2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2006 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
22 import jalview.schemes.*;
32 import java.util.jar.*;
36 import org.exolab.castor.xml.*;
38 import jalview.schemabinding.version2.*;
49 public class Jalview2XML
55 * This maintains a list of viewports, the key being the
56 * seqSetId. Important to set historyItem and redoList
59 Hashtable viewportsAdded;
61 String uniqueSetSuffix = "";
64 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
65 public void SaveState(File statefile)
67 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
76 FileOutputStream fos = new FileOutputStream(statefile);
77 JarOutputStream jout = new JarOutputStream(fos);
79 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
80 ////////////////////////////////////////////////////
81 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
84 Vector shortNames = new Vector();
87 for (int i = frames.length - 1; i > -1; i--)
89 if (frames[i] instanceof AlignFrame)
91 AlignFrame af = (AlignFrame) frames[i];
93 String shortName = af.getTitle();
95 if (shortName.indexOf(File.separatorChar) > -1)
97 shortName = shortName.substring(shortName.lastIndexOf(
98 File.separatorChar) + 1);
103 while (shortNames.contains(shortName))
105 if (shortName.endsWith("_" + (count - 1)))
107 shortName = shortName.substring(0,
108 shortName.lastIndexOf("_"));
111 shortName = shortName.concat("_" + count);
115 shortNames.addElement(shortName);
117 if (!shortName.endsWith(".xml"))
119 shortName = shortName + ".xml";
122 int ap, apSize= af.alignPanels.size();
123 for (ap = 0; ap < apSize; ap++)
125 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.
129 apSize == 1 ? shortName : ap+shortName,
140 ex.printStackTrace();
144 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
145 public void SaveAlignment(AlignFrame af, String jarFile,
150 int ap, apSize= af.alignPanels.size();
151 FileOutputStream fos = new FileOutputStream(jarFile);
152 JarOutputStream jout = new JarOutputStream(fos);
153 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
155 for( ap=0; ap<apSize; ap++)
157 AlignmentPanel apanel = (AlignmentPanel)af.alignPanels.elementAt(ap);
160 apSize==1?fileName:fileName+ap,
169 ex.printStackTrace();
176 * @param af DOCUMENT ME!
177 * @param timeStamp DOCUMENT ME!
178 * @param fileName DOCUMENT ME!
179 * @param jout DOCUMENT ME!
180 * @param out DOCUMENT ME!
182 public JalviewModel SaveState(AlignmentPanel ap,
184 JarOutputStream jout,
187 if (seqRefIds == null)
188 seqRefIds = new Hashtable();
190 Vector userColours = new Vector();
192 AlignViewport av = ap.av;
194 JalviewModel object = new JalviewModel();
195 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
197 object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
198 object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
200 jalview.datamodel.AlignmentI jal = av.alignment;
204 jal = jal.getHiddenSequences().getFullAlignment();
207 SequenceSet vamsasSet = new SequenceSet();
209 JalviewModelSequence jms = new JalviewModelSequence();
211 vamsasSet.setGapChar(jal.getGapCharacter() + "");
214 Vector pdbfiles = null;
218 jalview.datamodel.SequenceI jds;
219 for (int i = 0; i < jal.getHeight(); i++)
221 jds = jal.getSequenceAt(i);
224 if(seqRefIds.get(id+"")!=null)
230 vamsasSeq = new Sequence();
231 vamsasSeq.setId(id + "");
232 vamsasSeq.setName(jds.getName());
233 vamsasSeq.setSequence(jds.getSequence());
234 vamsasSeq.setDescription(jds.getDescription());
236 if (jds.getDatasetSequence().getDBRef() != null)
238 jalview.datamodel.DBRefEntry[] dbrefs =
239 jds.getDatasetSequence().getDBRef();
241 for (int d = 0; d < dbrefs.length; d++)
243 DBRef dbref = new DBRef();
244 dbref.setSource(dbrefs[d].getSource());
245 dbref.setVersion(dbrefs[d].getVersion());
246 dbref.setAccessionId(dbrefs[d].getAccessionId());
247 vamsasSeq.addDBRef(dbref);
251 vamsasSet.addSequence(vamsasSeq);
252 seqRefIds.put(id+"", jal.getSequenceAt(i));
256 jseq.setStart(jds.getStart());
257 jseq.setEnd(jds.getEnd());
258 jseq.setColour( av.getSequenceColour(jds).getRGB());
262 if (av.hasHiddenRows)
264 jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
266 if(jal.getSequenceAt(i).getHiddenSequences()!=null)
