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 for (int i = 0; i < jal.getHeight(); i++)
220 id = jal.getSequenceAt(i).hashCode();
222 if(seqRefIds.get(id+"")!=null)
228 vamsasSeq = new Sequence();
229 vamsasSeq.setId(id + "");
230 vamsasSeq.setName(jal.getSequenceAt(i).getName());
231 vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
232 vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());
234 if (jal.getSequenceAt(i).getDatasetSequence().getDBRef() != null)
236 jalview.datamodel.DBRefEntry[] dbrefs =
237 jal.getSequenceAt(i).getDatasetSequence().getDBRef();
239 for (int d = 0; d < dbrefs.length; d++)
241 DBRef dbref = new DBRef();
242 dbref.setSource(dbrefs[d].getSource());
243 dbref.setVersion(dbrefs[d].getVersion());
244 dbref.setAccessionId(dbrefs[d].getAccessionId());
245 vamsasSeq.addDBRef(dbref);
249 vamsasSet.addSequence(vamsasSeq);
250 seqRefIds.put(id+"", jal.getSequenceAt(i));
254 jseq.setStart(jal.getSequenceAt(i).getStart());
255 jseq.setEnd(jal.getSequenceAt(i).getEnd());
256 jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
260 if (av.hasHiddenRows)
262 jseq.setHidden(av.alignment.getHiddenSequences().isHidden(
263 jal.getSequenceAt(i)));
265 if(jal.getSequenceAt(i).getHiddenSequences()!=null)
267 jalview.datamodel.SequenceI [] reps =
268 jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal);
270 for(int h=0; h<reps.length; h++)
272 jseq.addHiddenSequences(
273 jal.findIndex(reps[h])
280 if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)
282 jalview.datamodel.SequenceFeature[] sf
283 = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
285 while(index < sf.length)
287 Features features = new Features();
289 features.setBegin(sf[index].getBegin());
290 features.setEnd(sf[index].getEnd());
291 features.setDescription(sf[index].getDescription());
292 features.setType(sf[index].getType());
293 features.setFeatureGroup(sf[index].getFeatureGroup());
294 features.setScore(sf[index].getScore());
295 if(sf[index].links!=null)
297 for(int l=0; l<sf[index].links.size(); l++)
299 OtherData keyValue = new OtherData();
300 keyValue.setKey("LINK_"+l);
301 keyValue.setValue(sf[index].links.elementAt(l).toString());
302 features.addOtherData(keyValue);
305 if(sf[index].otherDetails!=null)
308 Enumeration keys = sf[index].otherDetails.keys();
309 while(keys.hasMoreElements())
311 key = keys.nextElement().toString();
312 OtherData keyValue = new OtherData();
313 keyValue.setKey( key );
315 sf[index].otherDetails.get(key).toString());
316 features.addOtherData(keyValue);
320 jseq.addFeatures(features);
325 if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)
327 Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();
328 while(en.hasMoreElements())
330 Pdbids pdb = new Pdbids();
331 jalview.datamodel.PDBEntry entry
332 = (jalview.datamodel.PDBEntry)en.nextElement();
334 pdb.setId(entry.getId());
335 pdb.setType(entry.getType());
337 if(entry.getFile()!=null)
340 pdbfiles = new Vector();
343 if(!pdbfiles.contains(entry.getId()))
345 pdbfiles.addElement(entry.getId());
348 File file = new File(entry.getFile());
351 byte[] data = new byte[ (int) file.length()];
352 jout.putNextEntry(new JarEntry(entry.getId()));
353 DataInputStream dis = new DataInputStream(new
354 FileInputStream(file));
357 DataOutputStream dout = new DataOutputStream(jout);
358 dout.write(data, 0, data.length);
364 ex.printStackTrace();
370 if(entry.getProperty()!=null)
372 PdbentryItem item = new PdbentryItem();
