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 boolean 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,
170 ex.printStackTrace();
178 * @param af DOCUMENT ME!
179 * @param timeStamp DOCUMENT ME!
180 * @param fileName DOCUMENT ME!
181 * @param jout DOCUMENT ME!
182 * @param out DOCUMENT ME!
184 public JalviewModel SaveState(AlignmentPanel ap,
186 JarOutputStream jout,
189 if (seqRefIds == null)
190 seqRefIds = new Hashtable();
192 Vector userColours = new Vector();
194 AlignViewport av = ap.av;
196 JalviewModel object = new JalviewModel();
197 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
199 object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
200 object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
202 jalview.datamodel.AlignmentI jal = av.alignment;
206 jal = jal.getHiddenSequences().getFullAlignment();
209 SequenceSet vamsasSet = new SequenceSet();
211 JalviewModelSequence jms = new JalviewModelSequence();
213 vamsasSet.setGapChar(jal.getGapCharacter() + "");
216 Vector pdbfiles = null;
220 jalview.datamodel.SequenceI jds;
221 for (int i = 0; i < jal.getHeight(); i++)
223 jds = jal.getSequenceAt(i);
226 if(seqRefIds.get(id+"")!=null)
232 vamsasSeq = new Sequence();
233 vamsasSeq.setId(id + "");
234 vamsasSeq.setName(jds.getName());
235 vamsasSeq.setSequence(jds.getSequenceAsString());
236 vamsasSeq.setDescription(jds.getDescription());
238 if (jds.getDatasetSequence().getDBRef() != null)
240 jalview.datamodel.DBRefEntry[] dbrefs =
241 jds.getDatasetSequence().getDBRef();
243 for (int d = 0; d < dbrefs.length; d++)
245 DBRef dbref = new DBRef();
246 dbref.setSource(dbrefs[d].getSource());
247 dbref.setVersion(dbrefs[d].getVersion());
248 dbref.setAccessionId(dbrefs[d].getAccessionId());
249 vamsasSeq.addDBRef(dbref);
253 vamsasSet.addSequence(vamsasSeq);
254 seqRefIds.put(id+"", jal.getSequenceAt(i));
258 jseq.setStart(jds.getStart());
259 jseq.setEnd(jds.getEnd());
260 jseq.setColour( av.getSequenceColour(jds).getRGB());
264 if (av.hasHiddenRows)
266 jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
268 if(jal.getSequenceAt(i).getHiddenSequences()!=null)
270 jalview.datamodel.SequenceI [] reps =
271 jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal);
273 for(int h=0; h<reps.length; h++)
275 jseq.addHiddenSequences(
276 jal.findIndex(reps[h])
283 if(jds.getDatasetSequence().getSequenceFeatures()!=null)
285 jalview.datamodel.SequenceFeature[] sf
286 = jds.getDatasetSequence().getSequenceFeatures();
288 while(index < sf.length)
290 Features features = new Features();
292 features.setBegin(sf[index].getBegin());
293 features.setEnd(sf[index].getEnd());
294 features.setDescription(sf[index].getDescription());
295 features.setType(sf[index].getType());
296 features.setFeatureGroup(sf[index].getFeatureGroup());
297 features.setScore(sf[index].getScore());
298 if(sf[index].links!=null)
300 for(int l=0; l<sf[index].links.size(); l++)
302 OtherData keyValue = new OtherData();
303 keyValue.setKey("LINK_"+l);
304 keyValue.setValue(sf[index].links.elementAt(l).toString());
305 features.addOtherData(keyValue);
308 if(sf[index].otherDetails!=null)
311 Enumeration keys = sf[index].otherDetails.keys();
312 while(keys.hasMoreElements())
314 key = keys.nextElement().toString();
315 OtherData keyValue = new OtherData();
316 keyValue.setKey( key );
318 sf[index].otherDetails.get(key).toString());
319 features.addOtherData(keyValue);
323 jseq.addFeatures(features);
328 if(jds.getDatasetSequence().getPDBId()!=null)
330 Enumeration en = jds.getDatasetSequence().getPDBId().elements();
331 while(en.hasMoreElements())
333 Pdbids pdb = new Pdbids();
334 jalview.datamodel.PDBEntry entry
335 = (jalview.datamodel.PDBEntry)en.nextElement();
337 pdb.setId(entry.getId());
338 pdb.setType(entry.getType());
341 if(entry.getFile()!=null)
343 pdb.setFile(entry.getFile());
345 pdbfiles = new Vector();
347 if(!pdbfiles.contains(entry.getId()))
349 pdbfiles.addElement(entry.getId());