268 jalview.datamodel.SequenceI [] reps =
269 jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal);
271 for(int h=0; h<reps.length; h++)
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());
338 if(entry.getFile()!=null)
341 pdbfiles = new Vector();
344 if(!pdbfiles.contains(entry.getId()))
346 pdbfiles.addElement(entry.getId());
349 File file = new File(entry.getFile());
352 byte[] data = new byte[ (int) file.length()];
353 jout.putNextEntry(new JarEntry(entry.getId()));
354 DataInputStream dis = new DataInputStream(new
355 FileInputStream(file));
358 DataOutputStream dout = new DataOutputStream(jout);
359 dout.write(data, 0, data.length);
365 ex.printStackTrace();
371 if(entry.getProperty()!=null)
373 PdbentryItem item = new PdbentryItem();
374 Hashtable properties = entry.getProperty();
375 Enumeration en2 = properties.keys();
376 while(en2.hasMoreElements())
378 Property prop = new Property();
379 String key = en2.nextElement().toString();
381 prop.setValue( properties.get(key).toString() );
382 item.addProperty(prop);
384 pdb.addPdbentryItem(item);
399 ///////////////////////////////////
400 if (av.currentTree != null)
402 // FIND ANY ASSOCIATED TREES
403 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
404 if (Desktop.desktop != null)
406 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
408 for (int t = 0; t < frames.length; t++)
410 if (frames[t] instanceof TreePanel)
412 TreePanel tp = (TreePanel) frames[t];
414 if (tp.treeCanvas.av.alignment == jal)
416 Tree tree = new Tree();
417 tree.setTitle(tp.getTitle());
418 tree.setCurrentTree( (av.currentTree == tp.getTree()));
419 tree.setNewick(tp.getTree().toString());
420 tree.setThreshold(tp.treeCanvas.threshold);
422 tree.setFitToWindow(tp.fitToWindow.getState());
423 tree.setFontName(tp.getTreeFont().getName());
424 tree.setFontSize(tp.getTreeFont().getSize());
425 tree.setFontStyle(tp.getTreeFont().getStyle());
426 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
428 tree.setShowBootstrap(tp.bootstrapMenu.getState());
429 tree.setShowDistances(tp.distanceMenu.getState());
431 tree.setHeight(tp.getHeight());
432 tree.setWidth(tp.getWidth());
433 tree.setXpos(tp.getX());
434 tree.setYpos(tp.getY());
444 if (jal.getAlignmentAnnotation() != null)
446 jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
448 for (int i = 0; i < aa.length; i++)
450 Annotation an = new Annotation();
452 if (aa[i].label.equals("Quality") ||
453 aa[i].label.equals("Conservation") ||
454 aa[i].label.equals("Consensus"))
456 an.setLabel(aa[i].label);
458 vamsasSet.addAnnotation(an);
463 an.setDescription(aa[i].description);
465 if(aa[i].sequenceRef!=null)
467 an.setSequenceRef(aa[i].sequenceRef.getName());
473 an.setGraphType(aa[i].graph);
474 an.setGraphGroup(aa[i].graphGroup);
475 if(aa[i].getThreshold()!=null)
477 ThresholdLine line = new ThresholdLine();
478 line.setLabel(aa[i].getThreshold().label);
479 line.setValue(aa[i].getThreshold().value);
480 line.setColour(aa[i].getThreshold().colour.getRGB());
481 an.setThresholdLine(line);
487 an.setLabel(aa[i].label);
489 AnnotationElement ae;
491 for (int a = 0; a < aa[i].annotations.length; a++)
493 if ((aa[i] == null) || (aa[i].annotations[a] == null))
498 ae = new AnnotationElement();
499 ae.setDescription(aa[i].annotations[a].description);
500 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
501 ae.setValue(aa[i].annotations[a].value);
503 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
506 if(aa[i].annotations[a].colour!=java.awt.Color.black)
507 ae.setColour(aa[i].annotations[a].colour.getRGB());
509 an.addAnnotationElement(ae);
512 vamsasSet.addAnnotation(an);
517 if (jal.getGroups() != null)
519 JGroup[] groups = new JGroup[jal.getGroups().size()];
521 for (int i = 0; i < groups.length; i++)
523 groups[i] = new JGroup();
525 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
527 groups[i].setStart(sg.getStartRes());
528 groups[i].setEnd(sg.getEndRes());
529 groups[i].setName(sg.getName());
532 if (sg.cs.conservationApplied())
534 groups[i].setConsThreshold(sg.cs.getConservationInc());
536 if (sg.cs instanceof jalview.schemes.UserColourScheme)
538 groups[i].setColour(SetUserColourScheme(sg.cs,
544 groups[i].setColour(ColourSchemeProperty.getColourName(sg.
