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
51 // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
52 public void SaveState(File statefile)
54 long creation = System.currentTimeMillis();
55 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
64 FileOutputStream fos = new FileOutputStream(statefile);
65 JarOutputStream jout = new JarOutputStream(fos);
67 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
68 ////////////////////////////////////////////////////
69 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
72 Vector shortNames = new Vector();
75 for (int i = frames.length - 1; i > -1; i--)
77 if (frames[i] instanceof AlignFrame)
79 AlignFrame af = (AlignFrame) frames[i];
81 String shortName = af.getTitle();
83 if (shortName.indexOf(File.separatorChar) > -1)
85 shortName = shortName.substring(shortName.lastIndexOf(
86 File.separatorChar) + 1);
91 while (shortNames.contains(shortName))
93 if (shortName.endsWith("_" + (count - 1)))
95 shortName = shortName.substring(0,
96 shortName.lastIndexOf("_"));
99 shortName = shortName.concat("_" + count);
103 shortNames.addElement(shortName);
105 if (!shortName.endsWith(".xml"))
107 shortName = shortName + ".xml";
110 SaveState(af, creation, shortName, jout, out);
119 ex.printStackTrace();
123 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
124 public void SaveAlignment(AlignFrame af, String jarFile,
129 FileOutputStream fos = new FileOutputStream(jarFile);
130 JarOutputStream jout = new JarOutputStream(fos);
132 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
133 ////////////////////////////////////////////////////
134 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
137 SaveState(af, System.currentTimeMillis(), fileName, jout, out);
143 ex.printStackTrace();
150 * @param af DOCUMENT ME!
151 * @param timeStamp DOCUMENT ME!
152 * @param fileName DOCUMENT ME!
153 * @param jout DOCUMENT ME!
154 * @param out DOCUMENT ME!
156 public void SaveState(AlignFrame af, long timeStamp,
157 String fileName, JarOutputStream jout, PrintWriter out)
159 Vector seqids = new Vector();
160 Vector userColours = new Vector();
162 AlignViewport av = af.viewport;
164 JalviewModel object = new JalviewModel();
165 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
167 object.setCreationDate(new java.util.Date(timeStamp));
168 object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
170 jalview.datamodel.AlignmentI jal = af.viewport.alignment;
171 jalview.datamodel.AlignmentI jalhidden = null;
176 jal = jal.getHiddenSequences().getFullAlignment();
180 SequenceSet vamsasSet = new SequenceSet();
182 JalviewModelSequence jms = new JalviewModelSequence();
184 vamsasSet.setGapChar(jal.getGapCharacter() + "");
187 Vector pdbfiles = null;
191 for (int i = 0; i < jal.getHeight(); i++)
193 seqids.add(jal.getSequenceAt(i));
194 vamsasSeq = new Sequence();
195 vamsasSeq.setId(id + "");
196 vamsasSeq.setName(jal.getSequenceAt(i).getName());
197 vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
198 vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());
200 if(jal.getSequenceAt(i).getDatasetSequence().getDBRef()!=null)
202 jalview.datamodel.DBRefEntry [] dbrefs =
203 jal.getSequenceAt(i).getDatasetSequence().getDBRef();
205 for(int d=0; d<dbrefs.length; d++)
207 DBRef dbref = new DBRef();
208 dbref.setSource( dbrefs[d].getSource() );
209 dbref.setVersion( dbrefs[d].getVersion());
210 dbref.setAccessionId(dbrefs[d].getAccessionId());
211 vamsasSeq.addDBRef(dbref);
216 jseq.setStart(jal.getSequenceAt(i).getStart());
217 jseq.setEnd(jal.getSequenceAt(i).getEnd());
218 jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
222 if (av.hasHiddenRows)
224 jseq.setHidden(jalhidden.getHiddenSequences().isHidden(
225 jal.getSequenceAt(i)));
227 if(jal.getSequenceAt(i).getHiddenSequences()!=null)
229 jalview.datamodel.SequenceI [] reps =
230 jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal);
232 for(int h=0; h<reps.length; h++)
234 jseq.addHiddenSequences(
235 jal.findIndex(reps[h])
242 if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)
