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());
339 if(entry.getFile()!=null)
341 pdb.setFile(entry.getFile());
343 pdbfiles = new Vector();
345 if(!pdbfiles.contains(entry.getId()))
347 pdbfiles.addElement(entry.getId());
350 File file = new File(entry.getFile());
351 if(file.exists() && jout!=null)
353 byte[] data = new byte[ (int) file.length()];
354 jout.putNextEntry(new JarEntry(entry.getId()));
355 DataInputStream dis = new DataInputStream(new
356 FileInputStream(file));
359 DataOutputStream dout = new DataOutputStream(jout);
360 dout.write(data, 0, data.length);
366 ex.printStackTrace();
372 if(entry.getProperty()!=null)
374 PdbentryItem item = new PdbentryItem();
375 Hashtable properties = entry.getProperty();
376 Enumeration en2 = properties.keys();
377 while(en2.hasMoreElements())
379 Property prop = new Property();
380 String key = en2.nextElement().toString();
382 prop.setValue( properties.get(key).toString() );
383 item.addProperty(prop);
385 pdb.addPdbentryItem(item);
400 ///////////////////////////////////
401 if (av.currentTree != null)
403 // FIND ANY ASSOCIATED TREES
404 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
405 if (Desktop.desktop != null)
407 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
409 for (int t = 0; t < frames.length; t++)
411 if (frames[t] instanceof TreePanel)
413 TreePanel tp = (TreePanel) frames[t];
415 if (tp.treeCanvas.av.alignment == jal)
417 Tree tree = new Tree();
418 tree.setTitle(tp.getTitle());
419 tree.setCurrentTree( (av.currentTree == tp.getTree()));
420 tree.setNewick(tp.getTree().toString());
421 tree.setThreshold(tp.treeCanvas.threshold);
423 tree.setFitToWindow(tp.fitToWindow.getState());
424 tree.setFontName(tp.getTreeFont().getName());
425 tree.setFontSize(tp.getTreeFont().getSize());
426 tree.setFontStyle(tp.getTreeFont().getStyle());
427 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
429 tree.setShowBootstrap(tp.bootstrapMenu.getState());
430 tree.setShowDistances(tp.distanceMenu.getState());
432 tree.setHeight(tp.getHeight());
433 tree.setWidth(tp.getWidth());
434 tree.setXpos(tp.getX());
435 tree.setYpos(tp.getY());
445 if (jal.getAlignmentAnnotation() != null)
447 jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
449 for (int i = 0; i < aa.length; i++)
451 Annotation an = new Annotation();
453 if (aa[i].label.equals("Quality") ||
454 aa[i].label.equals("Conservation") ||
455 aa[i].label.equals("Consensus"))
457 an.setLabel(aa[i].label);
459 vamsasSet.addAnnotation(an);
464 an.setDescription(aa[i].description);
466 if(aa[i].sequenceRef!=null)
468 an.setSequenceRef(aa[i].sequenceRef.getName());
474 an.setGraphType(aa[i].graph);
475 an.setGraphGroup(aa[i].graphGroup);
476 if(aa[i].getThreshold()!=null)
478 ThresholdLine line = new ThresholdLine();
479 line.setLabel(aa[i].getThreshold().label);
480 line.setValue(aa[i].getThreshold().value);
481 line.setColour(aa[i].getThreshold().colour.getRGB());
482 an.setThresholdLine(line);
488 an.setLabel(aa[i].label);
490 AnnotationElement ae;
492 for (int a = 0; a < aa[i].annotations.length; a++)
494 if ((aa[i] == null) || (aa[i].annotations[a] == null))
499 ae = new AnnotationElement();
500 ae.setDescription(aa[i].annotations[a].description);
501 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
502 ae.setValue(aa[i].annotations[a].value);
504 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
507 if(aa[i].annotations[a].colour!=java.awt.Color.black)
508 ae.setColour(aa[i].annotations[a].colour.getRGB());
510 an.addAnnotationElement(ae);
513 vamsasSet.addAnnotation(an);
518 if (jal.getGroups() != null)
520 JGroup[] groups = new JGroup[jal.getGroups().size()];
522 for (int i = 0; i < groups.length; i++)
524 groups[i] = new JGroup();
526 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
528 groups[i].setStart(sg.getStartRes());
529 groups[i].setEnd(sg.getEndRes());
530 groups[i].setName(sg.getName());
533 if (sg.cs.conservationApplied())
535 groups[i].setConsThreshold(sg.cs.getConservationInc());
537 if (sg.cs instanceof jalview.schemes.UserColourScheme)
539 groups[i].setColour(SetUserColourScheme(sg.cs,
545 groups[i].setColour(ColourSchemeProperty.getColourName(sg.
