2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 import java.util.jar.*;
28 import org.exolab.castor.xml.*;
30 import uk.ac.vamsas.objects.utils.MapList;
31 import jalview.datamodel.Alignment;
32 import jalview.datamodel.AlignmentI;
33 import jalview.datamodel.SequenceI;
34 import jalview.schemabinding.version2.*;
35 import jalview.schemes.*;
36 import jalview.structure.StructureSelectionManager;
39 * Write out the current jalview desktop state
40 * as a Jalview XML stream.
42 * Note: the vamsas objects referred to here are primitive
43 * versions of the VAMSAS project schema elements - they are
44 * not the same and most likely never will be :)
49 public class Jalview2XML
52 * create/return unique hash string for sq
54 * @return new or existing unique string for sq
56 String seqHash(SequenceI sq)
62 if (seqsToIds.containsKey(sq))
64 return (String) seqsToIds.get(sq);
66 // create sequential key
67 String key = "sq"+(seqsToIds.size()+1);
68 seqsToIds.put(sq, key);
81 seqsToIds = new IdentityHashMap();
85 seqRefIds = new Hashtable();
88 java.util.IdentityHashMap seqsToIds = null; // SequenceI->key resolution
89 java.util.Hashtable seqRefIds = null; // key->SequenceI resolution
91 Vector frefedSequence = null;
92 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
96 public Jalview2XML(boolean raiseGUI)
98 this.raiseGUI = raiseGUI;
101 public void resolveFrefedSequences()
103 if (frefedSequence.size() > 0)
105 int r = 0, rSize = frefedSequence.size();
108 Object[] ref = (Object[]) frefedSequence.elementAt(r);
111 String sref = (String) ref[0];
112 if (seqRefIds.containsKey(sref))
114 if (ref[1] instanceof jalview.datamodel.Mapping)
116 SequenceI seq = (SequenceI) seqRefIds.get(sref);
117 while (seq.getDatasetSequence() != null)
119 seq = seq.getDatasetSequence();
121 ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
126 .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
127 + ref[1].getClass() + " type objects.");
129 frefedSequence.remove(r);
139 frefedSequence.remove(r);
147 * This maintains a list of viewports, the key being the
148 * seqSetId. Important to set historyItem and redoList
151 Hashtable viewportsAdded;
153 Hashtable annotationIds = new Hashtable();
155 String uniqueSetSuffix = "";
158 * List of pdbfiles added to Jar
160 Vector pdbfiles = null;
162 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
163 public void SaveState(File statefile)
165 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
174 FileOutputStream fos = new FileOutputStream(statefile);
175 JarOutputStream jout = new JarOutputStream(fos);
177 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
178 ////////////////////////////////////////////////////
179 //NOTE ALSO new PrintWriter must be used for each new JarEntry
180 PrintWriter out = null;
182 Vector shortNames = new Vector();
185 for (int i = frames.length - 1; i > -1; i--)
187 if (frames[i] instanceof AlignFrame)
189 AlignFrame af = (AlignFrame) frames[i];
191 String shortName = af.getTitle();
193 if (shortName.indexOf(File.separatorChar) > -1)
195 shortName = shortName.substring(shortName
196 .lastIndexOf(File.separatorChar) + 1);
201 while (shortNames.contains(shortName))
203 if (shortName.endsWith("_" + (count - 1)))
205 shortName = shortName
206 .substring(0, shortName.lastIndexOf("_"));
209 shortName = shortName.concat("_" + count);
213 shortNames.addElement(shortName);
215 if (!shortName.endsWith(".xml"))
217 shortName = shortName + ".xml";
220 int ap, apSize = af.alignPanels.size();
221 for (ap = 0; ap < apSize; ap++)
223 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
225 String fileName = apSize == 1 ? shortName : ap + shortName;
226 if (!fileName.endsWith(".xml"))
228 fileName = fileName + ".xml";
231 SaveState(apanel, fileName, jout);
235 try { jout.flush(); } catch (Exception foo) {};
237 } catch (Exception ex)
239 //TODO: inform user of the problem - they need to know if their data was not saved !
240 ex.printStackTrace();
244 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
245 public boolean SaveAlignment(AlignFrame af, String jarFile,
250 int ap, apSize = af.alignPanels.size();
251 FileOutputStream fos = new FileOutputStream(jarFile);
252 JarOutputStream jout = new JarOutputStream(fos);
253 for (ap = 0; ap < apSize; ap++)
255 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
257 String jfileName = apSize == 1 ? fileName : fileName + ap;
258 if (!jfileName.endsWith(".xml"))
260 jfileName = jfileName + ".xml";
262 SaveState(apanel, jfileName, jout);
265 try { jout.flush(); } catch (Exception foo) {};
268 } catch (Exception ex)
270 ex.printStackTrace();
276 * create a JalviewModel from an algnment view and marshall it
277 * to a JarOutputStream
279 * @param ap panel to create jalview model for
280 * @param fileName name of alignment panel written to output stream
281 * @param jout jar output stream
282 * @param out jar entry name
284 public JalviewModel SaveState(AlignmentPanel ap, String fileName,
285 JarOutputStream jout)
289 Vector userColours = new Vector();
291 AlignViewport av = ap.av;
293 JalviewModel object = new JalviewModel();
294 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
296 object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
297 object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
299 jalview.datamodel.AlignmentI jal = av.alignment;
301 if (av.hasHiddenRows)
303 jal = jal.getHiddenSequences().getFullAlignment();
306 SequenceSet vamsasSet = new SequenceSet();
308 JalviewModelSequence jms = new JalviewModelSequence();
310 vamsasSet.setGapChar(jal.getGapCharacter() + "");
312 if (jal.getDataset() != null)
314 // dataset id is the dataset's hashcode
315 vamsasSet.setDatasetId(jal.getDataset().hashCode() + "");
317 if (jal.getProperties() != null)
319 Enumeration en = jal.getProperties().keys();
320 while (en.hasMoreElements())
322 String key = en.nextElement().toString();
323 SequenceSetProperties ssp = new SequenceSetProperties();
325 ssp.setValue(jal.getProperties().get(key).toString());
326 vamsasSet.addSequenceSetProperties(ssp);
334 jalview.datamodel.SequenceI jds;
335 for (int i = 0; i < jal.getHeight(); i++)
337 jds = jal.getSequenceAt(i);
340 if (seqRefIds.get(id) != null)
342 // 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)
343 // JBPNote: Uncomment to debug writing out of files that do not read back in due to ArrayOutOfBoundExceptions.