244 jalview.datamodel.SequenceFeature[] sf
245 = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
247 while(index < sf.length)
249 Features features = new Features();
251 features.setBegin(sf[index].getBegin());
252 features.setEnd(sf[index].getEnd());
253 features.setDescription(sf[index].getDescription());
254 features.setType(sf[index].getType());
255 features.setFeatureGroup(sf[index].getFeatureGroup());
256 features.setScore(sf[index].getScore());
257 if(sf[index].links!=null)
259 for(int l=0; l<sf[index].links.size(); l++)
261 OtherData keyValue = new OtherData();
262 keyValue.setKey("LINK_"+l);
263 keyValue.setValue(sf[index].links.elementAt(l).toString());
264 features.addOtherData(keyValue);
267 if(sf[index].otherDetails!=null)
270 Enumeration keys = sf[index].otherDetails.keys();
271 while(keys.hasMoreElements())
273 key = keys.nextElement().toString();
274 OtherData keyValue = new OtherData();
275 keyValue.setKey( key );
277 sf[index].otherDetails.get(key).toString());
278 features.addOtherData(keyValue);
282 jseq.addFeatures(features);
287 if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)
289 Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();
290 while(en.hasMoreElements())
292 Pdbids pdb = new Pdbids();
293 jalview.datamodel.PDBEntry entry
294 = (jalview.datamodel.PDBEntry)en.nextElement();
296 pdb.setId(entry.getId());
297 pdb.setType(entry.getType());
299 if(entry.getFile()!=null)
302 pdbfiles = new Vector();
305 if(!pdbfiles.contains(entry.getId()))
307 pdbfiles.addElement(entry.getId());
310 File file = new File(entry.getFile());
313 byte[] data = new byte[ (int) file.length()];
314 jout.putNextEntry(new JarEntry(entry.getId()));
315 DataInputStream dis = new DataInputStream(new
316 FileInputStream(file));
319 DataOutputStream dout = new DataOutputStream(jout);
320 dout.write(data, 0, data.length);
326 ex.printStackTrace();
332 if(entry.getProperty()!=null)
334 PdbentryItem item = new PdbentryItem();
335 Hashtable properties = entry.getProperty();
336 Enumeration en2 = properties.keys();
337 while(en2.hasMoreElements())
339 Property prop = new Property();
340 String key = en2.nextElement().toString();
342 prop.setValue( properties.get(key).toString() );
343 item.addProperty(prop);
345 pdb.addPdbentryItem(item);
353 vamsasSet.addSequence(vamsasSeq);
358 ///////////////////////////////////
359 if (af.viewport.currentTree != null)
361 // FIND ANY ASSOCIATED TREES
362 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
363 if (Desktop.desktop != null)
365 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
367 for (int t = 0; t < frames.length; t++)
369 if (frames[t] instanceof TreePanel)
371 TreePanel tp = (TreePanel) frames[t];
373 if (tp.treeCanvas.av.alignment == jal)
375 Tree tree = new Tree();
376 tree.setTitle(tp.getTitle());
377 tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));
378 tree.setNewick(tp.getTree().toString());
379 tree.setThreshold(tp.treeCanvas.threshold);
381 tree.setFitToWindow(tp.fitToWindow.getState());
382 tree.setFontName(tp.getTreeFont().getName());
383 tree.setFontSize(tp.getTreeFont().getSize());
384 tree.setFontStyle(tp.getTreeFont().getStyle());
385 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
387 tree.setShowBootstrap(tp.bootstrapMenu.getState());
388 tree.setShowDistances(tp.distanceMenu.getState());
390 tree.setHeight(tp.getHeight());
391 tree.setWidth(tp.getWidth());
392 tree.setXpos(tp.getX());
393 tree.setYpos(tp.getY());
403 if (jal.getAlignmentAnnotation() != null)
405 jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
407 for (int i = 0; i < aa.length; i++)
409 Annotation an = new Annotation();
411 if (aa[i].label.equals("Quality") ||
412 aa[i].label.equals("Conservation") ||
413 aa[i].label.equals("Consensus"))
415 an.setLabel(aa[i].label);
417 vamsasSet.addAnnotation(an);
422 an.setDescription(aa[i].description);
424 if(aa[i].sequenceRef!=null)
426 an.setSequenceRef(aa[i].sequenceRef.getName());
432 an.setGraphType(aa[i].graph);
433 an.setGraphGroup(aa[i].graphGroup);
434 if(aa[i].getThreshold()!=null)