549 else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)
552 ColourSchemeProperty.getColourName(
553 ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));
555 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
557 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
562 groups[i].setColour(ColourSchemeProperty.getColourName(
566 groups[i].setPidThreshold(sg.cs.getThreshold());
569 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
570 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
571 groups[i].setDisplayText(sg.getDisplayText());
572 groups[i].setColourText(sg.getColourText());
573 groups[i].setTextCol1(sg.textColour.getRGB());
574 groups[i].setTextCol2(sg.textColour2.getRGB());
575 groups[i].setTextColThreshold(sg.thresholdTextColour);
577 for (int s = 0; s < sg.getSize(false); s++)
579 jalview.datamodel.Sequence seq =
580 (jalview.datamodel.Sequence) sg.getSequenceAt(s);
581 groups[i].addSeq(seq.hashCode());
585 jms.setJGroup(groups);
589 ///////////SAVE VIEWPORT
590 Viewport view = new Viewport();
591 view.setTitle(ap.alignFrame.getTitle());
592 view.setSequenceSetId(av.getSequenceSetId());
593 view.setViewName(av.viewName);
594 view.setGatheredViews(av.gatherViewsHere);
597 if (ap.av.explodedPosition != null)
599 view.setXpos(av.explodedPosition.x);
600 view.setYpos(av.explodedPosition.y);
601 view.setWidth(av.explodedPosition.width);
602 view.setHeight(av.explodedPosition.height);
606 view.setXpos(ap.alignFrame.getBounds().x);
607 view.setYpos(ap.alignFrame.getBounds().y);
608 view.setWidth(ap.alignFrame.getBounds().width);
609 view.setHeight(ap.alignFrame.getBounds().height);
612 view.setStartRes(av.startRes);
613 view.setStartSeq(av.startSeq);
615 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
617 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
620 else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
622 jalview.schemes.AnnotationColourGradient acg
623 = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();
625 AnnotationColours ac = new AnnotationColours();
626 ac.setAboveThreshold(acg.getAboveThreshold());
627 ac.setThreshold(acg.getAnnotationThreshold());
628 ac.setAnnotation(acg.getAnnotation());
629 if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
630 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
633 ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
635 ac.setMaxColour(acg.getMaxColour().getRGB());
636 ac.setMinColour(acg.getMinColour().getRGB());
637 view.setAnnotationColours(ac);
638 view.setBgColour("AnnotationColourGradient");
642 view.setBgColour(ColourSchemeProperty.getColourName(
643 av.getGlobalColourScheme()));
646 ColourSchemeI cs = av.getGlobalColourScheme();
650 if (cs.conservationApplied())
652 view.setConsThreshold(cs.getConservationInc());
653 if (cs instanceof jalview.schemes.UserColourScheme)
654 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
657 if (cs instanceof ResidueColourScheme)
659 view.setPidThreshold(cs.getThreshold());
663 view.setConservationSelected(av.getConservationSelected());
664 view.setPidSelected(av.getAbovePIDThreshold());
665 view.setFontName(av.font.getName());
666 view.setFontSize(av.font.getSize());
667 view.setFontStyle(av.font.getStyle());
668 view.setRenderGaps(av.renderGaps);
669 view.setShowAnnotation(av.getShowAnnotation());
670 view.setShowBoxes(av.getShowBoxes());
671 view.setShowColourText(av.getColourText());
672 view.setShowFullId(av.getShowJVSuffix());
673 view.setRightAlignIds(av.rightAlignIds);
674 view.setShowSequenceFeatures(av.showSequenceFeatures);
675 view.setShowText(av.getShowText());
676 view.setWrapAlignment(av.getWrapAlignment());
677 view.setTextCol1(av.textColour.getRGB());
678 view.setTextCol2(av.textColour2.getRGB());
