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 Hashtable seqRefIds = null;
54 Vector frefedSequence = null;
55 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
59 public Jalview2XML(boolean raiseGUI)
61 this.raiseGUI = raiseGUI;
64 public void resolveFrefedSequences()
66 if (frefedSequence.size() > 0)
68 int r = 0, rSize = frefedSequence.size();
71 Object[] ref = (Object[]) frefedSequence.elementAt(r);
74 String sref = (String) ref[0];
75 if (seqRefIds.containsKey(sref))
77 if (ref[1] instanceof jalview.datamodel.Mapping)
79 SequenceI seq = (SequenceI) seqRefIds.get(sref);
80 while (seq.getDatasetSequence() != null)
82 seq = seq.getDatasetSequence();
84 ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
89 .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
90 + ref[1].getClass() + " type objects.");
92 frefedSequence.remove(r);
102 frefedSequence.remove(r);
110 * This maintains a list of viewports, the key being the
111 * seqSetId. Important to set historyItem and redoList
114 Hashtable viewportsAdded;
116 Hashtable annotationIds = new Hashtable();
118 String uniqueSetSuffix = "";
121 * List of pdbfiles added to Jar
123 Vector pdbfiles = null;
125 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
126 public void SaveState(File statefile)
128 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
137 FileOutputStream fos = new FileOutputStream(statefile);
138 JarOutputStream jout = new JarOutputStream(fos);
140 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
141 ////////////////////////////////////////////////////
142 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
145 Vector shortNames = new Vector();
148 for (int i = frames.length - 1; i > -1; i--)
150 if (frames[i] instanceof AlignFrame)
152 AlignFrame af = (AlignFrame) frames[i];
154 String shortName = af.getTitle();
156 if (shortName.indexOf(File.separatorChar) > -1)
158 shortName = shortName.substring(shortName
159 .lastIndexOf(File.separatorChar) + 1);
164 while (shortNames.contains(shortName))
166 if (shortName.endsWith("_" + (count - 1)))
168 shortName = shortName
169 .substring(0, shortName.lastIndexOf("_"));
172 shortName = shortName.concat("_" + count);
176 shortNames.addElement(shortName);
178 if (!shortName.endsWith(".xml"))
180 shortName = shortName + ".xml";
183 int ap, apSize = af.alignPanels.size();
184 for (ap = 0; ap < apSize; ap++)
186 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
189 SaveState(apanel, apSize == 1 ? shortName : ap + shortName,
197 } catch (Exception ex)
199 //TODO: inform user of the problem - they need to know if their data was not saved !
200 ex.printStackTrace();
204 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
205 public boolean SaveAlignment(AlignFrame af, String jarFile,
210 int ap, apSize = af.alignPanels.size();
211 FileOutputStream fos = new FileOutputStream(jarFile);
212 JarOutputStream jout = new JarOutputStream(fos);
213 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
215 for (ap = 0; ap < apSize; ap++)
217 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
220 SaveState(apanel, apSize == 1 ? fileName : fileName + ap, jout, out);
226 } catch (Exception ex)
228 ex.printStackTrace();
236 * @param af DOCUMENT ME!
237 * @param timeStamp DOCUMENT ME!
238 * @param fileName DOCUMENT ME!
239 * @param jout DOCUMENT ME!
240 * @param out DOCUMENT ME!
242 public JalviewModel SaveState(AlignmentPanel ap, String fileName,
243 JarOutputStream jout, PrintWriter out)
245 if (seqRefIds == null)
247 seqRefIds = new Hashtable();
250 Vector userColours = new Vector();
252 AlignViewport av = ap.av;
254 JalviewModel object = new JalviewModel();
255 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
257 object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
258 object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
260 jalview.datamodel.AlignmentI jal = av.alignment;
262 if (av.hasHiddenRows)
264 jal = jal.getHiddenSequences().getFullAlignment();
267 SequenceSet vamsasSet = new SequenceSet();
269 JalviewModelSequence jms = new JalviewModelSequence();
271 vamsasSet.setGapChar(jal.getGapCharacter() + "");
273 if (jal.getDataset() != null)
275 // dataset id is the dataset's hashcode
276 vamsasSet.setDatasetId(jal.getDataset().hashCode() + "");
278 if (jal.getProperties() != null)
280 Enumeration en = jal.getProperties().keys();
281 while (en.hasMoreElements())
283 String key = en.nextElement().toString();
284 SequenceSetProperties ssp = new SequenceSetProperties();
286 ssp.setValue(jal.getProperties().get(key).toString());
287 vamsasSet.addSequenceSetProperties(ssp);
295 jalview.datamodel.SequenceI jds;
296 for (int i = 0; i < jal.getHeight(); i++)
298 jds = jal.getSequenceAt(i);
301 if (seqRefIds.get(id + "") != null)
307 vamsasSeq = createVamsasSequence(id, jds);
308 vamsasSet.addSequence(vamsasSeq);
309 seqRefIds.put(id + "", jal.getSequenceAt(i));
313 jseq.setStart(jds.getStart());
314 jseq.setEnd(jds.getEnd());
315 jseq.setColour(av.getSequenceColour(jds).getRGB());
319 if (av.hasHiddenRows)
321 jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
323 if (av.hiddenRepSequences != null
324 && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
326 jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences
327 .get(jal.getSequenceAt(i))).getSequencesInOrder(jal);
329 for (int h = 0; h < reps.length; h++)
331 if (reps[h] != jal.getSequenceAt(i))
333 jseq.addHiddenSequences(jal.findIndex(reps[h]));
339 if (jds.getDatasetSequence().getSequenceFeatures() != null)
341 jalview.datamodel.SequenceFeature[] sf = jds.getDatasetSequence()
342 .getSequenceFeatures();
344 while (index < sf.length)
346 Features features = new Features();
348 features.setBegin(sf[index].getBegin());
349 features.setEnd(sf[index].getEnd());
350 features.setDescription(sf[index].getDescription());
351 features.setType(sf[index].getType());
352 features.setFeatureGroup(sf[index].getFeatureGroup());
353 features.setScore(sf[index].getScore());
354 if (sf[index].links != null)
356 for (int l = 0; l < sf[index].links.size(); l++)
358 OtherData keyValue = new OtherData();
359 keyValue.setKey("LINK_" + l);
360 keyValue.setValue(sf[index].links.elementAt(l).toString());
361 features.addOtherData(keyValue);
364 if (sf[index].otherDetails != null)
367 Enumeration keys = sf[index].otherDetails.keys();
368 while (keys.hasMoreElements())
370 key = keys.nextElement().toString();
371 OtherData keyValue = new OtherData();
372 keyValue.setKey(key);
373 keyValue.setValue(sf[index].otherDetails.get(key).toString());
374 features.addOtherData(keyValue);
378 jseq.addFeatures(features);
383 if (jds.getDatasetSequence().getPDBId() != null)
385 Enumeration en = jds.getDatasetSequence().getPDBId().elements();
386 while (en.hasMoreElements())
388 Pdbids pdb = new Pdbids();
389 jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
392 pdb.setId(entry.getId());
393 pdb.setType(entry.getType());
396 //This must have been loaded, is it still visible?