344 //System.err.println("vamsasSeq backref: "+id+"");
345 //System.err.println(jds.getName()+" "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
346 //System.err.println("Hashcode: "+seqHash(jds));
347 //SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
348 //System.err.println(rsq.getName()+" "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
349 //System.err.println("Hashcode: "+seqHash(rsq));
353 vamsasSeq = createVamsasSequence(id, jds);
354 vamsasSet.addSequence(vamsasSeq);
355 seqRefIds.put(id, jds);
359 jseq.setStart(jds.getStart());
360 jseq.setEnd(jds.getEnd());
361 jseq.setColour(av.getSequenceColour(jds).getRGB());
363 jseq.setId(id); // jseq id should be a string not a number
365 if (av.hasHiddenRows)
367 jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
369 if (av.hiddenRepSequences != null
370 && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
372 jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences
373 .get(jal.getSequenceAt(i))).getSequencesInOrder(jal);
375 for (int h = 0; h < reps.length; h++)
377 if (reps[h] != jal.getSequenceAt(i))
379 jseq.addHiddenSequences(jal.findIndex(reps[h]));
385 if (jds.getDatasetSequence().getSequenceFeatures() != null)
387 jalview.datamodel.SequenceFeature[] sf = jds.getDatasetSequence()
388 .getSequenceFeatures();
390 while (index < sf.length)
392 Features features = new Features();
394 features.setBegin(sf[index].getBegin());
395 features.setEnd(sf[index].getEnd());
396 features.setDescription(sf[index].getDescription());
397 features.setType(sf[index].getType());
398 features.setFeatureGroup(sf[index].getFeatureGroup());
399 features.setScore(sf[index].getScore());
400 if (sf[index].links != null)
402 for (int l = 0; l < sf[index].links.size(); l++)
404 OtherData keyValue = new OtherData();
405 keyValue.setKey("LINK_" + l);
406 keyValue.setValue(sf[index].links.elementAt(l).toString());
407 features.addOtherData(keyValue);
410 if (sf[index].otherDetails != null)
413 Enumeration keys = sf[index].otherDetails.keys();
414 while (keys.hasMoreElements())
416 key = keys.nextElement().toString();
417 OtherData keyValue = new OtherData();
418 keyValue.setKey(key);
419 keyValue.setValue(sf[index].otherDetails.get(key).toString());
420 features.addOtherData(keyValue);
424 jseq.addFeatures(features);
429 if (jds.getDatasetSequence().getPDBId() != null)
431 Enumeration en = jds.getDatasetSequence().getPDBId().elements();
432 while (en.hasMoreElements())
434 Pdbids pdb = new Pdbids();
435 jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
438 pdb.setId(entry.getId());
439 pdb.setType(entry.getType());
442 //This must have been loaded, is it still visible?
443 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
444 for (int f = frames.length - 1; f > -1; f--)
446 if (frames[f] instanceof AppJmol)
448 jmol = (AppJmol) frames[f];
449 if (!jmol.pdbentry.getId().equals(entry.getId()))
452 StructureState state = new StructureState();
453 state.setVisible(true);
454 state.setXpos(jmol.getX());
455 state.setYpos(jmol.getY());
456 state.setWidth(jmol.getWidth());
457 state.setHeight(jmol.getHeight());
459 String statestring = jmol.viewer.getStateInfo();
462 state.setContent(statestring.replaceAll("\n", ""));
464 for (int s = 0; s < jmol.sequence.length; s++)
466 if (jal.findIndex(jmol.sequence[s]) > -1)
468 pdb.addStructureState(state);
474 if (entry.getFile() != null)
476 pdb.setFile(entry.getFile());
477 if (pdbfiles == null)
479 pdbfiles = new Vector();
482 if (!pdbfiles.contains(entry.getId()))
484 pdbfiles.addElement(entry.getId());
487 File file = new File(entry.getFile());
488 if (file.exists() && jout != null)
490 byte[] data = new byte[(int) file.length()];
491 jout.putNextEntry(new JarEntry(entry.getId()));
492 DataInputStream dis = new DataInputStream(
493 new FileInputStream(file));
496 DataOutputStream dout = new DataOutputStream(jout);
497 dout.write(data, 0, data.length);
501 } catch (Exception ex)
503 ex.printStackTrace();
509 if (entry.getProperty() != null)
511 PdbentryItem item = new PdbentryItem();
512 Hashtable properties = entry.getProperty();
513 Enumeration en2 = properties.keys();
514 while (en2.hasMoreElements())
516 Property prop = new Property();
517 String key = en2.nextElement().toString();
519 prop.setValue(properties.get(key).toString());
520 item.addProperty(prop);
522 pdb.addPdbentryItem(item);
532 if (av.hasHiddenRows)
537 if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
539 jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
540 for (int i = 0; i < jac.length; i++)
542 AlcodonFrame alc = new AlcodonFrame();
543 vamsasSet.addAlcodonFrame(alc);
544 for (int p = 0; p < jac[i].aaWidth; p++)
546 Alcodon cmap = new Alcodon();
547 cmap.setPos1(jac[i].codons[p][0]);
548 cmap.setPos2(jac[i].codons[p][1]);
549 cmap.setPos3(jac[i].codons[p][2]);
550 alc.addAlcodon(cmap);
552 if (jac[i].getProtMappings() != null
553 && jac[i].getProtMappings().length > 0)
555 SequenceI[] dnas = jac[i].getdnaSeqs();
556 jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings();
557 for (int m = 0; m < pmaps.length; m++)
559 AlcodMap alcmap = new AlcodMap();
560 alcmap.setDnasq("" + dnas[m].hashCode());
561 alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
563 alc.addAlcodMap(alcmap);
570 ///////////////////////////////////
571 if (av.currentTree != null)
573 // FIND ANY ASSOCIATED TREES
574 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
575 if (Desktop.desktop != null)
577 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
579 for (int t = 0; t < frames.length; t++)
581 if (frames[t] instanceof TreePanel)
583 TreePanel tp = (TreePanel) frames[t];
585 if (tp.treeCanvas.av.alignment == jal)
587 Tree tree = new Tree();
588 tree.setTitle(tp.getTitle());
589 tree.setCurrentTree((av.currentTree == tp.getTree()));
590 tree.setNewick(tp.getTree().toString());
591 tree.setThreshold(tp.treeCanvas.threshold);
593 tree.setFitToWindow(tp.fitToWindow.getState());
594 tree.setFontName(tp.getTreeFont().getName());
595 tree.setFontSize(tp.getTreeFont().getSize());
596 tree.setFontStyle(tp.getTreeFont().getStyle());
597 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
599 tree.setShowBootstrap(tp.bootstrapMenu.getState());
600 tree.setShowDistances(tp.distanceMenu.getState());
602 tree.setHeight(tp.getHeight());
603 tree.setWidth(tp.getWidth());
604 tree.setXpos(tp.getX());
605 tree.setYpos(tp.getY());
615 if (jal.getAlignmentAnnotation() != null)
617 jalview.datamodel.AlignmentAnnotation[] aa = jal
618 .getAlignmentAnnotation();
620 for (int i = 0; i < aa.length; i++)
622 Annotation an = new Annotation();
624 if (aa[i].annotationId != null)
626 annotationIds.put(aa[i].annotationId, aa[i]);
629 an.setId(aa[i].annotationId);
631 if (aa[i] == av.quality || aa[i] == av.conservation
632 || aa[i] == av.consensus)
634 an.setLabel(aa[i].label);
636 vamsasSet.addAnnotation(an);
640 an.setVisible(aa[i].visible);
642 an.setDescription(aa[i].description);
644 if (aa[i].sequenceRef != null)
646 an.setSequenceRef(aa[i].sequenceRef.getName());
652 an.setGraphType(aa[i].graph);
653 an.setGraphGroup(aa[i].graphGroup);
654 if (aa[i].getThreshold() != null)
656 ThresholdLine line = new ThresholdLine();
657 line.setLabel(aa[i].getThreshold().label);
658 line.setValue(aa[i].getThreshold().value);
659 line.setColour(aa[i].getThreshold().colour.getRGB());
660 an.setThresholdLine(line);
668 an.setLabel(aa[i].label);
669 if (aa[i].hasScore())
671 an.setScore(aa[i].getScore());
673 AnnotationElement ae;
674 if (aa[i].annotations != null)
676 an.setScoreOnly(false);
677 for (int a = 0; a < aa[i].annotations.length; a++)
679 if ((aa[i] == null) || (aa[i].annotations[a] == null))