679 view.setTextColThreshold(av.thresholdTextColour);
682 if(av.featuresDisplayed!=null)
684 jalview.schemabinding.version2.FeatureSettings fs
685 = new jalview.schemabinding.version2.FeatureSettings();
687 String [] renderOrder =
688 ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
690 Vector settingsAdded = new Vector();
691 for(int ro=0; ro<renderOrder.length; ro++)
693 Setting setting = new Setting();
694 setting.setType(renderOrder[ro]);
696 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
700 av.featuresDisplayed.containsKey(renderOrder[ro])
703 fs.addSetting(setting);
704 settingsAdded.addElement(renderOrder[ro]);
707 //Make sure we save none displayed feature settings
709 ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
710 while(en.hasMoreElements())
712 String key = en.nextElement().toString();
713 if(settingsAdded.contains(key))
716 Setting setting = new Setting();
717 setting.setType(key);
719 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
722 setting.setDisplay(false);
724 fs.addSetting(setting);
725 settingsAdded.addElement(key);
728 jms.setFeatureSettings(fs);
732 if(av.hasHiddenColumns)
734 for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)
736 int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);
737 HiddenColumns hc = new HiddenColumns();
738 hc.setStart(region[0]);
739 hc.setEnd(region[1]);
740 view.addHiddenColumns(hc);
744 jms.addViewport(view);
747 object.setJalviewModelSequence(jms);
748 object.getVamsasModel().addSequenceSet(vamsasSet);
752 //We may not want to right the object to disk,
753 //eg we can copy the alignViewport to a new view object
754 //using save and then load
757 if (!fileName.endsWith(".xml"))
759 fileName = fileName + ".xml";
762 JarEntry entry = new JarEntry(fileName);
763 jout.putNextEntry(entry);
769 ex.printStackTrace();
775 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
776 Vector userColours, JalviewModelSequence jms)
779 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
781 if (!userColours.contains(ucs))
783 userColours.add(ucs);
785 java.awt.Color[] colours = ucs.getColours();
786 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
787 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
789 for (int i = 0; i < colours.length; i++)
791 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
792 col.setName(ResidueProperties.aa[i]);
793 col.setRGB(jalview.util.Format.getHexString(colours[i]));
794 jbucs.addColour(col);
796 if(ucs.getLowerCaseColours()!=null)
798 colours = ucs.getLowerCaseColours();
799 for (int i = 0; i < colours.length; i++)
801 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
802 col.setName(ResidueProperties.aa[i].toLowerCase());
803 col.setRGB(jalview.util.Format.getHexString(colours[i]));
804 jbucs.addColour(col);
808 id = "ucs" + userColours.indexOf(ucs);
810 uc.setUserColourScheme(jbucs);
811 jms.addUserColours(uc);
817 jalview.schemes.UserColourScheme GetUserColourScheme(
818 JalviewModelSequence jms, String id)
820 UserColours[] uc = jms.getUserColours();
821 UserColours colours = null;
823 for (int i = 0; i < uc.length; i++)
825 if (uc[i].getId().equals(id))
833 java.awt.Color[] newColours = new java.awt.Color[24];
835 for (int i = 0; i < 24; i++)
837 newColours[i] = new java.awt.Color(Integer.parseInt(
838 colours.getUserColourScheme().getColour(i).getRGB(), 16));
841 jalview.schemes.UserColourScheme ucs =
842 new jalview.schemes.UserColourScheme(newColours);
844 if (colours.getUserColourScheme().getColourCount() > 24)
846 newColours = new java.awt.Color[23];
847 for (int i = 0; i < 23; i++)
849 newColours[i] = new java.awt.Color(Integer.parseInt(
850 colours.getUserColourScheme().getColour(i+24).getRGB(), 16));
852 ucs.setLowerCaseColours(newColours);
862 * @param file DOCUMENT ME!