397 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
398 for (int f = frames.length - 1; f > -1; f--)
400 if (frames[f] instanceof AppJmol)
402 jmol = (AppJmol) frames[f];
403 if (!jmol.pdbentry.getId().equals(entry.getId()))
406 StructureState state = new StructureState();
407 state.setVisible(true);
408 state.setXpos(jmol.getX());
409 state.setYpos(jmol.getY());
410 state.setWidth(jmol.getWidth());
411 state.setHeight(jmol.getHeight());
413 String statestring = jmol.viewer.getStateInfo();
416 state.setContent(statestring.replaceAll("\n", ""));
418 for (int s = 0; s < jmol.sequence.length; s++)
420 if (jal.findIndex(jmol.sequence[s]) > -1)
422 pdb.addStructureState(state);
428 if (entry.getFile() != null)
430 pdb.setFile(entry.getFile());
431 if (pdbfiles == null)
433 pdbfiles = new Vector();
436 if (!pdbfiles.contains(entry.getId()))
438 pdbfiles.addElement(entry.getId());
441 File file = new File(entry.getFile());
442 if (file.exists() && jout != null)
444 byte[] data = new byte[(int) file.length()];
445 jout.putNextEntry(new JarEntry(entry.getId()));
446 DataInputStream dis = new DataInputStream(
447 new FileInputStream(file));
450 DataOutputStream dout = new DataOutputStream(jout);
451 dout.write(data, 0, data.length);
454 } catch (Exception ex)
456 ex.printStackTrace();
462 if (entry.getProperty() != null)
464 PdbentryItem item = new PdbentryItem();
465 Hashtable properties = entry.getProperty();
466 Enumeration en2 = properties.keys();
467 while (en2.hasMoreElements())
469 Property prop = new Property();
470 String key = en2.nextElement().toString();
472 prop.setValue(properties.get(key).toString());
473 item.addProperty(prop);
475 pdb.addPdbentryItem(item);
485 if (av.hasHiddenRows)
490 if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
492 jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
493 for (int i = 0; i < jac.length; i++)
495 AlcodonFrame alc = new AlcodonFrame();
496 vamsasSet.addAlcodonFrame(alc);
497 for (int p = 0; p < jac[i].aaWidth; p++)
499 Alcodon cmap = new Alcodon();
500 cmap.setPos1(jac[i].codons[p][0]);
501 cmap.setPos2(jac[i].codons[p][1]);
502 cmap.setPos3(jac[i].codons[p][2]);
503 alc.addAlcodon(cmap);
505 if (jac[i].getProtMappings() != null
506 && jac[i].getProtMappings().length > 0)
508 SequenceI[] dnas = jac[i].getdnaSeqs();
509 jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings();
510 for (int m = 0; m < pmaps.length; m++)
512 AlcodMap alcmap = new AlcodMap();
513 alcmap.setDnasq("" + dnas[m].hashCode());
514 alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
516 alc.addAlcodMap(alcmap);
523 ///////////////////////////////////
524 if (av.currentTree != null)
526 // FIND ANY ASSOCIATED TREES
527 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
528 if (Desktop.desktop != null)
530 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
532 for (int t = 0; t < frames.length; t++)
534 if (frames[t] instanceof TreePanel)
536 TreePanel tp = (TreePanel) frames[t];
538 if (tp.treeCanvas.av.alignment == jal)
540 Tree tree = new Tree();
541 tree.setTitle(tp.getTitle());
542 tree.setCurrentTree((av.currentTree == tp.getTree()));
543 tree.setNewick(tp.getTree().toString());
544 tree.setThreshold(tp.treeCanvas.threshold);
546 tree.setFitToWindow(tp.fitToWindow.getState());
547 tree.setFontName(tp.getTreeFont().getName());
548 tree.setFontSize(tp.getTreeFont().getSize());
549 tree.setFontStyle(tp.getTreeFont().getStyle());
550 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
552 tree.setShowBootstrap(tp.bootstrapMenu.getState());
553 tree.setShowDistances(tp.distanceMenu.getState());
555 tree.setHeight(tp.getHeight());
556 tree.setWidth(tp.getWidth());
557 tree.setXpos(tp.getX());
558 tree.setYpos(tp.getY());
568 if (jal.getAlignmentAnnotation() != null)
570 jalview.datamodel.AlignmentAnnotation[] aa = jal
571 .getAlignmentAnnotation();
573 for (int i = 0; i < aa.length; i++)
575 Annotation an = new Annotation();
577 if (aa[i].annotationId != null)
579 annotationIds.put(aa[i].annotationId, aa[i]);
582 an.setId(aa[i].annotationId);
584 if (aa[i] == av.quality || aa[i] == av.conservation
585 || aa[i] == av.consensus)
587 an.setLabel(aa[i].label);
589 vamsasSet.addAnnotation(an);
593 an.setVisible(aa[i].visible);
595 an.setDescription(aa[i].description);
597 if (aa[i].sequenceRef != null)
599 an.setSequenceRef(aa[i].sequenceRef.getName());
605 an.setGraphType(aa[i].graph);
606 an.setGraphGroup(aa[i].graphGroup);
607 if (aa[i].getThreshold() != null)
609 ThresholdLine line = new ThresholdLine();
610 line.setLabel(aa[i].getThreshold().label);
611 line.setValue(aa[i].getThreshold().value);
612 line.setColour(aa[i].getThreshold().colour.getRGB());
613 an.setThresholdLine(line);
621 an.setLabel(aa[i].label);
622 if (aa[i].hasScore())
624 an.setScore(aa[i].getScore());
626 AnnotationElement ae;
627 if (aa[i].annotations != null)
629 an.setScoreOnly(false);
630 for (int a = 0; a < aa[i].annotations.length; a++)
632 if ((aa[i] == null) || (aa[i].annotations[a] == null))
637 ae = new AnnotationElement();
638 if (aa[i].annotations[a].description != null)
639 ae.setDescription(aa[i].annotations[a].description);
640 if (aa[i].annotations[a].displayCharacter != null)
641 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
643 if (!Float.isNaN(aa[i].annotations[a].value))
644 ae.setValue(aa[i].annotations[a].value);
647 if (aa[i].annotations[a].secondaryStructure != ' '
648 && aa[i].annotations[a].secondaryStructure != '\0')
650 .setSecondaryStructure(aa[i].annotations[a].secondaryStructure
653 if (aa[i].annotations[a].colour != null
654 && aa[i].annotations[a].colour != java.awt.Color.black)
656 ae.setColour(aa[i].annotations[a].colour.getRGB());
659 an.addAnnotationElement(ae);
664 an.setScoreOnly(true);
666 vamsasSet.addAnnotation(an);
671 if (jal.getGroups() != null)
673 JGroup[] groups = new JGroup[jal.getGroups().size()];
675 for (int i = 0; i < groups.length; i++)
677 groups[i] = new JGroup();
679 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal
680 .getGroups().elementAt(i);
681 groups[i].setStart(sg.getStartRes());
682 groups[i].setEnd(sg.getEndRes());
683 groups[i].setName(sg.getName());
686 if (sg.cs.conservationApplied())
688 groups[i].setConsThreshold(sg.cs.getConservationInc());
690 if (sg.cs instanceof jalview.schemes.UserColourScheme)