373 Hashtable properties = entry.getProperty();
374 Enumeration en2 = properties.keys();
375 while(en2.hasMoreElements())
377 Property prop = new Property();
378 String key = en2.nextElement().toString();
380 prop.setValue( properties.get(key).toString() );
381 item.addProperty(prop);
383 pdb.addPdbentryItem(item);
398 ///////////////////////////////////
399 if (av.currentTree != null)
401 // FIND ANY ASSOCIATED TREES
402 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
403 if (Desktop.desktop != null)
405 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
407 for (int t = 0; t < frames.length; t++)
409 if (frames[t] instanceof TreePanel)
411 TreePanel tp = (TreePanel) frames[t];
413 if (tp.treeCanvas.av.alignment == jal)
415 Tree tree = new Tree();
416 tree.setTitle(tp.getTitle());
417 tree.setCurrentTree( (av.currentTree == tp.getTree()));
418 tree.setNewick(tp.getTree().toString());
419 tree.setThreshold(tp.treeCanvas.threshold);
421 tree.setFitToWindow(tp.fitToWindow.getState());
422 tree.setFontName(tp.getTreeFont().getName());
423 tree.setFontSize(tp.getTreeFont().getSize());
424 tree.setFontStyle(tp.getTreeFont().getStyle());
425 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
427 tree.setShowBootstrap(tp.bootstrapMenu.getState());
428 tree.setShowDistances(tp.distanceMenu.getState());
430 tree.setHeight(tp.getHeight());
431 tree.setWidth(tp.getWidth());
432 tree.setXpos(tp.getX());
433 tree.setYpos(tp.getY());
443 if (jal.getAlignmentAnnotation() != null)
445 jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
447 for (int i = 0; i < aa.length; i++)
449 Annotation an = new Annotation();
451 if (aa[i].label.equals("Quality") ||
452 aa[i].label.equals("Conservation") ||
453 aa[i].label.equals("Consensus"))
455 an.setLabel(aa[i].label);
457 vamsasSet.addAnnotation(an);
462 an.setDescription(aa[i].description);
464 if(aa[i].sequenceRef!=null)
466 an.setSequenceRef(aa[i].sequenceRef.getName());
472 an.setGraphType(aa[i].graph);
473 an.setGraphGroup(aa[i].graphGroup);
474 if(aa[i].getThreshold()!=null)
476 ThresholdLine line = new ThresholdLine();
477 line.setLabel(aa[i].getThreshold().label);
478 line.setValue(aa[i].getThreshold().value);
479 line.setColour(aa[i].getThreshold().colour.getRGB());
480 an.setThresholdLine(line);
486 an.setLabel(aa[i].label);
488 AnnotationElement ae;
490 for (int a = 0; a < aa[i].annotations.length; a++)
492 if ((aa[i] == null) || (aa[i].annotations[a] == null))
497 ae = new AnnotationElement();
498 ae.setDescription(aa[i].annotations[a].description);
499 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
500 ae.setValue(aa[i].annotations[a].value);
502 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
505 if(aa[i].annotations[a].colour!=java.awt.Color.black)
506 ae.setColour(aa[i].annotations[a].colour.getRGB());
508 an.addAnnotationElement(ae);
511 vamsasSet.addAnnotation(an);
516 if (jal.getGroups() != null)
518 JGroup[] groups = new JGroup[jal.getGroups().size()];
520 for (int i = 0; i < groups.length; i++)
522 groups[i] = new JGroup();
524 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
526 groups[i].setStart(sg.getStartRes());
527 groups[i].setEnd(sg.getEndRes());
528 groups[i].setName(sg.getName());
531 if (sg.cs.conservationApplied())
533 groups[i].setConsThreshold(sg.cs.getConservationInc());
535 if (sg.cs instanceof jalview.schemes.UserColourScheme)
537 groups[i].setColour(SetUserColourScheme(sg.cs,
543 groups[i].setColour(ColourSchemeProperty.getColourName(sg.
