/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
*/
package jalview.gui;
-
-import jalview.schemes.*;
-
-import jalview.gui.*;
-
import java.io.*;
-
import java.net.*;
-
import java.util.*;
-
import java.util.jar.*;
import javax.swing.*;
import org.exolab.castor.xml.*;
+import uk.ac.vamsas.objects.utils.MapList;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
import jalview.schemabinding.version2.*;
-
-
-
+import jalview.schemes.*;
+import jalview.structure.StructureSelectionManager;
/**
- * DOCUMENT ME!
+ * Write out the current jalview desktop state
+ * as a Jalview XML stream.
+ *
+ * Note: the vamsas objects referred to here are primitive
+ * versions of the VAMSAS project schema elements - they are
+ * not the same and most likely never will be :)
*
* @author $author$
* @version $Revision$
*/
public class Jalview2XML
{
- // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
- public void SaveState(File statefile)
+ /**
+ * create/return unique hash string for sq
+ * @param sq
+ * @return new or existing unique string for sq
+ */
+ String seqHash(SequenceI sq)
+ {
+ if (seqsToIds==null)
{
- long creation = System.currentTimeMillis();
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-
- if (frames == null)
+ initSeqRefs();
+ }
+ if (seqsToIds.containsKey(sq))
+ {
+ return (String) seqsToIds.get(sq);
+ } else {
+ // create sequential key
+ String key = "sq"+(seqsToIds.size()+1);
+ seqsToIds.put(sq, key);
+ return key;
+ }
+ }
+ void clearSeqRefs()
+ {
+ seqRefIds.clear();
+ seqsToIds.clear();
+ }
+ void initSeqRefs()
+ {
+ if (seqsToIds==null)
+ {
+ seqsToIds = new IdentityHashMap();
+ }
+ if (seqRefIds==null)
+ {
+ seqRefIds = new Hashtable();
+ }
+ }
+ java.util.IdentityHashMap seqsToIds = null; // SequenceI->key resolution
+ java.util.Hashtable seqRefIds = null; // key->SequenceI resolution
+
+ Vector frefedSequence = null;
+ boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
+ public Jalview2XML()
+ {
+ }
+ public Jalview2XML(boolean raiseGUI)
+ {
+ this.raiseGUI = raiseGUI;
+ }
+
+ public void resolveFrefedSequences()
+ {
+ if (frefedSequence.size() > 0)
+ {
+ int r = 0, rSize = frefedSequence.size();
+ while (r < rSize)
+ {
+ Object[] ref = (Object[]) frefedSequence.elementAt(r);
+ if (ref != null)
+ {
+ String sref = (String) ref[0];
+ if (seqRefIds.containsKey(sref))
+ {
+ if (ref[1] instanceof jalview.datamodel.Mapping)
+ {
+ SequenceI seq = (SequenceI) seqRefIds.get(sref);
+ while (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
+ ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
+ }
+ else
+ {
+ System.err
+ .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
+ + ref[1].getClass() + " type objects.");
+ }
+ frefedSequence.remove(r);
+ rSize--;
+ }
+ else
+ {
+ r++;
+ }
+ }
+ else
{
- return;
+ frefedSequence.remove(r);
+ rSize--;
}
+ }
+ }
+ }
- try
- {
- FileOutputStream fos = new FileOutputStream(statefile);
- JarOutputStream jout = new JarOutputStream(fos);
+ /**
+ * This maintains a list of viewports, the key being the
+ * seqSetId. Important to set historyItem and redoList
+ * for multiple views
+ */
+ Hashtable viewportsAdded;
- //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
- ////////////////////////////////////////////////////
- PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
- "UTF-8"));
+ Hashtable annotationIds = new Hashtable();
- Vector shortNames = new Vector();
+ String uniqueSetSuffix = "";
- //REVERSE ORDER
- for (int i = frames.length - 1; i > -1; i--)
- {
- if (frames[i] instanceof AlignFrame)
- {
- AlignFrame af = (AlignFrame) frames[i];
+ /**
+ * List of pdbfiles added to Jar
+ */
+ Vector pdbfiles = null;
- String shortName = af.getTitle();
+ // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
+ public void SaveState(File statefile)
+ {
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- if (shortName.indexOf(File.separatorChar) > -1)
- {
- shortName = shortName.substring(shortName.lastIndexOf(
- File.separatorChar) + 1);
- }
+ if (frames == null)
+ {
+ return;
+ }
- int count = 1;
+ try
+ {
+ FileOutputStream fos = new FileOutputStream(statefile);
+ JarOutputStream jout = new JarOutputStream(fos);
- while (shortNames.contains(shortName))
- {
- if (shortName.endsWith("_" + (count - 1)))
- {
- shortName = shortName.substring(0,
- shortName.lastIndexOf("_"));
- }
-
- shortName = shortName.concat("_" + count);
- count++;
- }
+ //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
+ ////////////////////////////////////////////////////
+ //NOTE ALSO new PrintWriter must be used for each new JarEntry
+ PrintWriter out = null;
- shortNames.addElement(shortName);
+ Vector shortNames = new Vector();
- if (!shortName.endsWith(".xml"))
- {
- shortName = shortName + ".xml";
- }
+ //REVERSE ORDER
+ for (int i = frames.length - 1; i > -1; i--)
+ {
+ if (frames[i] instanceof AlignFrame)
+ {
+ AlignFrame af = (AlignFrame) frames[i];
- SaveState(af, creation, shortName, jout, out);
- }
+ String shortName = af.getTitle();
+
+ if (shortName.indexOf(File.separatorChar) > -1)
+ {
+ shortName = shortName.substring(shortName
+ .lastIndexOf(File.separatorChar) + 1);
+ }
+
+ int count = 1;
+
+ while (shortNames.contains(shortName))
+ {
+ if (shortName.endsWith("_" + (count - 1)))
+ {
+ shortName = shortName
+ .substring(0, shortName.lastIndexOf("_"));
}
- out.close();
- jout.close();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
+ shortName = shortName.concat("_" + count);
+ count++;
+ }
- // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
- public void SaveAlignment(AlignFrame af, String jarFile,
- String fileName)
- {
- try
- {
- FileOutputStream fos = new FileOutputStream(jarFile);
- JarOutputStream jout = new JarOutputStream(fos);
+ shortNames.addElement(shortName);
+
+ if (!shortName.endsWith(".xml"))
+ {
+ shortName = shortName + ".xml";
+ }
- //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
- ////////////////////////////////////////////////////
- PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
- "UTF-8"));
+ int ap, apSize = af.alignPanels.size();
+ for (ap = 0; ap < apSize; ap++)
+ {
+ AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
+ .elementAt(ap);
+ String fileName = apSize == 1 ? shortName : ap + shortName;
+ if (!fileName.endsWith(".xml"))
+ {
+ fileName = fileName + ".xml";
+ }
- SaveState(af, System.currentTimeMillis(), fileName, jout, out);
- out.close();
- jout.close();
+ SaveState(apanel, fileName, jout);
+ }
}
- catch (Exception ex)
+ }
+ try { jout.flush(); } catch (Exception foo) {};
+ jout.close();
+ } catch (Exception ex)
+ {
+ //TODO: inform user of the problem - they need to know if their data was not saved !
+ ex.printStackTrace();
+ }
+ }
+
+ // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
+ public boolean SaveAlignment(AlignFrame af, String jarFile,
+ String fileName)
+ {
+ try
+ {
+ int ap, apSize = af.alignPanels.size();
+ FileOutputStream fos = new FileOutputStream(jarFile);
+ JarOutputStream jout = new JarOutputStream(fos);
+ for (ap = 0; ap < apSize; ap++)
+ {
+ AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
+ .elementAt(ap);
+ String jfileName = apSize == 1 ? fileName : fileName + ap;
+ if (!jfileName.endsWith(".xml"))
{
- ex.printStackTrace();
+ jfileName = jfileName + ".xml";
}
- }
+ SaveState(apanel, jfileName, jout);
+ }
- /**
- * DOCUMENT ME!
- *
- * @param af DOCUMENT ME!
- * @param timeStamp DOCUMENT ME!
- * @param fileName DOCUMENT ME!
- * @param jout DOCUMENT ME!
- * @param out DOCUMENT ME!
- */
- public void SaveState(AlignFrame af, long timeStamp,
- String fileName, JarOutputStream jout, PrintWriter out)
+ try { jout.flush(); } catch (Exception foo) {};
+ jout.close();
+ return true;
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ return false;
+ }
+ }
+
+ /**
+ * create a JalviewModel from an algnment view and marshall it
+ * to a JarOutputStream
+ *
+ * @param ap panel to create jalview model for
+ * @param fileName name of alignment panel written to output stream
+ * @param jout jar output stream
+ * @param out jar entry name
+ */
+ public JalviewModel SaveState(AlignmentPanel ap, String fileName,
+ JarOutputStream jout)
+ {
+ initSeqRefs();
+
+ Vector userColours = new Vector();
+
+ AlignViewport av = ap.av;
+
+ JalviewModel object = new JalviewModel();
+ object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
+
+ object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
+ object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
+
+ jalview.datamodel.AlignmentI jal = av.alignment;
+
+ if (av.hasHiddenRows)
{
- Vector seqids = new Vector();
- Vector userColours = new Vector();
+ jal = jal.getHiddenSequences().getFullAlignment();
+ }
- AlignViewport av = af.viewport;
+ SequenceSet vamsasSet = new SequenceSet();
+ Sequence vamsasSeq;
+ JalviewModelSequence jms = new JalviewModelSequence();
- JalviewModel object = new JalviewModel();
- object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
+ vamsasSet.setGapChar(jal.getGapCharacter() + "");
- object.setCreationDate(new java.util.Date(timeStamp));
- object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
+ if (jal.getDataset() != null)
+ {
+ // dataset id is the dataset's hashcode
+ vamsasSet.setDatasetId(jal.getDataset().hashCode() + "");
+ }
+ if (jal.getProperties() != null)
+ {
+ Enumeration en = jal.getProperties().keys();
+ while (en.hasMoreElements())
+ {
+ String key = en.nextElement().toString();
+ SequenceSetProperties ssp = new SequenceSetProperties();
+ ssp.setKey(key);
+ ssp.setValue(jal.getProperties().get(key).toString());
+ vamsasSet.addSequenceSetProperties(ssp);
+ }
+ }
- jalview.datamodel.AlignmentI jal = af.viewport.alignment;
- jalview.datamodel.AlignmentI jalhidden = null;
+ JSeq jseq;
- if(av.hasHiddenRows)
- {
- jalhidden = jal;
- jal = jal.getHiddenSequences().getFullAlignment();
- }
+ //SAVE SEQUENCES
+ String id = "";
+ jalview.datamodel.SequenceI jds;
+ for (int i = 0; i < jal.getHeight(); i++)
+ {
+ jds = jal.getSequenceAt(i);
+ id = seqHash(jds);
+ if (seqRefIds.get(id) != null)
+ {
+ // This happens for two reasons: 1. multiple views are being serialised. 2. the hashCode has collided with another sequence's code. This DOES HAPPEN! (PF00072.15.stk does this)
+ // JBPNote: Uncomment to debug writing out of files that do not read back in due to ArrayOutOfBoundExceptions.
