elementAt(g);
2060 * (view.getAnnotationColours().getColourScheme().equals("None")) {
2061 * sg.cs = new AnnotationColourGradient(
2062 * af.viewport.alignment.getAlignmentAnnotation()[i], new
2063 * java.awt.Color(view.getAnnotationColours(). getMinColour()),
2064 * new java.awt.Color(view.getAnnotationColours().
2066 * view.getAnnotationColours().getAboveThreshold()); } else
2069 sg.cs = new AnnotationColourGradient(
2070 af.viewport.alignment.getAlignmentAnnotation()[i],
2071 sg.cs, view.getAnnotationColours()
2072 .getAboveThreshold());
2085 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
2090 cs.setThreshold(view.getPidThreshold(), true);
2091 cs.setConsensus(af.viewport.hconsensus);
2095 af.viewport.setGlobalColourScheme(cs);
2096 af.viewport.setColourAppliesToAllGroups(false);
2098 if (view.getConservationSelected() && cs != null)
2100 cs.setConservationInc(view.getConsThreshold());
2103 af.changeColour(cs);
2105 af.viewport.setColourAppliesToAllGroups(true);
2107 if (view.getShowSequenceFeatures())
2109 af.viewport.showSequenceFeatures = true;
2112 if (jms.getFeatureSettings() != null)
2114 af.viewport.featuresDisplayed = new Hashtable();
2115 String[] renderOrder = new String[jms.getFeatureSettings()
2116 .getSettingCount()];
2117 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
2119 Setting setting = jms.getFeatureSettings().getSetting(fs);
2121 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
2122 setting.getType(), new java.awt.Color(setting.getColour()));
2123 renderOrder[fs] = setting.getType();
2124 if (setting.hasOrder())
2125 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2126 setting.getType(), setting.getOrder());
2128 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2130 fs / jms.getFeatureSettings().getSettingCount());
2131 if (setting.getDisplay())
2133 af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
2134 setting.getColour()));
2137 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
2139 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
2140 for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
2142 Group grp = jms.getFeatureSettings().getGroup(gs);
2143 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
2147 if (view.getHiddenColumnsCount() > 0)
2149 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
2151 af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
2152 .getHiddenColumns(c).getEnd() // +1
2157 af.setMenusFromViewport(af.viewport);
2159 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
2163 // /////////////////////////////////////
2164 if (loadTreesAndStructures && jms.getTreeCount() > 0)
2168 for (int t = 0; t < jms.getTreeCount(); t++)
2171 Tree tree = jms.getTree(t);
2173 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(tree
2174 .getNewick()), tree.getTitle(), tree.getWidth(), tree
2175 .getHeight(), tree.getXpos(), tree.getYpos());
2177 tp.fitToWindow.setState(tree.getFitToWindow());
2178 tp.fitToWindow_actionPerformed(null);
2180 if (tree.getFontName() != null)
2182 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
2183 .getFontStyle(), tree.getFontSize()));
2187 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
2188 .getFontStyle(), tree.getFontSize()));
2191 tp.showPlaceholders(tree.getMarkUnlinked());
2192 tp.showBootstrap(tree.getShowBootstrap());
2193 tp.showDistances(tree.getShowDistances());
2195 tp.treeCanvas.threshold = tree.getThreshold();
2197 if (tree.getCurrentTree())
2199 af.viewport.setCurrentTree(tp.getTree());
2203 } catch (Exception ex)
2205 ex.printStackTrace();
2209 // //LOAD STRUCTURES
2210 if (loadTreesAndStructures)
2212 for (int i = 0; i < JSEQ.length; i++)
2214 if (JSEQ[i].getPdbidsCount() > 0)
2216 Pdbids[] ids = JSEQ[i].getPdbids();
2217 for (int p = 0; p < ids.length; p++)
2219 for (int s = 0; s < ids[p].getStructureStateCount(); s++)
2221 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
2223 jpdb.setFile(loadPDBFile(ids[p].getFile(), ids[p].getId()));
2224 jpdb.setId(ids[p].getId());
2226 int x = ids[p].getStructureState(s).getXpos();
2227 int y = ids[p].getStructureState(s).getYpos();
2228 int width = ids[p].getStructureState(s).getWidth();
2229 int height = ids[p].getStructureState(s).getHeight();
2231 java.awt.Component comp = null;
2233 JInternalFrame[] frames = null;
2238 frames = Desktop.desktop.getAllFrames();
2239 } catch (ArrayIndexOutOfBoundsException e)
2241 // occasional No such child exceptions are thrown here...