547 else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)
550 ColourSchemeProperty.getColourName(
551 ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));
553 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
555 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
560 groups[i].setColour(ColourSchemeProperty.getColourName(
564 groups[i].setPidThreshold(sg.cs.getThreshold());
567 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
568 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
569 groups[i].setDisplayText(sg.getDisplayText());
570 groups[i].setColourText(sg.getColourText());
572 for (int s = 0; s < sg.getSize(false); s++)
574 jalview.datamodel.Sequence seq =
575 (jalview.datamodel.Sequence) sg.getSequenceAt(s);
576 groups[i].addSeq(seq.hashCode());
580 jms.setJGroup(groups);
584 ///////////SAVE VIEWPORT
585 Viewport view = new Viewport();
586 view.setTitle(ap.alignFrame.getTitle());
587 view.setSequenceSetId(av.getSequenceSetId());
588 view.setViewName(av.viewName);
589 view.setGatheredViews(av.gatherViewsHere);
592 if (ap.av.explodedPosition != null)
594 view.setXpos(av.explodedPosition.x);
595 view.setYpos(av.explodedPosition.y);
596 view.setWidth(av.explodedPosition.width);
597 view.setHeight(av.explodedPosition.height);
601 view.setXpos(ap.alignFrame.getBounds().x);
602 view.setYpos(ap.alignFrame.getBounds().y);
603 view.setWidth(ap.alignFrame.getBounds().width);
604 view.setHeight(ap.alignFrame.getBounds().height);
607 view.setStartRes(av.startRes);
608 view.setStartSeq(av.startSeq);
610 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
612 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
615 else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
617 jalview.schemes.AnnotationColourGradient acg
618 = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();
620 AnnotationColours ac = new AnnotationColours();
621 ac.setAboveThreshold(acg.getAboveThreshold());
622 ac.setThreshold(acg.getAnnotationThreshold());
623 ac.setAnnotation(acg.getAnnotation());
624 if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
625 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
628 ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
630 ac.setMaxColour(acg.getMaxColour().getRGB());
631 ac.setMinColour(acg.getMinColour().getRGB());
632 view.setAnnotationColours(ac);
633 view.setBgColour("AnnotationColourGradient");
637 view.setBgColour(ColourSchemeProperty.getColourName(
638 av.getGlobalColourScheme()));
641 ColourSchemeI cs = av.getGlobalColourScheme();
645 if (cs.conservationApplied())
647 view.setConsThreshold(cs.getConservationInc());
648 if (cs instanceof jalview.schemes.UserColourScheme)
649 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
652 if (cs instanceof ResidueColourScheme)
654 view.setPidThreshold(cs.getThreshold());
658 view.setConservationSelected(av.getConservationSelected());
659 view.setPidSelected(av.getAbovePIDThreshold());
660 view.setFontName(av.font.getName());
661 view.setFontSize(av.font.getSize());
662 view.setFontStyle(av.font.getStyle());
663 view.setRenderGaps(av.renderGaps);
664 view.setShowAnnotation(av.getShowAnnotation());
665 view.setShowBoxes(av.getShowBoxes());
666 view.setShowColourText(av.getColourText());
667 view.setShowFullId(av.getShowJVSuffix());
668 view.setShowSequenceFeatures(av.showSequenceFeatures);
669 view.setShowText(av.getShowText());
670 view.setWrapAlignment(av.getWrapAlignment());
672 if(av.featuresDisplayed!=null)
674 jalview.schemabinding.version2.FeatureSettings fs
675 = new jalview.schemabinding.version2.FeatureSettings();
677 String [] renderOrder =
678 ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
680 Vector settingsAdded = new Vector();
681 for(int ro=0; ro<renderOrder.length; ro++)
683 Setting setting = new Setting();
684 setting.setType(renderOrder[ro]);
686 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
690 av.featuresDisplayed.containsKey(renderOrder[ro])
693 fs.addSetting(setting);
694 settingsAdded.addElement(renderOrder[ro]);
697 //Make sure we save none displayed feature settings
699 ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
700 while(en.hasMoreElements())
702 String key = en.nextElement().toString();
703 if(settingsAdded.contains(key))