864 public AlignFrame LoadJalviewAlign(final String file)
866 uniqueSetSuffix = System.currentTimeMillis()%100000 +"";
868 jalview.gui.AlignFrame af = null;
870 seqRefIds = new Hashtable();
871 viewportsAdded = new Hashtable();
873 Vector gatherToThisFrame= new Vector();
877 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
880 if (file.startsWith("http://"))
885 JarInputStream jin = null;
886 JarEntry jarentry = null;
893 jin = new JarInputStream(url.openStream());
897 jin = new JarInputStream(new FileInputStream(file));
900 for (int i = 0; i < entryCount; i++)
902 jarentry = jin.getNextJarEntry();
905 if (jarentry != null && jarentry.getName().endsWith(".xml"))
907 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
908 JalviewModel object = new JalviewModel();
910 Unmarshaller unmar = new Unmarshaller(object);
911 unmar.setValidation(false);
912 object = (JalviewModel) unmar.unmarshal( in );
914 af = LoadFromObject(object, file, true);
915 if(af.viewport.gatherViewsHere)
917 gatherToThisFrame.add(af);
921 else if (jarentry != null)
923 //Some other file here.
927 while (jarentry != null);
929 catch(java.net.UnknownHostException ex)
931 ex.printStackTrace();
932 System.err.println("Couldn't locate Jalview XML file : " +
935 javax.swing.SwingUtilities.invokeLater(new Runnable()
939 JOptionPane.showInternalMessageDialog(Desktop.desktop,
940 "Couldn't locate " + file,
942 JOptionPane.WARNING_MESSAGE);
948 //Is Version 1 Jar file?
949 af = new Jalview2XML_V1().LoadJalviewAlign(file);
953 System.out.println("Successfully loaded archive file");
957 System.err.println("Exception whilst loading jalview XML file : " +
959 javax.swing.SwingUtilities.invokeLater(new Runnable()
964 JOptionPane.showInternalMessageDialog(Desktop.desktop,
965 "Error loading " + file,
966 "Error loading Jalview file",
967 JOptionPane.WARNING_MESSAGE);
971 if (Desktop.instance != null)
972 Desktop.instance.stopLoading();
974 for (int i = 0; i < gatherToThisFrame.size(); i++)
976 Desktop.instance.gatherViews(
977 (AlignFrame) gatherToThisFrame.elementAt(i));
983 String loadPDBFile(String file, String pdbId)
985 System.out.println(file +" "+pdbId);
988 JarInputStream jin = null;
990 if (file.startsWith("http://"))
992 jin = new JarInputStream(new URL(file).openStream());
996 jin = new JarInputStream(new FileInputStream(file));
999 JarEntry entry = null;
1002 entry = jin.getNextJarEntry();
1004 while (!entry.getName().equals(pdbId));
1006 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1007 File outFile = File.createTempFile("jalview_pdb", ".txt");
1008 System.out.println("CREATE "+outFile);
1009 outFile.deleteOnExit();
1010 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1013 while ( (data = in.readLine()) != null)
1018 return outFile.getAbsolutePath();
1021 catch (Exception ex)
1023 ex.printStackTrace();
1030 AlignFrame LoadFromObject(JalviewModel object,
1034 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1035 Sequence[] vamsasSeq = vamsasSet.getSequence();
1037 JalviewModelSequence jms = object.getJalviewModelSequence();
1039 Viewport view = jms.getViewport(0);
1041 //////////////////////////////////
1044 Vector hiddenSeqs = null;
1045 jalview.datamodel.Sequence jseq;
1047 ArrayList tmpseqs = new ArrayList();
1049 boolean multipleView = false;
1051 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1052 for (int i = 0; i < JSEQ.length; i++)
1054 String seqId = JSEQ[i].getId() + "";
1056 if (seqRefIds.get(seqId) != null)
1058 tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1059 multipleView = true;
1063 jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
1064 vamsasSeq[i].getSequence());
1065 jseq.setDescription(vamsasSeq[i].getDescription());
