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.*;
29 import jalview.schemabinding.version2.*;
30 import jalview.schemes.*;
31 import jalview.structure.StructureSelectionManager;
39 public class Jalview2XML
45 * This maintains a list of viewports, the key being the
46 * seqSetId. Important to set historyItem and redoList
49 Hashtable viewportsAdded;
51 Hashtable annotationIds = new Hashtable();
53 String uniqueSetSuffix = "";
55 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
56 public void SaveState(File statefile)
58 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
67 FileOutputStream fos = new FileOutputStream(statefile);
68 JarOutputStream jout = new JarOutputStream(fos);
70 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
71 ////////////////////////////////////////////////////
72 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
75 Vector shortNames = new Vector();
78 for (int i = frames.length - 1; i > -1; i--)
80 if (frames[i] instanceof AlignFrame)
82 AlignFrame af = (AlignFrame) frames[i];
84 String shortName = af.getTitle();
86 if (shortName.indexOf(File.separatorChar) > -1)
88 shortName = shortName.substring(shortName.lastIndexOf(
89 File.separatorChar) + 1);
94 while (shortNames.contains(shortName))
96 if (shortName.endsWith("_" + (count - 1)))
98 shortName = shortName.substring(0,
99 shortName.lastIndexOf("_"));
102 shortName = shortName.concat("_" + count);
106 shortNames.addElement(shortName);
108 if (!shortName.endsWith(".xml"))
110 shortName = shortName + ".xml";
113 int ap, apSize = af.alignPanels.size();
114 for (ap = 0; ap < apSize; ap++)
116 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.
120 apSize == 1 ? shortName : ap + shortName,
131 ex.printStackTrace();
135 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
136 public boolean SaveAlignment(AlignFrame af, String jarFile,
141 int ap, apSize = af.alignPanels.size();
142 FileOutputStream fos = new FileOutputStream(jarFile);
143 JarOutputStream jout = new JarOutputStream(fos);
144 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
146 for (ap = 0; ap < apSize; ap++)
148 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.elementAt(ap);
151 apSize == 1 ? fileName : fileName + ap,
161 ex.printStackTrace();
169 * @param af DOCUMENT ME!
170 * @param timeStamp DOCUMENT ME!
171 * @param fileName DOCUMENT ME!
172 * @param jout DOCUMENT ME!
173 * @param out DOCUMENT ME!
175 public JalviewModel SaveState(AlignmentPanel ap,
177 JarOutputStream jout,
180 if (seqRefIds == null)
182 seqRefIds = new Hashtable();
185 Vector userColours = new Vector();
187 AlignViewport av = ap.av;
189 JalviewModel object = new JalviewModel();
190 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
192 object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
193 object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
195 jalview.datamodel.AlignmentI jal = av.alignment;
197 if (av.hasHiddenRows)
199 jal = jal.getHiddenSequences().getFullAlignment();
202 SequenceSet vamsasSet = new SequenceSet();
204 JalviewModelSequence jms = new JalviewModelSequence();
206 vamsasSet.setGapChar(jal.getGapCharacter() + "");
209 Vector pdbfiles = null;
213 jalview.datamodel.SequenceI jds;
214 for (int i = 0; i < jal.getHeight(); i++)
216 jds = jal.getSequenceAt(i);
219 if (seqRefIds.get(id + "") != null)
225 vamsasSeq = new Sequence();
226 vamsasSeq.setId(id + "");
227 vamsasSeq.setName(jds.getName());
228 vamsasSeq.setSequence(jds.getSequenceAsString());
229 vamsasSeq.setDescription(jds.getDescription());
231 if (jds.getDatasetSequence().getDBRef() != null)
233 jalview.datamodel.DBRefEntry[] dbrefs =
234 jds.getDatasetSequence().getDBRef();
236 for (int d = 0; d < dbrefs.length; d++)
238 DBRef dbref = new DBRef();
239 dbref.setSource(dbrefs[d].getSource());
240 dbref.setVersion(dbrefs[d].getVersion());
241 dbref.setAccessionId(dbrefs[d].getAccessionId());
242 vamsasSeq.addDBRef(dbref);
246 vamsasSet.addSequence(vamsasSeq);
247 seqRefIds.put(id + "", jal.getSequenceAt(i));
251 jseq.setStart(jds.getStart());
252 jseq.setEnd(jds.getEnd());
253 jseq.setColour(av.getSequenceColour(jds).getRGB());
257 if (av.hasHiddenRows)
259 jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
261 if (av.hiddenRepSequences != null
262 && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
264 jalview.datamodel.SequenceI[] reps =
265 ( (jalview.datamodel.SequenceGroup)
266 av.hiddenRepSequences.get(
267 jal.getSequenceAt(i))).getSequencesInOrder(jal);
269 for (int h = 0; h < reps.length; h++)
271 if (reps[h] != jal.getSequenceAt(i))
273 jseq.addHiddenSequences(
274 jal.findIndex(reps[h])
281 if (jds.getDatasetSequence().getSequenceFeatures() != null)
283 jalview.datamodel.SequenceFeature[] sf
284 = jds.getDatasetSequence().getSequenceFeatures();
286 while (index < sf.length)
288 Features features = new Features();
290 features.setBegin(sf[index].getBegin());
291 features.setEnd(sf[index].getEnd());
292 features.setDescription(sf[index].getDescription());
293 features.setType(sf[index].getType());
294 features.setFeatureGroup(sf[index].getFeatureGroup());
295 features.setScore(sf[index].getScore());
296 if (sf[index].links != null)
298 for (int l = 0; l < sf[index].links.size(); l++)
300 OtherData keyValue = new OtherData();
301 keyValue.setKey("LINK_" + l);
302 keyValue.setValue(sf[index].links.elementAt(l).toString());
303 features.addOtherData(keyValue);
306 if (sf[index].otherDetails != null)
309 Enumeration keys = sf[index].otherDetails.keys();
310 while (keys.hasMoreElements())
312 key = keys.nextElement().toString();
313 OtherData keyValue = new OtherData();
314 keyValue.setKey(key);
316 sf[index].otherDetails.get(key).toString());
317 features.addOtherData(keyValue);
321 jseq.addFeatures(features);
326 if (jds.getDatasetSequence().getPDBId() != null)
328 Enumeration en = jds.getDatasetSequence().getPDBId().elements();
329 while (en.hasMoreElements())
331 Pdbids pdb = new Pdbids();
332 jalview.datamodel.PDBEntry entry
333 = (jalview.datamodel.PDBEntry) en.nextElement();
335 pdb.setId(entry.getId());
336 pdb.setType(entry.getType());
339 //This must have been loaded, is it still visible?