706 Setting setting = new Setting();
707 setting.setType(key);
709 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
712 setting.setDisplay(false);
714 fs.addSetting(setting);
715 settingsAdded.addElement(key);
718 jms.setFeatureSettings(fs);
722 if(av.hasHiddenColumns)
724 for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)
726 int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);
727 HiddenColumns hc = new HiddenColumns();
728 hc.setStart(region[0]);
729 hc.setEnd(region[1]);
730 view.addHiddenColumns(hc);
734 jms.addViewport(view);
737 object.setJalviewModelSequence(jms);
738 object.getVamsasModel().addSequenceSet(vamsasSet);
742 //We may not want to right the object to disk,
743 //eg we can copy the alignViewport to a new view object
744 //using save and then load
747 if (!fileName.endsWith(".xml"))
749 fileName = fileName + ".xml";
752 JarEntry entry = new JarEntry(fileName);
753 jout.putNextEntry(entry);
759 ex.printStackTrace();
765 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
766 Vector userColours, JalviewModelSequence jms)
769 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
771 if (!userColours.contains(ucs))
773 userColours.add(ucs);
775 java.awt.Color[] colours = ucs.getColours();
776 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
777 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
779 for (int i = 0; i < colours.length; i++)
781 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
782 col.setName(ResidueProperties.aa[i]);
783 col.setRGB(jalview.util.Format.getHexString(colours[i]));
784 jbucs.addColour(col);
786 if(ucs.getLowerCaseColours()!=null)
788 colours = ucs.getLowerCaseColours();
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].toLowerCase());
793 col.setRGB(jalview.util.Format.getHexString(colours[i]));
794 jbucs.addColour(col);
798 id = "ucs" + userColours.indexOf(ucs);
800 uc.setUserColourScheme(jbucs);
801 jms.addUserColours(uc);
807 jalview.schemes.UserColourScheme GetUserColourScheme(
808 JalviewModelSequence jms, String id)
810 UserColours[] uc = jms.getUserColours();
811 UserColours colours = null;
813 for (int i = 0; i < uc.length; i++)
815 if (uc[i].getId().equals(id))
823 java.awt.Color[] newColours = new java.awt.Color[24];
825 for (int i = 0; i < 24; i++)
827 newColours[i] = new java.awt.Color(Integer.parseInt(
828 colours.getUserColourScheme().getColour(i).getRGB(), 16));
831 jalview.schemes.UserColourScheme ucs =
832 new jalview.schemes.UserColourScheme(newColours);
834 if (colours.getUserColourScheme().getColourCount() > 24)
836 newColours = new java.awt.Color[23];
837 for (int i = 0; i < 23; i++)
839 newColours[i] = new java.awt.Color(Integer.parseInt(
840 colours.getUserColourScheme().getColour(i+24).getRGB(), 16));
842 ucs.setLowerCaseColours(newColours);
852 * @param file DOCUMENT ME!
854 public AlignFrame LoadJalviewAlign(final String file)
856 uniqueSetSuffix = System.currentTimeMillis()%100000 +"";
858 jalview.gui.AlignFrame af = null;
860 seqRefIds = new Hashtable();
861 viewportsAdded = new Hashtable();
863 Vector gatherToThisFrame= new Vector();
867 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
870 if (file.startsWith("http://"))
875 JarInputStream jin = null;
876 JarEntry jarentry = null;
883 jin = new JarInputStream(url.openStream());
887 jin = new JarInputStream(new FileInputStream(file));
890 for (int i = 0; i < entryCount; i++)
892 jarentry = jin.getNextJarEntry();
895 if (jarentry != null && jarentry.getName().endsWith(".xml"))
897 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
898 JalviewModel object = new JalviewModel();
900 Unmarshaller unmar = new Unmarshaller(object);
901 unmar.setValidation(false);
902 object = (JalviewModel) unmar.unmarshal( in );
904 af = LoadFromObject(object, file);
905 if(af.viewport.gatherViewsHere)
907 gatherToThisFrame.add(af);
911 else if (jarentry != null)
913 //Some other file here.
917 while (jarentry != null);
919 catch(java.net.UnknownHostException ex)
921 ex.printStackTrace();
922 System.err.println("Couldn't locate Jalview XML file : " +
925 javax.swing.SwingUtilities.invokeLater(new Runnable()
929 JOptionPane.showInternalMessageDialog(Desktop.desktop,
930 "Couldn't locate " + file,
932 JOptionPane.WARNING_MESSAGE);
938 //Is Version 1 Jar file?