+ //System.err.println("vamsasSeq backref: "+id+"");
+ //System.err.println(jds.getName()+" "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
+ //System.err.println("Hashcode: "+seqHash(jds));
+ //SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
+ //System.err.println(rsq.getName()+" "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
+ //System.err.println("Hashcode: "+seqHash(rsq));
+ }
+ else
+ {
+ vamsasSeq = createVamsasSequence(id, jds);
+ vamsasSet.addSequence(vamsasSeq);
+ seqRefIds.put(id, jds);
+ }
- SequenceSet vamsasSet = new SequenceSet();
- Sequence vamsasSeq;
- JalviewModelSequence jms = new JalviewModelSequence();
+ jseq = new JSeq();
+ jseq.setStart(jds.getStart());
+ jseq.setEnd(jds.getEnd());
+ jseq.setColour(av.getSequenceColour(jds).getRGB());
- vamsasSet.setGapChar(jal.getGapCharacter() + "");
+ jseq.setId(id); // jseq id should be a string not a number
- JSeq jseq;
- Vector pdbfiles = null;
+ if (av.hasHiddenRows)
+ {
+ jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
- //SAVE SEQUENCES
- int id = 0;
- for (int i = 0; i < jal.getHeight(); i++)
+ if (av.hiddenRepSequences != null
+ && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
{
- seqids.add(jal.getSequenceAt(i));
- vamsasSeq = new Sequence();
- vamsasSeq.setId(id + "");
- vamsasSeq.setName(jal.getSequenceAt(i).getName());
- vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
- vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());
+ jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences
+ .get(jal.getSequenceAt(i))).getSequencesInOrder(jal);
- if(jal.getSequenceAt(i).getDatasetSequence().getDBRef()!=null)
+ for (int h = 0; h < reps.length; h++)
+ {
+ if (reps[h] != jal.getSequenceAt(i))
{
- jalview.datamodel.DBRefEntry [] dbrefs =
- jal.getSequenceAt(i).getDatasetSequence().getDBRef();
+ jseq.addHiddenSequences(jal.findIndex(reps[h]));
+ }
+ }
+ }
+ }
- for(int d=0; d<dbrefs.length; d++)
- {
- DBRef dbref = new DBRef();
- dbref.setSource( dbrefs[d].getSource() );
- dbref.setVersion( dbrefs[d].getVersion());
- dbref.setAccessionId(dbrefs[d].getAccessionId());
- vamsasSeq.addDBRef(dbref);
- }
+ if (jds.getDatasetSequence().getSequenceFeatures() != null)
+ {
+ jalview.datamodel.SequenceFeature[] sf = jds.getDatasetSequence()
+ .getSequenceFeatures();
+ int index = 0;
+ while (index < sf.length)
+ {
+ Features features = new Features();
+
+ features.setBegin(sf[index].getBegin());
+ features.setEnd(sf[index].getEnd());
+ features.setDescription(sf[index].getDescription());
+ features.setType(sf[index].getType());
+ features.setFeatureGroup(sf[index].getFeatureGroup());
+ features.setScore(sf[index].getScore());
+ if (sf[index].links != null)
+ {
+ for (int l = 0; l < sf[index].links.size(); l++)
+ {
+ OtherData keyValue = new OtherData();
+ keyValue.setKey("LINK_" + l);
+ keyValue.setValue(sf[index].links.elementAt(l).toString());
+ features.addOtherData(keyValue);
+ }
+ }
+ if (sf[index].otherDetails != null)
+ {
+ String key;
+ Enumeration keys = sf[index].otherDetails.keys();
+ while (keys.hasMoreElements())
+ {
+ key = keys.nextElement().toString();
+ OtherData keyValue = new OtherData();
+ keyValue.setKey(key);
+ keyValue.setValue(sf[index].otherDetails.get(key).toString());
+ features.addOtherData(keyValue);
}
+ }
- jseq = new JSeq();
- jseq.setStart(jal.getSequenceAt(i).getStart());
- jseq.setEnd(jal.getSequenceAt(i).getEnd());
- jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
+ jseq.addFeatures(features);
+ index++;
+ }
+ }
+
+ if (jds.getDatasetSequence().getPDBId() != null)
+ {
+ Enumeration en = jds.getDatasetSequence().getPDBId().elements();
+ while (en.hasMoreElements())
+ {
+ Pdbids pdb = new Pdbids();
+ jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
+ .nextElement();
- jseq.setId(id);
+ pdb.setId(entry.getId());
+ pdb.setType(entry.getType());
- if (av.hasHiddenRows)
+ AppJmol jmol;
+ //This must have been loaded, is it still visible?
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ for (int f = frames.length - 1; f > -1; f--)
+ {
+ if (frames[f] instanceof AppJmol)
{
- jseq.setHidden(jalhidden.getHiddenSequences().isHidden(
- jal.getSequenceAt(i)));
-
- if(jal.getSequenceAt(i).getHiddenSequences()!=null)
+ jmol = (AppJmol) frames[f];
+ if (!jmol.pdbentry.getId().equals(entry.getId()))
+ continue;
+
+ StructureState state = new StructureState();
+ state.setVisible(true);
+ state.setXpos(jmol.getX());
+ state.setYpos(jmol.getY());
+ state.setWidth(jmol.getWidth());
+ state.setHeight(jmol.getHeight());
+
+ String statestring = jmol.viewer.getStateInfo();
+ if (state != null)
{
- jalview.datamodel.SequenceI [] reps =
- jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal);
-
- for(int h=0; h<reps.length; h++)
+ state.setContent(statestring.replaceAll("\n", ""));
+ }
+ for (int s = 0; s < jmol.sequence.length; s++)
+ {
+ if (jal.findIndex(jmol.sequence[s]) > -1)
{
- jseq.addHiddenSequences(
- jal.findIndex(reps[h])
- );
+ pdb.addStructureState(state);
}
}
}
+ }
-
- if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)
+ if (entry.getFile() != null)
+ {
+ pdb.setFile(entry.getFile());
+ if (pdbfiles == null)
{
- jalview.datamodel.SequenceFeature[] sf
- = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
- int index = 0;
- while(index < sf.length)
- {
- Features features = new Features();
-
- features.setBegin(sf[index].getBegin());
- features.setEnd(sf[index].getEnd());
- features.setDescription(sf[index].getDescription());
- features.setType(sf[index].getType());
- features.setFeatureGroup(sf[index].getFeatureGroup());
- features.setScore(sf[index].getScore());
- if(sf[index].links!=null)
- {
- for(int l=0; l<sf[index].links.size(); l++)
- {
- OtherData keyValue = new OtherData();
- keyValue.setKey("LINK_"+l);
- keyValue.setValue(sf[index].links.elementAt(l).toString());
- features.addOtherData(keyValue);
- }
- }
- if(sf[index].otherDetails!=null)
- {
- String key;
- Enumeration keys = sf[index].otherDetails.keys();
- while(keys.hasMoreElements())
- {
- key = keys.nextElement().toString();
- OtherData keyValue = new OtherData();
- keyValue.setKey( key );
- keyValue.setValue(
- sf[index].otherDetails.get(key).toString());
- features.addOtherData(keyValue);
- }
- }
-
- jseq.addFeatures(features);
- index ++;
- }
+ pdbfiles = new Vector();
}
- if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)
+ if (!pdbfiles.contains(entry.getId()))
{
- Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();
- while(en.hasMoreElements())
+ pdbfiles.addElement(entry.getId());
+ try
{
- Pdbids pdb = new Pdbids();
- jalview.datamodel.PDBEntry entry
- = (jalview.datamodel.PDBEntry)en.nextElement();
-
- pdb.setId(entry.getId());
- pdb.setType(entry.getType());
-
- if(entry.getFile()!=null)
+ File file = new File(entry.getFile());
+ if (file.exists() && jout != null)
{
- if(pdbfiles==null)
- pdbfiles = new Vector();
-
-
- if(!pdbfiles.contains(entry.getId()))
- {
- pdbfiles.addElement(entry.getId());
- try
- {
- File file = new File(entry.getFile());
- if(file.exists())
- {
- byte[] data = new byte[ (int) file.length()];
- jout.putNextEntry(new JarEntry(entry.getId()));
- DataInputStream dis = new DataInputStream(new
- FileInputStream(file));
- dis.readFully(data);
-
- DataOutputStream dout = new DataOutputStream(jout);
- dout.write(data, 0, data.length);
- jout.closeEntry();
- }
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
+ byte[] data = new byte[(int) file.length()];
+ jout.putNextEntry(new JarEntry(entry.getId()));
+ DataInputStream dis = new DataInputStream(
+ new FileInputStream(file));
+ dis.readFully(data);
+
+ DataOutputStream dout = new DataOutputStream(jout);
+ dout.write(data, 0, data.length);
+ dout.flush();
+ jout.closeEntry();
}
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ }
- if(entry.getProperty()!=null)
- {
- PdbentryItem item = new PdbentryItem();
- Hashtable properties = entry.getProperty();
- Enumeration en2 = properties.keys();
- while(en2.hasMoreElements())
- {
- Property prop = new Property();
- String key = en2.nextElement().toString();
- prop.setName(key);
- prop.setValue( properties.get(key).toString() );
- item.addProperty(prop);
- }
- pdb.addPdbentryItem(item);
- }
-
- jseq.addPdbids(pdb);
- }
+ if (entry.getProperty() != null)
+ {
+ PdbentryItem item = new PdbentryItem();
+ Hashtable properties = entry.getProperty();
+ Enumeration en2 = properties.keys();
+ while (en2.hasMoreElements())
+ {
+ Property prop = new Property();
+ String key = en2.nextElement().toString();
+ prop.setName(key);
+ prop.setValue(properties.get(key).toString());
+ item.addProperty(prop);
}
+ pdb.addPdbentryItem(item);
+ }
- jms.addJSeq(jseq);
- vamsasSet.addSequence(vamsasSeq);
- id++;
+ jseq.addPdbids(pdb);
}
+ }
+
+ jms.addJSeq(jseq);
+ }
- //SAVE TREES
- ///////////////////////////////////
- if (af.viewport.currentTree != null)
+ if (av.hasHiddenRows)
+ {
+ jal = av.alignment;
+ }
+ // SAVE MAPPINGS
+ if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
+ {
+ jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
+ for (int i = 0; i < jac.length; i++)
+ {
+ AlcodonFrame alc = new AlcodonFrame();
+ vamsasSet.addAlcodonFrame(alc);
+ for (int p = 0; p < jac[i].aaWidth; p++)
{
- // FIND ANY ASSOCIATED TREES
- // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
- if (Desktop.desktop != null)
+ Alcodon cmap = new Alcodon();
+ cmap.setPos1(jac[i].codons[p][0]);
+ cmap.setPos2(jac[i].codons[p][1]);
+ cmap.setPos3(jac[i].codons[p][2]);
+ alc.addAlcodon(cmap);
+ }
+ if (jac[i].getProtMappings() != null
+ && jac[i].getProtMappings().length > 0)
+ {
+ SequenceI[] dnas = jac[i].getdnaSeqs();
+ jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings();
+ for (int m = 0; m < pmaps.length; m++)
{
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-
- for (int t = 0; t < frames.length; t++)
- {
- if (frames[t] instanceof TreePanel)
- {
- TreePanel tp = (TreePanel) frames[t];
-
- if (tp.treeCanvas.av.alignment == jal)
- {
- Tree tree = new Tree();
- tree.setTitle(tp.getTitle());
- tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));
- tree.setNewick(tp.getTree().toString());
- tree.setThreshold(tp.treeCanvas.threshold);
-
- tree.setFitToWindow(tp.fitToWindow.getState());
- tree.setFontName(tp.getTreeFont().getName());
- tree.setFontSize(tp.getTreeFont().getSize());
- tree.setFontStyle(tp.getTreeFont().getStyle());
- tree.setMarkUnlinked(tp.placeholdersMenu.getState());
-
- tree.setShowBootstrap(tp.bootstrapMenu.getState());
- tree.setShowDistances(tp.distanceMenu.getState());
-
- tree.setHeight(tp.getHeight());
- tree.setWidth(tp.getWidth());
- tree.setXpos(tp.getX());
- tree.setYpos(tp.getY());
-
- jms.addTree(tree);
- }
- }
- }
+ AlcodMap alcmap = new AlcodMap();
+ alcmap.setDnasq("" + dnas[m].hashCode());
+ alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
+ false));
+ alc.addAlcodMap(alcmap);
}
}
+ }
+ }
- //SAVE ANNOTATIONS
- if (jal.getAlignmentAnnotation() != null)
+ //SAVE TREES
+ ///////////////////////////////////
+ if (av.currentTree != null)
+ {
+ // FIND ANY ASSOCIATED TREES
+ // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
+ if (Desktop.desktop != null)
+ {
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+
+ for (int t = 0; t < frames.length; t++)
{
- jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
+ if (frames[t] instanceof TreePanel)
+ {
+ TreePanel tp = (TreePanel) frames[t];
- for (int i = 0; i < aa.length; i++)
+ if (tp.treeCanvas.av.alignment == jal)
{
- Annotation an = new Annotation();
-
- if (aa[i].label.equals("Quality") ||
- aa[i].label.equals("Conservation") ||
- aa[i].label.equals("Consensus"))
- {
- an.setLabel(aa[i].label);
- an.setGraph(true);
- vamsasSet.addAnnotation(an);
- continue;
- }
-
-
- an.setDescription(aa[i].description);
-
- if(aa[i].sequenceRef!=null)
- {
- an.setSequenceRef(aa[i].sequenceRef.getName());
- }
+ Tree tree = new Tree();
+ tree.setTitle(tp.getTitle());
+ tree.setCurrentTree((av.currentTree == tp.getTree()));
+ tree.setNewick(tp.getTree().toString());
+ tree.setThreshold(tp.treeCanvas.threshold);
+