692 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
698 .setColour(ColourSchemeProperty.getColourName(sg.cs));
701 else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
704 .setColour(ColourSchemeProperty
705 .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
708 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
711 .setColour(SetUserColourScheme(sg.cs, userColours, jms));
715 groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
718 groups[i].setPidThreshold(sg.cs.getThreshold());
721 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
722 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
723 groups[i].setDisplayText(sg.getDisplayText());
724 groups[i].setColourText(sg.getColourText());
725 groups[i].setTextCol1(sg.textColour.getRGB());
726 groups[i].setTextCol2(sg.textColour2.getRGB());
727 groups[i].setTextColThreshold(sg.thresholdTextColour);
729 for (int s = 0; s < sg.getSize(); s++)
731 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
733 groups[i].addSeq(seq.hashCode());
737 jms.setJGroup(groups);
740 ///////////SAVE VIEWPORT
741 Viewport view = new Viewport();
742 view.setTitle(ap.alignFrame.getTitle());
743 view.setSequenceSetId(av.getSequenceSetId());
744 view.setViewName(av.viewName);
745 view.setGatheredViews(av.gatherViewsHere);
747 if (ap.av.explodedPosition != null)
749 view.setXpos(av.explodedPosition.x);
750 view.setYpos(av.explodedPosition.y);
751 view.setWidth(av.explodedPosition.width);
752 view.setHeight(av.explodedPosition.height);
756 view.setXpos(ap.alignFrame.getBounds().x);
757 view.setYpos(ap.alignFrame.getBounds().y);
758 view.setWidth(ap.alignFrame.getBounds().width);
759 view.setHeight(ap.alignFrame.getBounds().height);
762 view.setStartRes(av.startRes);
763 view.setStartSeq(av.startSeq);
765 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
767 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
770 else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
772 jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
773 .getGlobalColourScheme();
775 AnnotationColours ac = new AnnotationColours();
776 ac.setAboveThreshold(acg.getAboveThreshold());
777 ac.setThreshold(acg.getAnnotationThreshold());
778 ac.setAnnotation(acg.getAnnotation());
779 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
781 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
786 ac.setColourScheme(ColourSchemeProperty.getColourName(acg
790 ac.setMaxColour(acg.getMaxColour().getRGB());
791 ac.setMinColour(acg.getMinColour().getRGB());
792 view.setAnnotationColours(ac);
793 view.setBgColour("AnnotationColourGradient");
797 view.setBgColour(ColourSchemeProperty.getColourName(av
798 .getGlobalColourScheme()));
801 ColourSchemeI cs = av.getGlobalColourScheme();
805 if (cs.conservationApplied())
807 view.setConsThreshold(cs.getConservationInc());
808 if (cs instanceof jalview.schemes.UserColourScheme)
810 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
814 if (cs instanceof ResidueColourScheme)
816 view.setPidThreshold(cs.getThreshold());
820 view.setConservationSelected(av.getConservationSelected());
821 view.setPidSelected(av.getAbovePIDThreshold());
822 view.setFontName(av.font.getName());
823 view.setFontSize(av.font.getSize());
824 view.setFontStyle(av.font.getStyle());
825 view.setRenderGaps(av.renderGaps);
826 view.setShowAnnotation(av.getShowAnnotation());
827 view.setShowBoxes(av.getShowBoxes());
828 view.setShowColourText(av.getColourText());
829 view.setShowFullId(av.getShowJVSuffix());
830 view.setRightAlignIds(av.rightAlignIds);
831 view.setShowSequenceFeatures(av.showSequenceFeatures);
832 view.setShowText(av.getShowText());
833 view.setWrapAlignment(av.getWrapAlignment());
834 view.setTextCol1(av.textColour.getRGB());
835 view.setTextCol2(av.textColour2.getRGB());
836 view.setTextColThreshold(av.thresholdTextColour);
838 if (av.featuresDisplayed != null)
840 jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
842 String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
844 Vector settingsAdded = new Vector();
845 for (int ro = 0; ro < renderOrder.length; ro++)
847 Setting setting = new Setting();
848 setting.setType(renderOrder[ro]);
849 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
850 .getColour(renderOrder[ro]).getRGB());
852 setting.setDisplay(av.featuresDisplayed
853 .containsKey(renderOrder[ro]));
854 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
858 setting.setOrder(rorder);
860 fs.addSetting(setting);
861 settingsAdded.addElement(renderOrder[ro]);
864 //Make sure we save none displayed feature settings
865 Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
867 while (en.hasMoreElements())
869 String key = en.nextElement().toString();
870 if (settingsAdded.contains(key))
875 Setting setting = new Setting();
876 setting.setType(key);
877 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
878 .getColour(key).getRGB());
880 setting.setDisplay(false);
881 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
885 setting.setOrder(rorder);
887 fs.addSetting(setting);
888 settingsAdded.addElement(key);
890 en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
891 Vector groupsAdded = new Vector();
892 while (en.hasMoreElements())
894 String grp = en.nextElement().toString();
895 if (groupsAdded.contains(grp))
899 Group g = new Group();
902 .setDisplay(((Boolean) ap.seqPanel.seqCanvas
903 .getFeatureRenderer().featureGroups.get(grp))
906 groupsAdded.addElement(grp);
908 jms.setFeatureSettings(fs);
912 if (av.hasHiddenColumns)
914 for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
916 int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
918 HiddenColumns hc = new HiddenColumns();
919 hc.setStart(region[0]);
920 hc.setEnd(region[1]);
921 view.addHiddenColumns(hc);
925 jms.addViewport(view);
927 object.setJalviewModelSequence(jms);
928 object.getVamsasModel().addSequenceSet(vamsasSet);
932 //We may not want to right the object to disk,
933 //eg we can copy the alignViewport to a new view object
934 //using save and then load
937 if (!fileName.endsWith(".xml"))
939 fileName = fileName + ".xml";
942 JarEntry entry = new JarEntry(fileName);
943 jout.putNextEntry(entry);
946 } catch (Exception ex)
948 ex.printStackTrace();
954 private Sequence createVamsasSequence(int id, SequenceI jds)