939 af = new Jalview2XML_V1().LoadJalviewAlign(file);
943 System.out.println("Successfully loaded archive file");
947 System.err.println("Exception whilst loading jalview XML file : " +
949 javax.swing.SwingUtilities.invokeLater(new Runnable()
954 JOptionPane.showInternalMessageDialog(Desktop.desktop,
955 "Error loading " + file,
956 "Error loading Jalview file",
957 JOptionPane.WARNING_MESSAGE);
961 if (Desktop.instance != null)
962 Desktop.instance.stopLoading();
964 for (int i = 0; i < gatherToThisFrame.size(); i++)
966 Desktop.instance.gatherViews(
967 (AlignFrame) gatherToThisFrame.elementAt(i));
973 String loadPDBFile(String file, String pdbId)
977 JarInputStream jin = null;
979 if (file.startsWith("http://"))
981 jin = new JarInputStream(new URL(file).openStream());
985 jin = new JarInputStream(new FileInputStream(file));
988 JarEntry entry = null;
991 entry = jin.getNextJarEntry();
993 while (!entry.getName().equals(pdbId));
995 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
996 File outFile = File.createTempFile("jalview_pdb", ".txt");
997 outFile.deleteOnExit();
998 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1001 while ( (data = in.readLine()) != null)
1006 return outFile.getAbsolutePath();
1009 catch (Exception ex)
1011 ex.printStackTrace();
1018 AlignFrame LoadFromObject(JalviewModel object, String file)
1020 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1021 Sequence[] vamsasSeq = vamsasSet.getSequence();
1023 JalviewModelSequence jms = object.getJalviewModelSequence();
1025 Viewport view = jms.getViewport(0);
1027 //////////////////////////////////
1030 Vector hiddenSeqs = null;
1031 jalview.datamodel.Sequence jseq;
1033 ArrayList tmpseqs = new ArrayList();
1036 boolean multipleView = false;
1038 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1039 for (int i = 0; i < JSEQ.length; i++)
1041 String seqId = JSEQ[i].getId() + "";
1043 if (seqRefIds.get(seqId) != null)
1045 tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1046 multipleView = true;
1050 jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
1051 vamsasSeq[i].getSequence());
1052 jseq.setDescription(vamsasSeq[i].getDescription());
1053 jseq.setStart(JSEQ[i].getStart());
1054 jseq.setEnd(JSEQ[i].getEnd());
1055 jseq.setColor(new java.awt.Color(JSEQ[i].getColour()));
1056 seqRefIds.put(vamsasSeq[i].getId(), jseq);
1057 tmpseqs.add( jseq );
1061 if (JSEQ[i].getHidden())
1063 if (hiddenSeqs == null)
1064 hiddenSeqs = new Vector();
1067 hiddenSeqs.addElement(
1068 (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1073 ///SequenceFeatures are added to the DatasetSequence,
1074 // so we must create the dataset before loading features
1075 /////////////////////////////////
1078 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
1081 tmpseqs.toArray(orderedSeqs) ;
1084 jalview.datamodel.Alignment al =
1085 new jalview.datamodel.Alignment(orderedSeqs);
1087 al.setDataset(null);
1088 /////////////////////////////////
1091 Hashtable pdbloaded = new Hashtable();
1094 for (int i = 0; i < vamsasSeq.length; i++)
1096 if (JSEQ[i].getFeaturesCount() > 0)
1098 Features[] features = JSEQ[i].getFeatures();
1099 for (int f = 0; f < features.length; f++)
1101 jalview.datamodel.SequenceFeature sf
1102 = new jalview.datamodel.SequenceFeature(features[f].getType(),
1103 features[f].getDescription(), features[f].getStatus(),
1104 features[f].getBegin(), features[f].getEnd(),
1105 features[f].getFeatureGroup());
1107 sf.setScore(features[f].getScore());
1108 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1110 OtherData keyValue = features[f].getOtherData(od);
1111 if (keyValue.getKey().startsWith("LINK"))
1112 sf.addLink(keyValue.getValue());
1114 sf.setValue(keyValue.getKey(), keyValue.getValue());
1118 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1121 if (JSEQ[i].getPdbidsCount() > 0)
1123 Pdbids[] ids = JSEQ[i].getPdbids();
1124 for (int p = 0; p < ids.length; p++)
1126 jalview.datamodel.PDBEntry entry = new jalview.datamodel.