548 else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)
551 ColourSchemeProperty.getColourName(
552 ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));
554 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
556 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
561 groups[i].setColour(ColourSchemeProperty.getColourName(
565 groups[i].setPidThreshold(sg.cs.getThreshold());
568 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
569 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
570 groups[i].setDisplayText(sg.getDisplayText());
571 groups[i].setColourText(sg.getColourText());
572 groups[i].setTextCol1(sg.textColour.getRGB());
573 groups[i].setTextCol2(sg.textColour2.getRGB());
574 groups[i].setTextColThreshold(sg.thresholdTextColour);
576 for (int s = 0; s < sg.getSize(false); s++)
578 jalview.datamodel.Sequence seq =
579 (jalview.datamodel.Sequence) sg.getSequenceAt(s);
580 groups[i].addSeq(seq.hashCode());
584 jms.setJGroup(groups);
588 ///////////SAVE VIEWPORT
589 Viewport view = new Viewport();
590 view.setTitle(ap.alignFrame.getTitle());
591 view.setSequenceSetId(av.getSequenceSetId());
592 view.setViewName(av.viewName);
593 view.setGatheredViews(av.gatherViewsHere);
596 if (ap.av.explodedPosition != null)
598 view.setXpos(av.explodedPosition.x);
599 view.setYpos(av.explodedPosition.y);
600 view.setWidth(av.explodedPosition.width);
601 view.setHeight(av.explodedPosition.height);
605 view.setXpos(ap.alignFrame.getBounds().x);
606 view.setYpos(ap.alignFrame.getBounds().y);
607 view.setWidth(ap.alignFrame.getBounds().width);
608 view.setHeight(ap.alignFrame.getBounds().height);
611 view.setStartRes(av.startRes);
612 view.setStartSeq(av.startSeq);
614 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
616 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
619 else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
621 jalview.schemes.AnnotationColourGradient acg
622 = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();
624 AnnotationColours ac = new AnnotationColours();
625 ac.setAboveThreshold(acg.getAboveThreshold());
626 ac.setThreshold(acg.getAnnotationThreshold());
627 ac.setAnnotation(acg.getAnnotation());
628 if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
629 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
632 ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
634 ac.setMaxColour(acg.getMaxColour().getRGB());
635 ac.setMinColour(acg.getMinColour().getRGB());
636 view.setAnnotationColours(ac);
637 view.setBgColour("AnnotationColourGradient");
641 view.setBgColour(ColourSchemeProperty.getColourName(
642 av.getGlobalColourScheme()));
645 ColourSchemeI cs = av.getGlobalColourScheme();
649 if (cs.conservationApplied())
651 view.setConsThreshold(cs.getConservationInc());
652 if (cs instanceof jalview.schemes.UserColourScheme)
653 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
656 if (cs instanceof ResidueColourScheme)
658 view.setPidThreshold(cs.getThreshold());
662 view.setConservationSelected(av.getConservationSelected());
663 view.setPidSelected(av.getAbovePIDThreshold());
664 view.setFontName(av.font.getName());
665 view.setFontSize(av.font.getSize());
666 view.setFontStyle(av.font.getStyle());
667 view.setRenderGaps(av.renderGaps);
668 view.setShowAnnotation(av.getShowAnnotation());
669 view.setShowBoxes(av.getShowBoxes());
670 view.setShowColourText(av.getColourText());
671 view.setShowFullId(av.getShowJVSuffix());
672 view.setRightAlignIds(av.rightAlignIds);
673 view.setShowSequenceFeatures(av.showSequenceFeatures);
674 view.setShowText(av.getShowText());
675 view.setWrapAlignment(av.getWrapAlignment());
676 view.setTextCol1(av.textColour.getRGB());
677 view.setTextCol2(av.textColour2.getRGB());
678 view.setTextColThreshold(av.thresholdTextColour);
681 if(av.featuresDisplayed!=null)
683 jalview.schemabinding.version2.FeatureSettings fs
684 = new jalview.schemabinding.version2.FeatureSettings();
686 String [] renderOrder =
687 ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
689 Vector settingsAdded = new Vector();
690 for(int ro=0; ro<renderOrder.length; ro++)
692 Setting setting = new Setting();
693 setting.setType(renderOrder[ro]);
695 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
699 av.featuresDisplayed.containsKey(renderOrder[ro])