1066 jseq.setStart(JSEQ[i].getStart());
1067 jseq.setEnd(JSEQ[i].getEnd());
1068 seqRefIds.put(vamsasSeq[i].getId(), jseq);
1069 tmpseqs.add( jseq );
1074 if (JSEQ[i].getHidden())
1076 if (hiddenSeqs == null)
1077 hiddenSeqs = new Vector();
1080 hiddenSeqs.addElement(
1081 (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1086 ///SequenceFeatures are added to the DatasetSequence,
1087 // so we must create the dataset before loading features
1088 /////////////////////////////////
1091 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
1094 tmpseqs.toArray(orderedSeqs) ;
1097 jalview.datamodel.Alignment al =
1098 new jalview.datamodel.Alignment(orderedSeqs);
1100 al.setDataset(null);
1101 /////////////////////////////////
1104 Hashtable pdbloaded = new Hashtable();
1107 for (int i = 0; i < vamsasSeq.length; i++)
1109 if (JSEQ[i].getFeaturesCount() > 0)
1111 Features[] features = JSEQ[i].getFeatures();
1112 for (int f = 0; f < features.length; f++)
1114 jalview.datamodel.SequenceFeature sf
1115 = new jalview.datamodel.SequenceFeature(features[f].getType(),
1116 features[f].getDescription(), features[f].getStatus(),
1117 features[f].getBegin(), features[f].getEnd(),
1118 features[f].getFeatureGroup());
1120 sf.setScore(features[f].getScore());
1121 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1123 OtherData keyValue = features[f].getOtherData(od);
1124 if (keyValue.getKey().startsWith("LINK"))
1125 sf.addLink(keyValue.getValue());
1127 sf.setValue(keyValue.getKey(), keyValue.getValue());
1131 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1134 if (JSEQ[i].getPdbidsCount() > 0)
1136 Pdbids[] ids = JSEQ[i].getPdbids();
1137 for (int p = 0; p < ids.length; p++)
1139 jalview.datamodel.PDBEntry entry = new jalview.datamodel.
1141 entry.setId(ids[p].getId());
1142 entry.setType(ids[p].getType());
1143 if (ids[p].getFile() != null)
1145 if (!pdbloaded.containsKey(ids[p].getFile()))
1147 String tmppdb = loadPDBFile(file, ids[p].getId());
1148 entry.setFile(tmppdb);
1149 pdbloaded.put(ids[p].getId(), tmppdb);
1152 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1155 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1158 if (vamsasSeq[i].getDBRefCount() > 0)
1160 for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
1162 jalview.datamodel.DBRefEntry entry =
1163 new jalview.datamodel.DBRefEntry(
1164 vamsasSeq[i].getDBRef(d).getSource(),
1165 vamsasSeq[i].getDBRef(d).getVersion(),
1166 vamsasSeq[i].getDBRef(d).getAccessionId()
1168 al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1176 /////////////////////////////////
1177 //////////////////////////////////
1179 boolean hideQuality = true,
1180 hideConservation = true,
1181 hideConsensus = true;
1183 if (vamsasSet.getAnnotationCount()>0)
1185 Annotation[] an = vamsasSet.getAnnotation();
1187 for (int i = 0; i < an.length; i++)
1189 if (an[i].getLabel().equals("Quality"))
1191 hideQuality = false;
1194 else if(an[i].getLabel().equals("Conservation"))
1196 hideConservation = false;
1199 else if(an[i].getLabel().equals("Consensus"))
1201 hideConsensus = false;
1205 AnnotationElement[] ae = an[i].getAnnotationElement();
1206 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
1208 for (int aa = 0; aa < ae.length; aa++)
1210 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
1211 ae[aa].getDescription(),
1212 ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
1214 anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
1217 jalview.datamodel.AlignmentAnnotation jaa = null;
1219 if (an[i].getGraph())
1221 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1222 an[i].getDescription(), anot, 0, 0,
1223 an[i].getGraphType());