1128 entry.setId(ids[p].getId());
1129 entry.setType(ids[p].getType());
1130 if (ids[p].getFile() != null)
1132 if (!pdbloaded.containsKey(ids[p].getFile()))
1134 String tmppdb = loadPDBFile(file, ids[p].getId());
1135 entry.setFile(tmppdb);
1136 pdbloaded.put(ids[p].getId(), tmppdb);
1139 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1142 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1145 if (vamsasSeq[i].getDBRefCount() > 0)
1147 for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
1149 jalview.datamodel.DBRefEntry entry =
1150 new jalview.datamodel.DBRefEntry(
1151 vamsasSeq[i].getDBRef(d).getSource(),
1152 vamsasSeq[i].getDBRef(d).getVersion(),
1153 vamsasSeq[i].getDBRef(d).getAccessionId()
1155 al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1163 /////////////////////////////////
1164 //////////////////////////////////
1166 boolean hideQuality = true,
1167 hideConservation = true,
1168 hideConsensus = true;
1170 if (vamsasSet.getAnnotationCount()>0)
1172 Annotation[] an = vamsasSet.getAnnotation();
1174 for (int i = 0; i < an.length; i++)
1176 if (an[i].getLabel().equals("Quality"))
1178 hideQuality = false;
1181 else if(an[i].getLabel().equals("Conservation"))
1183 hideConservation = false;
1186 else if(an[i].getLabel().equals("Consensus"))
1188 hideConsensus = false;
1192 AnnotationElement[] ae = an[i].getAnnotationElement();
1193 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
1195 for (int aa = 0; aa < ae.length; aa++)
1197 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
1198 ae[aa].getDescription(),
1199 ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
1201 anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
1204 jalview.datamodel.AlignmentAnnotation jaa = null;
1206 if (an[i].getGraph())
1208 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1209 an[i].getDescription(), anot, 0, 0,
1210 an[i].getGraphType());
1212 jaa.graphGroup = an[i].getGraphGroup();
1214 if (an[i].getThresholdLine() != null)
1216 jaa.setThreshold(new jalview.datamodel.GraphLine(
1217 an[i].getThresholdLine().getValue(),
1218 an[i].getThresholdLine().getLabel(),
1219 new java.awt.Color(an[i].getThresholdLine().getColour()))
1227 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1228 an[i].getDescription(), anot);
1231 if(an[i].getSequenceRef()!=null)
1233 jaa.createSequenceMapping(
1234 al.findName(an[i].getSequenceRef()), 1, true
1236 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1239 al.addAnnotation(jaa);
1243 /////////////////////////
1245 if (jms.getJGroupCount() > 0)
1247 JGroup[] groups = jms.getJGroup();
1249 for (int i = 0; i < groups.length; i++)
1251 ColourSchemeI cs = null;
1253 if (groups[i].getColour() != null)
1255 if (groups[i].getColour().startsWith("ucs"))
1257 cs = GetUserColourScheme(jms, groups[i].getColour());
1261 cs = ColourSchemeProperty.getColour(al,
1262 groups[i].getColour());
1266 cs.setThreshold(groups[i].getPidThreshold(), true);
1269 Vector seqs = new Vector();
1271 for (int s = 0; s < groups[i].getSeqCount(); s++)
1273 String seqId = groups[i].getSeq(s)+"";
1274 seqs.addElement((jalview.datamodel.SequenceI) seqRefIds.get(seqId));
1277 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
1278 groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1279 groups[i].getDisplayText(), groups[i].getColourText(),
1280 groups[i].getStart(), groups[i].getEnd());
1282 sg.setOutlineColour(new java.awt.Color(
1283 groups[i].getOutlineColour()));
1285 if (groups[i].getConsThreshold() != 0)
1287 jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
1288 ResidueProperties.propHash, 3, sg.getSequences(false), 0,
1291 c.verdict(false, 25);
1292 sg.cs.setConservation(c);
1300 /////////////////////////////////
1303 AlignFrame af = new AlignFrame(al,
1308 //If we just load in the same jar file again, the sequenceSetId