+ tree.setFitToWindow(tp.fitToWindow.getState());
+ tree.setFontName(tp.getTreeFont().getName());
+ tree.setFontSize(tp.getTreeFont().getSize());
+ tree.setFontStyle(tp.getTreeFont().getStyle());
+ tree.setMarkUnlinked(tp.placeholdersMenu.getState());
+
+ tree.setShowBootstrap(tp.bootstrapMenu.getState());
+ tree.setShowDistances(tp.distanceMenu.getState());
+
+ tree.setHeight(tp.getHeight());
+ tree.setWidth(tp.getWidth());
+ tree.setXpos(tp.getX());
+ tree.setYpos(tp.getY());
+
+ jms.addTree(tree);
+ }
+ }
+ }
+ }
+ }
- if(aa[i].graph>0)
- {
- an.setGraph(true);
- an.setGraphType(aa[i].graph);
- an.setGraphGroup(aa[i].graphGroup);
- if(aa[i].getThreshold()!=null)
- {
- ThresholdLine line = new ThresholdLine();
- line.setLabel(aa[i].getThreshold().label);
- line.setValue(aa[i].getThreshold().value);
- line.setColour(aa[i].getThreshold().colour.getRGB());
- an.setThresholdLine(line);
- }
- }
- else
- an.setGraph(false);
+ //SAVE ANNOTATIONS
+ if (jal.getAlignmentAnnotation() != null)
+ {
+ jalview.datamodel.AlignmentAnnotation[] aa = jal
+ .getAlignmentAnnotation();
- an.setLabel(aa[i].label);
+ for (int i = 0; i < aa.length; i++)
+ {
+ Annotation an = new Annotation();
- AnnotationElement ae;
+ if (aa[i].annotationId != null)
+ {
+ annotationIds.put(aa[i].annotationId, aa[i]);
+ }
- for (int a = 0; a < aa[i].annotations.length; a++)
- {
- if ((aa[i] == null) || (aa[i].annotations[a] == null))
- {
- continue;
- }
+ an.setId(aa[i].annotationId);
- ae = new AnnotationElement();
- ae.setDescription(aa[i].annotations[a].description);
- ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
- ae.setValue(aa[i].annotations[a].value);
- ae.setPosition(a);
- ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
- "");
+ if (aa[i] == av.quality || aa[i] == av.conservation
+ || aa[i] == av.consensus)
+ {
+ an.setLabel(aa[i].label);
+ an.setGraph(true);
+ vamsasSet.addAnnotation(an);
+ continue;
+ }
- if(aa[i].annotations[a].colour!=java.awt.Color.black)
- ae.setColour(aa[i].annotations[a].colour.getRGB());
+ an.setVisible(aa[i].visible);
- an.addAnnotationElement(ae);
- }
+ an.setDescription(aa[i].description);
- vamsasSet.addAnnotation(an);
- }
+ if (aa[i].sequenceRef != null)
+ {
+ an.setSequenceRef(aa[i].sequenceRef.getName());
}
- //SAVE GROUPS
- if (jal.getGroups() != null)
+ if (aa[i].graph > 0)
{
- JGroup[] groups = new JGroup[jal.getGroups().size()];
+ an.setGraph(true);
+ an.setGraphType(aa[i].graph);
+ an.setGraphGroup(aa[i].graphGroup);
+ if (aa[i].getThreshold() != null)
+ {
+ ThresholdLine line = new ThresholdLine();
+ line.setLabel(aa[i].getThreshold().label);
+ line.setValue(aa[i].getThreshold().value);
+ line.setColour(aa[i].getThreshold().colour.getRGB());
+ an.setThresholdLine(line);
+ }
+ }
+ else
+ {
+ an.setGraph(false);
+ }
- for (int i = 0; i < groups.length; i++)
+ an.setLabel(aa[i].label);
+ if (aa[i].hasScore())
+ {
+ an.setScore(aa[i].getScore());
+ }
+ AnnotationElement ae;
+ if (aa[i].annotations != null)
+ {
+ an.setScoreOnly(false);
+ for (int a = 0; a < aa[i].annotations.length; a++)
+ {
+ if ((aa[i] == null) || (aa[i].annotations[a] == null))
{
- groups[i] = new JGroup();
-
- jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
- .elementAt(i);
- groups[i].setStart(sg.getStartRes());
- groups[i].setEnd(sg.getEndRes());
- groups[i].setName(sg.getName());
- if(sg.cs!=null)
- {
- if (sg.cs.conservationApplied())
- {
- groups[i].setConsThreshold(sg.cs.getConservationInc());
+ continue;
+ }
- if (sg.cs instanceof jalview.schemes.UserColourScheme)
- {
- groups[i].setColour(SetUserColourScheme(sg.cs,
- userColours,
- jms));
- }
- else
- {
- groups[i].setColour(ColourSchemeProperty.getColourName(sg.
- cs));
- }
- }
- else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)
- {
- groups[i].setColour(
- ColourSchemeProperty.getColourName(
- ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));
- }
- else if (sg.cs instanceof jalview.schemes.UserColourScheme)
- {
- groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
- jms));
- }
- else
- {
- groups[i].setColour(ColourSchemeProperty.getColourName(
- sg.cs));
- }
+ ae = new AnnotationElement();
+ if (aa[i].annotations[a].description != null)
+ ae.setDescription(aa[i].annotations[a].description);
+ if (aa[i].annotations[a].displayCharacter != null)
+ ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
- groups[i].setPidThreshold(sg.cs.getThreshold());
- }
+ if (!Float.isNaN(aa[i].annotations[a].value))
+ ae.setValue(aa[i].annotations[a].value);
- groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
- groups[i].setDisplayBoxes(sg.getDisplayBoxes());
- groups[i].setDisplayText(sg.getDisplayText());
- groups[i].setColourText(sg.getColourText());
+ ae.setPosition(a);
+ if (aa[i].annotations[a].secondaryStructure != ' '
+ && aa[i].annotations[a].secondaryStructure != '\0')
+ ae
+ .setSecondaryStructure(aa[i].annotations[a].secondaryStructure
+ + "");
- for (int s = 0; s < sg.getSize(false); s++)
- {
- jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);
- int index = seqids.indexOf(seq);
- groups[i].addSeq(index);
- }
+ if (aa[i].annotations[a].colour != null
+ && aa[i].annotations[a].colour != java.awt.Color.black)
+ {
+ ae.setColour(aa[i].annotations[a].colour.getRGB());
}
- jms.setJGroup(groups);
+ an.addAnnotationElement(ae);
+ }
}
-
-
- ///////////SAVE VIEWPORT
- Viewport view = new Viewport();
- view.setTitle(af.getTitle());
- view.setXpos(af.getX());
- view.setYpos(af.getY());
- view.setWidth(af.getWidth());
- view.setHeight(af.getHeight());
- view.setStartRes(av.startRes);
- view.setStartSeq(av.startSeq);
-
- if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
+ else
{
- view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
- userColours, jms));
+ an.setScoreOnly(true);
}
- else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
- {
- jalview.schemes.AnnotationColourGradient acg
- = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();
+ vamsasSet.addAnnotation(an);
+ }
+ }
- AnnotationColours ac = new AnnotationColours();
- ac.setAboveThreshold(acg.getAboveThreshold());
- ac.setThreshold(acg.getAnnotationThreshold());
- ac.setAnnotation(acg.getAnnotation());
- if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
- ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
- userColours, jms));
- else
- ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
+ //SAVE GROUPS
+ if (jal.getGroups() != null)
+ {
+ JGroup[] groups = new JGroup[jal.getGroups().size()];
- ac.setMaxColour(acg.getMaxColour().getRGB());
- ac.setMinColour(acg.getMinColour().getRGB());
- view.setAnnotationColours(ac);
- view.setBgColour("AnnotationColourGradient");
- }
- else
+ for (int i = 0; i < groups.length; i++)
+ {
+ groups[i] = new JGroup();
+
+ jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal
+ .getGroups().elementAt(i);
+ groups[i].setStart(sg.getStartRes());
+ groups[i].setEnd(sg.getEndRes());
+ groups[i].setName(sg.getName());
+ if (sg.cs != null)
{
- view.setBgColour(ColourSchemeProperty.getColourName(
- av.getGlobalColourScheme()));
- }
-
- ColourSchemeI cs = av.getGlobalColourScheme();
+ if (sg.cs.conservationApplied())
+ {
+ groups[i].setConsThreshold(sg.cs.getConservationInc());
- if(cs!=null)
- {
- if (cs.conservationApplied())
+ if (sg.cs instanceof jalview.schemes.UserColourScheme)
+ {
+ groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
+ jms));
+ }
+ else
+ {
+ groups[i]
+ .setColour(ColourSchemeProperty.getColourName(sg.cs));
+ }
+ }
+ else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
{
- view.setConsThreshold(cs.getConservationInc());
- if (cs instanceof jalview.schemes.UserColourScheme)
- view.setBgColour(SetUserColourScheme(cs, userColours, jms));
+ groups[i]
+ .setColour(ColourSchemeProperty
+ .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
+ .getBaseColour()));
}
-
- if (cs instanceof ResidueColourScheme)
+ else if (sg.cs instanceof jalview.schemes.UserColourScheme)
+ {
+ groups[i]
+ .setColour(SetUserColourScheme(sg.cs, userColours, jms));
+ }
+ else
{
- view.setPidThreshold(cs.getThreshold());
+ groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
}
+
+ groups[i].setPidThreshold(sg.cs.getThreshold());
}
- view.setConservationSelected(av.getConservationSelected());
- view.setPidSelected(av.getAbovePIDThreshold());
- view.setFontName(av.font.getName());
- view.setFontSize(av.font.getSize());
- view.setFontStyle(av.font.getStyle());
- view.setRenderGaps(av.renderGaps);
- view.setShowAnnotation(av.getShowAnnotation());
- view.setShowBoxes(av.getShowBoxes());
- view.setShowColourText(av.getColourText());
- view.setShowConservation(av.showConservation);
- view.setShowFullId(av.getShowJVSuffix());
- view.setShowIdentity(av.showIdentity);
- view.setShowQuality(av.showQuality);
- view.setShowSequenceFeatures(av.showSequenceFeatures);
- view.setShowText(av.getShowText());
- view.setWrapAlignment(av.getWrapAlignment());
-
- if(av.featuresDisplayed!=null)
- {
- jalview.schemabinding.version2.FeatureSettings fs
- = new jalview.schemabinding.version2.FeatureSettings();
-
- String [] renderOrder =
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
-
- Vector settingsAdded = new Vector();
- for(int ro=0; ro<renderOrder.length; ro++)
- {
- Setting setting = new Setting();
- setting.setType(renderOrder[ro]);
- setting.setColour(
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
- );
+ groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
+ groups[i].setDisplayBoxes(sg.getDisplayBoxes());
+ groups[i].setDisplayText(sg.getDisplayText());
+ groups[i].setColourText(sg.getColourText());
+ groups[i].setTextCol1(sg.textColour.getRGB());
+ groups[i].setTextCol2(sg.textColour2.getRGB());
+ groups[i].setTextColThreshold(sg.thresholdTextColour);
- setting.setDisplay(
- av.featuresDisplayed.containsKey(renderOrder[ro])
- );
+ for (int s = 0; s < sg.getSize(); s++)
+ {
+ jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
+ .getSequenceAt(s);
+ groups[i].addSeq(seqHash(seq));
+ }
+ }
- fs.addSetting(setting);
- settingsAdded.addElement(renderOrder[ro]);
- }
+ jms.setJGroup(groups);
+ }
- //Make sure we save none displayed feature settings
- Enumeration en =
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
- while(en.hasMoreElements())
- {
- String key = en.nextElement().toString();
- if(settingsAdded.contains(key))
- continue;
+ ///////////SAVE VIEWPORT
+ Viewport view = new Viewport();
+ view.setTitle(ap.alignFrame.getTitle());
+ view.setSequenceSetId(av.getSequenceSetId());
+ view.setViewName(av.viewName);
+ view.setGatheredViews(av.gatherViewsHere);
- Setting setting = new Setting();
- setting.setType(key);
- setting.setColour(
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
- );
+ if (ap.av.explodedPosition != null)
+ {
+ view.setXpos(av.explodedPosition.x);
+ view.setYpos(av.explodedPosition.y);
+ view.setWidth(av.explodedPosition.width);
+ view.setHeight(av.explodedPosition.height);
+ }
+ else
+ {
+ view.setXpos(ap.alignFrame.getBounds().x);
+ view.setYpos(ap.alignFrame.getBounds().y);
+ view.setWidth(ap.alignFrame.getBounds().width);
+ view.setHeight(ap.alignFrame.getBounds().height);
+ }
- setting.setDisplay(false);
+ view.setStartRes(av.startRes);
+ view.setStartSeq(av.startSeq);
- fs.addSetting(setting);
- settingsAdded.addElement(key);
- }
+ if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
+ {
+ view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
+ userColours, jms));
+ }
+ else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
+ {
+ jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
+ .getGlobalColourScheme();
+
+ AnnotationColours ac = new AnnotationColours();
+ ac.setAboveThreshold(acg.getAboveThreshold());
+ ac.setThreshold(acg.getAnnotationThreshold());
+ ac.setAnnotation(acg.getAnnotation());
+ if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
+ {
+ ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
+ userColours, jms));
+ }
+ else
+ {
+ ac.setColourScheme(ColourSchemeProperty.getColourName(acg
+ .getBaseColour()));
+ }
- jms.setFeatureSettings(fs);
+ ac.setMaxColour(acg.getMaxColour().getRGB());