340 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
341 for (int f = frames.length - 1; f > -1; f--)
343 if (frames[f] instanceof AppJMol)
345 jmol = (AppJMol) frames[f];
346 if (!jmol.pdbentry.getId().equals(entry.getId()))
349 StructureState state = new StructureState();
350 state.setVisible(true);
351 state.setXpos(jmol.getX());
352 state.setYpos(jmol.getY());
353 state.setWidth(jmol.getWidth());
354 state.setHeight(jmol.getHeight());
356 state.setContent(jmol.viewer.getStateInfo().replaceAll("\n", ""));
358 for (int s = 0; s < jmol.sequence.length; s++)
360 if (jal.findIndex(jmol.sequence[s]) > -1)
362 pdb.addStructureState(state);
369 if (entry.getFile() != null)
371 pdb.setFile(entry.getFile());
372 if (pdbfiles == null)
374 pdbfiles = new Vector();
377 if (!pdbfiles.contains(entry.getId()))
379 pdbfiles.addElement(entry.getId());
382 File file = new File(entry.getFile());
383 if (file.exists() && jout != null)
385 byte[] data = new byte[ (int) file.length()];
386 jout.putNextEntry(new JarEntry(entry.getId()));
387 DataInputStream dis = new DataInputStream(new
388 FileInputStream(file));
391 DataOutputStream dout = new DataOutputStream(jout);
392 dout.write(data, 0, data.length);
398 ex.printStackTrace();
404 if (entry.getProperty() != null)
406 PdbentryItem item = new PdbentryItem();
407 Hashtable properties = entry.getProperty();
408 Enumeration en2 = properties.keys();
409 while (en2.hasMoreElements())
411 Property prop = new Property();
412 String key = en2.nextElement().toString();
414 prop.setValue(properties.get(key).toString());
415 item.addProperty(prop);
417 pdb.addPdbentryItem(item);
427 if (av.hasHiddenRows)
433 ///////////////////////////////////
434 if (av.currentTree != null)
436 // FIND ANY ASSOCIATED TREES
437 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
438 if (Desktop.desktop != null)
440 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
442 for (int t = 0; t < frames.length; t++)
444 if (frames[t] instanceof TreePanel)
446 TreePanel tp = (TreePanel) frames[t];
448 if (tp.treeCanvas.av.alignment == jal)
450 Tree tree = new Tree();
451 tree.setTitle(tp.getTitle());
452 tree.setCurrentTree( (av.currentTree == tp.getTree()));
453 tree.setNewick(tp.getTree().toString());
454 tree.setThreshold(tp.treeCanvas.threshold);
456 tree.setFitToWindow(tp.fitToWindow.getState());
457 tree.setFontName(tp.getTreeFont().getName());
458 tree.setFontSize(tp.getTreeFont().getSize());
459 tree.setFontStyle(tp.getTreeFont().getStyle());
460 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
462 tree.setShowBootstrap(tp.bootstrapMenu.getState());
463 tree.setShowDistances(tp.distanceMenu.getState());
465 tree.setHeight(tp.getHeight());
466 tree.setWidth(tp.getWidth());
467 tree.setXpos(tp.getX());
468 tree.setYpos(tp.getY());
478 if (jal.getAlignmentAnnotation() != null)
480 jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
482 for (int i = 0; i < aa.length; i++)
484 Annotation an = new Annotation();
486 if (aa[i].annotationId != null)
488 annotationIds.put(aa[i].annotationId, aa[i]);
491 an.setId(aa[i].annotationId);
493 if (aa[i] == av.quality ||
494 aa[i] == av.conservation ||
495 aa[i] == av.consensus)
497 an.setLabel(aa[i].label);
499 vamsasSet.addAnnotation(an);
503 an.setDescription(aa[i].description);
505 if (aa[i].sequenceRef != null)
507 an.setSequenceRef(aa[i].sequenceRef.getName());
513 an.setGraphType(aa[i].graph);
514 an.setGraphGroup(aa[i].graphGroup);
515 if (aa[i].getThreshold() != null)
517 ThresholdLine line = new ThresholdLine();
518 line.setLabel(aa[i].getThreshold().label);
519 line.setValue(aa[i].getThreshold().value);
520 line.setColour(aa[i].getThreshold().colour.getRGB());
521 an.setThresholdLine(line);
529 an.setLabel(aa[i].label);
531 AnnotationElement ae;
533 for (int a = 0; a < aa[i].annotations.length; a++)
535 if ( (aa[i] == null) || (aa[i].annotations[a] == null))
540 ae = new AnnotationElement();
541 ae.setDescription(aa[i].annotations[a].description);
542 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
543 ae.setValue(aa[i].annotations[a].value);
545 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
548 if (aa[i].annotations[a].colour != java.awt.Color.black)
550 ae.setColour(aa[i].annotations[a].colour.getRGB());
553 an.addAnnotationElement(ae);
556 vamsasSet.addAnnotation(an);
561 if (jal.getGroups() != null)
563 JGroup[] groups = new JGroup[jal.getGroups().size()];
565 for (int i = 0; i < groups.length; i++)
567 groups[i] = new JGroup();
569 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup)
572 groups[i].setStart(sg.getStartRes());
573 groups[i].setEnd(sg.getEndRes());