684 ae = new AnnotationElement();
685 if (aa[i].annotations[a].description != null)
686 ae.setDescription(aa[i].annotations[a].description);
687 if (aa[i].annotations[a].displayCharacter != null)
688 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
690 if (!Float.isNaN(aa[i].annotations[a].value))
691 ae.setValue(aa[i].annotations[a].value);
694 if (aa[i].annotations[a].secondaryStructure != ' '
695 && aa[i].annotations[a].secondaryStructure != '\0')
697 .setSecondaryStructure(aa[i].annotations[a].secondaryStructure
700 if (aa[i].annotations[a].colour != null
701 && aa[i].annotations[a].colour != java.awt.Color.black)
703 ae.setColour(aa[i].annotations[a].colour.getRGB());
706 an.addAnnotationElement(ae);
711 an.setScoreOnly(true);
713 vamsasSet.addAnnotation(an);
718 if (jal.getGroups() != null)
720 JGroup[] groups = new JGroup[jal.getGroups().size()];
722 for (int i = 0; i < groups.length; i++)
724 groups[i] = new JGroup();
726 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal
727 .getGroups().elementAt(i);
728 groups[i].setStart(sg.getStartRes());
729 groups[i].setEnd(sg.getEndRes());
730 groups[i].setName(sg.getName());
733 if (sg.cs.conservationApplied())
735 groups[i].setConsThreshold(sg.cs.getConservationInc());
737 if (sg.cs instanceof jalview.schemes.UserColourScheme)
739 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
745 .setColour(ColourSchemeProperty.getColourName(sg.cs));
748 else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
751 .setColour(ColourSchemeProperty
752 .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
755 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
758 .setColour(SetUserColourScheme(sg.cs, userColours, jms));
762 groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
765 groups[i].setPidThreshold(sg.cs.getThreshold());
768 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
769 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
770 groups[i].setDisplayText(sg.getDisplayText());
771 groups[i].setColourText(sg.getColourText());
772 groups[i].setTextCol1(sg.textColour.getRGB());
773 groups[i].setTextCol2(sg.textColour2.getRGB());
774 groups[i].setTextColThreshold(sg.thresholdTextColour);
776 for (int s = 0; s < sg.getSize(); s++)
778 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
780 groups[i].addSeq(seqHash(seq));
784 jms.setJGroup(groups);
787 ///////////SAVE VIEWPORT
788 Viewport view = new Viewport();
789 view.setTitle(ap.alignFrame.getTitle());
790 view.setSequenceSetId(av.getSequenceSetId());
791 view.setViewName(av.viewName);
792 view.setGatheredViews(av.gatherViewsHere);
794 if (ap.av.explodedPosition != null)
796 view.setXpos(av.explodedPosition.x);
797 view.setYpos(av.explodedPosition.y);
798 view.setWidth(av.explodedPosition.width);
799 view.setHeight(av.explodedPosition.height);
803 view.setXpos(ap.alignFrame.getBounds().x);
804 view.setYpos(ap.alignFrame.getBounds().y);
805 view.setWidth(ap.alignFrame.getBounds().width);
806 view.setHeight(ap.alignFrame.getBounds().height);
809 view.setStartRes(av.startRes);
810 view.setStartSeq(av.startSeq);
812 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
814 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
817 else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
819 jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
820 .getGlobalColourScheme();
822 AnnotationColours ac = new AnnotationColours();
823 ac.setAboveThreshold(acg.getAboveThreshold());
824 ac.setThreshold(acg.getAnnotationThreshold());
825 ac.setAnnotation(acg.getAnnotation());
826 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
828 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
833 ac.setColourScheme(ColourSchemeProperty.getColourName(acg
837 ac.setMaxColour(acg.getMaxColour().getRGB());
838 ac.setMinColour(acg.getMinColour().getRGB());
839 view.setAnnotationColours(ac);
840 view.setBgColour("AnnotationColourGradient");
844 view.setBgColour(ColourSchemeProperty.getColourName(av
845 .getGlobalColourScheme()));
848 ColourSchemeI cs = av.getGlobalColourScheme();
852 if (cs.conservationApplied())
854 view.setConsThreshold(cs.getConservationInc());
855 if (cs instanceof jalview.schemes.UserColourScheme)
857 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
861 if (cs instanceof ResidueColourScheme)
863 view.setPidThreshold(cs.getThreshold());
867 view.setConservationSelected(av.getConservationSelected());
868 view.setPidSelected(av.getAbovePIDThreshold());
869 view.setFontName(av.font.getName());
870 view.setFontSize(av.font.getSize());
871 view.setFontStyle(av.font.getStyle());
872 view.setRenderGaps(av.renderGaps);
873 view.setShowAnnotation(av.getShowAnnotation());
874 view.setShowBoxes(av.getShowBoxes());
875 view.setShowColourText(av.getColourText());
876 view.setShowFullId(av.getShowJVSuffix());
877 view.setRightAlignIds(av.rightAlignIds);
878 view.setShowSequenceFeatures(av.showSequenceFeatures);
879 view.setShowText(av.getShowText());
880 view.setWrapAlignment(av.getWrapAlignment());
881 view.setTextCol1(av.textColour.getRGB());
882 view.setTextCol2(av.textColour2.getRGB());
883 view.setTextColThreshold(av.thresholdTextColour);
885 if (av.featuresDisplayed != null)
887 jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
889 String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
891 Vector settingsAdded = new Vector();
892 for (int ro = 0; ro < renderOrder.length; ro++)
894 Setting setting = new Setting();
895 setting.setType(renderOrder[ro]);
896 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
897 .getColour(renderOrder[ro]).getRGB());
899 setting.setDisplay(av.featuresDisplayed
900 .containsKey(renderOrder[ro]));
901 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
905 setting.setOrder(rorder);
907 fs.addSetting(setting);
908 settingsAdded.addElement(renderOrder[ro]);
911 //Make sure we save none displayed feature settings
912 Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
914 while (en.hasMoreElements())
916 String key = en.nextElement().toString();
917 if (settingsAdded.contains(key))
922 Setting setting = new Setting();
923 setting.setType(key);
924 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
925 .getColour(key).getRGB());
927 setting.setDisplay(false);
928 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
932 setting.setOrder(rorder);
934 fs.addSetting(setting);
935 settingsAdded.addElement(key);
937 en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
938 Vector groupsAdded = new Vector();
939 while (en.hasMoreElements())
941 String grp = en.nextElement().toString();
942 if (groupsAdded.contains(grp))
946 Group g = new Group();
949 .setDisplay(((Boolean) ap.seqPanel.seqCanvas
950 .getFeatureRenderer().featureGroups.get(grp))
953 groupsAdded.addElement(grp);
955 jms.setFeatureSettings(fs);
959 if (av.hasHiddenColumns)
961 for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
963 int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
965 HiddenColumns hc = new HiddenColumns();
966 hc.setStart(region[0]);
967 hc.setEnd(region[1]);
968 view.addHiddenColumns(hc);
972 jms.addViewport(view);
974 object.setJalviewModelSequence(jms);
975 object.getVamsasModel().addSequenceSet(vamsasSet);
977 if (jout!=null && fileName!=null)
979 //We may not want to write the object to disk,
980 //eg we can copy the alignViewport to a new view object
981 //using save and then load
984 JarEntry entry = new JarEntry(fileName);
985 jout.putNextEntry(entry);
986 PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
988 org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(pout);
989 marshaller.marshal(object);
992 } catch (Exception ex)
994 // TODO: raise error in GUI if marshalling failed.