+ ac.setMinColour(acg.getMinColour().getRGB());
+ view.setAnnotationColours(ac);
+ view.setBgColour("AnnotationColourGradient");
+ }
+ else
+ {
+ view.setBgColour(ColourSchemeProperty.getColourName(av
+ .getGlobalColourScheme()));
+ }
- }
+ ColourSchemeI cs = av.getGlobalColourScheme();
- if(av.hasHiddenColumns)
+ if (cs != null)
+ {
+ if (cs.conservationApplied())
+ {
+ view.setConsThreshold(cs.getConservationInc());
+ if (cs instanceof jalview.schemes.UserColourScheme)
{
- for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)
- {
- int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);
- HiddenColumns hc = new HiddenColumns();
- hc.setStart(region[0]);
- hc.setEnd(region[1]);
- view.addHiddenColumns(hc);
- }
+ view.setBgColour(SetUserColourScheme(cs, userColours, jms));
}
+ }
- jms.addViewport(view);
+ if (cs instanceof ResidueColourScheme)
+ {
+ view.setPidThreshold(cs.getThreshold());
+ }
+ }
+ view.setConservationSelected(av.getConservationSelected());
+ view.setPidSelected(av.getAbovePIDThreshold());
+ view.setFontName(av.font.getName());
+ view.setFontSize(av.font.getSize());
+ view.setFontStyle(av.font.getStyle());
+ view.setRenderGaps(av.renderGaps);
+ view.setShowAnnotation(av.getShowAnnotation());
+ view.setShowBoxes(av.getShowBoxes());
+ view.setShowColourText(av.getColourText());
+ view.setShowFullId(av.getShowJVSuffix());
+ view.setRightAlignIds(av.rightAlignIds);
+ view.setShowSequenceFeatures(av.showSequenceFeatures);
+ view.setShowText(av.getShowText());
+ view.setWrapAlignment(av.getWrapAlignment());
+ view.setTextCol1(av.textColour.getRGB());
+ view.setTextCol2(av.textColour2.getRGB());
+ view.setTextColThreshold(av.thresholdTextColour);
+
+ if (av.featuresDisplayed != null)
+ {
+ jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
- object.setJalviewModelSequence(jms);
- object.getVamsasModel().addSequenceSet(vamsasSet);
+ String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
- try
+ Vector settingsAdded = new Vector();
+ for (int ro = 0; ro < renderOrder.length; ro++)
+ {
+ Setting setting = new Setting();
+ setting.setType(renderOrder[ro]);
+ setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getColour(renderOrder[ro]).getRGB());
+
+ setting.setDisplay(av.featuresDisplayed
+ .containsKey(renderOrder[ro]));
+ float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
+ renderOrder[ro]);
+ if (rorder > -1)
{
- if (!fileName.endsWith(".xml"))
- {
- fileName = fileName + ".xml";
- }
+ setting.setOrder(rorder);
+ }
+ fs.addSetting(setting);
+ settingsAdded.addElement(renderOrder[ro]);
+ }
+
+ //Make sure we save none displayed feature settings
+ Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
+ .keys();
+ while (en.hasMoreElements())
+ {
+ String key = en.nextElement().toString();
+ if (settingsAdded.contains(key))
+ {
+ continue;
+ }
- JarEntry entry = new JarEntry(fileName);
- jout.putNextEntry(entry);
+ Setting setting = new Setting();
+ setting.setType(key);
+ setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getColour(key).getRGB());
- object.marshal(out);
+ setting.setDisplay(false);
+ float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
+ key);
+ if (rorder > -1)
+ {
+ setting.setOrder(rorder);
}
- catch (Exception ex)
+ fs.addSetting(setting);
+ settingsAdded.addElement(key);
+ }
+ en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
+ Vector groupsAdded = new Vector();
+ while (en.hasMoreElements())
+ {
+ String grp = en.nextElement().toString();
+ if (groupsAdded.contains(grp))
{
- ex.printStackTrace();
+ continue;
}
+ Group g = new Group();
+ g.setName(grp);
+ g
+ .setDisplay(((Boolean) ap.seqPanel.seqCanvas
+ .getFeatureRenderer().featureGroups.get(grp))
+ .booleanValue());
+ fs.addGroup(g);
+ groupsAdded.addElement(grp);
+ }
+ jms.setFeatureSettings(fs);
+
}
- String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
- Vector userColours, JalviewModelSequence jms)
+ if (av.hasHiddenColumns)
{
- String id = null;
- jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
-
- if (!userColours.contains(ucs))
- {
- userColours.add(ucs);
-
- java.awt.Color[] colours = ucs.getColours();
- jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
- jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
+ for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
+ {
+ int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
+ .elementAt(c);
+ HiddenColumns hc = new HiddenColumns();
+ hc.setStart(region[0]);
+ hc.setEnd(region[1]);
+ view.addHiddenColumns(hc);
+ }
+ }
- for (int i = 0; i < colours.length; i++)
- {
- jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
- col.setName(ResidueProperties.aa[i]);
- col.setRGB(jalview.util.Format.getHexString(colours[i]));
- jbucs.addColour(col);
- }
- if(ucs.getLowerCaseColours()!=null)
- {
- colours = ucs.getLowerCaseColours();
- for (int i = 0; i < colours.length; i++)
- {
- jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
- col.setName(ResidueProperties.aa[i].toLowerCase());
- col.setRGB(jalview.util.Format.getHexString(colours[i]));
- jbucs.addColour(col);
- }
- }
+ jms.addViewport(view);
- id = "ucs" + userColours.indexOf(ucs);
- uc.setId(id);
- uc.setUserColourScheme(jbucs);
- jms.addUserColours(uc);
- }
+ object.setJalviewModelSequence(jms);
+ object.getVamsasModel().addSequenceSet(vamsasSet);
- return id;
+ if (jout!=null && fileName!=null)
+ {
+ //We may not want to write the object to disk,
+ //eg we can copy the alignViewport to a new view object
+ //using save and then load
+ try
+ {
+ JarEntry entry = new JarEntry(fileName);
+ jout.putNextEntry(entry);
+ PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
+ "UTF-8"));
+ org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(pout);
+ marshaller.marshal(object);
+ pout.flush();
+ jout.closeEntry();
+ } catch (Exception ex)
+ {
+ // TODO: raise error in GUI if marshalling failed.
+ ex.printStackTrace();
+ }
}
-
- jalview.schemes.UserColourScheme GetUserColourScheme(
- JalviewModelSequence jms, String id)
+ return object;
+ }
+
+ private Sequence createVamsasSequence(String id, SequenceI jds)
+ {
+ return createVamsasSequence(true, id, jds, null);
+ }
+
+ private Sequence createVamsasSequence(boolean recurse, String id,
+ SequenceI jds, SequenceI parentseq)
+ {
+ Sequence vamsasSeq = new Sequence();
+ vamsasSeq.setId(id);
+ vamsasSeq.setName(jds.getName());
+ vamsasSeq.setSequence(jds.getSequenceAsString());
+ vamsasSeq.setDescription(jds.getDescription());
+ jalview.datamodel.DBRefEntry[] dbrefs = null;
+ if (jds.getDatasetSequence() != null)
{
- UserColours[] uc = jms.getUserColours();
- UserColours colours = null;
-
- for (int i = 0; i < uc.length; i++)
+ vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
+ if (jds.getDatasetSequence().getDBRef() != null)
+ {
+ dbrefs = jds.getDatasetSequence().getDBRef();
+ }
+ }
+ else
+ {
+ vamsasSeq.setDsseqid(id); // so we can tell which sequences really are dataset sequences only
+ dbrefs = jds.getDBRef();
+ }
+ if (dbrefs != null)
+ {
+ for (int d = 0; d < dbrefs.length; d++)
+ {
+ DBRef dbref = new DBRef();
+ dbref.setSource(dbrefs[d].getSource());
+ dbref.setVersion(dbrefs[d].getVersion());
+ dbref.setAccessionId(dbrefs[d].getAccessionId());
+ if (dbrefs[d].hasMap())
{
- if (uc[i].getId().equals(id))
- {
- colours = uc[i];
-
- break;
- }
+ Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
+ jds, recurse);
+ dbref.setMapping(mp);
}
+ vamsasSeq.addDBRef(dbref);
+ }
+ }
+ return vamsasSeq;
+ }
+
+ private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
+ SequenceI parentseq, SequenceI jds, boolean recurse)
+ {
+ Mapping mp = null;
+ if (jmp.getMap() != null)
+ {
+ mp = new Mapping();
- java.awt.Color[] newColours = new java.awt.Color[24];
-
- for (int i = 0; i < 24; i++)
+ jalview.util.MapList mlst = jmp.getMap();
+ int r[] = mlst.getFromRanges();
+ for (int s = 0; s < r.length; s += 2)
+ {
+ MapListFrom mfrom = new MapListFrom();
+ mfrom.setStart(r[s]);
+ mfrom.setEnd(r[s + 1]);
+ mp.addMapListFrom(mfrom);
+ }
+ r = mlst.getToRanges();
+ for (int s = 0; s < r.length; s += 2)
+ {
+ MapListTo mto = new MapListTo();
+ mto.setStart(r[s]);
+ mto.setEnd(r[s + 1]);
+ mp.addMapListTo(mto);
+ }
+ mp.setMapFromUnit(mlst.getFromRatio());
+ mp.setMapToUnit(mlst.getToRatio());
+ if (jmp.getTo() != null)
+ {
+ MappingChoice mpc = new MappingChoice();
+ if (recurse
+ && (parentseq != jmp.getTo() || parentseq
+ .getDatasetSequence() != jmp.getTo()))
{
- newColours[i] = new java.awt.Color(Integer.parseInt(
- colours.getUserColourScheme().getColour(i).getRGB(), 16));
+ mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo())
+ , jmp.getTo(), jds));
}
-
- jalview.schemes.UserColourScheme ucs =
- new jalview.schemes.UserColourScheme(newColours);
-
- if (colours.getUserColourScheme().getColourCount() > 24)
+ else
{
- newColours = new java.awt.Color[23];
- for (int i = 0; i < 23; i++)
+ String jmpid = "";
+ SequenceI ps = null;
+ if (parentseq != jmp.getTo()
+ && parentseq.getDatasetSequence() != jmp.getTo())
+ {
+ // chaining dbref rather than a handshaking one
+ jmpid = seqHash(ps = jmp.getTo());
+ }
+ else
+ {
+ jmpid = seqHash(ps = parentseq);
+ }
+ mpc.setDseqFor(jmpid);
+ if (!seqRefIds.containsKey(mpc.getDseqFor()))
{
- newColours[i] = new java.awt.Color(Integer.parseInt(
- colours.getUserColourScheme().getColour(i+24).getRGB(), 16));
+ jalview.bin.Cache.log.debug("creatign new DseqFor ID");
+ seqRefIds.put(mpc.getDseqFor(), ps);
+ }
+ else
+ {
+ jalview.bin.Cache.log.debug("reusing DseqFor ID");
}
- ucs.setLowerCaseColours(newColours);
}
-
- return ucs;
+ mp.setMappingChoice(mpc);
+ }
}
+ return mp;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param file DOCUMENT ME!
- */
- public AlignFrame LoadJalviewAlign(final String file)
+ String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
+ Vector userColours, JalviewModelSequence jms)
+ {
+ String id = null;
+ jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
+
+ if (!userColours.contains(ucs))
{
- jalview.gui.AlignFrame af = null;
- try
+ userColours.add(ucs);
+
+ java.awt.Color[] colours = ucs.getColours();
+ jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
+ jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
+
+ for (int i = 0; i < colours.length; i++)
+ {
+ jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
+ col.setName(ResidueProperties.aa[i]);
+ col.setRGB(jalview.util.Format.getHexString(colours[i]));
+ jbucs.addColour(col);
+ }
+ if (ucs.getLowerCaseColours() != null)
+ {
+ colours = ucs.getLowerCaseColours();
+ for (int i = 0; i < colours.length; i++)
{
- //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
- URL url = null;
+ jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
+ col.setName(ResidueProperties.aa[i].toLowerCase());
+ col.setRGB(jalview.util.Format.getHexString(colours[i]));
+ jbucs.addColour(col);
+ }
+ }
- if (file.startsWith("http://"))
- {
- url = new URL(file);
- }
+ id = "ucs" + userColours.indexOf(ucs);
+ uc.setId(id);
+ uc.setUserColourScheme(jbucs);
+ jms.addUserColours(uc);
+ }
- JarInputStream jin = null;
- JarEntry jarentry = null;
- int entryCount = 1;
+ return id;
+ }
- do
- {
- if (url != null)
- {
- jin = new JarInputStream(url.openStream());
- }
- else
- {
- jin = new JarInputStream(new FileInputStream(file));
- }
+ jalview.schemes.UserColourScheme GetUserColourScheme(
+ JalviewModelSequence jms, String id)
+ {
+ UserColours[] uc = jms.getUserColours();
+ UserColours colours = null;
- for (int i = 0; i < entryCount; i++)
- {
- jarentry = jin.getNextJarEntry();
- }
+ for (int i = 0; i < uc.length; i++)
+ {
+ if (uc[i].getId().equals(id))
+ {
+ colours = uc[i];
- if (jarentry != null && jarentry.getName().endsWith(".xml"))
- {
- InputStreamReader in = new InputStreamReader(jin, "UTF-8");
- JalviewModel object = new JalviewModel();
+ break;
+ }
+ }
- Unmarshaller unmar = new Unmarshaller(object);
- unmar.setValidation(false);
- object = (JalviewModel) unmar.unmarshal( in );
+ java.awt.Color[] newColours = new java.awt.Color[24];
- af = LoadFromObject(object, file);
- entryCount++;
- }
- else if (jarentry != null)
- {
- //Some other file here.