2246 } catch (Exception f)
2251 } while (frames == null);
2252 for (int f = 0; f < frames.length; f++)
2254 if (frames[f] instanceof AppJmol)
2256 if (frames[f].getX() == x && frames[f].getY() == y
2257 && frames[f].getHeight() == height
2258 && frames[f].getWidth() == width)
2266 Desktop.desktop.getComponentAt(x, y);
2268 String pdbFile = loadPDBFile(file, ids[p].getId());
2270 jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
2271 { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId()
2276 String state = ids[p].getStructureState(s).getContent();
2278 StringBuffer newFileLoc = new StringBuffer(state.substring(
2279 0, state.indexOf("\"", state.indexOf("load")) + 1));
2281 newFileLoc.append(jpdb.getFile());
2282 newFileLoc.append(state.substring(state.indexOf("\"", state
2283 .indexOf("load \"") + 6)));
2285 new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel,
2286 newFileLoc.toString(), new java.awt.Rectangle(x, y,
2290 else if (comp != null)
2292 StructureSelectionManager.getStructureSelectionManager()
2293 .setMapping(seq, null, pdbFile,
2294 jalview.io.AppletFormatAdapter.FILE);
2296 ((AppJmol) comp).addSequence(seq);
2307 private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
2309 jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
2310 Vector dseqs = null;
2313 // create a list of new dataset sequences
2314 dseqs = new Vector();
2316 for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
2318 Sequence vamsasSeq = vamsasSet.getSequence(i);
2319 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
2321 // create a new dataset
2324 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
2325 dseqs.copyInto(dsseqs);
2326 ds = new jalview.datamodel.Alignment(dsseqs);
2327 addDatasetRef(vamsasSet.getDatasetId(), ds);
2329 // set the dataset for the newly imported alignment.
2330 if (al.getDataset() == null)
2339 * sequence definition to create/merge dataset sequence for
2343 * vector to add new dataset sequence to
2345 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
2346 AlignmentI ds, Vector dseqs)
2348 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
2350 jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds
2351 .get(vamsasSeq.getId());
2352 jalview.datamodel.SequenceI dsq = null;
2353 if (sq != null && sq.getDatasetSequence() != null)
2355 dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
2358 String sqid = vamsasSeq.getDsseqid();
2361 // need to create or add a new dataset sequence reference to this sequence
2364 dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
2369 // make a new dataset sequence
2370 dsq = sq.createDatasetSequence();
2373 // make up a new dataset reference for this sequence
2374 sqid = seqHash(dsq);
2376 dsq.setVamsasId(uniqueSetSuffix + sqid);
2377 seqRefIds.put(sqid, dsq);
2382 dseqs.addElement(dsq);
2387 ds.addSequence(dsq);
2393 { // make this dataset sequence sq's dataset sequence
2394 sq.setDatasetSequence(dsq);
2398 // TODO: refactor this as a merge dataset sequence function
2399 // now check that sq (the dataset sequence) sequence really is the union of
2400 // all references to it
2401 // boolean pre = sq.getStart() < dsq.getStart();
2402 // boolean post = sq.getEnd() > dsq.getEnd();
2406 StringBuffer sb = new StringBuffer();
2407 String newres = jalview.analysis.AlignSeq.extractGaps(
2408 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
2409 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
2410 && newres.length() > dsq.getLength())
2412 // Update with the longer sequence.