352 File file = new File(entry.getFile());
353 if(file.exists() && jout!=null)
355 byte[] data = new byte[ (int) file.length()];
356 jout.putNextEntry(new JarEntry(entry.getId()));
357 DataInputStream dis = new DataInputStream(new
358 FileInputStream(file));
361 DataOutputStream dout = new DataOutputStream(jout);
362 dout.write(data, 0, data.length);
368 ex.printStackTrace();
374 if(entry.getProperty()!=null)
376 PdbentryItem item = new PdbentryItem();
377 Hashtable properties = entry.getProperty();
378 Enumeration en2 = properties.keys();
379 while(en2.hasMoreElements())
381 Property prop = new Property();
382 String key = en2.nextElement().toString();
384 prop.setValue( properties.get(key).toString() );
385 item.addProperty(prop);
387 pdb.addPdbentryItem(item);
402 ///////////////////////////////////
403 if (av.currentTree != null)
405 // FIND ANY ASSOCIATED TREES
406 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
407 if (Desktop.desktop != null)
409 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
411 for (int t = 0; t < frames.length; t++)
413 if (frames[t] instanceof TreePanel)
415 TreePanel tp = (TreePanel) frames[t];
417 if (tp.treeCanvas.av.alignment == jal)
419 Tree tree = new Tree();
420 tree.setTitle(tp.getTitle());
421 tree.setCurrentTree( (av.currentTree == tp.getTree()));
422 tree.setNewick(tp.getTree().toString());
423 tree.setThreshold(tp.treeCanvas.threshold);
425 tree.setFitToWindow(tp.fitToWindow.getState());
426 tree.setFontName(tp.getTreeFont().getName());
427 tree.setFontSize(tp.getTreeFont().getSize());
428 tree.setFontStyle(tp.getTreeFont().getStyle());
429 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
431 tree.setShowBootstrap(tp.bootstrapMenu.getState());
432 tree.setShowDistances(tp.distanceMenu.getState());
434 tree.setHeight(tp.getHeight());
435 tree.setWidth(tp.getWidth());
436 tree.setXpos(tp.getX());
437 tree.setYpos(tp.getY());
447 if (jal.getAlignmentAnnotation() != null)
449 jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
451 for (int i = 0; i < aa.length; i++)
453 Annotation an = new Annotation();
455 if (aa[i].label.equals("Quality") ||
456 aa[i].label.equals("Conservation") ||
457 aa[i].label.equals("Consensus"))
459 an.setLabel(aa[i].label);
461 vamsasSet.addAnnotation(an);
466 an.setDescription(aa[i].description);
468 if(aa[i].sequenceRef!=null)
470 an.setSequenceRef(aa[i].sequenceRef.getName());
476 an.setGraphType(aa[i].graph);
477 an.setGraphGroup(aa[i].graphGroup);
478 if(aa[i].getThreshold()!=null)
480 ThresholdLine line = new ThresholdLine();
481 line.setLabel(aa[i].getThreshold().label);
482 line.setValue(aa[i].getThreshold().value);
483 line.setColour(aa[i].getThreshold().colour.getRGB());
484 an.setThresholdLine(line);
490 an.setLabel(aa[i].label);
492 AnnotationElement ae;
494 for (int a = 0; a < aa[i].annotations.length; a++)
496 if ((aa[i] == null) || (aa[i].annotations[a] == null))
501 ae = new AnnotationElement();
502 ae.setDescription(aa[i].annotations[a].description);
503 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
504 ae.setValue(aa[i].annotations[a].value);
506 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
509 if(aa[i].annotations[a].colour!=java.awt.Color.black)
510 ae.setColour(aa[i].annotations[a].colour.getRGB());
512 an.addAnnotationElement(ae);
515 vamsasSet.addAnnotation(an);
520 if (jal.getGroups() != null)
522 JGroup[] groups = new JGroup[jal.getGroups().size()];
524 for (int i = 0; i < groups.length; i++)
526 groups[i] = new JGroup();
528 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
530 groups[i].setStart(sg.getStartRes());
531 groups[i].setEnd(sg.getEndRes());
532 groups[i].setName(sg.getName());
535 if (sg.cs.conservationApplied())
537 groups[i].setConsThreshold(sg.cs.getConservationInc());
539 if (sg.cs instanceof jalview.schemes.UserColourScheme)
541 groups[i].setColour(SetUserColourScheme(sg.cs,
547 groups[i].setColour(ColourSchemeProperty.getColourName(sg.