995 ex.printStackTrace();
1001 private Sequence createVamsasSequence(String id, SequenceI jds)
1003 return createVamsasSequence(true, id, jds, null);
1006 private Sequence createVamsasSequence(boolean recurse, String id,
1007 SequenceI jds, SequenceI parentseq)
1009 Sequence vamsasSeq = new Sequence();
1010 vamsasSeq.setId(id);
1011 vamsasSeq.setName(jds.getName());
1012 vamsasSeq.setSequence(jds.getSequenceAsString());
1013 vamsasSeq.setDescription(jds.getDescription());
1014 jalview.datamodel.DBRefEntry[] dbrefs = null;
1015 if (jds.getDatasetSequence() != null)
1017 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
1018 if (jds.getDatasetSequence().getDBRef() != null)
1020 dbrefs = jds.getDatasetSequence().getDBRef();
1025 vamsasSeq.setDsseqid(id); // so we can tell which sequences really are dataset sequences only
1026 dbrefs = jds.getDBRef();
1030 for (int d = 0; d < dbrefs.length; d++)
1032 DBRef dbref = new DBRef();
1033 dbref.setSource(dbrefs[d].getSource());
1034 dbref.setVersion(dbrefs[d].getVersion());
1035 dbref.setAccessionId(dbrefs[d].getAccessionId());
1036 if (dbrefs[d].hasMap())
1038 Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
1040 dbref.setMapping(mp);
1042 vamsasSeq.addDBRef(dbref);
1048 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
1049 SequenceI parentseq, SequenceI jds, boolean recurse)
1052 if (jmp.getMap() != null)
1056 jalview.util.MapList mlst = jmp.getMap();
1057 int r[] = mlst.getFromRanges();
1058 for (int s = 0; s < r.length; s += 2)
1060 MapListFrom mfrom = new MapListFrom();
1061 mfrom.setStart(r[s]);
1062 mfrom.setEnd(r[s + 1]);
1063 mp.addMapListFrom(mfrom);
1065 r = mlst.getToRanges();
1066 for (int s = 0; s < r.length; s += 2)
1068 MapListTo mto = new MapListTo();
1070 mto.setEnd(r[s + 1]);
1071 mp.addMapListTo(mto);
1073 mp.setMapFromUnit(mlst.getFromRatio());
1074 mp.setMapToUnit(mlst.getToRatio());
1075 if (jmp.getTo() != null)
1077 MappingChoice mpc = new MappingChoice();
1079 && (parentseq != jmp.getTo() || parentseq
1080 .getDatasetSequence() != jmp.getTo()))
1082 mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo())
1083 , jmp.getTo(), jds));
1088 SequenceI ps = null;
1089 if (parentseq != jmp.getTo()
1090 && parentseq.getDatasetSequence() != jmp.getTo())
1092 // chaining dbref rather than a handshaking one
1093 jmpid = seqHash(ps = jmp.getTo());
1097 jmpid = seqHash(ps = parentseq);
1099 mpc.setDseqFor(jmpid);
1100 if (!seqRefIds.containsKey(mpc.getDseqFor()))
1102 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
1103 seqRefIds.put(mpc.getDseqFor(), ps);
1107 jalview.bin.Cache.log.debug("reusing DseqFor ID");
1110 mp.setMappingChoice(mpc);
1116 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
1117 Vector userColours, JalviewModelSequence jms)
1120 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
1122 if (!userColours.contains(ucs))
1124 userColours.add(ucs);
1126 java.awt.Color[] colours = ucs.getColours();
1127 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
1128 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
1130 for (int i = 0; i < colours.length; i++)
1132 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1133 col.setName(ResidueProperties.aa[i]);
1134 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1135 jbucs.addColour(col);
1137 if (ucs.getLowerCaseColours() != null)
1139 colours = ucs.getLowerCaseColours();
1140 for (int i = 0; i < colours.length; i++)
1142 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1143 col.setName(ResidueProperties.aa[i].toLowerCase());
1144 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1145 jbucs.addColour(col);
1149 id = "ucs" + userColours.indexOf(ucs);
1151 uc.setUserColourScheme(jbucs);
1152 jms.addUserColours(uc);
1158 jalview.schemes.UserColourScheme GetUserColourScheme(
1159 JalviewModelSequence jms, String id)
1161 UserColours[] uc = jms.getUserColours();
1162 UserColours colours = null;
1164 for (int i = 0; i < uc.length; i++)
1166 if (uc[i].getId().equals(id))
1174 java.awt.Color[] newColours = new java.awt.Color[24];
1176 for (int i = 0; i < 24; i++)
1178 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1179 .getUserColourScheme().getColour(i).getRGB(), 16));
1182 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
1185 if (colours.getUserColourScheme().getColourCount() > 24)
1187 newColours = new java.awt.Color[23];
1188 for (int i = 0; i < 23; i++)
1190 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1191 .getUserColourScheme().getColour(i + 24).getRGB(), 16));
1193 ucs.setLowerCaseColours(newColours);
1202 * @param file DOCUMENT ME!
1204 public AlignFrame LoadJalviewAlign(final String file)
1206 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
1208 jalview.gui.AlignFrame af = null;
1210 seqRefIds = new Hashtable();
1211 viewportsAdded = new Hashtable();
1212 frefedSequence = new Vector();
1213 Hashtable gatherToThisFrame = new Hashtable();
1215 String errorMessage = null;
1219 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
1222 if (file.startsWith("http://"))
1224 url = new URL(file);
1227 JarInputStream jin = null;
1228 JarEntry jarentry = null;
1235 jin = new JarInputStream(url.openStream());
1239 jin = new JarInputStream(new FileInputStream(file));
1242 for (int i = 0; i < entryCount; i++)
1244 jarentry = jin.getNextJarEntry();
1247 if (jarentry != null && jarentry.getName().endsWith(".xml"))
1249 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
1250 JalviewModel object = new JalviewModel();
1252 Unmarshaller unmar = new Unmarshaller(object);
1253 unmar.setValidation(false);
1254 object = (JalviewModel) unmar.unmarshal(in);
1256 af = LoadFromObject(object, file, true);
1257 if (af.viewport.gatherViewsHere)
1259 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
1263 else if (jarentry != null)
1265 //Some other file here.
1268 } while (jarentry != null);
1269 resolveFrefedSequences();
1270 } catch (java.io.FileNotFoundException ex)
1272 ex.printStackTrace();
1273 errorMessage = "Couldn't locate Jalview XML file : " + file;
1274 System.err.println("Exception whilst loading jalview XML file : "
1276 } catch (java.net.UnknownHostException ex)
1278 ex.printStackTrace();
1279 errorMessage = "Couldn't locate Jalview XML file : " + file;
1280 System.err.println("Exception whilst loading jalview XML file : "
1282 } catch (Exception ex)
1284 System.err.println("Parsing as Jalview Version 2 file failed.");
1285 ex.printStackTrace(System.err);
1287 //Is Version 1 Jar file?