- entryCount++;
- }
- }
- while (jarentry != null);
- }
- catch(java.net.UnknownHostException ex)
- {
- ex.printStackTrace();
- System.err.println("Couldn't locate Jalview XML file : " +
- ex + "\n");
+ for (int i = 0; i < 24; i++)
+ {
+ newColours[i] = new java.awt.Color(Integer.parseInt(colours
+ .getUserColourScheme().getColour(i).getRGB(), 16));
+ }
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Couldn't locate " + file,
- "URL not found",
- JOptionPane.WARNING_MESSAGE);
- }
- });
- }
- catch (Exception ex)
- {
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
+ newColours);
- //Is Version 1 Jar file?
- af = new Jalview2XML_V1().LoadJalviewAlign(file);
+ if (colours.getUserColourScheme().getColourCount() > 24)
+ {
+ newColours = new java.awt.Color[23];
+ for (int i = 0; i < 23; i++)
+ {
+ newColours[i] = new java.awt.Color(Integer.parseInt(colours
+ .getUserColourScheme().getColour(i + 24).getRGB(), 16));
+ }
+ ucs.setLowerCaseColours(newColours);
+ }
- if(af!=null)
- {
- System.out.println("Successfully loaded archive file");
- return af;
- }
- ex.printStackTrace();
- System.err.println("Exception whilst loading jalview XML file : " +
- ex + "\n");
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
+ return ucs;
+ }
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Error loading " + file,
- "Error loading Jalview file",
- JOptionPane.WARNING_MESSAGE);
- }});
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param file DOCUMENT ME!
+ */
+ public AlignFrame LoadJalviewAlign(final String file)
+ {
+ uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
- return af;
- }
+ jalview.gui.AlignFrame af = null;
- String loadPDBFile(String file, String pdbId)
+ seqRefIds = new Hashtable();
+ viewportsAdded = new Hashtable();
+ frefedSequence = new Vector();
+ Hashtable gatherToThisFrame = new Hashtable();
+
+ String errorMessage = null;
+
+ try
{
- System.out.println("load file "+file);
- try
+ //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
+ URL url = null;
+
+ if (file.startsWith("http://"))
{
- JarInputStream jin = null;
+ url = new URL(file);
+ }
+
+ JarInputStream jin = null;
+ JarEntry jarentry = null;
+ int entryCount = 1;
- if (file.startsWith("http://"))
+ do
+ {
+ if (url != null)
{
- jin = new JarInputStream(new URL(file).openStream());
+ jin = new JarInputStream(url.openStream());
}
else
{
jin = new JarInputStream(new FileInputStream(file));
}
- JarEntry entry = null;
- do
+ for (int i = 0; i < entryCount; i++)
{
- entry = jin.getNextJarEntry();
+ jarentry = jin.getNextJarEntry();
}
- while (!entry.getName().equals(pdbId));
- BufferedReader in = new BufferedReader(new InputStreamReader(jin));
- File outFile = File.createTempFile("jalview_pdb", ".txt");
- outFile.deleteOnExit();
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
- String data;
+ if (jarentry != null && jarentry.getName().endsWith(".xml"))
+ {
+ InputStreamReader in = new InputStreamReader(jin, "UTF-8");
+ JalviewModel object = new JalviewModel();
+
+ Unmarshaller unmar = new Unmarshaller(object);
+ unmar.setValidation(false);
+ object = (JalviewModel) unmar.unmarshal(in);
- while ( (data = in.readLine()) != null)
+ af = LoadFromObject(object, file, true);
+ if (af.viewport.gatherViewsHere)
+ {
+ gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+ }
+ entryCount++;
+ }
+ else if (jarentry != null)
{
- out.println(data);
+ //Some other file here.
+ entryCount++;
}
- out.close();
- return outFile.getAbsolutePath();
+ } while (jarentry != null);
+ resolveFrefedSequences();
+ } catch (java.io.FileNotFoundException ex)
+ {
+ ex.printStackTrace();
+ errorMessage = "Couldn't locate Jalview XML file : " + file;
+ System.err.println("Exception whilst loading jalview XML file : "
+ + ex + "\n");
+ } catch (java.net.UnknownHostException ex)
+ {
+ ex.printStackTrace();
+ errorMessage = "Couldn't locate Jalview XML file : " + file;
+ System.err.println("Exception whilst loading jalview XML file : "
+ + ex + "\n");
+ } catch (Exception ex)
+ {
+ System.err.println("Parsing as Jalview Version 2 file failed.");
+ ex.printStackTrace(System.err);
+
+ //Is Version 1 Jar file?
+ try {
+ af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(file);
+ } catch (Exception ex2) {
+ System.err.println("Exception whilst loading as jalviewXMLV1:");
+ ex2.printStackTrace();
+ af = null;
+ }
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
}
- catch (Exception ex)
+ if (af != null)
{
- ex.printStackTrace();
+ System.out.println("Successfully loaded archive file");
+ return af;
}
+ ex.printStackTrace();
- return null;
+ System.err.println("Exception whilst loading jalview XML file : "
+ + ex + "\n");
}
-
- AlignFrame LoadFromObject(JalviewModel object, String file)
+ if (Desktop.instance != null)
{
- Vector seqids = new Vector();
- SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
- Sequence[] vamsasSeq = vamsasSet.getSequence();
+ Desktop.instance.stopLoading();
+ }
- JalviewModelSequence jms = object.getJalviewModelSequence();
+ Enumeration en = gatherToThisFrame.elements();
+ while (en.hasMoreElements())
+ {
+ Desktop.instance.gatherViews((AlignFrame) en.nextElement());
+ }
- //////////////////////////////////
- //LOAD SEQUENCES
- Vector hiddenSeqs = null;
- jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
- JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
- for (int i = 0; i < vamsasSeq.length; i++)
+ if (errorMessage != null)
+ {
+ final String finalErrorMessage = errorMessage;
+ if (raiseGUI)
{
- jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
- vamsasSeq[i].getSequence());
- jseqs[i].setDescription( vamsasSeq[i].getDescription() );
-
- if(JSEQ[i].getHidden())
- {
- if(hiddenSeqs == null)
- hiddenSeqs = new Vector();
- hiddenSeqs.addElement(jseqs[i]);
- }
- jseqs[i].setStart(JSEQ[i].getStart());
- jseqs[i].setEnd(JSEQ[i].getEnd());
- jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
- seqids.add(jseqs[i]);
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ finalErrorMessage, "Error loading Jalview file",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ });
+ } else {
+ System.err.println("Problem loading Jalview file: "+errorMessage);
}
+ }
- ///SequenceFeatures are added to the DatasetSequence,
- // so we must create the dataset before loading features
- /////////////////////////////////
- jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
- al.setDataset(null);
- /////////////////////////////////
+ return af;
+ }
+ Hashtable alreadyLoadedPDB;
- Hashtable pdbloaded = new Hashtable();
- for (int i = 0; i < vamsasSeq.length; i++)
- {
- if (JSEQ[i].getFeaturesCount() > 0)
- {
- Features[] features = JSEQ[i].getFeatures();
- for (int f = 0; f < features.length; f++)
- {
- jalview.datamodel.SequenceFeature sf
- = new jalview.datamodel.SequenceFeature(features[f].getType(),
- features[f].getDescription(), features[f].getStatus(),
- features[f].getBegin(), features[f].getEnd(),
- features[f].getFeatureGroup());
-
- sf.setScore(features[f].getScore());
- for(int od=0; od<features[f].getOtherDataCount(); od++)
- {
- OtherData keyValue = features[f].getOtherData(od);
- if(keyValue.getKey().startsWith("LINK"))
- sf.addLink(keyValue.getValue());
- else
- sf.setValue(keyValue.getKey(), keyValue.getValue());
+ String loadPDBFile(String file, String pdbId)
+ {
+ if (alreadyLoadedPDB == null)
+ alreadyLoadedPDB = new Hashtable();
- }
+ if (alreadyLoadedPDB.containsKey(pdbId))
+ return alreadyLoadedPDB.get(pdbId).toString();
- al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
- }
- }
- if (JSEQ[i].getPdbidsCount() > 0)
- {
- Pdbids[] ids = JSEQ[i].getPdbids();
- for (int p = 0; p < ids.length; p++)
- {
- jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
- entry.setId(ids[p].getId());
- entry.setType(ids[p].getType());
- if (ids[p].getFile() != null)
- {
- if (!pdbloaded.containsKey(ids[p].getFile()))
- {
- String tmppdb = loadPDBFile(file, ids[p].getId());
- entry.setFile(tmppdb);
- pdbloaded.put(ids[p].getId(), tmppdb);
- }
- else
- entry.setFile(pdbloaded.get(ids[p].getId()).toString());
- }
+ try
+ {
+ JarInputStream jin = null;
- al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
- }
- }
- if(vamsasSeq[i].getDBRefCount()>0)
- {
- for(int d=0; d<vamsasSeq[i].getDBRefCount(); d++)
- {
- jalview.datamodel.DBRefEntry entry =
- new jalview.datamodel.DBRefEntry(
- vamsasSeq[i].getDBRef(d).getSource(),
- vamsasSeq[i].getDBRef(d).getVersion(),
- vamsasSeq[i].getDBRef(d).getAccessionId()
- );
- al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
- }
+ if (file.startsWith("http://"))
+ {
+ jin = new JarInputStream(new URL(file).openStream());
+ }
+ else
+ {
+ jin = new JarInputStream(new FileInputStream(file));
+ }
- }
- }
+ JarEntry entry = null;
+ do
+ {
+ entry = jin.getNextJarEntry();
+ } while (!entry.getName().equals(pdbId));
+ BufferedReader in = new BufferedReader(new InputStreamReader(jin));
+ File outFile = File.createTempFile("jalview_pdb", ".txt");
+ outFile.deleteOnExit();
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+ String data;
+ while ((data = in.readLine()) != null)
+ {
+ out.println(data);
+ }
+ try { out.flush(); } catch (Exception foo) {};
+ out.close();
- /////////////////////////////////
- //////////////////////////////////
- //LOAD ANNOTATIONS
- boolean hideQuality = true,
- hideConservation = true,
- hideConsensus = true;
+ alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
+ return outFile.getAbsolutePath();
- if (vamsasSet.getAnnotation() != null)
- {
- Annotation[] an = vamsasSet.getAnnotation();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
- for (int i = 0; i < an.length; i++)
- {
- if (an[i].getLabel().equals("Quality"))
- {
- hideQuality = false;
- continue;
- }
- else if(an[i].getLabel().equals("Conservation"))
- {
- hideConservation = false;
- continue;
- }
- else if(an[i].getLabel().equals("Consensus"))
- {
- hideConsensus = false;
- continue;
- }
-
- AnnotationElement[] ae = an[i].getAnnotationElement();
- jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
-
- for (int aa = 0; aa < ae.length; aa++)
- {
- anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
- ae[aa].getDescription(),
- ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
- ae[aa].getValue());
- anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
- }
+ return null;
+ }
- jalview.datamodel.AlignmentAnnotation jaa = null;
+ AlignFrame LoadFromObject(JalviewModel object, String file,
+ boolean loadTreesAndStructures)
+ {
+ SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
+ Sequence[] vamsasSeq = vamsasSet.getSequence();
- if (an[i].getGraph())
- {
- jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
- an[i].getDescription(), anot, 0, 0,
- an[i].getGraphType());
+ JalviewModelSequence jms = object.getJalviewModelSequence();
- jaa.graphGroup = an[i].getGraphGroup();
+ Viewport view = jms.getViewport(0);
- if (an[i].getThresholdLine() != null)
- {
- jaa.setThreshold(new jalview.datamodel.GraphLine(
- an[i].getThresholdLine().getValue(),
- an[i].getThresholdLine().getLabel(),
- new java.awt.Color(an[i].getThresholdLine().getColour()))
- );
+ //////////////////////////////////
+ //LOAD SEQUENCES
- }
+ Vector hiddenSeqs = null;
+ jalview.datamodel.Sequence jseq;
- }
- else
- {
- jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
- an[i].getDescription(), anot);
- }
+ ArrayList tmpseqs = new ArrayList();
- if(an[i].getSequenceRef()!=null)
- {
- jaa.createSequenceMapping(
- al.findName(an[i].getSequenceRef()), 1, true
- );
- al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
- }
+ boolean multipleView = false;
- al.addAnnotation(jaa);
- }
- }
+ JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
+ int vi=0; // counter in vamsasSeq array
+ for (int i = 0; i < JSEQ.length; i++)
+ {
+ String seqId = JSEQ[i].getId() + "";
+ if (seqRefIds.get(seqId) != null)
+ {
+ tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId));
+ multipleView = true;
+ }
+ else
+ {
+ jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
+ vamsasSeq[vi].getSequence());
+ jseq.setDescription(vamsasSeq[vi].getDescription());
+ jseq.setStart(JSEQ[i].getStart());
+ jseq.setEnd(JSEQ[i].getEnd());
+ jseq.setVamsasId(uniqueSetSuffix + seqId);
+ seqRefIds.put(vamsasSeq[vi].getId()+"", jseq);
+ tmpseqs.add(jseq);
+ vi++;
+ }
- // af.changeColour() );
- /////////////////////////
- //LOAD GROUPS
- if (jms.getJGroupCount() > 0)
+ if (JSEQ[i].getHidden())
+ {
+ if (hiddenSeqs == null)
{
- JGroup[] groups = jms.getJGroup();
+ hiddenSeqs = new Vector();
+ }
- for (int i = 0; i < groups.length; i++)
- {
- ColourSchemeI cs = null;
+ hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
+ .get(seqId));
+ }
- if (groups[i].getColour() != null)
- {
- if (groups[i].getColour().startsWith("ucs"))
- {
- cs = GetUserColourScheme(jms, groups[i].getColour());
- }
- else
- {
- cs = ColourSchemeProperty.getColour(al,
- groups[i].getColour());
- }
+ }
- if(cs!=null)
- cs.setThreshold(groups[i].getPidThreshold(), true);
- }
+ ///
+ // Create the alignment object from the sequence set
+ /////////////////////////////////
+ jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
+ .size()];
- Vector seqs = new Vector();
- int[] ids = groups[i].getSeq();
+ tmpseqs.toArray(orderedSeqs);
- for (int s = 0; s < ids.length; s++)
- {
- seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(
- ids[s]));
- }
+ jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
+ orderedSeqs);
- jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
- groups[i].getName(), cs, groups[i].getDisplayBoxes(),
- groups[i].getDisplayText(), groups[i].getColourText(),
- groups[i].getStart(), groups[i].getEnd());
+ /// Add the alignment properties
+ for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
+ {
+ SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
+ al.setProperty(ssp.getKey(), ssp.getValue());
+ }
- sg.setOutlineColour(new java.awt.Color(
- groups[i].getOutlineColour()));
+ ///
+ // SequenceFeatures are added to the DatasetSequence,
+ // so we must create or recover the dataset before loading features
+ /////////////////////////////////
+ if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
+ {
+ // older jalview projects do not have a dataset id.