436 ThresholdLine line = new ThresholdLine();
437 line.setLabel(aa[i].getThreshold().label);
438 line.setValue(aa[i].getThreshold().value);
439 line.setColour(aa[i].getThreshold().colour.getRGB());
440 an.setThresholdLine(line);
446 an.setLabel(aa[i].label);
448 AnnotationElement ae;
450 for (int a = 0; a < aa[i].annotations.length; a++)
452 if ((aa[i] == null) || (aa[i].annotations[a] == null))
457 ae = new AnnotationElement();
458 ae.setDescription(aa[i].annotations[a].description);
459 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
460 ae.setValue(aa[i].annotations[a].value);
462 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
465 if(aa[i].annotations[a].colour!=java.awt.Color.black)
466 ae.setColour(aa[i].annotations[a].colour.getRGB());
468 an.addAnnotationElement(ae);
471 vamsasSet.addAnnotation(an);
476 if (jal.getGroups() != null)
478 JGroup[] groups = new JGroup[jal.getGroups().size()];
480 for (int i = 0; i < groups.length; i++)
482 groups[i] = new JGroup();
484 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
486 groups[i].setStart(sg.getStartRes());
487 groups[i].setEnd(sg.getEndRes());
488 groups[i].setName(sg.getName());
491 if (sg.cs.conservationApplied())
493 groups[i].setConsThreshold(sg.cs.getConservationInc());
495 if (sg.cs instanceof jalview.schemes.UserColourScheme)
497 groups[i].setColour(SetUserColourScheme(sg.cs,
503 groups[i].setColour(ColourSchemeProperty.getColourName(sg.
507 else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)
510 ColourSchemeProperty.getColourName(
511 ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));
513 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
515 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
520 groups[i].setColour(ColourSchemeProperty.getColourName(
524 groups[i].setPidThreshold(sg.cs.getThreshold());
527 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
528 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
529 groups[i].setDisplayText(sg.getDisplayText());
530 groups[i].setColourText(sg.getColourText());
532 for (int s = 0; s < sg.getSize(false); s++)
534 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);
535 int index = seqids.indexOf(seq);
536 groups[i].addSeq(index);
540 jms.setJGroup(groups);
544 ///////////SAVE VIEWPORT
545 Viewport view = new Viewport();
546 view.setTitle(af.getTitle());
547 view.setXpos(af.getX());
548 view.setYpos(af.getY());
549 view.setWidth(af.getWidth());
550 view.setHeight(af.getHeight());
551 view.setStartRes(av.startRes);
552 view.setStartSeq(av.startSeq);
554 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
556 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
559 else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
561 jalview.schemes.AnnotationColourGradient acg
562 = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();
564 AnnotationColours ac = new AnnotationColours();
565 ac.setAboveThreshold(acg.getAboveThreshold());
566 ac.setThreshold(acg.getAnnotationThreshold());
567 ac.setAnnotation(acg.getAnnotation());
568 if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
569 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
572 ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
574 ac.setMaxColour(acg.getMaxColour().getRGB());
575 ac.setMinColour(acg.getMinColour().getRGB());
576 view.setAnnotationColours(ac);
577 view.setBgColour("AnnotationColourGradient");
581 view.setBgColour(ColourSchemeProperty.getColourName(
582 av.getGlobalColourScheme()));
585 ColourSchemeI cs = av.getGlobalColourScheme();
589 if (cs.conservationApplied())
591 view.setConsThreshold(cs.getConservationInc());
592 if (cs instanceof jalview.schemes.UserColourScheme)
593 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
596 if (cs instanceof ResidueColourScheme)
598 view.setPidThreshold(cs.getThreshold());
602 view.setConservationSelected(av.getConservationSelected());
603 view.setPidSelected(av.getAbovePIDThreshold());
604 view.setFontName(av.font.getName());
605 view.setFontSize(av.font.getSize());
606 view.setFontStyle(av.font.getStyle());