702 fs.addSetting(setting);
703 settingsAdded.addElement(renderOrder[ro]);
706 //Make sure we save none displayed feature settings
708 ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
709 while(en.hasMoreElements())
711 String key = en.nextElement().toString();
712 if(settingsAdded.contains(key))
715 Setting setting = new Setting();
716 setting.setType(key);
718 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
721 setting.setDisplay(false);
723 fs.addSetting(setting);
724 settingsAdded.addElement(key);
727 jms.setFeatureSettings(fs);
731 if(av.hasHiddenColumns)
733 for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)
735 int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);
736 HiddenColumns hc = new HiddenColumns();
737 hc.setStart(region[0]);
738 hc.setEnd(region[1]);
739 view.addHiddenColumns(hc);
743 jms.addViewport(view);
746 object.setJalviewModelSequence(jms);
747 object.getVamsasModel().addSequenceSet(vamsasSet);
751 //We may not want to right the object to disk,
752 //eg we can copy the alignViewport to a new view object
753 //using save and then load
756 if (!fileName.endsWith(".xml"))
758 fileName = fileName + ".xml";
761 JarEntry entry = new JarEntry(fileName);
762 jout.putNextEntry(entry);
768 ex.printStackTrace();
774 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
775 Vector userColours, JalviewModelSequence jms)
778 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
780 if (!userColours.contains(ucs))
782 userColours.add(ucs);
784 java.awt.Color[] colours = ucs.getColours();
785 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
786 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
788 for (int i = 0; i < colours.length; i++)
790 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
791 col.setName(ResidueProperties.aa[i]);
792 col.setRGB(jalview.util.Format.getHexString(colours[i]));
793 jbucs.addColour(col);
795 if(ucs.getLowerCaseColours()!=null)
797 colours = ucs.getLowerCaseColours();
798 for (int i = 0; i < colours.length; i++)
800 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
801 col.setName(ResidueProperties.aa[i].toLowerCase());
802 col.setRGB(jalview.util.Format.getHexString(colours[i]));
803 jbucs.addColour(col);
807 id = "ucs" + userColours.indexOf(ucs);
809 uc.setUserColourScheme(jbucs);
810 jms.addUserColours(uc);
816 jalview.schemes.UserColourScheme GetUserColourScheme(
817 JalviewModelSequence jms, String id)
819 UserColours[] uc = jms.getUserColours();
820 UserColours colours = null;
822 for (int i = 0; i < uc.length; i++)
824 if (uc[i].getId().equals(id))
832 java.awt.Color[] newColours = new java.awt.Color[24];
834 for (int i = 0; i < 24; i++)
836 newColours[i] = new java.awt.Color(Integer.parseInt(
837 colours.getUserColourScheme().getColour(i).getRGB(), 16));
840 jalview.schemes.UserColourScheme ucs =
841 new jalview.schemes.UserColourScheme(newColours);
843 if (colours.getUserColourScheme().getColourCount() > 24)
845 newColours = new java.awt.Color[23];
846 for (int i = 0; i < 23; i++)
848 newColours[i] = new java.awt.Color(Integer.parseInt(
849 colours.getUserColourScheme().getColour(i+24).getRGB(), 16));
851 ucs.setLowerCaseColours(newColours);
861 * @param file DOCUMENT ME!
863 public AlignFrame LoadJalviewAlign(final String file)
865 uniqueSetSuffix = System.currentTimeMillis()%100000 +"";
867 jalview.gui.AlignFrame af = null;
869 seqRefIds = new Hashtable();
870 viewportsAdded = new Hashtable();
872 Vector gatherToThisFrame= new Vector();
876 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
879 if (file.startsWith("http://"))
884 JarInputStream jin = null;
885 JarEntry jarentry = null;
892 jin = new JarInputStream(url.openStream());
896 jin = new JarInputStream(new FileInputStream(file));
899 for (int i = 0; i < entryCount; i++)
901 jarentry = jin.getNextJarEntry();
904 if (jarentry != null && jarentry.getName().endsWith(".xml"))
906 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
907 JalviewModel object = new JalviewModel();
909 Unmarshaller unmar = new Unmarshaller(object);
910 unmar.setValidation(false);
911 object = (JalviewModel) unmar.unmarshal( in );
913 af = LoadFromObject(object, file, true);
914 if(af.viewport.gatherViewsHere)
916 gatherToThisFrame.add(af);
920 else if (jarentry != null)
922 //Some other file here.