1309 //will be the same, and we end up with multiple references
1310 //to the same sequenceSet. We must modify this id on load
1311 //so that each load of the file gives a unique id
1312 String uniqueSeqSetId = view.getSequenceSetId()+uniqueSetSuffix;
1314 af.viewport.gatherViewsHere = view.getGatheredViews();
1316 if (view.getSequenceSetId() != null)
1318 jalview.gui.AlignViewport av =
1319 (jalview.gui.AlignViewport)
1320 viewportsAdded.get(uniqueSeqSetId);
1322 af.viewport.sequenceSetID = uniqueSeqSetId;
1326 af.viewport.historyList = av.historyList;
1327 af.viewport.redoList = av.redoList;
1331 viewportsAdded.put(uniqueSeqSetId, af.viewport);
1334 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1336 if(hiddenSeqs!=null)
1338 for(int s=0; s<JSEQ.length; s++)
1340 for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
1342 al.getSequenceAt(s).addHiddenSequence(
1343 al.getSequenceAt( JSEQ[s].getHiddenSequences(r) )
1348 jalview.datamodel.SequenceI [] hseqs = new
1349 jalview.datamodel.SequenceI[hiddenSeqs.size()];
1351 for(int s=0; s<hiddenSeqs.size(); s++)
1352 hseqs[s] = (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s);
1354 af.viewport.hideSequence( hseqs );
1359 if((hideConsensus || hideQuality || hideConservation)
1360 && al.getAlignmentAnnotation()!=null)
1362 int hSize = al.getAlignmentAnnotation().length;
1363 for (int h = 0; h < hSize; h++)
1367 al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1370 al.getAlignmentAnnotation()[h].label.equals("Quality"))
1372 (hideConservation &&
1373 al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1375 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1380 af.alignPanel.adjustAnnotationHeight();
1383 af.viewport.viewName = view.getViewName();
1384 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1386 af.viewport.setStartRes(view.getStartRes());
1387 af.viewport.setStartSeq(view.getStartSeq());
1388 af.viewport.setShowAnnotation(view.getShowAnnotation());
1389 af.viewport.setAbovePIDThreshold(view.getPidSelected());
1391 af.viewport.setColourText(view.getShowColourText());
1393 af.viewport.setConservationSelected(view.getConservationSelected());
1394 af.viewport.setShowJVSuffix(view.getShowFullId());
1395 af.viewport.setFont(new java.awt.Font(view.getFontName(),
1396 view.getFontStyle(), view.getFontSize()));
1397 af.alignPanel.fontChanged();
1398 af.viewport.setRenderGaps(view.getRenderGaps());
1399 af.viewport.setWrapAlignment(view.getWrapAlignment());
1400 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1401 af.viewport.setShowAnnotation(view.getShowAnnotation());
1402 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1404 af.viewport.setShowBoxes(view.getShowBoxes());
1406 af.viewport.setShowText(view.getShowText());
1409 ColourSchemeI cs = null;
1411 if (view.getBgColour() != null)
1413 if (view.getBgColour().startsWith("ucs"))
1415 cs = GetUserColourScheme(jms, view.getBgColour());
1417 else if(view.getBgColour().startsWith("Annotation"))
1419 //int find annotation
1420 for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1422 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1423 equals(view.getAnnotationColours().getAnnotation()))
1425 if (af.viewport.alignment.getAlignmentAnnotation()[i].
1426 getThreshold() == null)
1428 af.viewport.alignment.getAlignmentAnnotation()[i].
1430 new jalview.datamodel.GraphLine(
1431 view.getAnnotationColours().getThreshold(),
1432 "Threshold", java.awt.Color.black)
1438 if (view.getAnnotationColours().getColourScheme().equals(
1441 cs = new AnnotationColourGradient(
1442 af.viewport.alignment.getAlignmentAnnotation()[i],
1443 new java.awt.Color(view.getAnnotationColours().
1445 new java.awt.Color(view.getAnnotationColours().
1447 view.getAnnotationColours().getAboveThreshold());
1449 else if (view.getAnnotationColours().getColourScheme().