607 view.setRenderGaps(av.renderGaps);
608 view.setShowAnnotation(av.getShowAnnotation());
609 view.setShowBoxes(av.getShowBoxes());
610 view.setShowColourText(av.getColourText());
611 view.setShowConservation(av.showConservation);
612 view.setShowFullId(av.getShowJVSuffix());
613 view.setShowIdentity(av.showIdentity);
614 view.setShowQuality(av.showQuality);
615 view.setShowSequenceFeatures(av.showSequenceFeatures);
616 view.setShowText(av.getShowText());
617 view.setWrapAlignment(av.getWrapAlignment());
619 if(av.featuresDisplayed!=null)
621 jalview.schemabinding.version2.FeatureSettings fs
622 = new jalview.schemabinding.version2.FeatureSettings();
624 String [] renderOrder =
625 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
627 Vector settingsAdded = new Vector();
628 for(int ro=0; ro<renderOrder.length; ro++)
630 Setting setting = new Setting();
631 setting.setType(renderOrder[ro]);
633 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
637 av.featuresDisplayed.containsKey(renderOrder[ro])
640 fs.addSetting(setting);
641 settingsAdded.addElement(renderOrder[ro]);
644 //Make sure we save none displayed feature settings
646 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
647 while(en.hasMoreElements())
649 String key = en.nextElement().toString();
650 if(settingsAdded.contains(key))
653 Setting setting = new Setting();
654 setting.setType(key);
656 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
659 setting.setDisplay(false);
661 fs.addSetting(setting);
662 settingsAdded.addElement(key);
665 jms.setFeatureSettings(fs);
669 if(av.hasHiddenColumns)
671 for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)
673 int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);
674 HiddenColumns hc = new HiddenColumns();
675 hc.setStart(region[0]);
676 hc.setEnd(region[1]);
677 view.addHiddenColumns(hc);
681 jms.addViewport(view);
684 object.setJalviewModelSequence(jms);
685 object.getVamsasModel().addSequenceSet(vamsasSet);
689 if (!fileName.endsWith(".xml"))
691 fileName = fileName + ".xml";
694 JarEntry entry = new JarEntry(fileName);
695 jout.putNextEntry(entry);
701 ex.printStackTrace();
705 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
706 Vector userColours, JalviewModelSequence jms)
709 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
711 if (!userColours.contains(ucs))
713 userColours.add(ucs);
715 java.awt.Color[] colours = ucs.getColours();
716 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
717 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
719 for (int i = 0; i < colours.length; i++)
721 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
722 col.setName(ResidueProperties.aa[i]);
723 col.setRGB(jalview.util.Format.getHexString(colours[i]));
724 jbucs.addColour(col);
726 if(ucs.getLowerCaseColours()!=null)
728 colours = ucs.getLowerCaseColours();
729 for (int i = 0; i < colours.length; i++)
731 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
732 col.setName(ResidueProperties.aa[i].toLowerCase());
733 col.setRGB(jalview.util.Format.getHexString(colours[i]));
734 jbucs.addColour(col);
738 id = "ucs" + userColours.indexOf(ucs);
740 uc.setUserColourScheme(jbucs);
741 jms.addUserColours(uc);
747 jalview.schemes.UserColourScheme GetUserColourScheme(
748 JalviewModelSequence jms, String id)
750 UserColours[] uc = jms.getUserColours();
751 UserColours colours = null;
753 for (int i = 0; i < uc.length; i++)
755 if (uc[i].getId().equals(id))
763 java.awt.Color[] newColours = new java.awt.Color[24];
765 for (int i = 0; i < 24; i++)
767 newColours[i] = new java.awt.Color(Integer.parseInt(
768 colours.getUserColourScheme().getColour(i).getRGB(), 16));
771 jalview.schemes.UserColourScheme ucs =
772 new jalview.schemes.UserColourScheme(newColours);
774 if (colours.getUserColourScheme().getColourCount() > 24)
776 newColours = new java.awt.Color[23];
777 for (int i = 0; i < 23; i++)
779 newColours[i] = new java.awt.Color(Integer.parseInt(
780 colours.getUserColourScheme().getColour(i+24).getRGB(), 16));
782 ucs.setLowerCaseColours(newColours);
791 * @param file DOCUMENT ME!