+ al.setDataset(null);
+ }
+ else
+ {
+ recoverDatasetFor(vamsasSet, al);
+ }
+ /////////////////////////////////
- if (groups[i].getConsThreshold() != 0)
- {
- jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
- ResidueProperties.propHash, 3, sg.getSequences(false), 0,
- sg.getWidth() - 1);
- c.calculate();
- c.verdict(false, 25);
- sg.cs.setConservation(c);
- }
+ Hashtable pdbloaded = new Hashtable();
+ if (!multipleView)
+ {
+ for (int i = 0; i < vamsasSeq.length; i++)
+ {
+ if (JSEQ[i].getFeaturesCount() > 0)
+ {
+ Features[] features = JSEQ[i].getFeatures();
+ for (int f = 0; f < features.length; f++)
+ {
+ jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
+ features[f].getType(), features[f].getDescription(),
+ features[f].getStatus(), features[f].getBegin(),
+ features[f].getEnd(), features[f].getFeatureGroup());
+
+ sf.setScore(features[f].getScore());
+ for (int od = 0; od < features[f].getOtherDataCount(); od++)
+ {
+ OtherData keyValue = features[f].getOtherData(od);
+ if (keyValue.getKey().startsWith("LINK"))
+ {
+ sf.addLink(keyValue.getValue());
+ }
+ else
+ {
+ sf.setValue(keyValue.getKey(), keyValue.getValue());
+ }
- al.addGroup(sg);
}
+
+ al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
+ }
+ }
+ if (vamsasSeq[i].getDBRefCount() > 0)
+ {
+ addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
}
+ if (JSEQ[i].getPdbidsCount() > 0)
+ {
+ Pdbids[] ids = JSEQ[i].getPdbids();
+ for (int p = 0; p < ids.length; p++)
+ {
+ jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
+ entry.setId(ids[p].getId());
+ entry.setType(ids[p].getType());
+ if (ids[p].getFile() != null)
+ {
+ if (!pdbloaded.containsKey(ids[p].getFile()))
+ {
+ entry.setFile(loadPDBFile(file, ids[p].getId()));
+ }
+ else
+ {
+ entry.setFile(pdbloaded.get(ids[p].getId()).toString());
+ }
+ }
+ al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+ }
+ }
+ }
+ }
- /////////////////////////////////
- // LOAD VIEWPORT
- Viewport[] views = jms.getViewport();
- Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
+ /////////////////////////////////
+ // LOAD SEQUENCE MAPPINGS
+ if (vamsasSet.getAlcodonFrameCount() > 0)
+ {
+ AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
+ for (int i = 0; i < alc.length; i++)
+ {
+ jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
+ alc[i].getAlcodonCount());
+ if (alc[i].getAlcodonCount() > 0)
+ {
+ Alcodon[] alcods = alc[i].getAlcodon();
+ for (int p = 0; p < cf.codons.length; p++)
+ {
+ cf.codons[p] = new int[3];
+ cf.codons[p][0] = (int) alcods[p].getPos1();
+ cf.codons[p][1] = (int) alcods[p].getPos2();
+ cf.codons[p][2] = (int) alcods[p].getPos3();
+ }
+ }
+ if (alc[i].getAlcodMapCount() > 0)
+ {
+ AlcodMap[] maps = alc[i].getAlcodMap();
+ for (int m = 0; m < maps.length; m++)
+ {
+ SequenceI dnaseq = (SequenceI) seqRefIds
+ .get(maps[m].getDnasq());
+ // Load Mapping
+ // attach to dna sequence reference.
+ if (dnaseq != null)
+ {
+ if (maps[m].getMapping() != null)
+ {
+ jalview.datamodel.Mapping mapping = addMapping(maps[m]
+ .getMapping());
+ cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
+ }
+ }
+ }
+ }
+ al.addCodonFrame(cf);
+ }
+ }
- AlignFrame af = new AlignFrame(al);
+ //////////////////////////////////
+ //LOAD ANNOTATIONS
+ boolean hideQuality = true, hideConservation = true, hideConsensus = true;
- if(hiddenSeqs!=null)
+ if (vamsasSet.getAnnotationCount() > 0)
+ {
+ Annotation[] an = vamsasSet.getAnnotation();
+
+ for (int i = 0; i < an.length; i++)
+ {
+ if (an[i].getLabel().equals("Quality"))
+ {
+ hideQuality = false;
+ continue;
+ }
+ else if (an[i].getLabel().equals("Conservation"))
+ {
+ hideConservation = false;
+ continue;
+ }
+ else if (an[i].getLabel().equals("Consensus"))
{
- for(int s=0; s<JSEQ.length; s++)
+ hideConsensus = false;
+ continue;
+ }
+
+ if (an[i].getId() != null
+ && annotationIds.containsKey(an[i].getId()))
+ {
+ jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
+ .get(an[i].getId());
+ if (an[i].hasVisible())
+ jda.visible = an[i].getVisible();
+
+ al.addAnnotation(jda);
+
+ continue;
+ }
+
+ AnnotationElement[] ae = an[i].getAnnotationElement();
+ jalview.datamodel.Annotation[] anot = null;
+
+ if (!an[i].getScoreOnly())
+ {
+ anot = new jalview.datamodel.Annotation[al.getWidth()];
+
+ for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
{
- for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
- {
- al.getSequenceAt(s).addHiddenSequence(
- al.getSequenceAt( JSEQ[s].getHiddenSequences(r) )
- );
- }
+ if (ae[aa].getPosition() >= anot.length)
+ continue;
+
+ anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
+
+ ae[aa].getDisplayCharacter(), ae[aa].getDescription(), (ae[aa]
+ .getSecondaryStructure() == null || ae[aa]
+ .getSecondaryStructure().length() == 0) ? ' ' : ae[aa]
+ .getSecondaryStructure().charAt(0), ae[aa].getValue()
+
+ );
+ // JBPNote: Consider verifying dataflow for IO of secondary structure annotation read from Stockholm files
+ // this was added to try to ensure that
+ //if (anot[ae[aa].getPosition()].secondaryStructure>' ')
+ //{
+ // anot[ae[aa].getPosition()].displayCharacter = "";
+ //}
+ anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]
+ .getColour());
}
+ }
+ jalview.datamodel.AlignmentAnnotation jaa = null;
+
+ if (an[i].getGraph())
+ {
+ jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+ an[i].getDescription(), anot, 0, 0, an[i].getGraphType());
+
+ jaa.graphGroup = an[i].getGraphGroup();
- for(int s=0; s<hiddenSeqs.size(); s++)
+ if (an[i].getThresholdLine() != null)
{
- af.viewport.hideSequence(
- (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s));
+ jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
+ .getThresholdLine().getValue(), an[i]
+ .getThresholdLine().getLabel(), new java.awt.Color(
+ an[i].getThresholdLine().getColour())));
+
}
+
+ }
+ else
+ {
+ jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+ an[i].getDescription(), anot);
}
+ if (an[i].getId() != null)
+ {
+ annotationIds.put(an[i].getId(), jaa);
+ jaa.annotationId = an[i].getId();
+ }
- if(hideConsensus || hideQuality || hideConservation)
+ if (an[i].getSequenceRef() != null)
{
- int hSize = al.getAlignmentAnnotation().length;
- for (int h = 0; h < hSize; h++)
+ if (al.findName(an[i].getSequenceRef()) != null)
{
- if (
- (hideConsensus &&
- al.getAlignmentAnnotation()[h].label.equals("Consensus"))
- ||
- (hideQuality &&
- al.getAlignmentAnnotation()[h].label.equals("Quality"))
- ||
- (hideConservation &&
- al.getAlignmentAnnotation()[h].label.equals("Conservation")))
- {
- al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
- hSize--;
- h--;
- }
+ jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
+ 1, true);
+ al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
}
- af.alignPanel.adjustAnnotationHeight();
+ }
+ if (an[i].hasScore())
+ {
+ jaa.setScore(an[i].getScore());
}
- af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
- view.getHeight());
- af.viewport.setStartRes(view.getStartRes());
- af.viewport.setStartSeq(view.getStartSeq());
- af.viewport.setShowAnnotation(view.getShowAnnotation());
- af.viewport.showConservation = view.getShowConservation();
- af.viewport.showQuality = view.getShowQuality();
- af.viewport.showIdentity = view.getShowIdentity();
- af.viewport.setAbovePIDThreshold(view.getPidSelected());
- af.abovePIDThreshold.setSelected(view.getPidSelected());
- af.viewport.setColourText(view.getShowColourText());
- af.colourTextMenuItem.setSelected(view.getShowColourText());
- af.viewport.setConservationSelected(view.getConservationSelected());
- af.conservationMenuItem.setSelected(view.getConservationSelected());
+ if (an[i].hasVisible())
+ jaa.visible = an[i].getVisible();
- af.viewport.setShowJVSuffix(view.getShowFullId());
- af.seqLimits.setSelected(view.getShowFullId());
+ al.addAnnotation(jaa);
+ }
+ }
- af.viewport.setFont(new java.awt.Font(view.getFontName(),
- view.getFontStyle(), view.getFontSize()));
- af.alignPanel.fontChanged();
+ /////////////////////////
+ //LOAD GROUPS
+ if (jms.getJGroupCount() > 0)
+ {
+ JGroup[] groups = jms.getJGroup();
- af.viewport.setRenderGaps(view.getRenderGaps());
- af.renderGapsMenuItem.setSelected(view.getRenderGaps());
+ for (int i = 0; i < groups.length; i++)
+ {
+ ColourSchemeI cs = null;
- af.viewport.setWrapAlignment(view.getWrapAlignment());
- af.wrapMenuItem.setSelected(view.getWrapAlignment());
+ if (groups[i].getColour() != null)
+ {
+ if (groups[i].getColour().startsWith("ucs"))
+ {
+ cs = GetUserColourScheme(jms, groups[i].getColour());
+ }
+ else
+ {
+ cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
+ }
- af.alignPanel.setWrapAlignment(view.getWrapAlignment());
+ if (cs != null)
+ {
+ cs.setThreshold(groups[i].getPidThreshold(), true);
+ }
+ }
- af.annotationPanelMenuItem.setState(view.getShowAnnotation());
- af.viewport.setShowAnnotation(view.getShowAnnotation());
- af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
+ Vector seqs = new Vector();
- af.viewport.setShowBoxes(view.getShowBoxes());
- af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
- af.viewport.setShowText(view.getShowText());
- af.viewTextMenuItem.setSelected(view.getShowText());
+ for (int s = 0; s < groups[i].getSeqCount(); s++)
+ {
+ String seqId = groups[i].getSeq(s) + "";
+ jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds
+ .get(seqId);
- ColourSchemeI cs = null;
+ if (ts != null)
+ {
+ seqs.addElement(ts);
+ }
+ }
- if (view.getBgColour() != null)
+ if (seqs.size() < 1)
{
- if (view.getBgColour().startsWith("ucs"))
- {
- cs = GetUserColourScheme(jms, view.getBgColour());
- }
- else if(view.getBgColour().startsWith("Annotation"))
- {
- //int find annotation
- for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
- {
- if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
- equals(view.getAnnotationColours().getAnnotation()))
- {
- if (af.viewport.alignment.getAlignmentAnnotation()[i].