574 groups[i].setName(sg.getName());
577 if (sg.cs.conservationApplied())
579 groups[i].setConsThreshold(sg.cs.getConservationInc());
581 if (sg.cs instanceof jalview.schemes.UserColourScheme)
583 groups[i].setColour(SetUserColourScheme(sg.cs,
589 groups[i].setColour(ColourSchemeProperty.getColourName(sg.
593 else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
596 ColourSchemeProperty.getColourName(
597 ( (jalview.schemes.AnnotationColourGradient) sg.cs).
600 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
602 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
607 groups[i].setColour(ColourSchemeProperty.getColourName(
611 groups[i].setPidThreshold(sg.cs.getThreshold());
614 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
615 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
616 groups[i].setDisplayText(sg.getDisplayText());
617 groups[i].setColourText(sg.getColourText());
618 groups[i].setTextCol1(sg.textColour.getRGB());
619 groups[i].setTextCol2(sg.textColour2.getRGB());
620 groups[i].setTextColThreshold(sg.thresholdTextColour);
622 for (int s = 0; s < sg.getSize(); s++)
624 jalview.datamodel.Sequence seq =
625 (jalview.datamodel.Sequence) sg.getSequenceAt(s);
626 groups[i].addSeq(seq.hashCode());
630 jms.setJGroup(groups);
633 ///////////SAVE VIEWPORT
634 Viewport view = new Viewport();
635 view.setTitle(ap.alignFrame.getTitle());
636 view.setSequenceSetId(av.getSequenceSetId());
637 view.setViewName(av.viewName);
638 view.setGatheredViews(av.gatherViewsHere);
642 if (ap.av.explodedPosition != null)
644 view.setXpos(av.explodedPosition.x);
645 view.setYpos(av.explodedPosition.y);
646 view.setWidth(av.explodedPosition.width);
647 view.setHeight(av.explodedPosition.height);
651 view.setXpos(ap.alignFrame.getBounds().x);
652 view.setYpos(ap.alignFrame.getBounds().y);
653 view.setWidth(ap.alignFrame.getBounds().width);
654 view.setHeight(ap.alignFrame.getBounds().height);
657 view.setStartRes(av.startRes);
658 view.setStartSeq(av.startSeq);
660 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
662 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
665 else if (av.getGlobalColourScheme() instanceof jalview.schemes.
666 AnnotationColourGradient)
668 jalview.schemes.AnnotationColourGradient acg
669 = (jalview.schemes.AnnotationColourGradient) av.getGlobalColourScheme();
671 AnnotationColours ac = new AnnotationColours();
672 ac.setAboveThreshold(acg.getAboveThreshold());
673 ac.setThreshold(acg.getAnnotationThreshold());
674 ac.setAnnotation(acg.getAnnotation());
675 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
677 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
682 ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
685 ac.setMaxColour(acg.getMaxColour().getRGB());
686 ac.setMinColour(acg.getMinColour().getRGB());
687 view.setAnnotationColours(ac);
688 view.setBgColour("AnnotationColourGradient");
692 view.setBgColour(ColourSchemeProperty.getColourName(
693 av.getGlobalColourScheme()));
696 ColourSchemeI cs = av.getGlobalColourScheme();
700 if (cs.conservationApplied())
702 view.setConsThreshold(cs.getConservationInc());
703 if (cs instanceof jalview.schemes.UserColourScheme)
705 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
709 if (cs instanceof ResidueColourScheme)
711 view.setPidThreshold(cs.getThreshold());
715 view.setConservationSelected(av.getConservationSelected());
716 view.setPidSelected(av.getAbovePIDThreshold());
717 view.setFontName(av.font.getName());
718 view.setFontSize(av.font.getSize());
719 view.setFontStyle(av.font.getStyle());
720 view.setRenderGaps(av.renderGaps);
721 view.setShowAnnotation(av.getShowAnnotation());
722 view.setShowBoxes(av.getShowBoxes());
723 view.setShowColourText(av.getColourText());
724 view.setShowFullId(av.getShowJVSuffix());
725 view.setRightAlignIds(av.rightAlignIds);
726 view.setShowSequenceFeatures(av.showSequenceFeatures);
727 view.setShowText(av.getShowText());
728 view.setWrapAlignment(av.getWrapAlignment());
729 view.setTextCol1(av.textColour.getRGB());
730 view.setTextCol2(av.textColour2.getRGB());
731 view.setTextColThreshold(av.thresholdTextColour);
733 if (av.featuresDisplayed != null)
735 jalview.schemabinding.version2.FeatureSettings fs
736 = new jalview.schemabinding.version2.FeatureSettings();
738 String[] renderOrder =
739 ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
741 Vector settingsAdded = new Vector();
742 for (int ro = 0; ro < renderOrder.length; ro++)
744 Setting setting = new Setting();
745 setting.setType(renderOrder[ro]);
747 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).