1289 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(file);
1290 } catch (Exception ex2) {
1291 System.err.println("Exception whilst loading as jalviewXMLV1:");
1292 ex2.printStackTrace();
1296 if (Desktop.instance != null)
1298 Desktop.instance.stopLoading();
1302 System.out.println("Successfully loaded archive file");
1305 ex.printStackTrace();
1307 System.err.println("Exception whilst loading jalview XML file : "
1311 if (Desktop.instance != null)
1313 Desktop.instance.stopLoading();
1316 Enumeration en = gatherToThisFrame.elements();
1317 while (en.hasMoreElements())
1319 Desktop.instance.gatherViews((AlignFrame) en.nextElement());
1322 if (errorMessage != null)
1324 final String finalErrorMessage = errorMessage;
1327 javax.swing.SwingUtilities.invokeLater(new Runnable()
1331 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1332 finalErrorMessage, "Error loading Jalview file",
1333 JOptionPane.WARNING_MESSAGE);
1337 System.err.println("Problem loading Jalview file: "+errorMessage);
1344 Hashtable alreadyLoadedPDB;
1346 String loadPDBFile(String file, String pdbId)
1348 if (alreadyLoadedPDB == null)
1349 alreadyLoadedPDB = new Hashtable();
1351 if (alreadyLoadedPDB.containsKey(pdbId))
1352 return alreadyLoadedPDB.get(pdbId).toString();
1356 JarInputStream jin = null;
1358 if (file.startsWith("http://"))
1360 jin = new JarInputStream(new URL(file).openStream());
1364 jin = new JarInputStream(new FileInputStream(file));
1367 JarEntry entry = null;
1370 entry = jin.getNextJarEntry();
1371 } while (!entry.getName().equals(pdbId));
1373 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1374 File outFile = File.createTempFile("jalview_pdb", ".txt");
1375 outFile.deleteOnExit();
1376 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1379 while ((data = in.readLine()) != null)
1383 try { out.flush(); } catch (Exception foo) {};
1386 alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
1387 return outFile.getAbsolutePath();
1389 } catch (Exception ex)
1391 ex.printStackTrace();
1397 AlignFrame LoadFromObject(JalviewModel object, String file,
1398 boolean loadTreesAndStructures)
1400 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1401 Sequence[] vamsasSeq = vamsasSet.getSequence();
1403 JalviewModelSequence jms = object.getJalviewModelSequence();
1405 Viewport view = jms.getViewport(0);
1407 //////////////////////////////////
1410 Vector hiddenSeqs = null;
1411 jalview.datamodel.Sequence jseq;
1413 ArrayList tmpseqs = new ArrayList();
1415 boolean multipleView = false;
1417 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1418 int vi=0; // counter in vamsasSeq array
1419 for (int i = 0; i < JSEQ.length; i++)
1421 String seqId = JSEQ[i].getId() + "";
1423 if (seqRefIds.get(seqId) != null)
1425 tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId));
1426 multipleView = true;
1430 jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
1431 vamsasSeq[vi].getSequence());
1432 jseq.setDescription(vamsasSeq[vi].getDescription());
1433 jseq.setStart(JSEQ[i].getStart());
1434 jseq.setEnd(JSEQ[i].getEnd());
1435 jseq.setVamsasId(uniqueSetSuffix + seqId);
1436 seqRefIds.put(vamsasSeq[vi].getId()+"", jseq);
1441 if (JSEQ[i].getHidden())
1443 if (hiddenSeqs == null)
1445 hiddenSeqs = new Vector();
1448 hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
1455 // Create the alignment object from the sequence set
1456 /////////////////////////////////
1457 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
1460 tmpseqs.toArray(orderedSeqs);
1462 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
1465 /// Add the alignment properties
1466 for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
1468 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
1469 al.setProperty(ssp.getKey(), ssp.getValue());
1473 // SequenceFeatures are added to the DatasetSequence,
1474 // so we must create or recover the dataset before loading features
1475 /////////////////////////////////
1476 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
1478 // older jalview projects do not have a dataset id.
1479 al.setDataset(null);
1483 recoverDatasetFor(vamsasSet, al);
1485 /////////////////////////////////
1487 Hashtable pdbloaded = new Hashtable();
1490 for (int i = 0; i < vamsasSeq.length; i++)
1492 if (JSEQ[i].getFeaturesCount() > 0)
1494 Features[] features = JSEQ[i].getFeatures();
1495 for (int f = 0; f < features.length; f++)
1497 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
1498 features[f].getType(), features[f].getDescription(),
1499 features[f].getStatus(), features[f].getBegin(),
1500 features[f].getEnd(), features[f].getFeatureGroup());
1502 sf.setScore(features[f].getScore());
1503 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1505 OtherData keyValue = features[f].getOtherData(od);
1506 if (keyValue.getKey().startsWith("LINK"))
1508 sf.addLink(keyValue.getValue());
1512 sf.setValue(keyValue.getKey(), keyValue.getValue());
1517 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1520 if (vamsasSeq[i].getDBRefCount() > 0)
1522 addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
1524 if (JSEQ[i].getPdbidsCount() > 0)
1526 Pdbids[] ids = JSEQ[i].getPdbids();
1527 for (int p = 0; p < ids.length; p++)
1529 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
1530 entry.setId(ids[p].getId());
1531 entry.setType(ids[p].getType());
1532 if (ids[p].getFile() != null)
1534 if (!pdbloaded.containsKey(ids[p].getFile()))
1536 entry.setFile(loadPDBFile(file, ids[p].getId()));
1540 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1544 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1550 /////////////////////////////////
1551 // LOAD SEQUENCE MAPPINGS
1552 if (vamsasSet.getAlcodonFrameCount() > 0)
1554 AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
1555 for (int i = 0; i < alc.length; i++)
1557 jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
1558 alc[i].getAlcodonCount());
1559 if (alc[i].getAlcodonCount() > 0)
1561 Alcodon[] alcods = alc[i].getAlcodon();
1562 for (int p = 0; p < cf.codons.length; p++)
1564 cf.codons[p] = new int[3];
1565 cf.codons[p][0] = (int) alcods[p].getPos1();
1566 cf.codons[p][1] = (int) alcods[p].getPos2();
1567 cf.codons[p][2] = (int) alcods[p].getPos3();
1570 if (alc[i].getAlcodMapCount() > 0)
1572 AlcodMap[] maps = alc[i].getAlcodMap();
1573 for (int m = 0; m < maps.length; m++)
1575 SequenceI dnaseq = (SequenceI) seqRefIds
1576 .get(maps[m].getDnasq());
1578 // attach to dna sequence reference.