551 else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)
554 ColourSchemeProperty.getColourName(
555 ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));
557 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
559 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
564 groups[i].setColour(ColourSchemeProperty.getColourName(
568 groups[i].setPidThreshold(sg.cs.getThreshold());
571 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
572 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
573 groups[i].setDisplayText(sg.getDisplayText());
574 groups[i].setColourText(sg.getColourText());
575 groups[i].setTextCol1(sg.textColour.getRGB());
576 groups[i].setTextCol2(sg.textColour2.getRGB());
577 groups[i].setTextColThreshold(sg.thresholdTextColour);
579 for (int s = 0; s < sg.getSize(false); s++)
581 jalview.datamodel.Sequence seq =
582 (jalview.datamodel.Sequence) sg.getSequenceAt(s);
583 groups[i].addSeq(seq.hashCode());
587 jms.setJGroup(groups);
591 ///////////SAVE VIEWPORT
592 Viewport view = new Viewport();
593 view.setTitle(ap.alignFrame.getTitle());
594 view.setSequenceSetId(av.getSequenceSetId());
595 view.setViewName(av.viewName);
596 view.setGatheredViews(av.gatherViewsHere);
599 if (ap.av.explodedPosition != null)
601 view.setXpos(av.explodedPosition.x);
602 view.setYpos(av.explodedPosition.y);
603 view.setWidth(av.explodedPosition.width);
604 view.setHeight(av.explodedPosition.height);
608 view.setXpos(ap.alignFrame.getBounds().x);
609 view.setYpos(ap.alignFrame.getBounds().y);
610 view.setWidth(ap.alignFrame.getBounds().width);
611 view.setHeight(ap.alignFrame.getBounds().height);
614 view.setStartRes(av.startRes);
615 view.setStartSeq(av.startSeq);
617 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
619 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
622 else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
624 jalview.schemes.AnnotationColourGradient acg
625 = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();
627 AnnotationColours ac = new AnnotationColours();
628 ac.setAboveThreshold(acg.getAboveThreshold());
629 ac.setThreshold(acg.getAnnotationThreshold());
630 ac.setAnnotation(acg.getAnnotation());
631 if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
632 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
635 ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
637 ac.setMaxColour(acg.getMaxColour().getRGB());
638 ac.setMinColour(acg.getMinColour().getRGB());
639 view.setAnnotationColours(ac);
640 view.setBgColour("AnnotationColourGradient");
644 view.setBgColour(ColourSchemeProperty.getColourName(
645 av.getGlobalColourScheme()));
648 ColourSchemeI cs = av.getGlobalColourScheme();
652 if (cs.conservationApplied())
654 view.setConsThreshold(cs.getConservationInc());
655 if (cs instanceof jalview.schemes.UserColourScheme)
656 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
659 if (cs instanceof ResidueColourScheme)
661 view.setPidThreshold(cs.getThreshold());
665 view.setConservationSelected(av.getConservationSelected());
666 view.setPidSelected(av.getAbovePIDThreshold());
667 view.setFontName(av.font.getName());
668 view.setFontSize(av.font.getSize());
669 view.setFontStyle(av.font.getStyle());
670 view.setRenderGaps(av.renderGaps);
671 view.setShowAnnotation(av.getShowAnnotation());
672 view.setShowBoxes(av.getShowBoxes());
673 view.setShowColourText(av.getColourText());
674 view.setShowFullId(av.getShowJVSuffix());
675 view.setRightAlignIds(av.rightAlignIds);
676 view.setShowSequenceFeatures(av.showSequenceFeatures);
677 view.setShowText(av.getShowText());
678 view.setWrapAlignment(av.getWrapAlignment());
679 view.setTextCol1(av.textColour.getRGB());
680 view.setTextCol2(av.textColour2.getRGB());
681 view.setTextColThreshold(av.thresholdTextColour);
684 if(av.featuresDisplayed!=null)
686 jalview.schemabinding.version2.FeatureSettings fs
687 = new jalview.schemabinding.version2.FeatureSettings();
689 String [] renderOrder =
690 ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
692 Vector settingsAdded = new Vector();
693 for(int ro=0; ro<renderOrder.length; ro++)
695 Setting setting = new Setting();
696 setting.setType(renderOrder[ro]);
698 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
702 av.featuresDisplayed.containsKey(renderOrder[ro])