752 av.featuresDisplayed.containsKey(renderOrder[ro])
755 fs.addSetting(setting);
756 settingsAdded.addElement(renderOrder[ro]);
759 //Make sure we save none displayed feature settings
761 ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
762 while (en.hasMoreElements())
764 String key = en.nextElement().toString();
765 if (settingsAdded.contains(key))
770 Setting setting = new Setting();
771 setting.setType(key);
773 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
776 setting.setDisplay(false);
778 fs.addSetting(setting);
779 settingsAdded.addElement(key);
782 jms.setFeatureSettings(fs);
786 if (av.hasHiddenColumns)
788 for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
790 int[] region = (int[]) av.getColumnSelection().getHiddenColumns().
792 HiddenColumns hc = new HiddenColumns();
793 hc.setStart(region[0]);
794 hc.setEnd(region[1]);
795 view.addHiddenColumns(hc);
799 jms.addViewport(view);
801 object.setJalviewModelSequence(jms);
802 object.getVamsasModel().addSequenceSet(vamsasSet);
806 //We may not want to right the object to disk,
807 //eg we can copy the alignViewport to a new view object
808 //using save and then load
811 if (!fileName.endsWith(".xml"))
813 fileName = fileName + ".xml";
816 JarEntry entry = new JarEntry(fileName);
817 jout.putNextEntry(entry);
823 ex.printStackTrace();
829 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
830 Vector userColours, JalviewModelSequence jms)
833 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)
836 if (!userColours.contains(ucs))
838 userColours.add(ucs);
840 java.awt.Color[] colours = ucs.getColours();
841 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.
842 version2.UserColours();
843 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.
844 schemabinding.version2.UserColourScheme();
846 for (int i = 0; i < colours.length; i++)
848 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.
850 col.setName(ResidueProperties.aa[i]);
851 col.setRGB(jalview.util.Format.getHexString(colours[i]));
852 jbucs.addColour(col);
854 if (ucs.getLowerCaseColours() != null)
856 colours = ucs.getLowerCaseColours();
857 for (int i = 0; i < colours.length; i++)
859 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.
861 col.setName(ResidueProperties.aa[i].toLowerCase());
862 col.setRGB(jalview.util.Format.getHexString(colours[i]));
863 jbucs.addColour(col);
867 id = "ucs" + userColours.indexOf(ucs);
869 uc.setUserColourScheme(jbucs);
870 jms.addUserColours(uc);
876 jalview.schemes.UserColourScheme GetUserColourScheme(
877 JalviewModelSequence jms, String id)
879 UserColours[] uc = jms.getUserColours();
880 UserColours colours = null;
882 for (int i = 0; i < uc.length; i++)
884 if (uc[i].getId().equals(id))
892 java.awt.Color[] newColours = new java.awt.Color[24];
894 for (int i = 0; i < 24; i++)
896 newColours[i] = new java.awt.Color(Integer.parseInt(
897 colours.getUserColourScheme().getColour(i).getRGB(), 16));
900 jalview.schemes.UserColourScheme ucs =
901 new jalview.schemes.UserColourScheme(newColours);
903 if (colours.getUserColourScheme().getColourCount() > 24)
905 newColours = new java.awt.Color[23];
906 for (int i = 0; i < 23; i++)
908 newColours[i] = new java.awt.Color(Integer.parseInt(
909 colours.getUserColourScheme().getColour(i + 24).getRGB(), 16));
911 ucs.setLowerCaseColours(newColours);
920 * @param file DOCUMENT ME!
922 public AlignFrame LoadJalviewAlign(final String file)
924 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
926 jalview.gui.AlignFrame af = null;
928 seqRefIds = new Hashtable();
929 viewportsAdded = new Hashtable();
931 Hashtable gatherToThisFrame = new Hashtable();
935 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
938 if (file.startsWith("http://"))
943 JarInputStream jin = null;
944 JarEntry jarentry = null;
951 jin = new JarInputStream(url.openStream());
955 jin = new JarInputStream(new FileInputStream(file));
958 for (int i = 0; i < entryCount; i++)
960 jarentry = jin.getNextJarEntry();
963 if (jarentry != null && jarentry.getName().endsWith(".xml"))
965 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
966 JalviewModel object = new JalviewModel();
968 Unmarshaller unmar = new Unmarshaller(object);
969 unmar.setValidation(false);
970 object = (JalviewModel) unmar.unmarshal(in);
972 af = LoadFromObject(object, file, true);
973 if (af.viewport.gatherViewsHere)
975 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
979 else if (jarentry != null)
981 //Some other file here.