1581 if (maps[m].getMapping() != null)
1583 jalview.datamodel.Mapping mapping = addMapping(maps[m]
1585 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
1590 al.addCodonFrame(cf);
1595 //////////////////////////////////
1597 boolean hideQuality = true, hideConservation = true, hideConsensus = true;
1599 if (vamsasSet.getAnnotationCount() > 0)
1601 Annotation[] an = vamsasSet.getAnnotation();
1603 for (int i = 0; i < an.length; i++)
1605 if (an[i].getLabel().equals("Quality"))
1607 hideQuality = false;
1610 else if (an[i].getLabel().equals("Conservation"))
1612 hideConservation = false;
1615 else if (an[i].getLabel().equals("Consensus"))
1617 hideConsensus = false;
1621 if (an[i].getId() != null
1622 && annotationIds.containsKey(an[i].getId()))
1624 jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
1625 .get(an[i].getId());
1626 if (an[i].hasVisible())
1627 jda.visible = an[i].getVisible();
1629 al.addAnnotation(jda);
1634 AnnotationElement[] ae = an[i].getAnnotationElement();
1635 jalview.datamodel.Annotation[] anot = null;
1637 if (!an[i].getScoreOnly())
1639 anot = new jalview.datamodel.Annotation[al.getWidth()];
1641 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
1643 if (ae[aa].getPosition() >= anot.length)
1646 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
1648 ae[aa].getDisplayCharacter(), ae[aa].getDescription(), (ae[aa]
1649 .getSecondaryStructure() == null || ae[aa]
1650 .getSecondaryStructure().length() == 0) ? ' ' : ae[aa]
1651 .getSecondaryStructure().charAt(0), ae[aa].getValue()
1654 // JBPNote: Consider verifying dataflow for IO of secondary structure annotation read from Stockholm files
1655 // this was added to try to ensure that
1656 //if (anot[ae[aa].getPosition()].secondaryStructure>' ')
1658 // anot[ae[aa].getPosition()].displayCharacter = "";
1660 anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]
1664 jalview.datamodel.AlignmentAnnotation jaa = null;
1666 if (an[i].getGraph())
1668 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1669 an[i].getDescription(), anot, 0, 0, an[i].getGraphType());
1671 jaa.graphGroup = an[i].getGraphGroup();
1673 if (an[i].getThresholdLine() != null)
1675 jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
1676 .getThresholdLine().getValue(), an[i]
1677 .getThresholdLine().getLabel(), new java.awt.Color(
1678 an[i].getThresholdLine().getColour())));
1685 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1686 an[i].getDescription(), anot);
1689 if (an[i].getId() != null)
1691 annotationIds.put(an[i].getId(), jaa);
1692 jaa.annotationId = an[i].getId();
1695 if (an[i].getSequenceRef() != null)
1697 if (al.findName(an[i].getSequenceRef()) != null)
1699 jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
1701 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1704 if (an[i].hasScore())
1706 jaa.setScore(an[i].getScore());
1709 if (an[i].hasVisible())
1710 jaa.visible = an[i].getVisible();
1712 al.addAnnotation(jaa);
1716 /////////////////////////
1718 if (jms.getJGroupCount() > 0)
1720 JGroup[] groups = jms.getJGroup();
1722 for (int i = 0; i < groups.length; i++)
1724 ColourSchemeI cs = null;
1726 if (groups[i].getColour() != null)
1728 if (groups[i].getColour().startsWith("ucs"))
1730 cs = GetUserColourScheme(jms, groups[i].getColour());
1734 cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
1739 cs.setThreshold(groups[i].getPidThreshold(), true);
1743 Vector seqs = new Vector();
1745 for (int s = 0; s < groups[i].getSeqCount(); s++)
1747 String seqId = groups[i].getSeq(s) + "";
1748 jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds
1753 seqs.addElement(ts);
1757 if (seqs.size() < 1)
1762 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
1763 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1764 groups[i].getDisplayText(), groups[i].getColourText(),
1765 groups[i].getStart(), groups[i].getEnd());
1768 .setOutlineColour(new java.awt.Color(groups[i]
1769 .getOutlineColour()));
1771 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
1772 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
1773 sg.thresholdTextColour = groups[i].getTextColThreshold();
1775 if (groups[i].getConsThreshold() != 0)
1777 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
1778 "All", ResidueProperties.propHash, 3, sg
1779 .getSequences(null), 0, sg.getWidth() - 1);
1781 c.verdict(false, 25);
1782 sg.cs.setConservation(c);
1789 /////////////////////////////////
1792 AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
1794 af.setFileName(file, "Jalview");
1796 for (int i = 0; i < JSEQ.length; i++)
1798 af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
1799 new java.awt.Color(JSEQ[i].getColour()));
1802 //If we just load in the same jar file again, the sequenceSetId
1803 //will be the same, and we end up with multiple references
1804 //to the same sequenceSet. We must modify this id on load
1805 //so that each load of the file gives a unique id
1806 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
1808 af.viewport.gatherViewsHere = view.getGatheredViews();
1810 if (view.getSequenceSetId() != null)
1812 jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
1813 .get(uniqueSeqSetId);
1815 af.viewport.sequenceSetID = uniqueSeqSetId;
1819 af.viewport.historyList = av.historyList;
1820 af.viewport.redoList = av.redoList;
1824 viewportsAdded.put(uniqueSeqSetId, af.viewport);
1827 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1829 if (hiddenSeqs != null)
1831 for (int s = 0; s < JSEQ.length; s++)
1833 jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
1835 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
1837 hidden.addSequence(al
1838 .getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
1840 af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
1843 jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
1846 for (int s = 0; s < hiddenSeqs.size(); s++)
1848 hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
1851 af.viewport.hideSequence(hseqs);
1855 if ((hideConsensus || hideQuality || hideConservation)
1856 && al.getAlignmentAnnotation() != null)
1858 int hSize = al.getAlignmentAnnotation().length;
1859 for (int h = 0; h < hSize; h++)
1861 if ((hideConsensus && al.getAlignmentAnnotation()[h].label
1862 .equals("Consensus"))
1863 || (hideQuality && al.getAlignmentAnnotation()[h].label
1865 || (hideConservation && al.getAlignmentAnnotation()[h].label
1866 .equals("Conservation")))
1868 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1873 af.alignPanel.adjustAnnotationHeight();
1876 if (view.getViewName() != null)
1878 af.viewport.viewName = view.getViewName();
1879 af.setInitialTabVisible();
1881 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
1884 af.viewport.setShowAnnotation(view.getShowAnnotation());
1885 af.viewport.setAbovePIDThreshold(view.getPidSelected());
1887 af.viewport.setColourText(view.getShowColourText());
1889 af.viewport.setConservationSelected(view.getConservationSelected());
1890 af.viewport.setShowJVSuffix(view.getShowFullId());
1891 af.viewport.rightAlignIds = view.getRightAlignIds();