956 return createVamsasSequence(true, id, jds, null);
959 private Sequence createVamsasSequence(boolean recurse, int id,
960 SequenceI jds, SequenceI parentseq)
962 Sequence vamsasSeq = new Sequence();
963 vamsasSeq.setId(id + "");
964 vamsasSeq.setName(jds.getName());
965 vamsasSeq.setSequence(jds.getSequenceAsString());
966 vamsasSeq.setDescription(jds.getDescription());
967 jalview.datamodel.DBRefEntry[] dbrefs = null;
968 if (jds.getDatasetSequence() != null)
970 vamsasSeq.setDsseqid(jds.getDatasetSequence().hashCode() + "");
971 if (jds.getDatasetSequence().getDBRef() != null)
973 dbrefs = jds.getDatasetSequence().getDBRef();
978 vamsasSeq.setDsseqid(id + ""); // so we can tell which sequences really are dataset sequences only
979 dbrefs = jds.getDBRef();
983 for (int d = 0; d < dbrefs.length; d++)
985 DBRef dbref = new DBRef();
986 dbref.setSource(dbrefs[d].getSource());
987 dbref.setVersion(dbrefs[d].getVersion());
988 dbref.setAccessionId(dbrefs[d].getAccessionId());
989 if (dbrefs[d].hasMap())
991 Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
993 dbref.setMapping(mp);
995 vamsasSeq.addDBRef(dbref);
1001 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
1002 SequenceI parentseq, SequenceI jds, boolean recurse)
1005 if (jmp.getMap() != null)
1009 jalview.util.MapList mlst = jmp.getMap();
1010 int r[] = mlst.getFromRanges();
1011 for (int s = 0; s < r.length; s += 2)
1013 MapListFrom mfrom = new MapListFrom();
1014 mfrom.setStart(r[s]);
1015 mfrom.setEnd(r[s + 1]);
1016 mp.addMapListFrom(mfrom);
1018 r = mlst.getToRanges();
1019 for (int s = 0; s < r.length; s += 2)
1021 MapListTo mto = new MapListTo();
1023 mto.setEnd(r[s + 1]);
1024 mp.addMapListTo(mto);
1026 mp.setMapFromUnit(mlst.getFromRatio());
1027 mp.setMapToUnit(mlst.getToRatio());
1028 if (jmp.getTo() != null)
1030 MappingChoice mpc = new MappingChoice();
1032 && (parentseq != jmp.getTo() || parentseq
1033 .getDatasetSequence() != jmp.getTo()))
1035 mpc.setSequence(createVamsasSequence(false, jmp.getTo()
1036 .hashCode(), jmp.getTo(), jds));
1041 SequenceI ps = null;
1042 if (parentseq != jmp.getTo()
1043 && parentseq.getDatasetSequence() != jmp.getTo())
1045 // chaining dbref rather than a handshaking one
1046 jmpid = (ps = jmp.getTo()).hashCode();
1050 jmpid = (ps = parentseq).hashCode();
1052 mpc.setDseqFor("" + jmpid);
1053 if (!seqRefIds.containsKey(mpc.getDseqFor()))
1055 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
1056 seqRefIds.put(mpc.getDseqFor(), ps);
1060 jalview.bin.Cache.log.debug("reusing DseqFor ID");
1063 mp.setMappingChoice(mpc);
1069 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
1070 Vector userColours, JalviewModelSequence jms)
1073 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
1075 if (!userColours.contains(ucs))
1077 userColours.add(ucs);
1079 java.awt.Color[] colours = ucs.getColours();
1080 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
1081 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
1083 for (int i = 0; i < colours.length; i++)
1085 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1086 col.setName(ResidueProperties.aa[i]);
1087 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1088 jbucs.addColour(col);
1090 if (ucs.getLowerCaseColours() != null)
1092 colours = ucs.getLowerCaseColours();
1093 for (int i = 0; i < colours.length; i++)
1095 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1096 col.setName(ResidueProperties.aa[i].toLowerCase());
1097 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1098 jbucs.addColour(col);
1102 id = "ucs" + userColours.indexOf(ucs);
1104 uc.setUserColourScheme(jbucs);
1105 jms.addUserColours(uc);
1111 jalview.schemes.UserColourScheme GetUserColourScheme(
1112 JalviewModelSequence jms, String id)
1114 UserColours[] uc = jms.getUserColours();
1115 UserColours colours = null;
1117 for (int i = 0; i < uc.length; i++)
1119 if (uc[i].getId().equals(id))
1127 java.awt.Color[] newColours = new java.awt.Color[24];
1129 for (int i = 0; i < 24; i++)
1131 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1132 .getUserColourScheme().getColour(i).getRGB(), 16));
1135 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
1138 if (colours.getUserColourScheme().getColourCount() > 24)
1140 newColours = new java.awt.Color[23];
1141 for (int i = 0; i < 23; i++)
1143 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1144 .getUserColourScheme().getColour(i + 24).getRGB(), 16));
1146 ucs.setLowerCaseColours(newColours);
1155 * @param file DOCUMENT ME!
1157 public AlignFrame LoadJalviewAlign(final String file)
1159 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
1161 jalview.gui.AlignFrame af = null;
1163 seqRefIds = new Hashtable();
1164 viewportsAdded = new Hashtable();
1165 frefedSequence = new Vector();
1166 Hashtable gatherToThisFrame = new Hashtable();
1168 String errorMessage = null;
1172 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
1175 if (file.startsWith("http://"))
1177 url = new URL(file);
1180 JarInputStream jin = null;
1181 JarEntry jarentry = null;
1188 jin = new JarInputStream(url.openStream());
1192 jin = new JarInputStream(new FileInputStream(file));
1195 for (int i = 0; i < entryCount; i++)
1197 jarentry = jin.getNextJarEntry();
1200 if (jarentry != null && jarentry.getName().endsWith(".xml"))
1202 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
1203 JalviewModel object = new JalviewModel();
1205 Unmarshaller unmar = new Unmarshaller(object);
1206 unmar.setValidation(false);
1207 object = (JalviewModel) unmar.unmarshal(in);
1209 af = LoadFromObject(object, file, true);
1210 if (af.viewport.gatherViewsHere)
1212 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
1216 else if (jarentry != null)
1218 //Some other file here.
1221 } while (jarentry != null);
1222 resolveFrefedSequences();
1223 } catch (java.io.FileNotFoundException ex)
1225 ex.printStackTrace();
1226 errorMessage = "Couldn't locate Jalview XML file : " + file;
1227 System.err.println("Exception whilst loading jalview XML file : "
1229 } catch (java.net.UnknownHostException ex)
1231 ex.printStackTrace();
1232 errorMessage = "Couldn't locate Jalview XML file : " + file;
1233 System.err.println("Exception whilst loading jalview XML file : "
1235 } catch (Exception ex)
1237 //Is Version 1 Jar file?