705 fs.addSetting(setting);
706 settingsAdded.addElement(renderOrder[ro]);
709 //Make sure we save none displayed feature settings
711 ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
712 while(en.hasMoreElements())
714 String key = en.nextElement().toString();
715 if(settingsAdded.contains(key))
718 Setting setting = new Setting();
719 setting.setType(key);
721 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
724 setting.setDisplay(false);
726 fs.addSetting(setting);
727 settingsAdded.addElement(key);
730 jms.setFeatureSettings(fs);
734 if(av.hasHiddenColumns)
736 for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)
738 int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);
739 HiddenColumns hc = new HiddenColumns();
740 hc.setStart(region[0]);
741 hc.setEnd(region[1]);
742 view.addHiddenColumns(hc);
746 jms.addViewport(view);
749 object.setJalviewModelSequence(jms);
750 object.getVamsasModel().addSequenceSet(vamsasSet);
754 //We may not want to right the object to disk,
755 //eg we can copy the alignViewport to a new view object
756 //using save and then load
759 if (!fileName.endsWith(".xml"))
761 fileName = fileName + ".xml";
764 JarEntry entry = new JarEntry(fileName);
765 jout.putNextEntry(entry);
771 ex.printStackTrace();
777 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
778 Vector userColours, JalviewModelSequence jms)
781 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
783 if (!userColours.contains(ucs))
785 userColours.add(ucs);
787 java.awt.Color[] colours = ucs.getColours();
788 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
789 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
791 for (int i = 0; i < colours.length; i++)
793 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
794 col.setName(ResidueProperties.aa[i]);
795 col.setRGB(jalview.util.Format.getHexString(colours[i]));
796 jbucs.addColour(col);
798 if(ucs.getLowerCaseColours()!=null)
800 colours = ucs.getLowerCaseColours();
801 for (int i = 0; i < colours.length; i++)
803 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
804 col.setName(ResidueProperties.aa[i].toLowerCase());
805 col.setRGB(jalview.util.Format.getHexString(colours[i]));
806 jbucs.addColour(col);
810 id = "ucs" + userColours.indexOf(ucs);
812 uc.setUserColourScheme(jbucs);
813 jms.addUserColours(uc);
819 jalview.schemes.UserColourScheme GetUserColourScheme(
820 JalviewModelSequence jms, String id)
822 UserColours[] uc = jms.getUserColours();
823 UserColours colours = null;
825 for (int i = 0; i < uc.length; i++)
827 if (uc[i].getId().equals(id))
835 java.awt.Color[] newColours = new java.awt.Color[24];
837 for (int i = 0; i < 24; i++)
839 newColours[i] = new java.awt.Color(Integer.parseInt(
840 colours.getUserColourScheme().getColour(i).getRGB(), 16));
843 jalview.schemes.UserColourScheme ucs =
844 new jalview.schemes.UserColourScheme(newColours);
846 if (colours.getUserColourScheme().getColourCount() > 24)
848 newColours = new java.awt.Color[23];
849 for (int i = 0; i < 23; i++)
851 newColours[i] = new java.awt.Color(Integer.parseInt(
852 colours.getUserColourScheme().getColour(i+24).getRGB(), 16));
854 ucs.setLowerCaseColours(newColours);
864 * @param file DOCUMENT ME!
866 public AlignFrame LoadJalviewAlign(final String file)
868 uniqueSetSuffix = System.currentTimeMillis()%100000 +"";
870 jalview.gui.AlignFrame af = null;
872 seqRefIds = new Hashtable();
873 viewportsAdded = new Hashtable();
875 Vector gatherToThisFrame= new Vector();
879 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
882 if (file.startsWith("http://"))
887 JarInputStream jin = null;
888 JarEntry jarentry = null;
895 jin = new JarInputStream(url.openStream());
899 jin = new JarInputStream(new FileInputStream(file));
902 for (int i = 0; i < entryCount; i++)
904 jarentry = jin.getNextJarEntry();
907 if (jarentry != null && jarentry.getName().endsWith(".xml"))
909 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
910 JalviewModel object = new JalviewModel();
912 Unmarshaller unmar = new Unmarshaller(object);
913 unmar.setValidation(false);
914 object = (JalviewModel) unmar.unmarshal( in );
916 af = LoadFromObject(object, file, true);
917 if(af.viewport.gatherViewsHere)
919 gatherToThisFrame.add(af);
923 else if (jarentry != null)
925 //Some other file here.