793 public AlignFrame LoadJalviewAlign(final String file)
795 jalview.gui.AlignFrame af = null;
798 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
801 if (file.startsWith("http://"))
806 JarInputStream jin = null;
807 JarEntry jarentry = null;
814 jin = new JarInputStream(url.openStream());
818 jin = new JarInputStream(new FileInputStream(file));
821 for (int i = 0; i < entryCount; i++)
823 jarentry = jin.getNextJarEntry();
826 if (jarentry != null && jarentry.getName().endsWith(".xml"))
828 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
829 JalviewModel object = new JalviewModel();
831 Unmarshaller unmar = new Unmarshaller(object);
832 unmar.setValidation(false);
833 object = (JalviewModel) unmar.unmarshal( in );
835 af = LoadFromObject(object, file);
838 else if (jarentry != null)
840 //Some other file here.
844 while (jarentry != null);
846 catch(java.net.UnknownHostException ex)
848 ex.printStackTrace();
849 System.err.println("Couldn't locate Jalview XML file : " +
852 javax.swing.SwingUtilities.invokeLater(new Runnable()
856 JOptionPane.showInternalMessageDialog(Desktop.desktop,
857 "Couldn't locate " + file,
859 JOptionPane.WARNING_MESSAGE);
866 //Is Version 1 Jar file?
867 af = new Jalview2XML_V1().LoadJalviewAlign(file);
871 System.out.println("Successfully loaded archive file");
874 ex.printStackTrace();
875 System.err.println("Exception whilst loading jalview XML file : " +
877 javax.swing.SwingUtilities.invokeLater(new Runnable()
882 JOptionPane.showInternalMessageDialog(Desktop.desktop,
883 "Error loading " + file,
884 "Error loading Jalview file",
885 JOptionPane.WARNING_MESSAGE);
892 String loadPDBFile(String file, String pdbId)
894 System.out.println("load file "+file);
897 JarInputStream jin = null;
899 if (file.startsWith("http://"))
901 jin = new JarInputStream(new URL(file).openStream());
905 jin = new JarInputStream(new FileInputStream(file));
908 JarEntry entry = null;
911 entry = jin.getNextJarEntry();
913 while (!entry.getName().equals(pdbId));
915 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
916 File outFile = File.createTempFile("jalview_pdb", ".txt");
917 outFile.deleteOnExit();
918 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
921 while ( (data = in.readLine()) != null)
926 return outFile.getAbsolutePath();
931 ex.printStackTrace();
938 AlignFrame LoadFromObject(JalviewModel object, String file)
940 Vector seqids = new Vector();
941 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
942 Sequence[] vamsasSeq = vamsasSet.getSequence();
944 JalviewModelSequence jms = object.getJalviewModelSequence();
946 //////////////////////////////////
948 Vector hiddenSeqs = null;
949 jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
950 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
951 for (int i = 0; i < vamsasSeq.length; i++)
953 jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
954 vamsasSeq[i].getSequence());
955 jseqs[i].setDescription( vamsasSeq[i].getDescription() );
957 if(JSEQ[i].getHidden())
959 if(hiddenSeqs == null)
960 hiddenSeqs = new Vector();
961 hiddenSeqs.addElement(jseqs[i]);
963 jseqs[i].setStart(JSEQ[i].getStart());
964 jseqs[i].setEnd(JSEQ[i].getEnd());
965 jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
966 seqids.add(jseqs[i]);
969 ///SequenceFeatures are added to the DatasetSequence,
970 // so we must create the dataset before loading features
971 /////////////////////////////////
972 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
974 /////////////////////////////////
977 Hashtable pdbloaded = new Hashtable();
978 for (int i = 0; i < vamsasSeq.length; i++)
980 if (JSEQ[i].getFeaturesCount() > 0)
982 Features[] features = JSEQ[i].getFeatures();
983 for (int f = 0; f < features.length; f++)
985 jalview.datamodel.SequenceFeature sf
986 = new jalview.datamodel.SequenceFeature(features[f].getType(),
987 features[f].getDescription(), features[f].getStatus(),
988 features[f].getBegin(), features[f].getEnd(),
989 features[f].getFeatureGroup());