1239 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(file);
1240 } catch (Exception ex2) {
1241 System.err.println("Exception whilst loading as jalviewXMLV1:");
1242 ex2.printStackTrace();
1246 if (Desktop.instance != null)
1248 Desktop.instance.stopLoading();
1252 System.out.println("Successfully loaded archive file");
1255 ex.printStackTrace();
1257 System.err.println("Exception whilst loading jalview XML file : "
1261 if (Desktop.instance != null)
1263 Desktop.instance.stopLoading();
1266 Enumeration en = gatherToThisFrame.elements();
1267 while (en.hasMoreElements())
1269 Desktop.instance.gatherViews((AlignFrame) en.nextElement());
1272 if (errorMessage != null)
1274 final String finalErrorMessage = errorMessage;
1277 javax.swing.SwingUtilities.invokeLater(new Runnable()
1281 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1282 finalErrorMessage, "Error loading Jalview file",
1283 JOptionPane.WARNING_MESSAGE);
1287 System.err.println("Problem loading Jalview file: "+errorMessage);
1294 Hashtable alreadyLoadedPDB;
1296 String loadPDBFile(String file, String pdbId)
1298 if (alreadyLoadedPDB == null)
1299 alreadyLoadedPDB = new Hashtable();
1301 if (alreadyLoadedPDB.containsKey(pdbId))
1302 return alreadyLoadedPDB.get(pdbId).toString();
1306 JarInputStream jin = null;
1308 if (file.startsWith("http://"))
1310 jin = new JarInputStream(new URL(file).openStream());
1314 jin = new JarInputStream(new FileInputStream(file));
1317 JarEntry entry = null;
1320 entry = jin.getNextJarEntry();
1321 } while (!entry.getName().equals(pdbId));
1323 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1324 File outFile = File.createTempFile("jalview_pdb", ".txt");
1325 outFile.deleteOnExit();
1326 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1329 while ((data = in.readLine()) != null)
1335 alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
1336 return outFile.getAbsolutePath();
1338 } catch (Exception ex)
1340 ex.printStackTrace();
1346 AlignFrame LoadFromObject(JalviewModel object, String file,
1347 boolean loadTreesAndStructures)
1349 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1350 Sequence[] vamsasSeq = vamsasSet.getSequence();
1352 JalviewModelSequence jms = object.getJalviewModelSequence();
1354 Viewport view = jms.getViewport(0);
1356 //////////////////////////////////
1359 Vector hiddenSeqs = null;
1360 jalview.datamodel.Sequence jseq;
1362 ArrayList tmpseqs = new ArrayList();
1364 boolean multipleView = false;
1366 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1367 for (int i = 0; i < JSEQ.length; i++)
1369 String seqId = JSEQ[i].getId() + "";
1371 if (seqRefIds.get(seqId) != null)
1373 tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId));
1374 multipleView = true;
1378 jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
1379 vamsasSeq[i].getSequence());
1380 jseq.setDescription(vamsasSeq[i].getDescription());
1381 jseq.setStart(JSEQ[i].getStart());
1382 jseq.setEnd(JSEQ[i].getEnd());
1383 jseq.setVamsasId(uniqueSetSuffix + seqId);
1384 seqRefIds.put(vamsasSeq[i].getId(), jseq);
1388 if (JSEQ[i].getHidden())
1390 if (hiddenSeqs == null)
1392 hiddenSeqs = new Vector();
1395 hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
1402 // Create the alignment object from the sequence set
1403 /////////////////////////////////
1404 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
1407 tmpseqs.toArray(orderedSeqs);
1409 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
1412 /// Add the alignment properties
1413 for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
1415 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
1416 al.setProperty(ssp.getKey(), ssp.getValue());
1420 // SequenceFeatures are added to the DatasetSequence,
1421 // so we must create or recover the dataset before loading features
1422 /////////////////////////////////
1423 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
1425 // older jalview projects do not have a dataset id.
1426 al.setDataset(null);
1430 recoverDatasetFor(vamsasSet, al);
1432 /////////////////////////////////
1434 Hashtable pdbloaded = new Hashtable();
1437 for (int i = 0; i < vamsasSeq.length; i++)
1439 if (JSEQ[i].getFeaturesCount() > 0)
1441 Features[] features = JSEQ[i].getFeatures();
1442 for (int f = 0; f < features.length; f++)
1444 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
1445 features[f].getType(), features[f].getDescription(),
1446 features[f].getStatus(), features[f].getBegin(),
1447 features[f].getEnd(), features[f].getFeatureGroup());
1449 sf.setScore(features[f].getScore());
1450 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1452 OtherData keyValue = features[f].getOtherData(od);
1453 if (keyValue.getKey().startsWith("LINK"))
1455 sf.addLink(keyValue.getValue());
1459 sf.setValue(keyValue.getKey(), keyValue.getValue());
1464 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1467 if (vamsasSeq[i].getDBRefCount() > 0)
1469 addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
1471 if (JSEQ[i].getPdbidsCount() > 0)
1473 Pdbids[] ids = JSEQ[i].getPdbids();
1474 for (int p = 0; p < ids.length; p++)
1476 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
1477 entry.setId(ids[p].getId());
1478 entry.setType(ids[p].getType());
1479 if (ids[p].getFile() != null)
1481 if (!pdbloaded.containsKey(ids[p].getFile()))
1483 entry.setFile(loadPDBFile(file, ids[p].getId()));
1487 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1491 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1497 /////////////////////////////////
1498 // LOAD SEQUENCE MAPPINGS
1499 if (vamsasSet.getAlcodonFrameCount() > 0)
1501 AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
1502 for (int i = 0; i < alc.length; i++)
1504 jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
1505 alc[i].getAlcodonCount());
1506 if (alc[i].getAlcodonCount() > 0)
1508 Alcodon[] alcods = alc[i].getAlcodon();
1509 for (int p = 0; p < cf.codons.length; p++)
1511 cf.codons[p] = new int[3];
1512 cf.codons[p][0] = (int) alcods[p].getPos1();
1513 cf.codons[p][1] = (int) alcods[p].getPos2();
1514 cf.codons[p][2] = (int) alcods[p].getPos3();
1517 if (alc[i].getAlcodMapCount() > 0)
1519 AlcodMap[] maps = alc[i].getAlcodMap();
1520 for (int m = 0; m < maps.length; m++)
1522 SequenceI dnaseq = (SequenceI) seqRefIds
1523 .get(maps[m].getDnasq());
1525 // attach to dna sequence reference.