926 while (jarentry != null);
928 catch(java.net.UnknownHostException ex)
930 ex.printStackTrace();
931 System.err.println("Couldn't locate Jalview XML file : " +
934 javax.swing.SwingUtilities.invokeLater(new Runnable()
938 JOptionPane.showInternalMessageDialog(Desktop.desktop,
939 "Couldn't locate " + file,
941 JOptionPane.WARNING_MESSAGE);
947 //Is Version 1 Jar file?
948 af = new Jalview2XML_V1().LoadJalviewAlign(file);
952 System.out.println("Successfully loaded archive file");
956 System.err.println("Exception whilst loading jalview XML file : " +
958 javax.swing.SwingUtilities.invokeLater(new Runnable()
963 JOptionPane.showInternalMessageDialog(Desktop.desktop,
964 "Error loading " + file,
965 "Error loading Jalview file",
966 JOptionPane.WARNING_MESSAGE);
970 if (Desktop.instance != null)
971 Desktop.instance.stopLoading();
973 for (int i = 0; i < gatherToThisFrame.size(); i++)
975 Desktop.instance.gatherViews(
976 (AlignFrame) gatherToThisFrame.elementAt(i));
982 String loadPDBFile(String file, String pdbId)
986 JarInputStream jin = null;
988 if (file.startsWith("http://"))
990 jin = new JarInputStream(new URL(file).openStream());
994 jin = new JarInputStream(new FileInputStream(file));
997 JarEntry entry = null;
1000 entry = jin.getNextJarEntry();
1002 while (!entry.getName().equals(pdbId));
1004 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1005 File outFile = File.createTempFile("jalview_pdb", ".txt");
1006 outFile.deleteOnExit();
1007 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1010 while ( (data = in.readLine()) != null)
1015 return outFile.getAbsolutePath();
1018 catch (Exception ex)
1020 ex.printStackTrace();
1027 AlignFrame LoadFromObject(JalviewModel object,
1031 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1032 Sequence[] vamsasSeq = vamsasSet.getSequence();
1034 JalviewModelSequence jms = object.getJalviewModelSequence();
1036 Viewport view = jms.getViewport(0);
1038 //////////////////////////////////
1041 Vector hiddenSeqs = null;
1042 jalview.datamodel.Sequence jseq;
1044 ArrayList tmpseqs = new ArrayList();
1046 boolean multipleView = false;
1048 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1049 for (int i = 0; i < JSEQ.length; i++)
1051 String seqId = JSEQ[i].getId() + "";
1053 if (seqRefIds.get(seqId) != null)
1055 tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1056 multipleView = true;
1060 jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
1061 vamsasSeq[i].getSequence());
1062 jseq.setDescription(vamsasSeq[i].getDescription());
1063 jseq.setStart(JSEQ[i].getStart());
1064 jseq.setEnd(JSEQ[i].getEnd());
1065 seqRefIds.put(vamsasSeq[i].getId(), jseq);
1066 tmpseqs.add( jseq );
1071 if (JSEQ[i].getHidden())
1073 if (hiddenSeqs == null)
1074 hiddenSeqs = new Vector();
1077 hiddenSeqs.addElement(
1078 (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1083 ///SequenceFeatures are added to the DatasetSequence,
1084 // so we must create the dataset before loading features
1085 /////////////////////////////////
1088 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
1091 tmpseqs.toArray(orderedSeqs) ;
1094 jalview.datamodel.Alignment al =
1095 new jalview.datamodel.Alignment(orderedSeqs);
1097 al.setDataset(null);
1098 /////////////////////////////////
1101 Hashtable pdbloaded = new Hashtable();
1104 for (int i = 0; i < vamsasSeq.length; i++)
1106 if (JSEQ[i].getFeaturesCount() > 0)
1108 Features[] features = JSEQ[i].getFeatures();
1109 for (int f = 0; f < features.length; f++)
1111 jalview.datamodel.SequenceFeature sf
1112 = new jalview.datamodel.SequenceFeature(features[f].getType(),
1113 features[f].getDescription(), features[f].getStatus(),
1114 features[f].getBegin(), features[f].getEnd(),
1115 features[f].getFeatureGroup());
1117 sf.setScore(features[f].getScore());
1118 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1120 OtherData keyValue = features[f].getOtherData(od);
1121 if (keyValue.getKey().startsWith("LINK"))
1122 sf.addLink(keyValue.getValue());
1124 sf.setValue(keyValue.getKey(), keyValue.getValue());
1128 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1131 if (JSEQ[i].getPdbidsCount() > 0)
1133 Pdbids[] ids = JSEQ[i].getPdbids();
1134 for (int p = 0; p < ids.length; p++)
1136 jalview.datamodel.PDBEntry entry = new jalview.datamodel.