991 sf.setScore(features[f].getScore());
992 for(int od=0; od<features[f].getOtherDataCount(); od++)
994 OtherData keyValue = features[f].getOtherData(od);
995 if(keyValue.getKey().startsWith("LINK"))
996 sf.addLink(keyValue.getValue());
998 sf.setValue(keyValue.getKey(), keyValue.getValue());
1002 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1005 if (JSEQ[i].getPdbidsCount() > 0)
1007 Pdbids[] ids = JSEQ[i].getPdbids();
1008 for (int p = 0; p < ids.length; p++)
1010 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
1011 entry.setId(ids[p].getId());
1012 entry.setType(ids[p].getType());
1013 if (ids[p].getFile() != null)
1015 if (!pdbloaded.containsKey(ids[p].getFile()))
1017 String tmppdb = loadPDBFile(file, ids[p].getId());
1018 entry.setFile(tmppdb);
1019 pdbloaded.put(ids[p].getId(), tmppdb);
1022 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1025 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1028 if(vamsasSeq[i].getDBRefCount()>0)
1030 for(int d=0; d<vamsasSeq[i].getDBRefCount(); d++)
1032 jalview.datamodel.DBRefEntry entry =
1033 new jalview.datamodel.DBRefEntry(
1034 vamsasSeq[i].getDBRef(d).getSource(),
1035 vamsasSeq[i].getDBRef(d).getVersion(),
1036 vamsasSeq[i].getDBRef(d).getAccessionId()
1038 al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1046 /////////////////////////////////
1047 //////////////////////////////////
1049 boolean hideQuality = true,
1050 hideConservation = true,
1051 hideConsensus = true;
1053 if (vamsasSet.getAnnotation() != null)
1055 Annotation[] an = vamsasSet.getAnnotation();
1057 for (int i = 0; i < an.length; i++)
1059 if (an[i].getLabel().equals("Quality"))
1061 hideQuality = false;
1064 else if(an[i].getLabel().equals("Conservation"))
1066 hideConservation = false;
1069 else if(an[i].getLabel().equals("Consensus"))
1071 hideConsensus = false;
1075 AnnotationElement[] ae = an[i].getAnnotationElement();
1076 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
1078 for (int aa = 0; aa < ae.length; aa++)
1080 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
1081 ae[aa].getDescription(),
1082 ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
1084 anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
1087 jalview.datamodel.AlignmentAnnotation jaa = null;
1089 if (an[i].getGraph())
1091 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1092 an[i].getDescription(), anot, 0, 0,
1093 an[i].getGraphType());
1095 jaa.graphGroup = an[i].getGraphGroup();
1097 if (an[i].getThresholdLine() != null)
1099 jaa.setThreshold(new jalview.datamodel.GraphLine(
1100 an[i].getThresholdLine().getValue(),
1101 an[i].getThresholdLine().getLabel(),
1102 new java.awt.Color(an[i].getThresholdLine().getColour()))
1110 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1111 an[i].getDescription(), anot);
1114 if(an[i].getSequenceRef()!=null)
1116 jaa.createSequenceMapping(
1117 al.findName(an[i].getSequenceRef()), 1, true
1119 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1122 al.addAnnotation(jaa);
1127 // af.changeColour() );
1128 /////////////////////////
1130 if (jms.getJGroupCount() > 0)
1132 JGroup[] groups = jms.getJGroup();
1134 for (int i = 0; i < groups.length; i++)
1136 ColourSchemeI cs = null;
1138 if (groups[i].getColour() != null)
1140 if (groups[i].getColour().startsWith("ucs"))
1142 cs = GetUserColourScheme(jms, groups[i].getColour());
1146 cs = ColourSchemeProperty.getColour(al,
1147 groups[i].getColour());
1151 cs.setThreshold(groups[i].getPidThreshold(), true);
1154 Vector seqs = new Vector();
1155 int[] ids = groups[i].getSeq();
1157 for (int s = 0; s < ids.length; s++)
1159 seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(
1163 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
1164 groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1165 groups[i].getDisplayText(), groups[i].getColourText(),
1166 groups[i].getStart(), groups[i].getEnd());
1168 sg.setOutlineColour(new java.awt.Color(
1169 groups[i].getOutlineColour()));
1171 if (groups[i].getConsThreshold() != 0)