1528 if (maps[m].getMapping() != null)
1530 jalview.datamodel.Mapping mapping = addMapping(maps[m]
1532 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
1537 al.addCodonFrame(cf);
1542 //////////////////////////////////
1544 boolean hideQuality = true, hideConservation = true, hideConsensus = true;
1546 if (vamsasSet.getAnnotationCount() > 0)
1548 Annotation[] an = vamsasSet.getAnnotation();
1550 for (int i = 0; i < an.length; i++)
1552 if (an[i].getLabel().equals("Quality"))
1554 hideQuality = false;
1557 else if (an[i].getLabel().equals("Conservation"))
1559 hideConservation = false;
1562 else if (an[i].getLabel().equals("Consensus"))
1564 hideConsensus = false;
1568 if (an[i].getId() != null
1569 && annotationIds.containsKey(an[i].getId()))
1571 jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
1572 .get(an[i].getId());
1573 if (an[i].hasVisible())
1574 jda.visible = an[i].getVisible();
1576 al.addAnnotation(jda);
1581 AnnotationElement[] ae = an[i].getAnnotationElement();
1582 jalview.datamodel.Annotation[] anot = null;
1584 if (!an[i].getScoreOnly())
1586 anot = new jalview.datamodel.Annotation[al.getWidth()];
1588 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
1590 if (ae[aa].getPosition() >= anot.length)
1593 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
1595 ae[aa].getDisplayCharacter(), ae[aa].getDescription(), (ae[aa]
1596 .getSecondaryStructure() == null || ae[aa]
1597 .getSecondaryStructure().length() == 0) ? ' ' : ae[aa]
1598 .getSecondaryStructure().charAt(0), ae[aa].getValue()
1602 anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]
1606 jalview.datamodel.AlignmentAnnotation jaa = null;
1608 if (an[i].getGraph())
1610 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1611 an[i].getDescription(), anot, 0, 0, an[i].getGraphType());
1613 jaa.graphGroup = an[i].getGraphGroup();
1615 if (an[i].getThresholdLine() != null)
1617 jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
1618 .getThresholdLine().getValue(), an[i]
1619 .getThresholdLine().getLabel(), new java.awt.Color(
1620 an[i].getThresholdLine().getColour())));
1627 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1628 an[i].getDescription(), anot);
1631 if (an[i].getId() != null)
1633 annotationIds.put(an[i].getId(), jaa);
1634 jaa.annotationId = an[i].getId();
1637 if (an[i].getSequenceRef() != null)
1639 if (al.findName(an[i].getSequenceRef()) != null)
1641 jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
1643 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1646 if (an[i].hasScore())
1648 jaa.setScore(an[i].getScore());
1651 if (an[i].hasVisible())
1652 jaa.visible = an[i].getVisible();
1654 al.addAnnotation(jaa);
1658 /////////////////////////
1660 if (jms.getJGroupCount() > 0)
1662 JGroup[] groups = jms.getJGroup();
1664 for (int i = 0; i < groups.length; i++)
1666 ColourSchemeI cs = null;
1668 if (groups[i].getColour() != null)
1670 if (groups[i].getColour().startsWith("ucs"))
1672 cs = GetUserColourScheme(jms, groups[i].getColour());
1676 cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
1681 cs.setThreshold(groups[i].getPidThreshold(), true);
1685 Vector seqs = new Vector();
1687 for (int s = 0; s < groups[i].getSeqCount(); s++)
1689 String seqId = groups[i].getSeq(s) + "";
1690 jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds
1695 seqs.addElement(ts);
1699 if (seqs.size() < 1)
1704 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
1705 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1706 groups[i].getDisplayText(), groups[i].getColourText(),
1707 groups[i].getStart(), groups[i].getEnd());
1710 .setOutlineColour(new java.awt.Color(groups[i]
1711 .getOutlineColour()));
1713 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
1714 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
1715 sg.thresholdTextColour = groups[i].getTextColThreshold();
1717 if (groups[i].getConsThreshold() != 0)
1719 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
1720 "All", ResidueProperties.propHash, 3, sg
1721 .getSequences(null), 0, sg.getWidth() - 1);
1723 c.verdict(false, 25);
1724 sg.cs.setConservation(c);
1731 /////////////////////////////////
1734 AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
1736 af.setFileName(file, "Jalview");
1738 for (int i = 0; i < JSEQ.length; i++)
1740 af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
1741 new java.awt.Color(JSEQ[i].getColour()));
1744 //If we just load in the same jar file again, the sequenceSetId
1745 //will be the same, and we end up with multiple references
1746 //to the same sequenceSet. We must modify this id on load
1747 //so that each load of the file gives a unique id
1748 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
1750 af.viewport.gatherViewsHere = view.getGatheredViews();
1752 if (view.getSequenceSetId() != null)
1754 jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
1755 .get(uniqueSeqSetId);
1757 af.viewport.sequenceSetID = uniqueSeqSetId;
1761 af.viewport.historyList = av.historyList;
1762 af.viewport.redoList = av.redoList;
1766 viewportsAdded.put(uniqueSeqSetId, af.viewport);
1769 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1771 if (hiddenSeqs != null)
1773 for (int s = 0; s < JSEQ.length; s++)
1775 jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
1777 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
1779 hidden.addSequence(al
1780 .getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
1782 af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
1785 jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
1788 for (int s = 0; s < hiddenSeqs.size(); s++)
1790 hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
1793 af.viewport.hideSequence(hseqs);
1797 if ((hideConsensus || hideQuality || hideConservation)
1798 && al.getAlignmentAnnotation() != null)
1800 int hSize = al.getAlignmentAnnotation().length;
1801 for (int h = 0; h < hSize; h++)
1803 if ((hideConsensus && al.getAlignmentAnnotation()[h].label
1804 .equals("Consensus"))
1805 || (hideQuality && al.getAlignmentAnnotation()[h].label
1807 || (hideConservation && al.getAlignmentAnnotation()[h].label
1808 .equals("Conservation")))
1810 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1815 af.alignPanel.adjustAnnotationHeight();
1818 if (view.getViewName() != null)
1820 af.viewport.viewName = view.getViewName();
1821 af.setInitialTabVisible();
1823 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
1826 af.viewport.setShowAnnotation(view.getShowAnnotation());
1827 af.viewport.setAbovePIDThreshold(view.getPidSelected());
1829 af.viewport.setColourText(view.getShowColourText());
1831 af.viewport.setConservationSelected(view.getConservationSelected());
1832 af.viewport.setShowJVSuffix(view.getShowFullId());
1833 af.viewport.rightAlignIds = view.getRightAlignIds();
1834 af.viewport.setFont(new java.awt.Font(view.getFontName(), view
1835 .getFontStyle(), view.getFontSize()));
1836 af.alignPanel.fontChanged();
1837 af.viewport.setRenderGaps(view.getRenderGaps());
1838 af.viewport.setWrapAlignment(view.getWrapAlignment());
1839 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1840 af.viewport.setShowAnnotation(view.getShowAnnotation());
1841 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1843 af.viewport.setShowBoxes(view.getShowBoxes());
1845 af.viewport.setShowText(view.getShowText());
1847 af.viewport.textColour = new java.awt.Color(view.getTextCol1());
1848 af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
1849 af.viewport.thresholdTextColour = view.getTextColThreshold();
1851 af.viewport.setStartRes(view.getStartRes());
1852 af.viewport.setStartSeq(view.getStartSeq());
1854 ColourSchemeI cs = null;
1856 if (view.getBgColour() != null)
1858 if (view.getBgColour().startsWith("ucs"))
1860 cs = GetUserColourScheme(jms, view.getBgColour());
1862 else if (view.getBgColour().startsWith("Annotation"))
1864 //int find annotation
1865 for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1867 if (af.viewport.alignment.getAlignmentAnnotation()[i].label
1868 .equals(view.getAnnotationColours().getAnnotation()))
1870 if (af.viewport.alignment.getAlignmentAnnotation()[i]
1871 .getThreshold() == null)
1873 af.viewport.alignment.getAlignmentAnnotation()[i]
1874 .setThreshold(new jalview.datamodel.GraphLine(view
1875 .getAnnotationColours().getThreshold(),
1876 "Threshold", java.awt.Color.black)
1881 if (view.getAnnotationColours().getColourScheme()
1884 cs = new AnnotationColourGradient(af.viewport.alignment
1885 .getAlignmentAnnotation()[i], new java.awt.Color(view
1886 .getAnnotationColours().getMinColour()),
1887 new java.awt.Color(view.getAnnotationColours()
1888 .getMaxColour()), view.getAnnotationColours()
1889 .getAboveThreshold());
1891 else if (view.getAnnotationColours().getColourScheme()
1894 cs = new AnnotationColourGradient(af.viewport.alignment
1895 .getAlignmentAnnotation()[i], GetUserColourScheme(
1896 jms, view.getAnnotationColours().getColourScheme()),
1897 view.getAnnotationColours().getAboveThreshold());
1901 cs = new AnnotationColourGradient(af.viewport.alignment
1902 .getAlignmentAnnotation()[i], ColourSchemeProperty
1903 .getColour(al, view.getAnnotationColours()
1904 .getColourScheme()), view
1905 .getAnnotationColours().getAboveThreshold());
1908 // Also use these settings for all the groups
1909 if (al.getGroups() != null)
1911 for (int g = 0; g < al.getGroups().size(); g++)
1913 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
1914 .getGroups().elementAt(g);
1921 /* if (view.getAnnotationColours().getColourScheme().equals("None"))
1923 sg.cs = new AnnotationColourGradient(
1924 af.viewport.alignment.getAlignmentAnnotation()[i],
1925 new java.awt.Color(view.getAnnotationColours().