985 while (jarentry != null);
987 catch (java.net.UnknownHostException ex)
989 ex.printStackTrace();
990 System.err.println("Couldn't locate Jalview XML file : " +
993 javax.swing.SwingUtilities.invokeLater(new Runnable()
997 JOptionPane.showInternalMessageDialog(Desktop.desktop,
998 "Couldn't locate " + file,
1000 JOptionPane.WARNING_MESSAGE);
1004 catch (Exception ex)
1006 //Is Version 1 Jar file?
1007 af = new Jalview2XML_V1().LoadJalviewAlign(file);
1011 System.out.println("Successfully loaded archive file");
1014 ex.printStackTrace();
1016 System.err.println("Exception whilst loading jalview XML file : " +
1018 javax.swing.SwingUtilities.invokeLater(new Runnable()
1023 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1024 "Error loading " + file,
1025 "Error loading Jalview file",
1026 JOptionPane.WARNING_MESSAGE);
1031 if (Desktop.instance != null)
1033 Desktop.instance.stopLoading();
1036 Enumeration en = gatherToThisFrame.elements();
1037 while(en.hasMoreElements())
1039 Desktop.instance.gatherViews(
1040 (AlignFrame) en.nextElement());
1046 Hashtable alreadyLoadedPDB;
1047 String loadPDBFile(String file, String pdbId)
1049 if (alreadyLoadedPDB == null)
1050 alreadyLoadedPDB = new Hashtable();
1052 if (alreadyLoadedPDB.containsKey(pdbId))
1053 return alreadyLoadedPDB.get(pdbId).toString();
1057 JarInputStream jin = null;
1059 if (file.startsWith("http://"))
1061 jin = new JarInputStream(new URL(file).openStream());
1065 jin = new JarInputStream(new FileInputStream(file));
1068 JarEntry entry = null;
1071 entry = jin.getNextJarEntry();
1073 while (!entry.getName().equals(pdbId));
1075 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1076 File outFile = File.createTempFile("jalview_pdb", ".txt");
1077 outFile.deleteOnExit();
1078 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1081 while ( (data = in.readLine()) != null)
1087 alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
1088 return outFile.getAbsolutePath();
1091 catch (Exception ex)
1093 ex.printStackTrace();
1099 AlignFrame LoadFromObject(JalviewModel object,
1101 boolean loadTreesAndStructures)
1103 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1104 Sequence[] vamsasSeq = vamsasSet.getSequence();
1106 JalviewModelSequence jms = object.getJalviewModelSequence();
1108 Viewport view = jms.getViewport(0);
1110 //////////////////////////////////
1113 Vector hiddenSeqs = null;
1114 jalview.datamodel.Sequence jseq;
1116 ArrayList tmpseqs = new ArrayList();
1118 boolean multipleView = false;
1120 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1121 for (int i = 0; i < JSEQ.length; i++)
1123 String seqId = JSEQ[i].getId() + "";
1125 if (seqRefIds.get(seqId) != null)
1127 tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1128 multipleView = true;
1132 jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
1133 vamsasSeq[i].getSequence());
1134 jseq.setDescription(vamsasSeq[i].getDescription());
1135 jseq.setStart(JSEQ[i].getStart());
1136 jseq.setEnd(JSEQ[i].getEnd());
1137 seqRefIds.put(vamsasSeq[i].getId(), jseq);
1141 if (JSEQ[i].getHidden())
1143 if (hiddenSeqs == null)
1145 hiddenSeqs = new Vector();
1148 hiddenSeqs.addElement(
1149 (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1154 ///SequenceFeatures are added to the DatasetSequence,
1155 // so we must create the dataset before loading features
1156 /////////////////////////////////
1159 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
1162 tmpseqs.toArray(orderedSeqs);
1164 jalview.datamodel.Alignment al =
1165 new jalview.datamodel.Alignment(orderedSeqs);
1167 al.setDataset(null);
1168 /////////////////////////////////
1171 Hashtable pdbloaded = new Hashtable();
1175 for (int i = 0; i < vamsasSeq.length; i++)
1177 if (JSEQ[i].getFeaturesCount() > 0)
1179 Features[] features = JSEQ[i].getFeatures();
1180 for (int f = 0; f < features.length; f++)
1182 jalview.datamodel.SequenceFeature sf
1183 = new jalview.datamodel.SequenceFeature(features[f].getType(),
1184 features[f].getDescription(), features[f].getStatus(),
1185 features[f].getBegin(), features[f].getEnd(),
1186 features[f].getFeatureGroup());
1188 sf.setScore(features[f].getScore());
1189 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1191 OtherData keyValue = features[f].getOtherData(od);
1192 if (keyValue.getKey().startsWith("LINK"))
1194 sf.addLink(keyValue.getValue());
1198 sf.setValue(keyValue.getKey(), keyValue.getValue());
1203 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1207 if (JSEQ[i].getPdbidsCount() > 0)
1209 Pdbids[] ids = JSEQ[i].getPdbids();
1210 for (int p = 0; p < ids.length; p++)
1212 jalview.datamodel.PDBEntry entry = new jalview.datamodel.