1138 entry.setId(ids[p].getId());
1139 entry.setType(ids[p].getType());
1140 if (ids[p].getFile() != null)
1142 if (!pdbloaded.containsKey(ids[p].getFile()))
1144 String tmppdb = loadPDBFile(file, ids[p].getId());
1145 entry.setFile(tmppdb);
1146 pdbloaded.put(ids[p].getId(), tmppdb);
1149 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1152 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1155 if (vamsasSeq[i].getDBRefCount() > 0)
1157 for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
1159 jalview.datamodel.DBRefEntry entry =
1160 new jalview.datamodel.DBRefEntry(
1161 vamsasSeq[i].getDBRef(d).getSource(),
1162 vamsasSeq[i].getDBRef(d).getVersion(),
1163 vamsasSeq[i].getDBRef(d).getAccessionId()
1165 al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1173 /////////////////////////////////
1174 //////////////////////////////////
1176 boolean hideQuality = true,
1177 hideConservation = true,
1178 hideConsensus = true;
1180 if (vamsasSet.getAnnotationCount()>0)
1182 Annotation[] an = vamsasSet.getAnnotation();
1184 for (int i = 0; i < an.length; i++)
1186 if (an[i].getLabel().equals("Quality"))
1188 hideQuality = false;
1191 else if(an[i].getLabel().equals("Conservation"))
1193 hideConservation = false;
1196 else if(an[i].getLabel().equals("Consensus"))
1198 hideConsensus = false;
1202 AnnotationElement[] ae = an[i].getAnnotationElement();
1203 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
1205 for (int aa = 0; aa < ae.length; aa++)
1207 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
1208 ae[aa].getDescription(),
1209 ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
1211 anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
1214 jalview.datamodel.AlignmentAnnotation jaa = null;
1216 if (an[i].getGraph())
1218 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1219 an[i].getDescription(), anot, 0, 0,
1220 an[i].getGraphType());
1222 jaa.graphGroup = an[i].getGraphGroup();
1224 if (an[i].getThresholdLine() != null)
1226 jaa.setThreshold(new jalview.datamodel.GraphLine(
1227 an[i].getThresholdLine().getValue(),
1228 an[i].getThresholdLine().getLabel(),
1229 new java.awt.Color(an[i].getThresholdLine().getColour()))
1237 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1238 an[i].getDescription(), anot);
1241 if(an[i].getSequenceRef()!=null)
1243 jaa.createSequenceMapping(
1244 al.findName(an[i].getSequenceRef()), 1, true
1246 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1249 al.addAnnotation(jaa);
1253 /////////////////////////
1255 if (jms.getJGroupCount() > 0)
1257 JGroup[] groups = jms.getJGroup();
1259 for (int i = 0; i < groups.length; i++)
1261 ColourSchemeI cs = null;
1263 if (groups[i].getColour() != null)
1265 if (groups[i].getColour().startsWith("ucs"))
1267 cs = GetUserColourScheme(jms, groups[i].getColour());
1271 cs = ColourSchemeProperty.getColour(al,
1272 groups[i].getColour());
1276 cs.setThreshold(groups[i].getPidThreshold(), true);
1279 Vector seqs = new Vector();
1281 for (int s = 0; s < groups[i].getSeqCount(); s++)
1283 String seqId = groups[i].getSeq(s)+"";
1284 seqs.addElement((jalview.datamodel.SequenceI) seqRefIds.get(seqId));
1287 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
1288 groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1289 groups[i].getDisplayText(), groups[i].getColourText(),
1290 groups[i].getStart(), groups[i].getEnd());
1292 sg.setOutlineColour(new java.awt.Color(
1293 groups[i].getOutlineColour()));
1295 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
1296 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
1297 sg.thresholdTextColour = groups[i].getTextColThreshold();
1299 if (groups[i].getConsThreshold() != 0)
1301 jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
1302 ResidueProperties.propHash, 3, sg.getSequences(false), 0,
1305 c.verdict(false, 25);
1306 sg.cs.setConservation(c);
1314 /////////////////////////////////
1317 AlignFrame af = new AlignFrame(al,
1321 af.setFileName(file, "Jalview");
1323 for (int i = 0; i < JSEQ.length; i++)
1325 af.viewport.setSequenceColour(
1326 af.viewport.alignment.getSequenceAt(i),
1328 JSEQ[i].getColour()));
1331 //If we just load in the same jar file again, the sequenceSetId