929 while (jarentry != null);
931 catch(java.net.UnknownHostException ex)
933 ex.printStackTrace();
934 System.err.println("Couldn't locate Jalview XML file : " +
937 javax.swing.SwingUtilities.invokeLater(new Runnable()
941 JOptionPane.showInternalMessageDialog(Desktop.desktop,
942 "Couldn't locate " + file,
944 JOptionPane.WARNING_MESSAGE);
950 //Is Version 1 Jar file?
951 af = new Jalview2XML_V1().LoadJalviewAlign(file);
955 System.out.println("Successfully loaded archive file");
959 System.err.println("Exception whilst loading jalview XML file : " +
961 javax.swing.SwingUtilities.invokeLater(new Runnable()
966 JOptionPane.showInternalMessageDialog(Desktop.desktop,
967 "Error loading " + file,
968 "Error loading Jalview file",
969 JOptionPane.WARNING_MESSAGE);
973 if (Desktop.instance != null)
974 Desktop.instance.stopLoading();
976 for (int i = 0; i < gatherToThisFrame.size(); i++)
978 Desktop.instance.gatherViews(
979 (AlignFrame) gatherToThisFrame.elementAt(i));
985 String loadPDBFile(String file, String pdbId)
987 System.out.println(file +" "+pdbId);
990 JarInputStream jin = null;
992 if (file.startsWith("http://"))
994 jin = new JarInputStream(new URL(file).openStream());
998 jin = new JarInputStream(new FileInputStream(file));
1001 JarEntry entry = null;
1004 entry = jin.getNextJarEntry();
1006 while (!entry.getName().equals(pdbId));
1008 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1009 File outFile = File.createTempFile("jalview_pdb", ".txt");
1010 outFile.deleteOnExit();
1011 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1014 while ( (data = in.readLine()) != null)
1019 return outFile.getAbsolutePath();
1022 catch (Exception ex)
1024 ex.printStackTrace();
1031 AlignFrame LoadFromObject(JalviewModel object,
1035 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1036 Sequence[] vamsasSeq = vamsasSet.getSequence();
1038 JalviewModelSequence jms = object.getJalviewModelSequence();
1040 Viewport view = jms.getViewport(0);
1042 //////////////////////////////////
1045 Vector hiddenSeqs = null;
1046 jalview.datamodel.Sequence jseq;
1048 ArrayList tmpseqs = new ArrayList();
1050 boolean multipleView = false;
1052 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1053 for (int i = 0; i < JSEQ.length; i++)
1055 String seqId = JSEQ[i].getId() + "";
1057 if (seqRefIds.get(seqId) != null)
1059 tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1060 multipleView = true;
1064 jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
1065 vamsasSeq[i].getSequence());
1066 jseq.setDescription(vamsasSeq[i].getDescription());
1067 jseq.setStart(JSEQ[i].getStart());
1068 jseq.setEnd(JSEQ[i].getEnd());
1069 seqRefIds.put(vamsasSeq[i].getId(), jseq);
1070 tmpseqs.add( jseq );
1075 if (JSEQ[i].getHidden())
1077 if (hiddenSeqs == null)
1078 hiddenSeqs = new Vector();
1081 hiddenSeqs.addElement(
1082 (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1087 ///SequenceFeatures are added to the DatasetSequence,
1088 // so we must create the dataset before loading features
1089 /////////////////////////////////
1092 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
1095 tmpseqs.toArray(orderedSeqs) ;
1098 jalview.datamodel.Alignment al =
1099 new jalview.datamodel.Alignment(orderedSeqs);
1101 al.setDataset(null);
1102 /////////////////////////////////
1105 Hashtable pdbloaded = new Hashtable();
1108 for (int i = 0; i < vamsasSeq.length; i++)
1110 if (JSEQ[i].getFeaturesCount() > 0)
1112 Features[] features = JSEQ[i].getFeatures();
1113 for (int f = 0; f < features.length; f++)
1115 jalview.datamodel.SequenceFeature sf
1116 = new jalview.datamodel.SequenceFeature(features[f].getType(),
1117 features[f].getDescription(), features[f].getStatus(),
1118 features[f].getBegin(), features[f].getEnd(),
1119 features[f].getFeatureGroup());
1121 sf.setScore(features[f].getScore());
1122 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1124 OtherData keyValue = features[f].getOtherData(od);
1125 if (keyValue.getKey().startsWith("LINK"))
1126 sf.addLink(keyValue.getValue());
1128 sf.setValue(keyValue.getKey(), keyValue.getValue());
1132 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1135 if (JSEQ[i].getPdbidsCount() > 0)
1137 Pdbids[] ids = JSEQ[i].getPdbids();
1138 for (int p = 0; p < ids.length; p++)
1140 jalview.datamodel.PDBEntry entry = new jalview.datamodel.