1452 cs = new AnnotationColourGradient(
1453 af.viewport.alignment.getAlignmentAnnotation()[i],
1454 GetUserColourScheme(jms, view.getAnnotationColours().
1456 view.getAnnotationColours().getAboveThreshold()
1461 cs = new AnnotationColourGradient(
1462 af.viewport.alignment.getAlignmentAnnotation()[i],
1463 ColourSchemeProperty.getColour(al,
1464 view.getAnnotationColours().getColourScheme()),
1465 view.getAnnotationColours().getAboveThreshold()
1469 // Also use these settings for all the groups
1470 if (al.getGroups() != null)
1471 for (int g = 0; g < al.getGroups().size(); g++)
1473 jalview.datamodel.SequenceGroup sg
1474 = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
1480 /* if (view.getAnnotationColours().getColourScheme().equals("None"))
1482 sg.cs = new AnnotationColourGradient(
1483 af.viewport.alignment.getAlignmentAnnotation()[i],
1484 new java.awt.Color(view.getAnnotationColours().
1486 new java.awt.Color(view.getAnnotationColours().
1488 view.getAnnotationColours().getAboveThreshold());
1492 sg.cs = new AnnotationColourGradient(
1493 af.viewport.alignment.getAlignmentAnnotation()[i],
1495 view.getAnnotationColours().getAboveThreshold()
1509 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1514 cs.setThreshold(view.getPidThreshold(), true);
1515 cs.setConsensus(af.viewport.hconsensus);
1520 af.viewport.setGlobalColourScheme(cs);
1521 af.viewport.setColourAppliesToAllGroups(false);
1523 if (view.getConservationSelected() && cs!=null)
1525 cs.setConservationInc(view.getConsThreshold());
1528 af.changeColour(cs);
1530 af.viewport.setColourAppliesToAllGroups(true);
1534 if (view.getShowSequenceFeatures())
1536 af.viewport.showSequenceFeatures = true;
1539 if(jms.getFeatureSettings()!=null)
1541 af.viewport.featuresDisplayed = new Hashtable();
1542 String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
1543 for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
1545 Setting setting = jms.getFeatureSettings().getSetting(fs);
1547 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
1548 new java.awt.Color(setting.getColour()));
1550 renderOrder[fs] = setting.getType();
1552 if(setting.getDisplay())
1553 af.viewport.featuresDisplayed.put(
1554 setting.getType(), new Integer(setting.getColour()));
1556 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
1559 if (view.getHiddenColumnsCount() > 0)
1561 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1563 af.viewport.hideColumns(
1564 view.getHiddenColumns(c).getStart(),
1565 view.getHiddenColumns(c).getEnd() //+1
1570 af.setMenusFromViewport(af.viewport);
1573 Desktop.addInternalFrame(af, view.getTitle(),
1574 view.getWidth(), view.getHeight());
1577 ///////////////////////////////////////
1578 if (jms.getTreeCount() > 0)
1582 for (int t = 0; t < jms.getTreeCount(); t++)
1585 Tree tree = jms.getTree(t);
1587 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1588 tree.getNewick()), tree.getTitle(),
1589 tree.getWidth(), tree.getHeight(),
1590 tree.getXpos(), tree.getYpos());
1592 tp.fitToWindow.setState(tree.getFitToWindow());
1593 tp.fitToWindow_actionPerformed(null);
1595 if(tree.getFontName()!=null)
1596 tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1597 tree.getFontStyle(),
1598 tree.getFontSize()));
1600 tp.setTreeFont(new java.awt.Font(view.getFontName(),
1601 view.getFontStyle(),
1602 tree.getFontSize()));
1604 tp.showPlaceholders(tree.getMarkUnlinked());
1605 tp.showBootstrap(tree.getShowBootstrap());
1606 tp.showDistances(tree.getShowDistances());
1608 tp.treeCanvas.threshold = tree.getThreshold();
1610 if (tree.getCurrentTree())
1611 af.viewport.setCurrentTree(tp.getTree());
1615 catch (Exception ex)
1617 ex.printStackTrace();
1625 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, boolean keepSeqRefs )
1627 jalview.schemabinding.version2.JalviewModel jm
1628 = SaveState(ap, null, null, null);
1633 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
1636 uniqueSetSuffix = "";
1638 viewportsAdded = new Hashtable();
1640 AlignFrame af = LoadFromObject(jm, null);
1641 af.alignPanels.clear();
1642 af.closeMenuItem_actionPerformed(null);
1644 return af.alignPanel;