1214 entry.setId(ids[p].getId());
1215 entry.setType(ids[p].getType());
1216 if (ids[p].getFile() != null)
1218 if (!pdbloaded.containsKey(ids[p].getFile()))
1220 entry.setFile(loadPDBFile(file, ids[p].getId()));
1224 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1228 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1231 if (vamsasSeq[i].getDBRefCount() > 0)
1233 for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
1235 jalview.datamodel.DBRefEntry entry =
1236 new jalview.datamodel.DBRefEntry(
1237 vamsasSeq[i].getDBRef(d).getSource(),
1238 vamsasSeq[i].getDBRef(d).getVersion(),
1239 vamsasSeq[i].getDBRef(d).getAccessionId()
1241 al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1248 /////////////////////////////////
1249 //////////////////////////////////
1251 boolean hideQuality = true,
1252 hideConservation = true,
1253 hideConsensus = true;
1255 if (vamsasSet.getAnnotationCount() > 0)
1257 Annotation[] an = vamsasSet.getAnnotation();
1259 for (int i = 0; i < an.length; i++)
1261 if (an[i].getLabel().equals("Quality"))
1263 hideQuality = false;
1266 else if (an[i].getLabel().equals("Conservation"))
1268 hideConservation = false;
1271 else if (an[i].getLabel().equals("Consensus"))
1273 hideConsensus = false;
1277 if (an[i].getId() != null
1278 && annotationIds.containsKey(an[i].getId()))
1281 (jalview.datamodel.AlignmentAnnotation) annotationIds.get(an[i].
1288 AnnotationElement[] ae = an[i].getAnnotationElement();
1289 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[
1292 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
1294 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].
1295 getDisplayCharacter(),
1296 ae[aa].getDescription(),
1297 ae[aa].getSecondaryStructure().length() == 0 ? ' ' :
1298 ae[aa].getSecondaryStructure().charAt(0),
1300 anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa].
1304 jalview.datamodel.AlignmentAnnotation jaa = null;
1306 if (an[i].getGraph())
1308 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1309 an[i].getDescription(), anot, 0, 0,
1310 an[i].getGraphType());
1312 jaa.graphGroup = an[i].getGraphGroup();
1314 if (an[i].getThresholdLine() != null)
1316 jaa.setThreshold(new jalview.datamodel.GraphLine(
1317 an[i].getThresholdLine().getValue(),
1318 an[i].getThresholdLine().getLabel(),
1319 new java.awt.Color(an[i].getThresholdLine().getColour()))
1327 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1328 an[i].getDescription(), anot);
1331 if (an[i].getId() != null)
1333 annotationIds.put(an[i].getId(), jaa);
1334 jaa.annotationId = an[i].getId();
1337 if (an[i].getSequenceRef() != null)
1339 jaa.createSequenceMapping(
1340 al.findName(an[i].getSequenceRef()), 1, true
1342 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1345 al.addAnnotation(jaa);
1349 /////////////////////////
1351 if (jms.getJGroupCount() > 0)
1353 JGroup[] groups = jms.getJGroup();
1355 for (int i = 0; i < groups.length; i++)
1357 ColourSchemeI cs = null;
1359 if (groups[i].getColour() != null)
1361 if (groups[i].getColour().startsWith("ucs"))
1363 cs = GetUserColourScheme(jms, groups[i].getColour());
1367 cs = ColourSchemeProperty.getColour(al,
1368 groups[i].getColour());
1373 cs.setThreshold(groups[i].getPidThreshold(), true);
1377 Vector seqs = new Vector();
1379 for (int s = 0; s < groups[i].getSeqCount(); s++)
1381 String seqId = groups[i].getSeq(s) + "";
1382 jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI)
1383 seqRefIds.get(seqId);
1387 seqs.addElement(ts);
1391 if (seqs.size() < 1)
1396 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.