1225 jaa.graphGroup = an[i].getGraphGroup();
1227 if (an[i].getThresholdLine() != null)
1229 jaa.setThreshold(new jalview.datamodel.GraphLine(
1230 an[i].getThresholdLine().getValue(),
1231 an[i].getThresholdLine().getLabel(),
1232 new java.awt.Color(an[i].getThresholdLine().getColour()))
1240 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1241 an[i].getDescription(), anot);
1244 if(an[i].getSequenceRef()!=null)
1246 jaa.createSequenceMapping(
1247 al.findName(an[i].getSequenceRef()), 1, true
1249 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1252 al.addAnnotation(jaa);
1256 /////////////////////////
1258 if (jms.getJGroupCount() > 0)
1260 JGroup[] groups = jms.getJGroup();
1262 for (int i = 0; i < groups.length; i++)
1264 ColourSchemeI cs = null;
1266 if (groups[i].getColour() != null)
1268 if (groups[i].getColour().startsWith("ucs"))
1270 cs = GetUserColourScheme(jms, groups[i].getColour());
1274 cs = ColourSchemeProperty.getColour(al,
1275 groups[i].getColour());
1279 cs.setThreshold(groups[i].getPidThreshold(), true);
1282 Vector seqs = new Vector();
1284 for (int s = 0; s < groups[i].getSeqCount(); s++)
1286 String seqId = groups[i].getSeq(s)+"";
1287 seqs.addElement((jalview.datamodel.SequenceI) seqRefIds.get(seqId));
1290 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
1291 groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1292 groups[i].getDisplayText(), groups[i].getColourText(),
1293 groups[i].getStart(), groups[i].getEnd());
1295 sg.setOutlineColour(new java.awt.Color(
1296 groups[i].getOutlineColour()));
1298 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
1299 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
1300 sg.thresholdTextColour = groups[i].getTextColThreshold();
1302 if (groups[i].getConsThreshold() != 0)
1304 jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
1305 ResidueProperties.propHash, 3, sg.getSequences(false), 0,
1308 c.verdict(false, 25);
1309 sg.cs.setConservation(c);
1317 /////////////////////////////////
1320 AlignFrame af = new AlignFrame(al,
1324 af.setFileName(file, "Jalview");
1326 for (int i = 0; i < JSEQ.length; i++)
1328 af.viewport.setSequenceColour(
1329 af.viewport.alignment.getSequenceAt(i),
1331 JSEQ[i].getColour()));
1334 //If we just load in the same jar file again, the sequenceSetId
1335 //will be the same, and we end up with multiple references
1336 //to the same sequenceSet. We must modify this id on load
1337 //so that each load of the file gives a unique id
1338 String uniqueSeqSetId = view.getSequenceSetId()+uniqueSetSuffix;
1340 af.viewport.gatherViewsHere = view.getGatheredViews();
1342 if (view.getSequenceSetId() != null)
1344 jalview.gui.AlignViewport av =
1345 (jalview.gui.AlignViewport)
1346 viewportsAdded.get(uniqueSeqSetId);
1348 af.viewport.sequenceSetID = uniqueSeqSetId;
1352 af.viewport.historyList = av.historyList;
1353 af.viewport.redoList = av.redoList;
1357 viewportsAdded.put(uniqueSeqSetId, af.viewport);
1360 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1362 if(hiddenSeqs!=null)
1364 for(int s=0; s<JSEQ.length; s++)
1366 for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
1368 al.getSequenceAt(s).addHiddenSequence(
1369 al.getSequenceAt( JSEQ[s].getHiddenSequences(r) )
1374 jalview.datamodel.SequenceI [] hseqs = new
1375 jalview.datamodel.SequenceI[hiddenSeqs.size()];
1377 for(int s=0; s<hiddenSeqs.size(); s++)
1378 hseqs[s] = (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s);
1380 af.viewport.hideSequence( hseqs );
1385 if((hideConsensus || hideQuality || hideConservation)
1386 && al.getAlignmentAnnotation()!=null)
1388 int hSize = al.getAlignmentAnnotation().length;
1389 for (int h = 0; h < hSize; h++)