1332 //will be the same, and we end up with multiple references
1333 //to the same sequenceSet. We must modify this id on load
1334 //so that each load of the file gives a unique id
1335 String uniqueSeqSetId = view.getSequenceSetId()+uniqueSetSuffix;
1337 af.viewport.gatherViewsHere = view.getGatheredViews();
1339 if (view.getSequenceSetId() != null)
1341 jalview.gui.AlignViewport av =
1342 (jalview.gui.AlignViewport)
1343 viewportsAdded.get(uniqueSeqSetId);
1345 af.viewport.sequenceSetID = uniqueSeqSetId;
1349 af.viewport.historyList = av.historyList;
1350 af.viewport.redoList = av.redoList;
1354 viewportsAdded.put(uniqueSeqSetId, af.viewport);
1357 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1359 if(hiddenSeqs!=null)
1361 for(int s=0; s<JSEQ.length; s++)
1363 for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
1365 al.getSequenceAt(s).addHiddenSequence(
1366 al.getSequenceAt( JSEQ[s].getHiddenSequences(r) )
1371 jalview.datamodel.SequenceI [] hseqs = new
1372 jalview.datamodel.SequenceI[hiddenSeqs.size()];
1374 for(int s=0; s<hiddenSeqs.size(); s++)
1375 hseqs[s] = (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s);
1377 af.viewport.hideSequence( hseqs );
1382 if((hideConsensus || hideQuality || hideConservation)
1383 && al.getAlignmentAnnotation()!=null)
1385 int hSize = al.getAlignmentAnnotation().length;
1386 for (int h = 0; h < hSize; h++)
1390 al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1393 al.getAlignmentAnnotation()[h].label.equals("Quality"))
1395 (hideConservation &&
1396 al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1398 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1403 af.alignPanel.adjustAnnotationHeight();
1406 if(view.getViewName()!=null)
1408 af.viewport.viewName = view.getViewName();
1409 af.setInitialTabVisible();
1411 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1413 af.viewport.setStartRes(view.getStartRes());
1414 af.viewport.setStartSeq(view.getStartSeq());
1415 af.viewport.setShowAnnotation(view.getShowAnnotation());
1416 af.viewport.setAbovePIDThreshold(view.getPidSelected());
1418 af.viewport.setColourText(view.getShowColourText());
1420 af.viewport.setConservationSelected(view.getConservationSelected());
1421 af.viewport.setShowJVSuffix(view.getShowFullId());
1422 af.viewport.rightAlignIds=view.getRightAlignIds();
1423 af.viewport.setFont(new java.awt.Font(view.getFontName(),
1424 view.getFontStyle(), view.getFontSize()));
1425 af.alignPanel.fontChanged();
1426 af.viewport.setRenderGaps(view.getRenderGaps());
1427 af.viewport.setWrapAlignment(view.getWrapAlignment());
1428 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1429 af.viewport.setShowAnnotation(view.getShowAnnotation());
1430 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1432 af.viewport.setShowBoxes(view.getShowBoxes());
1434 af.viewport.setShowText(view.getShowText());
1436 af.viewport.textColour = new java.awt.Color(view.getTextCol1());
1437 af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
1438 af.viewport.thresholdTextColour = view.getTextColThreshold();
1441 ColourSchemeI cs = null;
1443 if (view.getBgColour() != null)
1445 if (view.getBgColour().startsWith("ucs"))
1447 cs = GetUserColourScheme(jms, view.getBgColour());
1449 else if(view.getBgColour().startsWith("Annotation"))
1451 //int find annotation
1452 for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1454 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1455 equals(view.getAnnotationColours().getAnnotation()))
1457 if (af.viewport.alignment.getAlignmentAnnotation()[i].
1458 getThreshold() == null)
1460 af.viewport.alignment.getAlignmentAnnotation()[i].
1462 new jalview.datamodel.GraphLine(
1463 view.getAnnotationColours().getThreshold(),
1464 "Threshold", java.awt.Color.black)
1470 if (view.getAnnotationColours().getColourScheme().equals(
1473 cs = new AnnotationColourGradient(
1474 af.viewport.alignment.getAlignmentAnnotation()[i],
1475 new java.awt.Color(view.getAnnotationColours().
1477 new java.awt.Color(view.getAnnotationColours().
1479 view.getAnnotationColours().getAboveThreshold());
1481 else if (view.getAnnotationColours().getColourScheme().