1398 groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1399 groups[i].getDisplayText(), groups[i].getColourText(),
1400 groups[i].getStart(), groups[i].getEnd());
1402 sg.setOutlineColour(new java.awt.Color(
1403 groups[i].getOutlineColour()));
1405 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
1406 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
1407 sg.thresholdTextColour = groups[i].getTextColThreshold();
1409 if (groups[i].getConsThreshold() != 0)
1411 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
1413 ResidueProperties.propHash, 3, sg.getSequences(null), 0,
1416 c.verdict(false, 25);
1417 sg.cs.setConservation(c);
1424 /////////////////////////////////
1427 AlignFrame af = new AlignFrame(al,
1431 af.setFileName(file, "Jalview");
1433 for (int i = 0; i < JSEQ.length; i++)
1435 af.viewport.setSequenceColour(
1436 af.viewport.alignment.getSequenceAt(i),
1438 JSEQ[i].getColour()));
1441 //If we just load in the same jar file again, the sequenceSetId
1442 //will be the same, and we end up with multiple references
1443 //to the same sequenceSet. We must modify this id on load
1444 //so that each load of the file gives a unique id
1445 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
1447 af.viewport.gatherViewsHere = view.getGatheredViews();
1449 if (view.getSequenceSetId() != null)
1451 jalview.gui.AlignViewport av =
1452 (jalview.gui.AlignViewport)
1453 viewportsAdded.get(uniqueSeqSetId);
1455 af.viewport.sequenceSetID = uniqueSeqSetId;
1459 af.viewport.historyList = av.historyList;
1460 af.viewport.redoList = av.redoList;
1464 viewportsAdded.put(uniqueSeqSetId, af.viewport);
1467 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1469 if (hiddenSeqs != null)
1471 for (int s = 0; s < JSEQ.length; s++)
1473 jalview.datamodel.SequenceGroup hidden =
1474 new jalview.datamodel.SequenceGroup();
1476 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
1479 al.getSequenceAt(JSEQ[s].getHiddenSequences(r))
1483 af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
1486 jalview.datamodel.SequenceI[] hseqs = new
1487 jalview.datamodel.SequenceI[hiddenSeqs.size()];
1489 for (int s = 0; s < hiddenSeqs.size(); s++)
1491 hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
1494 af.viewport.hideSequence(hseqs);
1498 if ( (hideConsensus || hideQuality || hideConservation)
1499 && al.getAlignmentAnnotation() != null)
1501 int hSize = al.getAlignmentAnnotation().length;
1502 for (int h = 0; h < hSize; h++)
1506 al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1509 al.getAlignmentAnnotation()[h].label.equals("Quality"))
1511 (hideConservation &&
1512 al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1514 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1519 af.alignPanel.adjustAnnotationHeight();
1522 if (view.getViewName() != null)
1524 af.viewport.viewName = view.getViewName();
1525 af.setInitialTabVisible();
1527 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1530 af.viewport.setShowAnnotation(view.getShowAnnotation());
1531 af.viewport.setAbovePIDThreshold(view.getPidSelected());
1533 af.viewport.setColourText(view.getShowColourText());
1535 af.viewport.setConservationSelected(view.getConservationSelected());
1536 af.viewport.setShowJVSuffix(view.getShowFullId());
1537 af.viewport.rightAlignIds = view.getRightAlignIds();
1538 af.viewport.setFont(new java.awt.Font(view.getFontName(),
1539 view.getFontStyle(), view.getFontSize()));
1540 af.alignPanel.fontChanged();
1541 af.viewport.setRenderGaps(view.getRenderGaps());
1542 af.viewport.setWrapAlignment(view.getWrapAlignment());
1543 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1544 af.viewport.setShowAnnotation(view.getShowAnnotation());
1545 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1547 af.viewport.setShowBoxes(view.getShowBoxes());
1549 af.viewport.setShowText(view.getShowText());
1551 af.viewport.textColour = new java.awt.Color(view.getTextCol1());
1552 af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
1553 af.viewport.thresholdTextColour = view.getTextColThreshold();
1555 af.viewport.setStartRes(view.getStartRes());
1556 af.viewport.setStartSeq(view.getStartSeq());
1558 ColourSchemeI cs = null;
1560 if (view.getBgColour() != null)
1562 if (view.getBgColour().startsWith("ucs"))
1564 cs = GetUserColourScheme(jms, view.getBgColour());
1566 else if (view.getBgColour().startsWith("Annotation"))
1568 //int find annotation
1570 i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1572 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1573 equals(view.getAnnotationColours().getAnnotation()))
1575 if (af.viewport.alignment.getAlignmentAnnotation()[i].
1576 getThreshold() == null)
1578 af.viewport.alignment.getAlignmentAnnotation()[i].
1580 new jalview.datamodel.GraphLine(
1581 view.getAnnotationColours().getThreshold(),
1582 "Threshold", java.awt.Color.black)
1587 if (view.getAnnotationColours().getColourScheme().equals(
1590 cs = new AnnotationColourGradient(
1591 af.viewport.alignment.getAlignmentAnnotation()[i],
1592 new java.awt.Color(view.getAnnotationColours().
1594 new java.awt.Color(view.getAnnotationColours().
1596 view.getAnnotationColours().getAboveThreshold());
1598 else if (view.getAnnotationColours().getColourScheme().
1601 cs = new AnnotationColourGradient(
1602 af.viewport.alignment.getAlignmentAnnotation()[i],
1603 GetUserColourScheme(jms, view.getAnnotationColours().
1605 view.getAnnotationColours().getAboveThreshold()
1610 cs = new AnnotationColourGradient(
1611 af.viewport.alignment.getAlignmentAnnotation()[i],
1612 ColourSchemeProperty.getColour(al,
1613 view.getAnnotationColours().
1615 view.getAnnotationColours().getAboveThreshold()
1619 // Also use these settings for all the groups
1620 if (al.getGroups() != null)
1622 for (int g = 0; g < al.getGroups().size(); g++)
1624 jalview.datamodel.SequenceGroup sg
1625 = (jalview.datamodel.SequenceGroup) al.getGroups().
1633 /* if (view.getAnnotationColours().getColourScheme().equals("None"))
1635 sg.cs = new AnnotationColourGradient(
1636 af.viewport.alignment.getAlignmentAnnotation()[i],
1637 new java.awt.Color(view.getAnnotationColours().
1639 new java.awt.Color(view.getAnnotationColours().