1142 entry.setId(ids[p].getId());
1143 entry.setType(ids[p].getType());
1144 if (ids[p].getFile() != null)
1146 if (!pdbloaded.containsKey(ids[p].getFile()))
1148 String tmppdb = loadPDBFile(file, ids[p].getId());
1149 entry.setFile(tmppdb);
1150 pdbloaded.put(ids[p].getId(), tmppdb);
1153 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1156 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1159 if (vamsasSeq[i].getDBRefCount() > 0)
1161 for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
1163 jalview.datamodel.DBRefEntry entry =
1164 new jalview.datamodel.DBRefEntry(
1165 vamsasSeq[i].getDBRef(d).getSource(),
1166 vamsasSeq[i].getDBRef(d).getVersion(),
1167 vamsasSeq[i].getDBRef(d).getAccessionId()
1169 al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1177 /////////////////////////////////
1178 //////////////////////////////////
1180 boolean hideQuality = true,
1181 hideConservation = true,
1182 hideConsensus = true;
1184 if (vamsasSet.getAnnotationCount()>0)
1186 Annotation[] an = vamsasSet.getAnnotation();
1188 for (int i = 0; i < an.length; i++)
1190 if (an[i].getLabel().equals("Quality"))
1192 hideQuality = false;
1195 else if(an[i].getLabel().equals("Conservation"))
1197 hideConservation = false;
1200 else if(an[i].getLabel().equals("Consensus"))
1202 hideConsensus = false;
1206 AnnotationElement[] ae = an[i].getAnnotationElement();
1207 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
1209 for (int aa = 0; aa < ae.length; aa++)
1211 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
1212 ae[aa].getDescription(),
1213 ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
1215 anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
1218 jalview.datamodel.AlignmentAnnotation jaa = null;
1220 if (an[i].getGraph())
1222 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1223 an[i].getDescription(), anot, 0, 0,
1224 an[i].getGraphType());
1226 jaa.graphGroup = an[i].getGraphGroup();
1228 if (an[i].getThresholdLine() != null)
1230 jaa.setThreshold(new jalview.datamodel.GraphLine(
1231 an[i].getThresholdLine().getValue(),
1232 an[i].getThresholdLine().getLabel(),
1233 new java.awt.Color(an[i].getThresholdLine().getColour()))
1241 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1242 an[i].getDescription(), anot);
1245 if(an[i].getSequenceRef()!=null)
1247 jaa.createSequenceMapping(
1248 al.findName(an[i].getSequenceRef()), 1, true
1250 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1253 al.addAnnotation(jaa);
1257 /////////////////////////
1259 if (jms.getJGroupCount() > 0)
1261 JGroup[] groups = jms.getJGroup();
1263 for (int i = 0; i < groups.length; i++)
1265 ColourSchemeI cs = null;
1267 if (groups[i].getColour() != null)
1269 if (groups[i].getColour().startsWith("ucs"))
1271 cs = GetUserColourScheme(jms, groups[i].getColour());
1275 cs = ColourSchemeProperty.getColour(al,
1276 groups[i].getColour());
1280 cs.setThreshold(groups[i].getPidThreshold(), true);
1283 Vector seqs = new Vector();
1285 for (int s = 0; s < groups[i].getSeqCount(); s++)
1287 String seqId = groups[i].getSeq(s)+"";
1288 seqs.addElement((jalview.datamodel.SequenceI) seqRefIds.get(seqId));
1291 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
1292 groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1293 groups[i].getDisplayText(), groups[i].getColourText(),
1294 groups[i].getStart(), groups[i].getEnd());
1296 sg.setOutlineColour(new java.awt.Color(
1297 groups[i].getOutlineColour()));
1299 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
1300 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
1301 sg.thresholdTextColour = groups[i].getTextColThreshold();
1303 if (groups[i].getConsThreshold() != 0)
1305 jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
1306 ResidueProperties.propHash, 3, sg.getSequences(false), 0,
1309 c.verdict(false, 25);
1310 sg.cs.setConservation(c);
1318 /////////////////////////////////
1321 AlignFrame af = new AlignFrame(al,
1325 af.setFileName(file, "Jalview");
1327 for (int i = 0; i < JSEQ.length; i++)
1329 af.viewport.setSequenceColour(
1330 af.viewport.alignment.getSequenceAt(i),
1332 JSEQ[i].getColour()));
1335 //If we just load in the same jar file again, the sequenceSetId