1393 al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1396 al.getAlignmentAnnotation()[h].label.equals("Quality"))
1398 (hideConservation &&
1399 al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1401 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1406 af.alignPanel.adjustAnnotationHeight();
1409 if(view.getViewName()!=null)
1411 af.viewport.viewName = view.getViewName();
1412 af.setInitialTabVisible();
1414 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1417 af.viewport.setShowAnnotation(view.getShowAnnotation());
1418 af.viewport.setAbovePIDThreshold(view.getPidSelected());
1420 af.viewport.setColourText(view.getShowColourText());
1422 af.viewport.setConservationSelected(view.getConservationSelected());
1423 af.viewport.setShowJVSuffix(view.getShowFullId());
1424 af.viewport.rightAlignIds=view.getRightAlignIds();
1425 af.viewport.setFont(new java.awt.Font(view.getFontName(),
1426 view.getFontStyle(), view.getFontSize()));
1427 af.alignPanel.fontChanged();
1428 af.viewport.setRenderGaps(view.getRenderGaps());
1429 af.viewport.setWrapAlignment(view.getWrapAlignment());
1430 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1431 af.viewport.setShowAnnotation(view.getShowAnnotation());
1432 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1434 af.viewport.setShowBoxes(view.getShowBoxes());
1436 af.viewport.setShowText(view.getShowText());
1438 af.viewport.textColour = new java.awt.Color(view.getTextCol1());
1439 af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
1440 af.viewport.thresholdTextColour = view.getTextColThreshold();
1442 af.viewport.setStartRes(view.getStartRes());
1443 af.viewport.setStartSeq(view.getStartSeq());
1445 ColourSchemeI cs = null;
1447 if (view.getBgColour() != null)
1449 if (view.getBgColour().startsWith("ucs"))
1451 cs = GetUserColourScheme(jms, view.getBgColour());
1453 else if(view.getBgColour().startsWith("Annotation"))
1455 //int find annotation
1456 for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1458 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1459 equals(view.getAnnotationColours().getAnnotation()))
1461 if (af.viewport.alignment.getAlignmentAnnotation()[i].
1462 getThreshold() == null)
1464 af.viewport.alignment.getAlignmentAnnotation()[i].
1466 new jalview.datamodel.GraphLine(
1467 view.getAnnotationColours().getThreshold(),
1468 "Threshold", java.awt.Color.black)
1474 if (view.getAnnotationColours().getColourScheme().equals(
1477 cs = new AnnotationColourGradient(
1478 af.viewport.alignment.getAlignmentAnnotation()[i],
1479 new java.awt.Color(view.getAnnotationColours().
1481 new java.awt.Color(view.getAnnotationColours().
1483 view.getAnnotationColours().getAboveThreshold());
1485 else if (view.getAnnotationColours().getColourScheme().
1488 cs = new AnnotationColourGradient(
1489 af.viewport.alignment.getAlignmentAnnotation()[i],
1490 GetUserColourScheme(jms, view.getAnnotationColours().
1492 view.getAnnotationColours().getAboveThreshold()
1497 cs = new AnnotationColourGradient(
1498 af.viewport.alignment.getAlignmentAnnotation()[i],
1499 ColourSchemeProperty.getColour(al,
1500 view.getAnnotationColours().getColourScheme()),
1501 view.getAnnotationColours().getAboveThreshold()
1505 // Also use these settings for all the groups
1506 if (al.getGroups() != null)
1507 for (int g = 0; g < al.getGroups().size(); g++)
1509 jalview.datamodel.SequenceGroup sg
1510 = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
1516 /* if (view.getAnnotationColours().getColourScheme().equals("None"))
1518 sg.cs = new AnnotationColourGradient(
1519 af.viewport.alignment.getAlignmentAnnotation()[i],
1520 new java.awt.Color(view.getAnnotationColours().