1927 new java.awt.Color(view.getAnnotationColours().
1929 view.getAnnotationColours().getAboveThreshold());
1933 sg.cs = new AnnotationColourGradient(
1934 af.viewport.alignment.getAlignmentAnnotation()[i],
1935 sg.cs, view.getAnnotationColours()
1936 .getAboveThreshold());
1949 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1954 cs.setThreshold(view.getPidThreshold(), true);
1955 cs.setConsensus(af.viewport.hconsensus);
1959 af.viewport.setGlobalColourScheme(cs);
1960 af.viewport.setColourAppliesToAllGroups(false);
1962 if (view.getConservationSelected() && cs != null)
1964 cs.setConservationInc(view.getConsThreshold());
1967 af.changeColour(cs);
1969 af.viewport.setColourAppliesToAllGroups(true);
1971 if (view.getShowSequenceFeatures())
1973 af.viewport.showSequenceFeatures = true;
1976 if (jms.getFeatureSettings() != null)
1978 af.viewport.featuresDisplayed = new Hashtable();
1979 String[] renderOrder = new String[jms.getFeatureSettings()
1980 .getSettingCount()];
1981 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
1983 Setting setting = jms.getFeatureSettings().getSetting(fs);
1985 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
1986 setting.getType(), new java.awt.Color(setting.getColour()));
1987 renderOrder[fs] = setting.getType();
1988 if (setting.hasOrder())
1989 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
1990 setting.getType(), setting.getOrder());
1992 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
1994 fs / jms.getFeatureSettings().getSettingCount());
1995 if (setting.getDisplay())
1997 af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
1998 setting.getColour()));
2001 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
2003 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
2004 for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
2006 Group grp = jms.getFeatureSettings().getGroup(gs);
2007 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
2011 if (view.getHiddenColumnsCount() > 0)
2013 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
2015 af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
2016 .getHiddenColumns(c).getEnd() //+1
2021 af.setMenusFromViewport(af.viewport);
2023 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
2027 ///////////////////////////////////////
2028 if (loadTreesAndStructures && jms.getTreeCount() > 0)
2032 for (int t = 0; t < jms.getTreeCount(); t++)
2035 Tree tree = jms.getTree(t);
2037 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(tree
2038 .getNewick()), tree.getTitle(), tree.getWidth(), tree
2039 .getHeight(), tree.getXpos(), tree.getYpos());
2041 tp.fitToWindow.setState(tree.getFitToWindow());
2042 tp.fitToWindow_actionPerformed(null);
2044 if (tree.getFontName() != null)
2046 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
2047 .getFontStyle(), tree.getFontSize()));
2051 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
2052 .getFontStyle(), tree.getFontSize()));
2055 tp.showPlaceholders(tree.getMarkUnlinked());
2056 tp.showBootstrap(tree.getShowBootstrap());
2057 tp.showDistances(tree.getShowDistances());
2059 tp.treeCanvas.threshold = tree.getThreshold();
2061 if (tree.getCurrentTree())
2063 af.viewport.setCurrentTree(tp.getTree());
2067 } catch (Exception ex)
2069 ex.printStackTrace();
2074 if (loadTreesAndStructures)
2076 for (int i = 0; i < JSEQ.length; i++)
2078 if (JSEQ[i].getPdbidsCount() > 0)
2080 Pdbids[] ids = JSEQ[i].getPdbids();
2081 for (int p = 0; p < ids.length; p++)
2083 for (int s = 0; s < ids[p].getStructureStateCount(); s++)
2085 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
2087 jpdb.setFile(loadPDBFile(ids[p].getFile(), ids[p].getId()));
2088 jpdb.setId(ids[p].getId());
2090 int x = ids[p].getStructureState(s).getXpos();
2091 int y = ids[p].getStructureState(s).getYpos();
2092 int width = ids[p].getStructureState(s).getWidth();
2093 int height = ids[p].getStructureState(s).getHeight();
2095 java.awt.Component comp = null;
2097 JInternalFrame[] frames = null;
2100 frames = Desktop.desktop.getAllFrames();
2102 catch (ArrayIndexOutOfBoundsException e)
2104 // occasional No such child exceptions are thrown here...