1336 //will be the same, and we end up with multiple references
1337 //to the same sequenceSet. We must modify this id on load
1338 //so that each load of the file gives a unique id
1339 String uniqueSeqSetId = view.getSequenceSetId()+uniqueSetSuffix;
1341 af.viewport.gatherViewsHere = view.getGatheredViews();
1343 if (view.getSequenceSetId() != null)
1345 jalview.gui.AlignViewport av =
1346 (jalview.gui.AlignViewport)
1347 viewportsAdded.get(uniqueSeqSetId);
1349 af.viewport.sequenceSetID = uniqueSeqSetId;
1353 af.viewport.historyList = av.historyList;
1354 af.viewport.redoList = av.redoList;
1358 viewportsAdded.put(uniqueSeqSetId, af.viewport);
1361 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1363 if(hiddenSeqs!=null)
1365 for(int s=0; s<JSEQ.length; s++)
1367 for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
1369 al.getSequenceAt(s).addHiddenSequence(
1370 al.getSequenceAt( JSEQ[s].getHiddenSequences(r) )
1375 jalview.datamodel.SequenceI [] hseqs = new
1376 jalview.datamodel.SequenceI[hiddenSeqs.size()];
1378 for(int s=0; s<hiddenSeqs.size(); s++)
1379 hseqs[s] = (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s);
1381 af.viewport.hideSequence( hseqs );
1386 if((hideConsensus || hideQuality || hideConservation)
1387 && al.getAlignmentAnnotation()!=null)
1389 int hSize = al.getAlignmentAnnotation().length;
1390 for (int h = 0; h < hSize; h++)
1394 al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1397 al.getAlignmentAnnotation()[h].label.equals("Quality"))
1399 (hideConservation &&
1400 al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1402 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1407 af.alignPanel.adjustAnnotationHeight();
1410 if(view.getViewName()!=null)
1412 af.viewport.viewName = view.getViewName();
1413 af.setInitialTabVisible();
1415 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1418 af.viewport.setShowAnnotation(view.getShowAnnotation());
1419 af.viewport.setAbovePIDThreshold(view.getPidSelected());
1421 af.viewport.setColourText(view.getShowColourText());
1423 af.viewport.setConservationSelected(view.getConservationSelected());
1424 af.viewport.setShowJVSuffix(view.getShowFullId());
1425 af.viewport.rightAlignIds=view.getRightAlignIds();
1426 af.viewport.setFont(new java.awt.Font(view.getFontName(),
1427 view.getFontStyle(), view.getFontSize()));
1428 af.alignPanel.fontChanged();
1429 af.viewport.setRenderGaps(view.getRenderGaps());
1430 af.viewport.setWrapAlignment(view.getWrapAlignment());
1431 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1432 af.viewport.setShowAnnotation(view.getShowAnnotation());
1433 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1435 af.viewport.setShowBoxes(view.getShowBoxes());
1437 af.viewport.setShowText(view.getShowText());
1439 af.viewport.textColour = new java.awt.Color(view.getTextCol1());
1440 af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
1441 af.viewport.thresholdTextColour = view.getTextColThreshold();
1443 af.viewport.setStartRes(view.getStartRes());
1444 af.viewport.setStartSeq(view.getStartSeq());
1446 ColourSchemeI cs = null;
1448 if (view.getBgColour() != null)
1450 if (view.getBgColour().startsWith("ucs"))
1452 cs = GetUserColourScheme(jms, view.getBgColour());
1454 else if(view.getBgColour().startsWith("Annotation"))
1456 //int find annotation
1457 for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1459 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1460 equals(view.getAnnotationColours().getAnnotation()))
1462 if (af.viewport.alignment.getAlignmentAnnotation()[i].
1463 getThreshold() == null)
1465 af.viewport.alignment.getAlignmentAnnotation()[i].
1467 new jalview.datamodel.GraphLine(
1468 view.getAnnotationColours().getThreshold(),
1469 "Threshold", java.awt.Color.black)
1475 if (view.getAnnotationColours().getColourScheme().equals(
1478 cs = new AnnotationColourGradient(
1479 af.viewport.alignment.getAlignmentAnnotation()[i],
1480 new java.awt.Color(view.getAnnotationColours().
1482 new java.awt.Color(view.getAnnotationColours().
1484 view.getAnnotationColours().getAboveThreshold());
1486 else if (view.getAnnotationColours().getColourScheme().