1641 view.getAnnotationColours().getAboveThreshold());
1645 sg.cs = new AnnotationColourGradient(
1646 af.viewport.alignment.getAlignmentAnnotation()[i],
1648 view.getAnnotationColours().getAboveThreshold()
1662 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1667 cs.setThreshold(view.getPidThreshold(), true);
1668 cs.setConsensus(af.viewport.hconsensus);
1672 af.viewport.setGlobalColourScheme(cs);
1673 af.viewport.setColourAppliesToAllGroups(false);
1675 if (view.getConservationSelected() && cs != null)
1677 cs.setConservationInc(view.getConsThreshold());
1680 af.changeColour(cs);
1682 af.viewport.setColourAppliesToAllGroups(true);
1684 if (view.getShowSequenceFeatures())
1686 af.viewport.showSequenceFeatures = true;
1689 if (jms.getFeatureSettings() != null)
1691 af.viewport.featuresDisplayed = new Hashtable();
1692 String[] renderOrder = new String[jms.getFeatureSettings().
1694 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
1696 Setting setting = jms.getFeatureSettings().getSetting(fs);
1698 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.
1700 new java.awt.Color(setting.getColour()));
1702 renderOrder[fs] = setting.getType();
1704 if (setting.getDisplay())
1706 af.viewport.featuresDisplayed.put(
1707 setting.getType(), new Integer(setting.getColour()));
1710 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder =
1714 if (view.getHiddenColumnsCount() > 0)
1716 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1718 af.viewport.hideColumns(
1719 view.getHiddenColumns(c).getStart(),
1720 view.getHiddenColumns(c).getEnd() //+1
1725 af.setMenusFromViewport(af.viewport);
1727 Desktop.addInternalFrame(af, view.getTitle(),
1728 view.getWidth(), view.getHeight());
1731 ///////////////////////////////////////
1732 if (loadTreesAndStructures && jms.getTreeCount() > 0)
1736 for (int t = 0; t < jms.getTreeCount(); t++)
1739 Tree tree = jms.getTree(t);
1741 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1742 tree.getNewick()), tree.getTitle(),
1743 tree.getWidth(), tree.getHeight(),
1744 tree.getXpos(), tree.getYpos());
1746 tp.fitToWindow.setState(tree.getFitToWindow());
1747 tp.fitToWindow_actionPerformed(null);
1749 if (tree.getFontName() != null)
1751 tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1752 tree.getFontStyle(),
1753 tree.getFontSize()));
1757 tp.setTreeFont(new java.awt.Font(view.getFontName(),
1758 view.getFontStyle(),
1759 tree.getFontSize()));
1762 tp.showPlaceholders(tree.getMarkUnlinked());
1763 tp.showBootstrap(tree.getShowBootstrap());
1764 tp.showDistances(tree.getShowDistances());
1766 tp.treeCanvas.threshold = tree.getThreshold();
1768 if (tree.getCurrentTree())
1770 af.viewport.setCurrentTree(tp.getTree());
1775 catch (Exception ex)
1777 ex.printStackTrace();
1782 if(loadTreesAndStructures)
1784 for (int i = 0; i < JSEQ.length; i++)
1786 if (JSEQ[i].getPdbidsCount() > 0)
1788 Pdbids[] ids = JSEQ[i].getPdbids();
1789 for (int p = 0; p < ids.length; p++)
1791 for (int s = 0; s < ids[p].getStructureStateCount(); s++)
1793 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
1795 jpdb.setFile(loadPDBFile(ids[p].getFile(), ids[p].getId()));
1796 jpdb.setId(ids[p].getId());
1798 int x = ids[p].getStructureState(s).getXpos();
1799 int y = ids[p].getStructureState(s).getYpos();
1800 int width = ids[p].getStructureState(s).getWidth();
1801 int height = ids[p].getStructureState(s).getHeight();
1803 java.awt.Component comp = Desktop.desktop.getComponentAt(x, y);
1805 String pdbFile = loadPDBFile(file, ids[p].getId());
1807 jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
1809 al.getSequenceAt(i)};
1812 (comp.getWidth() != width && comp.getHeight() != height))
1814 String state = ids[p].getStructureState(s).getContent();
1816 StringBuffer newFileLoc = new StringBuffer(state.substring(0,
1817 state.indexOf("\"", state.indexOf("load")) + 1));
1819 newFileLoc.append(jpdb.getFile());
1820 newFileLoc.append(state.substring(
1821 state.indexOf("\"", state.indexOf("load \"") + 6)));
1823 new AppJMol(pdbFile,
1827 newFileLoc.toString(),
1828 new java.awt.Rectangle(x, y, width, height));
1833 StructureSelectionManager.getStructureSelectionManager()
1834 .setMapping(seq, pdbFile,
1835 jalview.io.AppletFormatAdapter.FILE);
1837 ( (AppJMol) comp).addSequence(seq);
1848 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
1849 boolean keepSeqRefs)
1851 jalview.schemabinding.version2.JalviewModel jm
1852 = SaveState(ap, null, null, null);
1857 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
1861 uniqueSetSuffix = "";
1864 viewportsAdded = new Hashtable();
1866 AlignFrame af = LoadFromObject(jm, null, false);
1867 af.alignPanels.clear();
1868 af.closeMenuItem_actionPerformed(true);
1870 /* if(ap.av.alignment.getAlignmentAnnotation()!=null)
1872 for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length; i++)
1874 if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated)
1876 af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
1877 ap.av.alignment.getAlignmentAnnotation()[i];
1882 return af.alignPanel;