1173 jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
1174 ResidueProperties.propHash, 3, sg.getSequences(false), 0,
1177 c.verdict(false, 25);
1178 sg.cs.setConservation(c);
1186 /////////////////////////////////
1188 Viewport[] views = jms.getViewport();
1189 Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
1192 AlignFrame af = new AlignFrame(al);
1194 if(hiddenSeqs!=null)
1196 for(int s=0; s<JSEQ.length; s++)
1198 for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
1200 al.getSequenceAt(s).addHiddenSequence(
1201 al.getSequenceAt( JSEQ[s].getHiddenSequences(r) )
1206 jalview.datamodel.SequenceI [] hseqs = new
1207 jalview.datamodel.SequenceI[hiddenSeqs.size()];
1209 for(int s=0; s<hiddenSeqs.size(); s++)
1210 hseqs[s] = (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s);
1212 af.viewport.hideSequence( hseqs );
1217 if(hideConsensus || hideQuality || hideConservation)
1219 int hSize = al.getAlignmentAnnotation().length;
1220 for (int h = 0; h < hSize; h++)
1224 al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1227 al.getAlignmentAnnotation()[h].label.equals("Quality"))
1229 (hideConservation &&
1230 al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1232 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1237 af.alignPanel.adjustAnnotationHeight();
1240 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1242 af.viewport.setStartRes(view.getStartRes());
1243 af.viewport.setStartSeq(view.getStartSeq());
1244 af.viewport.setShowAnnotation(view.getShowAnnotation());
1245 af.viewport.showConservation = view.getShowConservation();
1246 af.viewport.showQuality = view.getShowQuality();
1247 af.viewport.showIdentity = view.getShowIdentity();
1248 af.viewport.setAbovePIDThreshold(view.getPidSelected());
1249 af.abovePIDThreshold.setSelected(view.getPidSelected());
1250 af.viewport.setColourText(view.getShowColourText());
1251 af.colourTextMenuItem.setSelected(view.getShowColourText());
1252 af.viewport.setConservationSelected(view.getConservationSelected());
1253 af.conservationMenuItem.setSelected(view.getConservationSelected());
1255 af.viewport.setShowJVSuffix(view.getShowFullId());
1256 af.seqLimits.setSelected(view.getShowFullId());
1258 af.viewport.setFont(new java.awt.Font(view.getFontName(),
1259 view.getFontStyle(), view.getFontSize()));
1260 af.alignPanel.fontChanged();
1262 af.viewport.setRenderGaps(view.getRenderGaps());
1263 af.renderGapsMenuItem.setSelected(view.getRenderGaps());
1265 af.viewport.setWrapAlignment(view.getWrapAlignment());
1266 af.wrapMenuItem.setSelected(view.getWrapAlignment());
1268 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1270 af.annotationPanelMenuItem.setState(view.getShowAnnotation());
1271 af.viewport.setShowAnnotation(view.getShowAnnotation());
1272 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1274 af.viewport.setShowBoxes(view.getShowBoxes());
1275 af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
1276 af.viewport.setShowText(view.getShowText());
1277 af.viewTextMenuItem.setSelected(view.getShowText());
1279 ColourSchemeI cs = null;
1281 if (view.getBgColour() != null)
1283 if (view.getBgColour().startsWith("ucs"))
1285 cs = GetUserColourScheme(jms, view.getBgColour());
1287 else if(view.getBgColour().startsWith("Annotation"))
1289 //int find annotation
1290 for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1292 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1293 equals(view.getAnnotationColours().getAnnotation()))
1295 if (af.viewport.alignment.getAlignmentAnnotation()[i].
1296 getThreshold() == null)
1298 af.viewport.alignment.getAlignmentAnnotation()[i].
1300 new jalview.datamodel.GraphLine(
1301 view.getAnnotationColours().getThreshold(),
1302 "Threshold", java.awt.Color.black)
1308 if (view.getAnnotationColours().getColourScheme().equals(
1311 cs = new AnnotationColourGradient(
1312 af.viewport.alignment.getAlignmentAnnotation()[i],
1313 new java.awt.Color(view.getAnnotationColours().
1315 new java.awt.Color(view.getAnnotationColours().