2416 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
2417 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
2418 * sb.append(newres.substring(newres.length() - sq.getEnd() -
2419 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
2421 dsq.setSequence(sb.toString());
2423 // TODO: merges will never happen if we 'know' we have the real dataset
2424 // sequence - this should be detected when id==dssid
2425 System.err.println("DEBUG Notice: Merged dataset sequence"); // ("
2426 // + (pre ? "prepended" : "") + " "
2427 // + (post ? "appended" : ""));
2432 java.util.Hashtable datasetIds = null;
2434 private Alignment getDatasetFor(String datasetId)
2436 if (datasetIds == null)
2438 datasetIds = new Hashtable();
2441 if (datasetIds.containsKey(datasetId))
2443 return (Alignment) datasetIds.get(datasetId);
2448 private void addDatasetRef(String datasetId, Alignment dataset)
2450 if (datasetIds == null)
2452 datasetIds = new Hashtable();
2454 datasetIds.put(datasetId, dataset);
2457 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
2459 for (int d = 0; d < sequence.getDBRefCount(); d++)
2461 DBRef dr = sequence.getDBRef(d);
2462 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
2463 sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
2464 .getVersion(), sequence.getDBRef(d).getAccessionId());
2465 if (dr.getMapping() != null)
2467 entry.setMap(addMapping(dr.getMapping()));
2469 datasetSequence.addDBRef(entry);
2473 private jalview.datamodel.Mapping addMapping(Mapping m)
2475 SequenceI dsto = null;
2476 // Mapping m = dr.getMapping();
2477 int fr[] = new int[m.getMapListFromCount() * 2];
2478 Enumeration f = m.enumerateMapListFrom();
2479 for (int _i = 0; f.hasMoreElements(); _i += 2)
2481 MapListFrom mf = (MapListFrom) f.nextElement();
2482 fr[_i] = mf.getStart();
2483 fr[_i + 1] = mf.getEnd();
2485 int fto[] = new int[m.getMapListToCount() * 2];
2486 f = m.enumerateMapListTo();
2487 for (int _i = 0; f.hasMoreElements(); _i += 2)
2489 MapListTo mf = (MapListTo) f.nextElement();
2490 fto[_i] = mf.getStart();
2491 fto[_i + 1] = mf.getEnd();
2493 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
2494 fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
2495 if (m.getMappingChoice() != null)
2497 MappingChoice mc = m.getMappingChoice();
2498 if (mc.getDseqFor() != null)
2500 if (seqRefIds.containsKey(mc.getDseqFor()))
2505 jmap.setTo((SequenceI) seqRefIds.get(mc.getDseqFor()));
2509 frefedSequence.add(new Object[]
2510 { mc.getDseqFor(), jmap });
2516 * local sequence definition
2518 Sequence ms = mc.getSequence();
2519 jalview.datamodel.Sequence djs = null;
2520 String sqid = ms.getDsseqid();
2521 if (sqid != null && sqid.length() > 0)
2524 * recover dataset sequence
2526 djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
2531 .println("Warning - making up dataset sequence id for DbRef sequence map reference");
2532 sqid = ((Object) ms).toString(); // make up a new hascode for
2533 // undefined dataset sequence hash
2534 // (unlikely to happen)
2540 * make a new dataset sequence and add it to refIds hash
2542 djs = new jalview.datamodel.Sequence(ms.getName(), ms
2544 djs.setStart(jmap.getMap().getToLowest());
2545 djs.setEnd(jmap.getMap().getToHighest());
2546 djs.setVamsasId(uniqueSetSuffix + sqid);
2548 seqRefIds.put(sqid, djs);
2551 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
2560 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
2561 boolean keepSeqRefs)
2563 jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
2569 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
2573 uniqueSetSuffix = "";
2576 viewportsAdded = new Hashtable();
2578 AlignFrame af = LoadFromObject(jm, null, false);
2579 af.alignPanels.clear();
2580 af.closeMenuItem_actionPerformed(true);
2583 * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length;
2584 * i++) { if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated) {
2585 * af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
2586 * ap.av.alignment.getAlignmentAnnotation()[i]; } } }
2589 return af.alignPanel;
2595 * @see java.lang.Object#finalize()
2597 protected void finalize() throws Throwable
2599 // really make sure we have no buried refs left.
2601 this.seqRefIds = null;
2602 this.seqsToIds = null;