- getThreshold() == null)
- {
- af.viewport.alignment.getAlignmentAnnotation()[i].
- setThreshold(
- new jalview.datamodel.GraphLine(
- view.getAnnotationColours().getThreshold(),
- "Threshold", java.awt.Color.black)
+ continue;
+ }
- );
- }
+ jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
+ seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
+ groups[i].getDisplayText(), groups[i].getColourText(),
+ groups[i].getStart(), groups[i].getEnd());
+ sg
+ .setOutlineColour(new java.awt.Color(groups[i]
+ .getOutlineColour()));
- if (view.getAnnotationColours().getColourScheme().equals(
- "None"))
- {
- cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
- new java.awt.Color(view.getAnnotationColours().
- getMinColour()),
- new java.awt.Color(view.getAnnotationColours().
- getMaxColour()),
- view.getAnnotationColours().getAboveThreshold());
- }
- else if (view.getAnnotationColours().getColourScheme().
- startsWith("ucs"))
- {
- cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
- GetUserColourScheme(jms, view.getAnnotationColours().
- getColourScheme()),
- view.getAnnotationColours().getAboveThreshold()
- );
- }
- else
- {
- cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
- ColourSchemeProperty.getColour(al,
- view.getAnnotationColours().getColourScheme()),
- view.getAnnotationColours().getAboveThreshold()
- );
- }
-
- // Also use these settings for all the groups
- if (al.getGroups() != null)
- for (int g = 0; g < al.getGroups().size(); g++)
- {
- jalview.datamodel.SequenceGroup sg
- = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
-
- if(sg.cs == null)
- continue;
-
-
- /* if (view.getAnnotationColours().getColourScheme().equals("None"))
- {
- sg.cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
- new java.awt.Color(view.getAnnotationColours().
- getMinColour()),
- new java.awt.Color(view.getAnnotationColours().
- getMaxColour()),
- view.getAnnotationColours().getAboveThreshold());
- }
- else*/
- {
- sg.cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
- sg.cs,
- view.getAnnotationColours().getAboveThreshold()
- );
- }
+ sg.textColour = new java.awt.Color(groups[i].getTextCol1());
+ sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
+ sg.thresholdTextColour = groups[i].getTextColThreshold();
- }
+ if (groups[i].getConsThreshold() != 0)
+ {
+ jalview.analysis.Conservation c = new jalview.analysis.Conservation(
+ "All", ResidueProperties.propHash, 3, sg
+ .getSequences(null), 0, sg.getWidth() - 1);
+ c.calculate();
+ c.verdict(false, 25);
+ sg.cs.setConservation(c);
+ }
+ al.addGroup(sg);
+ }
+ }
- break;
- }
+ /////////////////////////////////
+ // LOAD VIEWPORT
- }
+ AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
+
+ af.setFileName(file, "Jalview");
+
+ for (int i = 0; i < JSEQ.length; i++)
+ {
+ af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
+ new java.awt.Color(JSEQ[i].getColour()));
+ }
+
+ //If we just load in the same jar file again, the sequenceSetId
+ //will be the same, and we end up with multiple references
+ //to the same sequenceSet. We must modify this id on load
+ //so that each load of the file gives a unique id
+ String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
+
+ af.viewport.gatherViewsHere = view.getGatheredViews();
+
+ if (view.getSequenceSetId() != null)
+ {
+ jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
+ .get(uniqueSeqSetId);
+
+ af.viewport.sequenceSetID = uniqueSeqSetId;
+ if (av != null)
+ {
+
+ af.viewport.historyList = av.historyList;
+ af.viewport.redoList = av.redoList;
+ }
+ else
+ {
+ viewportsAdded.put(uniqueSeqSetId, af.viewport);
+ }
+
+ PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
+ }
+ if (hiddenSeqs != null)
+ {
+ for (int s = 0; s < JSEQ.length; s++)
+ {
+ jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
+
+ for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
+ {
+ hidden.addSequence(al
+ .getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
+ }
+ af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
+ }
+
+ jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
+ .size()];
+
+ for (int s = 0; s < hiddenSeqs.size(); s++)
+ {
+ hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
+ }
+
+ af.viewport.hideSequence(hseqs);
+
+ }
+
+ if ((hideConsensus || hideQuality || hideConservation)
+ && al.getAlignmentAnnotation() != null)
+ {
+ int hSize = al.getAlignmentAnnotation().length;
+ for (int h = 0; h < hSize; h++)
+ {
+ if ((hideConsensus && al.getAlignmentAnnotation()[h].label
+ .equals("Consensus"))
+ || (hideQuality && al.getAlignmentAnnotation()[h].label
+ .equals("Quality"))
+ || (hideConservation && al.getAlignmentAnnotation()[h].label
+ .equals("Conservation")))
+ {
+ al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
+ hSize--;
+ h--;
+ }
+ }
+ af.alignPanel.adjustAnnotationHeight();
+ }
+
+ if (view.getViewName() != null)
+ {
+ af.viewport.viewName = view.getViewName();
+ af.setInitialTabVisible();
+ }
+ af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
+ .getHeight());
+
+ af.viewport.setShowAnnotation(view.getShowAnnotation());
+ af.viewport.setAbovePIDThreshold(view.getPidSelected());
+
+ af.viewport.setColourText(view.getShowColourText());
+
+ af.viewport.setConservationSelected(view.getConservationSelected());
+ af.viewport.setShowJVSuffix(view.getShowFullId());
+ af.viewport.rightAlignIds = view.getRightAlignIds();
+ af.viewport.setFont(new java.awt.Font(view.getFontName(), view
+ .getFontStyle(), view.getFontSize()));
+ af.alignPanel.fontChanged();
+ af.viewport.setRenderGaps(view.getRenderGaps());
+ af.viewport.setWrapAlignment(view.getWrapAlignment());
+ af.alignPanel.setWrapAlignment(view.getWrapAlignment());
+ af.viewport.setShowAnnotation(view.getShowAnnotation());
+ af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
+
+ af.viewport.setShowBoxes(view.getShowBoxes());
+
+ af.viewport.setShowText(view.getShowText());
+
+ af.viewport.textColour = new java.awt.Color(view.getTextCol1());
+ af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
+ af.viewport.thresholdTextColour = view.getTextColThreshold();
+
+ af.viewport.setStartRes(view.getStartRes());
+ af.viewport.setStartSeq(view.getStartSeq());
+
+ ColourSchemeI cs = null;
+
+ if (view.getBgColour() != null)
+ {
+ if (view.getBgColour().startsWith("ucs"))
+ {
+ cs = GetUserColourScheme(jms, view.getBgColour());
+ }
+ else if (view.getBgColour().startsWith("Annotation"))
+ {
+ //int find annotation
+ for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
+ {
+ if (af.viewport.alignment.getAlignmentAnnotation()[i].label
+ .equals(view.getAnnotationColours().getAnnotation()))
+ {
+ if (af.viewport.alignment.getAlignmentAnnotation()[i]
+ .getThreshold() == null)
+ {
+ af.viewport.alignment.getAlignmentAnnotation()[i]
+ .setThreshold(new jalview.datamodel.GraphLine(view
+ .getAnnotationColours().getThreshold(),
+ "Threshold", java.awt.Color.black)
+
+ );
+ }
+
+ if (view.getAnnotationColours().getColourScheme()
+ .equals("None"))
+ {
+ cs = new AnnotationColourGradient(af.viewport.alignment
+ .getAlignmentAnnotation()[i], new java.awt.Color(view
+ .getAnnotationColours().getMinColour()),
+ new java.awt.Color(view.getAnnotationColours()
+ .getMaxColour()), view.getAnnotationColours()
+ .getAboveThreshold());
+ }
+ else if (view.getAnnotationColours().getColourScheme()
+ .startsWith("ucs"))
+ {
+ cs = new AnnotationColourGradient(af.viewport.alignment
+ .getAlignmentAnnotation()[i], GetUserColourScheme(
+ jms, view.getAnnotationColours().getColourScheme()),
+ view.getAnnotationColours().getAboveThreshold());
}
else
{
- cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+ cs = new AnnotationColourGradient(af.viewport.alignment
+ .getAlignmentAnnotation()[i], ColourSchemeProperty
+ .getColour(al, view.getAnnotationColours()
+ .getColourScheme()), view
+ .getAnnotationColours().getAboveThreshold());
}
- if(cs!=null)
+ // Also use these settings for all the groups
+ if (al.getGroups() != null)
{
- cs.setThreshold(view.getPidThreshold(), true);
- cs.setConsensus(af.viewport.vconsensus);
+ for (int g = 0; g < al.getGroups().size(); g++)
+ {
+ jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
+ .getGroups().elementAt(g);
+
+ if (sg.cs == null)
+ {
+ continue;
+ }
+
+ /* if (view.getAnnotationColours().getColourScheme().equals("None"))
+ {
+ sg.cs = new AnnotationColourGradient(
+ af.viewport.alignment.getAlignmentAnnotation()[i],
+ new java.awt.Color(view.getAnnotationColours().
+ getMinColour()),
+ new java.awt.Color(view.getAnnotationColours().