1484 cs = new AnnotationColourGradient(
1485 af.viewport.alignment.getAlignmentAnnotation()[i],
1486 GetUserColourScheme(jms, view.getAnnotationColours().
1488 view.getAnnotationColours().getAboveThreshold()
1493 cs = new AnnotationColourGradient(
1494 af.viewport.alignment.getAlignmentAnnotation()[i],
1495 ColourSchemeProperty.getColour(al,
1496 view.getAnnotationColours().getColourScheme()),
1497 view.getAnnotationColours().getAboveThreshold()
1501 // Also use these settings for all the groups
1502 if (al.getGroups() != null)
1503 for (int g = 0; g < al.getGroups().size(); g++)
1505 jalview.datamodel.SequenceGroup sg
1506 = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
1512 /* if (view.getAnnotationColours().getColourScheme().equals("None"))
1514 sg.cs = new AnnotationColourGradient(
1515 af.viewport.alignment.getAlignmentAnnotation()[i],
1516 new java.awt.Color(view.getAnnotationColours().
1518 new java.awt.Color(view.getAnnotationColours().
1520 view.getAnnotationColours().getAboveThreshold());
1524 sg.cs = new AnnotationColourGradient(
1525 af.viewport.alignment.getAlignmentAnnotation()[i],
1527 view.getAnnotationColours().getAboveThreshold()
1541 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1546 cs.setThreshold(view.getPidThreshold(), true);
1547 cs.setConsensus(af.viewport.hconsensus);
1552 af.viewport.setGlobalColourScheme(cs);
1553 af.viewport.setColourAppliesToAllGroups(false);
1555 if (view.getConservationSelected() && cs!=null)
1557 cs.setConservationInc(view.getConsThreshold());
1560 af.changeColour(cs);
1562 af.viewport.setColourAppliesToAllGroups(true);
1566 if (view.getShowSequenceFeatures())
1568 af.viewport.showSequenceFeatures = true;
1571 if(jms.getFeatureSettings()!=null)
1573 af.viewport.featuresDisplayed = new Hashtable();
1574 String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
1575 for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
1577 Setting setting = jms.getFeatureSettings().getSetting(fs);
1579 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
1580 new java.awt.Color(setting.getColour()));
1582 renderOrder[fs] = setting.getType();
1584 if(setting.getDisplay())
1585 af.viewport.featuresDisplayed.put(
1586 setting.getType(), new Integer(setting.getColour()));
1588 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
1591 if (view.getHiddenColumnsCount() > 0)
1593 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1595 af.viewport.hideColumns(
1596 view.getHiddenColumns(c).getStart(),
1597 view.getHiddenColumns(c).getEnd() //+1
1602 af.setMenusFromViewport(af.viewport);
1605 Desktop.addInternalFrame(af, view.getTitle(),
1606 view.getWidth(), view.getHeight());
1609 ///////////////////////////////////////
1610 if (loadTrees && jms.getTreeCount() > 0)
1614 for (int t = 0; t < jms.getTreeCount(); t++)
1617 Tree tree = jms.getTree(t);
1619 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1620 tree.getNewick()), tree.getTitle(),
1621 tree.getWidth(), tree.getHeight(),
1622 tree.getXpos(), tree.getYpos());
1624 tp.fitToWindow.setState(tree.getFitToWindow());
1625 tp.fitToWindow_actionPerformed(null);
1627 if(tree.getFontName()!=null)
1628 tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1629 tree.getFontStyle(),
1630 tree.getFontSize()));
1632 tp.setTreeFont(new java.awt.Font(view.getFontName(),
1633 view.getFontStyle(),
1634 tree.getFontSize()));
1636 tp.showPlaceholders(tree.getMarkUnlinked());
1637 tp.showBootstrap(tree.getShowBootstrap());
1638 tp.showDistances(tree.getShowDistances());
1640 tp.treeCanvas.threshold = tree.getThreshold();
1642 if (tree.getCurrentTree())
1643 af.viewport.setCurrentTree(tp.getTree());
1647 catch (Exception ex)
1649 ex.printStackTrace();
1657 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, boolean keepSeqRefs )
1659 jalview.schemabinding.version2.JalviewModel jm
1660 = SaveState(ap, null, null, null);
1665 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
1668 uniqueSetSuffix = "";
1670 viewportsAdded = new Hashtable();
1672 AlignFrame af = LoadFromObject(jm, null, false);
1673 af.alignPanels.clear();
1674 af.closeMenuItem_actionPerformed(true);
1676 return af.alignPanel;