1489 cs = new AnnotationColourGradient(
1490 af.viewport.alignment.getAlignmentAnnotation()[i],
1491 GetUserColourScheme(jms, view.getAnnotationColours().
1493 view.getAnnotationColours().getAboveThreshold()
1498 cs = new AnnotationColourGradient(
1499 af.viewport.alignment.getAlignmentAnnotation()[i],
1500 ColourSchemeProperty.getColour(al,
1501 view.getAnnotationColours().getColourScheme()),
1502 view.getAnnotationColours().getAboveThreshold()
1506 // Also use these settings for all the groups
1507 if (al.getGroups() != null)
1508 for (int g = 0; g < al.getGroups().size(); g++)
1510 jalview.datamodel.SequenceGroup sg
1511 = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
1517 /* if (view.getAnnotationColours().getColourScheme().equals("None"))
1519 sg.cs = new AnnotationColourGradient(
1520 af.viewport.alignment.getAlignmentAnnotation()[i],
1521 new java.awt.Color(view.getAnnotationColours().
1523 new java.awt.Color(view.getAnnotationColours().
1525 view.getAnnotationColours().getAboveThreshold());
1529 sg.cs = new AnnotationColourGradient(
1530 af.viewport.alignment.getAlignmentAnnotation()[i],
1532 view.getAnnotationColours().getAboveThreshold()
1546 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1551 cs.setThreshold(view.getPidThreshold(), true);
1552 cs.setConsensus(af.viewport.hconsensus);
1557 af.viewport.setGlobalColourScheme(cs);
1558 af.viewport.setColourAppliesToAllGroups(false);
1560 if (view.getConservationSelected() && cs!=null)
1562 cs.setConservationInc(view.getConsThreshold());
1565 af.changeColour(cs);
1567 af.viewport.setColourAppliesToAllGroups(true);
1571 if (view.getShowSequenceFeatures())
1573 af.viewport.showSequenceFeatures = true;
1576 if(jms.getFeatureSettings()!=null)
1578 af.viewport.featuresDisplayed = new Hashtable();
1579 String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
1580 for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
1582 Setting setting = jms.getFeatureSettings().getSetting(fs);
1584 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
1585 new java.awt.Color(setting.getColour()));
1587 renderOrder[fs] = setting.getType();
1589 if(setting.getDisplay())
1590 af.viewport.featuresDisplayed.put(
1591 setting.getType(), new Integer(setting.getColour()));
1593 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
1596 if (view.getHiddenColumnsCount() > 0)
1598 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1600 af.viewport.hideColumns(
1601 view.getHiddenColumns(c).getStart(),
1602 view.getHiddenColumns(c).getEnd() //+1
1607 af.setMenusFromViewport(af.viewport);
1610 Desktop.addInternalFrame(af, view.getTitle(),
1611 view.getWidth(), view.getHeight());
1614 ///////////////////////////////////////
1615 if (loadTrees && jms.getTreeCount() > 0)
1619 for (int t = 0; t < jms.getTreeCount(); t++)
1622 Tree tree = jms.getTree(t);
1624 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1625 tree.getNewick()), tree.getTitle(),
1626 tree.getWidth(), tree.getHeight(),
1627 tree.getXpos(), tree.getYpos());
1629 tp.fitToWindow.setState(tree.getFitToWindow());
1630 tp.fitToWindow_actionPerformed(null);
1632 if(tree.getFontName()!=null)
1633 tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1634 tree.getFontStyle(),
1635 tree.getFontSize()));
1637 tp.setTreeFont(new java.awt.Font(view.getFontName(),
1638 view.getFontStyle(),
1639 tree.getFontSize()));
1641 tp.showPlaceholders(tree.getMarkUnlinked());
1642 tp.showBootstrap(tree.getShowBootstrap());
1643 tp.showDistances(tree.getShowDistances());
1645 tp.treeCanvas.threshold = tree.getThreshold();
1647 if (tree.getCurrentTree())
1648 af.viewport.setCurrentTree(tp.getTree());
1652 catch (Exception ex)
1654 ex.printStackTrace();
1662 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, boolean keepSeqRefs )
1664 jalview.schemabinding.version2.JalviewModel jm
1665 = SaveState(ap, null, null, null);
1670 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
1673 uniqueSetSuffix = "";
1675 viewportsAdded = new Hashtable();
1677 AlignFrame af = LoadFromObject(jm, null, false);
1678 af.alignPanels.clear();
1679 af.closeMenuItem_actionPerformed(true);
1681 return af.alignPanel;