1317 view.getAnnotationColours().getAboveThreshold());
1319 else if (view.getAnnotationColours().getColourScheme().
1322 cs = new AnnotationColourGradient(
1323 af.viewport.alignment.getAlignmentAnnotation()[i],
1324 GetUserColourScheme(jms, view.getAnnotationColours().
1326 view.getAnnotationColours().getAboveThreshold()
1331 cs = new AnnotationColourGradient(
1332 af.viewport.alignment.getAlignmentAnnotation()[i],
1333 ColourSchemeProperty.getColour(al,
1334 view.getAnnotationColours().getColourScheme()),
1335 view.getAnnotationColours().getAboveThreshold()
1339 // Also use these settings for all the groups
1340 if (al.getGroups() != null)
1341 for (int g = 0; g < al.getGroups().size(); g++)
1343 jalview.datamodel.SequenceGroup sg
1344 = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
1350 /* if (view.getAnnotationColours().getColourScheme().equals("None"))
1352 sg.cs = new AnnotationColourGradient(
1353 af.viewport.alignment.getAlignmentAnnotation()[i],
1354 new java.awt.Color(view.getAnnotationColours().
1356 new java.awt.Color(view.getAnnotationColours().
1358 view.getAnnotationColours().getAboveThreshold());
1362 sg.cs = new AnnotationColourGradient(
1363 af.viewport.alignment.getAlignmentAnnotation()[i],
1365 view.getAnnotationColours().getAboveThreshold()
1379 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1384 cs.setThreshold(view.getPidThreshold(), true);
1385 cs.setConsensus(af.viewport.vconsensus);
1389 af.setColourSelected(view.getBgColour());
1390 af.viewport.setGlobalColourScheme(cs);
1391 af.viewport.setColourAppliesToAllGroups(false);
1392 af.changeColour(cs);
1393 if (view.getConservationSelected() && cs!=null)
1395 cs.setConservationInc(view.getConsThreshold());
1398 af.viewport.setColourAppliesToAllGroups(true);
1400 if (view.getShowSequenceFeatures())
1402 af.viewport.showSequenceFeatures = true;
1403 af.showSeqFeatures.setSelected(true);
1406 if(jms.getFeatureSettings()!=null)
1408 af.viewport.featuresDisplayed = new Hashtable();
1409 String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
1410 for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
1412 Setting setting = jms.getFeatureSettings().getSetting(fs);
1414 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
1415 new java.awt.Color(setting.getColour()));
1417 renderOrder[fs] = setting.getType();
1419 if(setting.getDisplay())
1420 af.viewport.featuresDisplayed.put(
1421 setting.getType(), new Integer(setting.getColour()));
1423 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
1426 if (view.getHiddenColumnsCount() > 0)
1428 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1430 af.viewport.hideColumns(
1431 view.getHiddenColumns(c).getStart(),
1432 view.getHiddenColumns(c).getEnd() //+1
1438 Desktop.addInternalFrame(af, view.getTitle(),
1439 view.getWidth(), view.getHeight());
1442 ///////////////////////////////////////
1443 if (jms.getTreeCount() > 0)
1447 for (int t = 0; t < jms.getTreeCount(); t++)
1450 Tree tree = jms.getTree(t);
1452 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1453 tree.getNewick()), tree.getTitle(),
1454 tree.getWidth(), tree.getHeight(),
1455 tree.getXpos(), tree.getYpos());
1457 tp.fitToWindow.setState(tree.getFitToWindow());
1458 tp.fitToWindow_actionPerformed(null);
1460 if(tree.getFontName()!=null)
1461 tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1462 tree.getFontStyle(),
1463 tree.getFontSize()));
1465 tp.setTreeFont(new java.awt.Font(view.getFontName(),
1466 view.getFontStyle(),
1467 tree.getFontSize()));
1469 tp.showPlaceholders(tree.getMarkUnlinked());
1470 tp.showBootstrap(tree.getShowBootstrap());
1471 tp.showDistances(tree.getShowDistances());
1473 tp.treeCanvas.threshold = tree.getThreshold();
1475 if (tree.getCurrentTree())
1476 af.viewport.setCurrentTree(tp.getTree());
1480 catch (Exception ex)
1482 ex.printStackTrace();