1892 af.viewport.setFont(new java.awt.Font(view.getFontName(), view
1893 .getFontStyle(), view.getFontSize()));
1894 af.alignPanel.fontChanged();
1895 af.viewport.setRenderGaps(view.getRenderGaps());
1896 af.viewport.setWrapAlignment(view.getWrapAlignment());
1897 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1898 af.viewport.setShowAnnotation(view.getShowAnnotation());
1899 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1901 af.viewport.setShowBoxes(view.getShowBoxes());
1903 af.viewport.setShowText(view.getShowText());
1905 af.viewport.textColour = new java.awt.Color(view.getTextCol1());
1906 af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
1907 af.viewport.thresholdTextColour = view.getTextColThreshold();
1909 af.viewport.setStartRes(view.getStartRes());
1910 af.viewport.setStartSeq(view.getStartSeq());
1912 ColourSchemeI cs = null;
1914 if (view.getBgColour() != null)
1916 if (view.getBgColour().startsWith("ucs"))
1918 cs = GetUserColourScheme(jms, view.getBgColour());
1920 else if (view.getBgColour().startsWith("Annotation"))
1922 //int find annotation
1923 for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1925 if (af.viewport.alignment.getAlignmentAnnotation()[i].label
1926 .equals(view.getAnnotationColours().getAnnotation()))
1928 if (af.viewport.alignment.getAlignmentAnnotation()[i]
1929 .getThreshold() == null)
1931 af.viewport.alignment.getAlignmentAnnotation()[i]
1932 .setThreshold(new jalview.datamodel.GraphLine(view
1933 .getAnnotationColours().getThreshold(),
1934 "Threshold", java.awt.Color.black)
1939 if (view.getAnnotationColours().getColourScheme()
1942 cs = new AnnotationColourGradient(af.viewport.alignment
1943 .getAlignmentAnnotation()[i], new java.awt.Color(view
1944 .getAnnotationColours().getMinColour()),
1945 new java.awt.Color(view.getAnnotationColours()
1946 .getMaxColour()), view.getAnnotationColours()
1947 .getAboveThreshold());
1949 else if (view.getAnnotationColours().getColourScheme()
1952 cs = new AnnotationColourGradient(af.viewport.alignment
1953 .getAlignmentAnnotation()[i], GetUserColourScheme(
1954 jms, view.getAnnotationColours().getColourScheme()),
1955 view.getAnnotationColours().getAboveThreshold());
1959 cs = new AnnotationColourGradient(af.viewport.alignment
1960 .getAlignmentAnnotation()[i], ColourSchemeProperty
1961 .getColour(al, view.getAnnotationColours()
1962 .getColourScheme()), view
1963 .getAnnotationColours().getAboveThreshold());
1966 // Also use these settings for all the groups
1967 if (al.getGroups() != null)
1969 for (int g = 0; g < al.getGroups().size(); g++)
1971 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
1972 .getGroups().elementAt(g);
1979 /* if (view.getAnnotationColours().getColourScheme().equals("None"))
1981 sg.cs = new AnnotationColourGradient(
1982 af.viewport.alignment.getAlignmentAnnotation()[i],
1983 new java.awt.Color(view.getAnnotationColours().
1985 new java.awt.Color(view.getAnnotationColours().
1987 view.getAnnotationColours().getAboveThreshold());
1991 sg.cs = new AnnotationColourGradient(
1992 af.viewport.alignment.getAlignmentAnnotation()[i],
1993 sg.cs, view.getAnnotationColours()
1994 .getAboveThreshold());
2007 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
2012 cs.setThreshold(view.getPidThreshold(), true);
2013 cs.setConsensus(af.viewport.hconsensus);
2017 af.viewport.setGlobalColourScheme(cs);
2018 af.viewport.setColourAppliesToAllGroups(false);
2020 if (view.getConservationSelected() && cs != null)
2022 cs.setConservationInc(view.getConsThreshold());
2025 af.changeColour(cs);
2027 af.viewport.setColourAppliesToAllGroups(true);
2029 if (view.getShowSequenceFeatures())
2031 af.viewport.showSequenceFeatures = true;
2034 if (jms.getFeatureSettings() != null)
2036 af.viewport.featuresDisplayed = new Hashtable();
2037 String[] renderOrder = new String[jms.getFeatureSettings()
2038 .getSettingCount()];
2039 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
2041 Setting setting = jms.getFeatureSettings().getSetting(fs);
2043 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
2044 setting.getType(), new java.awt.Color(setting.getColour()));
2045 renderOrder[fs] = setting.getType();
2046 if (setting.hasOrder())
2047 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2048 setting.getType(), setting.getOrder());
2050 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2052 fs / jms.getFeatureSettings().getSettingCount());
2053 if (setting.getDisplay())
2055 af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
2056 setting.getColour()));
2059 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
2061 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
2062 for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
2064 Group grp = jms.getFeatureSettings().getGroup(gs);
2065 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
2069 if (view.getHiddenColumnsCount() > 0)
2071 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
2073 af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
2074 .getHiddenColumns(c).getEnd() //+1
2079 af.setMenusFromViewport(af.viewport);
2081 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
2085 ///////////////////////////////////////
2086 if (loadTreesAndStructures && jms.getTreeCount() > 0)
2090 for (int t = 0; t < jms.getTreeCount(); t++)
2093 Tree tree = jms.getTree(t);
2095 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(tree
2096 .getNewick()), tree.getTitle(), tree.getWidth(), tree
2097 .getHeight(), tree.getXpos(), tree.getYpos());
2099 tp.fitToWindow.setState(tree.getFitToWindow());
2100 tp.fitToWindow_actionPerformed(null);
2102 if (tree.getFontName() != null)
2104 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
2105 .getFontStyle(), tree.getFontSize()));
2109 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
2110 .getFontStyle(), tree.getFontSize()));
2113 tp.showPlaceholders(tree.getMarkUnlinked());
2114 tp.showBootstrap(tree.getShowBootstrap());
2115 tp.showDistances(tree.getShowDistances());
2117 tp.treeCanvas.threshold = tree.getThreshold();
2119 if (tree.getCurrentTree())
2121 af.viewport.setCurrentTree(tp.getTree());
2125 } catch (Exception ex)
2127 ex.printStackTrace();
2132 if (loadTreesAndStructures)
2134 for (int i = 0; i < JSEQ.length; i++)
2136 if (JSEQ[i].getPdbidsCount() > 0)
2138 Pdbids[] ids = JSEQ[i].getPdbids();
2139 for (int p = 0; p < ids.length; p++)
2141 for (int s = 0; s < ids[p].getStructureStateCount(); s++)
2143 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
2145 jpdb.setFile(loadPDBFile(ids[p].getFile(), ids[p].getId()));
2146 jpdb.setId(ids[p].getId());
2148 int x = ids[p].getStructureState(s).getXpos();
2149 int y = ids[p].getStructureState(s).getYpos();
2150 int width = ids[p].getStructureState(s).getWidth();
2151 int height = ids[p].getStructureState(s).getHeight();
2153 java.awt.Component comp = null;
2155 JInternalFrame[] frames = null;
2158 frames = Desktop.desktop.getAllFrames();
2160 catch (ArrayIndexOutOfBoundsException e)
2162 // occasional No such child exceptions are thrown here...