2108 } catch (Exception f) {};
2110 } while (frames==null);
2111 for (int f = 0; f < frames.length; f++)
2113 if (frames[f] instanceof AppJmol)
2115 if (frames[f].getX() == x && frames[f].getY() == y
2116 && frames[f].getHeight() == height
2117 && frames[f].getWidth() == width)
2125 Desktop.desktop.getComponentAt(x, y);
2127 String pdbFile = loadPDBFile(file, ids[p].getId());
2129 jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
2130 { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId()
2135 String state = ids[p].getStructureState(s).getContent();
2137 StringBuffer newFileLoc = new StringBuffer(state.substring(
2138 0, state.indexOf("\"", state.indexOf("load")) + 1));
2140 newFileLoc.append(jpdb.getFile());
2141 newFileLoc.append(state.substring(state.indexOf("\"", state
2142 .indexOf("load \"") + 6)));
2144 new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel,
2145 newFileLoc.toString(), new java.awt.Rectangle(x, y,
2149 else if (comp != null)
2151 StructureSelectionManager.getStructureSelectionManager()
2152 .setMapping(seq, null, pdbFile,
2153 jalview.io.AppletFormatAdapter.FILE);
2155 ((AppJmol) comp).addSequence(seq);
2166 private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
2168 jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
2169 Vector dseqs = null;
2172 // create a list of new dataset sequences
2173 dseqs = new Vector();
2175 for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
2177 Sequence vamsasSeq = vamsasSet.getSequence(i);
2178 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
2180 // create a new dataset
2183 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
2184 dseqs.copyInto(dsseqs);
2185 ds = new jalview.datamodel.Alignment(dsseqs);
2186 addDatasetRef(vamsasSet.getDatasetId(), ds);
2188 // set the dataset for the newly imported alignment.
2189 if (al.getDataset() == null)
2198 * @param vamsasSeq sequence definition to create/merge dataset sequence for
2199 * @param ds dataset alignment
2200 * @param dseqs vector to add new dataset sequence to
2202 private void ensureJalviewDatasetSequence(Sequence vamsasSeq, AlignmentI ds, Vector dseqs)
2204 jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds.get(vamsasSeq.getId());
2205 jalview.datamodel.SequenceI dsq = null;
2206 if (sq!=null && sq.getDatasetSequence()!=null)
2208 dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
2211 String sqid = vamsasSeq.getDsseqid();
2214 // need to create or add a new dataset sequence reference to this sequence
2217 dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
2222 // make a new dataset sequence
2223 dsq = sq.createDatasetSequence();
2226 // make up a new dataset reference for this sequence
2227 sqid = "" + dsq.hashCode();
2229 dsq.setVamsasId(uniqueSetSuffix + sqid);
2230 seqRefIds.put(sqid, dsq);
2235 dseqs.addElement(dsq);
2240 ds.addSequence(dsq);
2244 { // make this dataset sequence sq's dataset sequence
2245 sq.setDatasetSequence(dsq);
2249 // TODO: refactor this as a merge dataset sequence function
2250 // now check that sq (the dataset sequence) sequence really is the union of all references to it
2251 //boolean pre = sq.getStart() < dsq.getStart();
2252 //boolean post = sq.getEnd() > dsq.getEnd();
2256 StringBuffer sb = new StringBuffer();
2257 String newres = jalview.analysis.AlignSeq.extractGaps(
2258 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
2259 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString()) && newres.length()>dsq.getLength())
2261 // Update with the longer sequence.
2267 .substring(0, dsq.getStart() - sq.getStart()));
2268 dsq.setStart(sq.getStart());
2272 sb.append(newres.substring(newres.length() - sq.getEnd()
2274 dsq.setEnd(sq.getEnd());
2277 dsq.setSequence(sb.toString());
2279 //TODO: merges will never happen if we 'know' we have the real dataset sequence - this should be detected when id==dssid
2281 .println("DEBUG Notice: Merged dataset sequence"); // ("
2282 // + (pre ? "prepended" : "") + " "
2283 //+ (post ? "appended" : ""));
2288 java.util.Hashtable datasetIds = null;
2290 private Alignment getDatasetFor(String datasetId)
2292 if (datasetIds == null)
2294 datasetIds = new Hashtable();
2297 if (datasetIds.containsKey(datasetId))
2299 return (Alignment) datasetIds.get(datasetId);
2304 private void addDatasetRef(String datasetId, Alignment dataset)
2306 if (datasetIds == null)
2308 datasetIds = new Hashtable();
2310 datasetIds.put(datasetId, dataset);
2313 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
2315 for (int d = 0; d < sequence.getDBRefCount(); d++)
2317 DBRef dr = sequence.getDBRef(d);
2318 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
2319 sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
2320 .getVersion(), sequence.getDBRef(d).getAccessionId());
2321 if (dr.getMapping() != null)
2323 entry.setMap(addMapping(dr.getMapping()));
2325 datasetSequence.addDBRef(entry);
2329 private jalview.datamodel.Mapping addMapping(Mapping m)
2331 SequenceI dsto = null;
2332 // Mapping m = dr.getMapping();
2333 int fr[] = new int[m.getMapListFromCount() * 2];
2334 Enumeration f = m.enumerateMapListFrom();
2335 for (int _i = 0; f.hasMoreElements(); _i += 2)
2337 MapListFrom mf = (MapListFrom) f.nextElement();
2338 fr[_i] = mf.getStart();
2339 fr[_i + 1] = mf.getEnd();
2341 int fto[] = new int[m.getMapListToCount() * 2];
2342 f = m.enumerateMapListTo();
2343 for (int _i = 0; f.hasMoreElements(); _i += 2)
2345 MapListTo mf = (MapListTo) f.nextElement();
2346 fto[_i] = mf.getStart();
2347 fto[_i + 1] = mf.getEnd();
2349 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
2350 fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
2351 if (m.getMappingChoice() != null)
2353 MappingChoice mc = m.getMappingChoice();
2354 if (mc.getDseqFor() != null)
2356 if (seqRefIds.containsKey(mc.getDseqFor()))
2361 jmap.setTo((SequenceI) seqRefIds.get(mc.getDseqFor()));
2365 frefedSequence.add(new Object[]
2366 { mc.getDseqFor(), jmap });
2372 * local sequence definition
2374 Sequence ms = mc.getSequence();
2375 jalview.datamodel.Sequence djs=null;
2376 String sqid = ms.getDsseqid();
2377 if (sqid!=null && sqid.length()>0)
2380 * recover dataset sequence
2382 djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
2384 System.err.println("Warning - making up dataset sequence id for DbRef sequence map reference");
2385 sqid = ""+ms.hashCode(); // make up a new hascode for undefined dataset sequence hash (unlikely to happen)
2390 * make a new dataset sequence and add it to refIds hash
2392 djs = new jalview.datamodel.Sequence(ms
2393 .getName(), ms.getSequence());
2394 djs.setStart(jmap.getMap().getToLowest());
2395 djs.setEnd(jmap.getMap().getToHighest());
2396 djs.setVamsasId(uniqueSetSuffix + sqid);
2398 seqRefIds.put(sqid, djs);
2401 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
2410 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
2411 boolean keepSeqRefs)
2413 jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
2419 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
2423 uniqueSetSuffix = "";
2426 viewportsAdded = new Hashtable();
2428 AlignFrame af = LoadFromObject(jm, null, false);
2429 af.alignPanels.clear();
2430 af.closeMenuItem_actionPerformed(true);
2432 /* if(ap.av.alignment.getAlignmentAnnotation()!=null)
2434 for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length; i++)
2436 if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated)
2438 af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
2439 ap.av.alignment.getAlignmentAnnotation()[i];
2444 return af.alignPanel;