1522 new java.awt.Color(view.getAnnotationColours().
1524 view.getAnnotationColours().getAboveThreshold());
1528 sg.cs = new AnnotationColourGradient(
1529 af.viewport.alignment.getAlignmentAnnotation()[i],
1531 view.getAnnotationColours().getAboveThreshold()
1545 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1550 cs.setThreshold(view.getPidThreshold(), true);
1551 cs.setConsensus(af.viewport.hconsensus);
1556 af.viewport.setGlobalColourScheme(cs);
1557 af.viewport.setColourAppliesToAllGroups(false);
1559 if (view.getConservationSelected() && cs!=null)
1561 cs.setConservationInc(view.getConsThreshold());
1564 af.changeColour(cs);
1566 af.viewport.setColourAppliesToAllGroups(true);
1570 if (view.getShowSequenceFeatures())
1572 af.viewport.showSequenceFeatures = true;
1575 if(jms.getFeatureSettings()!=null)
1577 af.viewport.featuresDisplayed = new Hashtable();
1578 String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
1579 for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
1581 Setting setting = jms.getFeatureSettings().getSetting(fs);
1583 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
1584 new java.awt.Color(setting.getColour()));
1586 renderOrder[fs] = setting.getType();
1588 if(setting.getDisplay())
1589 af.viewport.featuresDisplayed.put(
1590 setting.getType(), new Integer(setting.getColour()));
1592 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
1595 if (view.getHiddenColumnsCount() > 0)
1597 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1599 af.viewport.hideColumns(
1600 view.getHiddenColumns(c).getStart(),
1601 view.getHiddenColumns(c).getEnd() //+1
1606 af.setMenusFromViewport(af.viewport);
1609 Desktop.addInternalFrame(af, view.getTitle(),
1610 view.getWidth(), view.getHeight());
1613 ///////////////////////////////////////
1614 if (loadTrees && jms.getTreeCount() > 0)
1618 for (int t = 0; t < jms.getTreeCount(); t++)
1621 Tree tree = jms.getTree(t);
1623 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1624 tree.getNewick()), tree.getTitle(),
1625 tree.getWidth(), tree.getHeight(),
1626 tree.getXpos(), tree.getYpos());
1628 tp.fitToWindow.setState(tree.getFitToWindow());
1629 tp.fitToWindow_actionPerformed(null);
1631 if(tree.getFontName()!=null)
1632 tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1633 tree.getFontStyle(),
1634 tree.getFontSize()));
1636 tp.setTreeFont(new java.awt.Font(view.getFontName(),
1637 view.getFontStyle(),
1638 tree.getFontSize()));
1640 tp.showPlaceholders(tree.getMarkUnlinked());
1641 tp.showBootstrap(tree.getShowBootstrap());
1642 tp.showDistances(tree.getShowDistances());
1644 tp.treeCanvas.threshold = tree.getThreshold();
1646 if (tree.getCurrentTree())
1647 af.viewport.setCurrentTree(tp.getTree());
1651 catch (Exception ex)
1653 ex.printStackTrace();
1661 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, boolean keepSeqRefs )
1663 jalview.schemabinding.version2.JalviewModel jm
1664 = SaveState(ap, null, null, null);
1669 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
1672 uniqueSetSuffix = "";
1674 viewportsAdded = new Hashtable();
1676 AlignFrame af = LoadFromObject(jm, null, false);
1677 af.alignPanels.clear();
1678 af.closeMenuItem_actionPerformed(true);
1680 return af.alignPanel;