2166 } catch (Exception f) {};
2168 } while (frames==null);
2169 for (int f = 0; f < frames.length; f++)
2171 if (frames[f] instanceof AppJmol)
2173 if (frames[f].getX() == x && frames[f].getY() == y
2174 && frames[f].getHeight() == height
2175 && frames[f].getWidth() == width)
2183 Desktop.desktop.getComponentAt(x, y);
2185 String pdbFile = loadPDBFile(file, ids[p].getId());
2187 jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
2188 { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId()
2193 String state = ids[p].getStructureState(s).getContent();
2195 StringBuffer newFileLoc = new StringBuffer(state.substring(
2196 0, state.indexOf("\"", state.indexOf("load")) + 1));
2198 newFileLoc.append(jpdb.getFile());
2199 newFileLoc.append(state.substring(state.indexOf("\"", state
2200 .indexOf("load \"") + 6)));
2202 new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel,
2203 newFileLoc.toString(), new java.awt.Rectangle(x, y,
2207 else if (comp != null)
2209 StructureSelectionManager.getStructureSelectionManager()
2210 .setMapping(seq, null, pdbFile,
2211 jalview.io.AppletFormatAdapter.FILE);
2213 ((AppJmol) comp).addSequence(seq);
2224 private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
2226 jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
2227 Vector dseqs = null;
2230 // create a list of new dataset sequences
2231 dseqs = new Vector();
2233 for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
2235 Sequence vamsasSeq = vamsasSet.getSequence(i);
2236 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
2238 // create a new dataset
2241 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
2242 dseqs.copyInto(dsseqs);
2243 ds = new jalview.datamodel.Alignment(dsseqs);
2244 addDatasetRef(vamsasSet.getDatasetId(), ds);
2246 // set the dataset for the newly imported alignment.
2247 if (al.getDataset() == null)
2256 * @param vamsasSeq sequence definition to create/merge dataset sequence for
2257 * @param ds dataset alignment
2258 * @param dseqs vector to add new dataset sequence to
2260 private void ensureJalviewDatasetSequence(Sequence vamsasSeq, AlignmentI ds, Vector dseqs)
2262 jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds.get(vamsasSeq.getId());
2263 jalview.datamodel.SequenceI dsq = null;
2264 if (sq!=null && sq.getDatasetSequence()!=null)
2266 dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
2269 String sqid = vamsasSeq.getDsseqid();
2272 // need to create or add a new dataset sequence reference to this sequence
2275 dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
2280 // make a new dataset sequence
2281 dsq = sq.createDatasetSequence();
2284 // make up a new dataset reference for this sequence
2285 sqid = seqHash(dsq);
2287 dsq.setVamsasId(uniqueSetSuffix + sqid);
2288 seqRefIds.put(sqid, dsq);
2293 dseqs.addElement(dsq);
2298 ds.addSequence(dsq);
2302 { // make this dataset sequence sq's dataset sequence
2303 sq.setDatasetSequence(dsq);
2307 // TODO: refactor this as a merge dataset sequence function
2308 // now check that sq (the dataset sequence) sequence really is the union of all references to it
2309 //boolean pre = sq.getStart() < dsq.getStart();
2310 //boolean post = sq.getEnd() > dsq.getEnd();
2314 StringBuffer sb = new StringBuffer();
2315 String newres = jalview.analysis.AlignSeq.extractGaps(
2316 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
2317 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString()) && newres.length()>dsq.getLength())
2319 // Update with the longer sequence.
2325 .substring(0, dsq.getStart() - sq.getStart()));
2326 dsq.setStart(sq.getStart());
2330 sb.append(newres.substring(newres.length() - sq.getEnd()
2332 dsq.setEnd(sq.getEnd());
2335 dsq.setSequence(sb.toString());
2337 //TODO: merges will never happen if we 'know' we have the real dataset sequence - this should be detected when id==dssid
2339 .println("DEBUG Notice: Merged dataset sequence"); // ("
2340 // + (pre ? "prepended" : "") + " "
2341 //+ (post ? "appended" : ""));
2346 java.util.Hashtable datasetIds = null;
2348 private Alignment getDatasetFor(String datasetId)
2350 if (datasetIds == null)
2352 datasetIds = new Hashtable();
2355 if (datasetIds.containsKey(datasetId))
2357 return (Alignment) datasetIds.get(datasetId);
2362 private void addDatasetRef(String datasetId, Alignment dataset)
2364 if (datasetIds == null)
2366 datasetIds = new Hashtable();
2368 datasetIds.put(datasetId, dataset);
2371 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
2373 for (int d = 0; d < sequence.getDBRefCount(); d++)
2375 DBRef dr = sequence.getDBRef(d);
2376 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
2377 sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
2378 .getVersion(), sequence.getDBRef(d).getAccessionId());
2379 if (dr.getMapping() != null)
2381 entry.setMap(addMapping(dr.getMapping()));
2383 datasetSequence.addDBRef(entry);
2387 private jalview.datamodel.Mapping addMapping(Mapping m)
2389 SequenceI dsto = null;
2390 // Mapping m = dr.getMapping();
2391 int fr[] = new int[m.getMapListFromCount() * 2];
2392 Enumeration f = m.enumerateMapListFrom();
2393 for (int _i = 0; f.hasMoreElements(); _i += 2)
2395 MapListFrom mf = (MapListFrom) f.nextElement();
2396 fr[_i] = mf.getStart();
2397 fr[_i + 1] = mf.getEnd();
2399 int fto[] = new int[m.getMapListToCount() * 2];
2400 f = m.enumerateMapListTo();
2401 for (int _i = 0; f.hasMoreElements(); _i += 2)
2403 MapListTo mf = (MapListTo) f.nextElement();
2404 fto[_i] = mf.getStart();
2405 fto[_i + 1] = mf.getEnd();
2407 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
2408 fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
2409 if (m.getMappingChoice() != null)
2411 MappingChoice mc = m.getMappingChoice();
2412 if (mc.getDseqFor() != null)
2414 if (seqRefIds.containsKey(mc.getDseqFor()))
2419 jmap.setTo((SequenceI) seqRefIds.get(mc.getDseqFor()));
2423 frefedSequence.add(new Object[]
2424 { mc.getDseqFor(), jmap });
2430 * local sequence definition
2432 Sequence ms = mc.getSequence();
2433 jalview.datamodel.Sequence djs=null;
2434 String sqid = ms.getDsseqid();
2435 if (sqid!=null && sqid.length()>0)
2438 * recover dataset sequence
2440 djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
2442 System.err.println("Warning - making up dataset sequence id for DbRef sequence map reference");
2443 sqid = ((Object)ms).toString(); // make up a new hascode for undefined dataset sequence hash (unlikely to happen)
2448 * make a new dataset sequence and add it to refIds hash
2450 djs = new jalview.datamodel.Sequence(ms
2451 .getName(), ms.getSequence());
2452 djs.setStart(jmap.getMap().getToLowest());
2453 djs.setEnd(jmap.getMap().getToHighest());
2454 djs.setVamsasId(uniqueSetSuffix + sqid);
2456 seqRefIds.put(sqid, djs);
2459 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
2468 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
2469 boolean keepSeqRefs)
2471 jalview.schemabinding.version2.JalviewModel jm =
2472 SaveState(ap, null, null);
2477 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
2481 uniqueSetSuffix = "";
2484 viewportsAdded = new Hashtable();
2486 AlignFrame af = LoadFromObject(jm, null, false);
2487 af.alignPanels.clear();
2488 af.closeMenuItem_actionPerformed(true);
2490 /* if(ap.av.alignment.getAlignmentAnnotation()!=null)
2492 for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length; i++)
2494 if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated)
2496 af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
2497 ap.av.alignment.getAlignmentAnnotation()[i];
2502 return af.alignPanel;
2505 * @see java.lang.Object#finalize()
2507 protected void finalize() throws Throwable
2509 // really make sure we have no buried refs left.
2511 this.seqRefIds = null;
2512 this.seqsToIds = null;