+ getMaxColour()),
+ view.getAnnotationColours().getAboveThreshold());
+ }
+ else*/
+ {
+ sg.cs = new AnnotationColourGradient(
+ af.viewport.alignment.getAlignmentAnnotation()[i],
+ sg.cs, view.getAnnotationColours()
+ .getAboveThreshold());
+ }
+
+ }
}
- }
- af.setColourSelected(view.getBgColour());
- af.viewport.setGlobalColourScheme(cs);
- af.viewport.setColourAppliesToAllGroups(false);
- af.changeColour(cs);
- if (view.getConservationSelected() && cs!=null)
- {
- cs.setConservationInc(view.getConsThreshold());
+ break;
+ }
+
}
+ }
+ else
+ {
+ cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+ }
+
+ if (cs != null)
+ {
+ cs.setThreshold(view.getPidThreshold(), true);
+ cs.setConsensus(af.viewport.hconsensus);
+ }
+ }
- af.viewport.setColourAppliesToAllGroups(true);
+ af.viewport.setGlobalColourScheme(cs);
+ af.viewport.setColourAppliesToAllGroups(false);
+
+ if (view.getConservationSelected() && cs != null)
+ {
+ cs.setConservationInc(view.getConsThreshold());
+ }
- if (view.getShowSequenceFeatures())
+ af.changeColour(cs);
+
+ af.viewport.setColourAppliesToAllGroups(true);
+
+ if (view.getShowSequenceFeatures())
+ {
+ af.viewport.showSequenceFeatures = true;
+ }
+
+ if (jms.getFeatureSettings() != null)
+ {
+ af.viewport.featuresDisplayed = new Hashtable();
+ String[] renderOrder = new String[jms.getFeatureSettings()
+ .getSettingCount()];
+ for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
+ {
+ Setting setting = jms.getFeatureSettings().getSetting(fs);
+
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
+ setting.getType(), new java.awt.Color(setting.getColour()));
+ renderOrder[fs] = setting.getType();
+ if (setting.hasOrder())
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
+ setting.getType(), setting.getOrder());
+ else
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
+ setting.getType(),
+ fs / jms.getFeatureSettings().getSettingCount());
+ if (setting.getDisplay())
{
- af.viewport.showSequenceFeatures = true;
- af.showSeqFeatures.setSelected(true);
+ af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
+ setting.getColour()));
}
+ }
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
+ Hashtable fgtable;
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
+ for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
+ {
+ Group grp = jms.getFeatureSettings().getGroup(gs);
+ fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
+ }
+ }
+
+ if (view.getHiddenColumnsCount() > 0)
+ {
+ for (int c = 0; c < view.getHiddenColumnsCount(); c++)
+ {
+ af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
+ .getHiddenColumns(c).getEnd() //+1
+ );
+ }
+ }
+
+ af.setMenusFromViewport(af.viewport);
+
+ Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
+ .getHeight());
- if(jms.getFeatureSettings()!=null)
+ //LOAD TREES
+ ///////////////////////////////////////
+ if (loadTreesAndStructures && jms.getTreeCount() > 0)
+ {
+ try
+ {
+ for (int t = 0; t < jms.getTreeCount(); t++)
{
- af.viewport.featuresDisplayed = new Hashtable();
- String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
- for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
- {
- Setting setting = jms.getFeatureSettings().getSetting(fs);
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
- new java.awt.Color(setting.getColour()));
+ Tree tree = jms.getTree(t);
- renderOrder[fs] = setting.getType();
+ TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(tree
+ .getNewick()), tree.getTitle(), tree.getWidth(), tree
+ .getHeight(), tree.getXpos(), tree.getYpos());
- if(setting.getDisplay())
- af.viewport.featuresDisplayed.put(
- setting.getType(), new Integer(setting.getColour()));
- }
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
- }
+ tp.fitToWindow.setState(tree.getFitToWindow());
+ tp.fitToWindow_actionPerformed(null);
- if (view.getHiddenColumnsCount() > 0)
- {
- for (int c = 0; c < view.getHiddenColumnsCount(); c++)
+ if (tree.getFontName() != null)
{
- af.viewport.hideColumns(
- view.getHiddenColumns(c).getStart(),
- view.getHiddenColumns(c).getEnd() //+1
- );
+ tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
+ .getFontStyle(), tree.getFontSize()));
+ }
+ else
+ {
+ tp.setTreeFont(new java.awt.Font(view.getFontName(), view
+ .getFontStyle(), tree.getFontSize()));
}
- }
+ tp.showPlaceholders(tree.getMarkUnlinked());
+ tp.showBootstrap(tree.getShowBootstrap());
+ tp.showDistances(tree.getShowDistances());
- Desktop.addInternalFrame(af, view.getTitle(),
- view.getWidth(), view.getHeight());
+ tp.treeCanvas.threshold = tree.getThreshold();
- //LOAD TREES
- ///////////////////////////////////////
- if (jms.getTreeCount() > 0)
+ if (tree.getCurrentTree())
+ {
+ af.viewport.setCurrentTree(tp.getTree());
+ }
+ }
+
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ ////LOAD STRUCTURES
+ if (loadTreesAndStructures)
+ {
+ for (int i = 0; i < JSEQ.length; i++)
+ {
+ if (JSEQ[i].getPdbidsCount() > 0)
{
- try
+ Pdbids[] ids = JSEQ[i].getPdbids();
+ for (int p = 0; p < ids.length; p++)
+ {
+ for (int s = 0; s < ids[p].getStructureStateCount(); s++)
{
- for (int t = 0; t < jms.getTreeCount(); t++)
+ jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
+
+ jpdb.setFile(loadPDBFile(ids[p].getFile(), ids[p].getId()));
+ jpdb.setId(ids[p].getId());
+
+ int x = ids[p].getStructureState(s).getXpos();
+ int y = ids[p].getStructureState(s).getYpos();
+ int width = ids[p].getStructureState(s).getWidth();
+ int height = ids[p].getStructureState(s).getHeight();
+
+ java.awt.Component comp = null;
+
+ JInternalFrame[] frames = null;
+ do {
+ try {
+ frames = Desktop.desktop.getAllFrames();
+ }
+ catch (ArrayIndexOutOfBoundsException e)
+ {
+ // occasional No such child exceptions are thrown here...
+ frames = null;
+ try {
+ Thread.sleep(10);
+ } catch (Exception f) {};
+ }
+ } while (frames==null);
+ for (int f = 0; f < frames.length; f++)
+ {
+ if (frames[f] instanceof AppJmol)
{
+ if (frames[f].getX() == x && frames[f].getY() == y
+ && frames[f].getHeight() == height
+ && frames[f].getWidth() == width)
+ {
+ comp = frames[f];
+ break;
+ }
+ }
+ }
- Tree tree = jms.getTree(t);
+ Desktop.desktop.getComponentAt(x, y);
- TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
- tree.getNewick()), tree.getTitle(),
- tree.getWidth(), tree.getHeight(),
- tree.getXpos(), tree.getYpos());
+ String pdbFile = loadPDBFile(file, ids[p].getId());
- tp.fitToWindow.setState(tree.getFitToWindow());
- tp.fitToWindow_actionPerformed(null);
+ jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
+ { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId()
+ + "") };
- if(tree.getFontName()!=null)
- tp.setTreeFont(new java.awt.Font(tree.getFontName(),
- tree.getFontStyle(),
- tree.getFontSize()));
- else
- tp.setTreeFont(new java.awt.Font(view.getFontName(),
- view.getFontStyle(),
- tree.getFontSize()));
+ if (comp == null)
+ {
+ String state = ids[p].getStructureState(s).getContent();
- tp.showPlaceholders(tree.getMarkUnlinked());
- tp.showBootstrap(tree.getShowBootstrap());
- tp.showDistances(tree.getShowDistances());
+ StringBuffer newFileLoc = new StringBuffer(state.substring(
+ 0, state.indexOf("\"", state.indexOf("load")) + 1));
- tp.treeCanvas.threshold = tree.getThreshold();
+ newFileLoc.append(jpdb.getFile());
+ newFileLoc.append(state.substring(state.indexOf("\"", state
+ .indexOf("load \"") + 6)));
- if (tree.getCurrentTree())
- af.viewport.setCurrentTree(tp.getTree());
- }
+ new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel,
+ newFileLoc.toString(), new java.awt.Rectangle(x, y,
+ width, height));
+ }
+ else if (comp != null)
+ {
+ StructureSelectionManager.getStructureSelectionManager()
+ .setMapping(seq, null, pdbFile,
+ jalview.io.AppletFormatAdapter.FILE);
+
+ ((AppJmol) comp).addSequence(seq);
+ }
}
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ }
+ }
+ }
+ }
+ return af;
+ }
+
+ private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
+ {
+ jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
+ Vector dseqs = null;
+ if (ds == null)
+ {
+ // create a list of new dataset sequences
+ dseqs = new Vector();
+ }
+ for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
+ {
+ Sequence vamsasSeq = vamsasSet.getSequence(i);
+ ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
+ }
+ // create a new dataset
+ if (ds == null)
+ {
+ SequenceI[] dsseqs = new SequenceI[dseqs.size()];
+ dseqs.copyInto(dsseqs);
+ ds = new jalview.datamodel.Alignment(dsseqs);
+ addDatasetRef(vamsasSet.getDatasetId(), ds);
+ }
+ // set the dataset for the newly imported alignment.
+ if (al.getDataset() == null)
+ {
+ al.setDataset(ds);
+ }
+ }
+
+
+ /**
+ *
+ * @param vamsasSeq sequence definition to create/merge dataset sequence for
+ * @param ds dataset alignment
+ * @param dseqs vector to add new dataset sequence to
+ */
+ private void ensureJalviewDatasetSequence(Sequence vamsasSeq, AlignmentI ds, Vector dseqs)
+ {
+ jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds.get(vamsasSeq.getId());
+ jalview.datamodel.SequenceI dsq = null;
+ if (sq!=null && sq.getDatasetSequence()!=null)
+ {
+ dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
+ }
+
+ String sqid = vamsasSeq.getDsseqid();
+ if (dsq==null)
+ {
+ // need to create or add a new dataset sequence reference to this sequence
+ if (sqid != null)
+ {
+ dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
+ }
+ // check again
+ if (dsq == null)
+ {
+ // make a new dataset sequence
+ dsq = sq.createDatasetSequence();
+ if (sqid == null)
+ {
+ // make up a new dataset reference for this sequence
+ sqid = seqHash(dsq);
}
+ dsq.setVamsasId(uniqueSetSuffix + sqid);
+ seqRefIds.put(sqid, dsq);
+ if (ds == null)
+ {
+ if (dseqs!=null)
+ {
+ dseqs.addElement(dsq);
+ }
+ }
+ else
+ {
+ ds.addSequence(dsq);
+ }
+ } else {
+ if (sq!=dsq)
+ { // make this dataset sequence sq's dataset sequence
+ sq.setDatasetSequence(dsq);
+ }
+ }
+ }
+ // TODO: refactor this as a merge dataset sequence function
+ // now check that sq (the dataset sequence) sequence really is the union of all references to it
+ //boolean pre = sq.getStart() < dsq.getStart();
+ //boolean post = sq.getEnd() > dsq.getEnd();
+ //if (pre || post)
+ if (sq!=dsq)
+ {
+ StringBuffer sb = new StringBuffer();
+ String newres = jalview.analysis.AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars, sq.getSequenceAsString());
+ if (!newres.equalsIgnoreCase(dsq.getSequenceAsString()) && newres.length()>dsq.getLength())
+ {
+ // Update with the longer sequence.
+ synchronized (dsq)
+ {
+ /*if (pre)
+ {
+ sb.insert(0, newres
+ .substring(0, dsq.getStart() - sq.getStart()));
+ dsq.setStart(sq.getStart());
+ }
+ if (post)
+ {
+ sb.append(newres.substring(newres.length() - sq.getEnd()
+ - dsq.getEnd()));
+ dsq.setEnd(sq.getEnd());
+ }
+ */
+ dsq.setSequence(sb.toString());
+ }
+ //TODO: merges will never happen if we 'know' we have the real dataset sequence - this should be detected when id==dssid
+ System.err
+ .println("DEBUG Notice: Merged dataset sequence"); // ("
+ // + (pre ? "prepended" : "") + " "
+ //+ (post ? "appended" : ""));
+ }
+ }
+ }
- return af;
+ java.util.Hashtable datasetIds = null;
+
+ private Alignment getDatasetFor(String datasetId)
+ {
+ if (datasetIds == null)
+ {
+ datasetIds = new Hashtable();
+ return null;
}
-}
+ if (datasetIds.containsKey(datasetId))
+ {
+ return (Alignment) datasetIds.get(datasetId);
+ }
+ return null;
+ }
+
+ private void addDatasetRef(String datasetId, Alignment dataset)
+ {
+ if (datasetIds == null)
+ {
+ datasetIds = new Hashtable();
+ }
+ datasetIds.put(datasetId, dataset);
+ }
+ private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
+ {
+ for (int d = 0; d < sequence.getDBRefCount(); d++)
+ {
+ DBRef dr = sequence.getDBRef(d);
+ jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
+ sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
+ .getVersion(), sequence.getDBRef(d).getAccessionId());
+ if (dr.getMapping() != null)
+ {
+ entry.setMap(addMapping(dr.getMapping()));
+ }
+ datasetSequence.addDBRef(entry);
+ }
+ }
+
+ private jalview.datamodel.Mapping addMapping(Mapping m)
+ {
+ SequenceI dsto = null;
+ // Mapping m = dr.getMapping();
+ int fr[] = new int[m.getMapListFromCount() * 2];
+ Enumeration f = m.enumerateMapListFrom();
+ for (int _i = 0; f.hasMoreElements(); _i += 2)
+ {
+ MapListFrom mf = (MapListFrom) f.nextElement();
+ fr[_i] = mf.getStart();
+ fr[_i + 1] = mf.getEnd();
+ }
+ int fto[] = new int[m.getMapListToCount() * 2];
+ f = m.enumerateMapListTo();
+ for (int _i = 0; f.hasMoreElements(); _i += 2)
+ {
+ MapListTo mf = (MapListTo) f.nextElement();
+ fto[_i] = mf.getStart();
+ fto[_i + 1] = mf.getEnd();
+ }
+ jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
+ fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
+ if (m.getMappingChoice() != null)
+ {
+ MappingChoice mc = m.getMappingChoice();
+ if (mc.getDseqFor() != null)
+ {
+ if (seqRefIds.containsKey(mc.getDseqFor()))
+ {
+ /**
+ * recover from hash
+ */
+ jmap.setTo((SequenceI) seqRefIds.get(mc.getDseqFor()));
+ }
+ else
+ {
+ frefedSequence.add(new Object[]
+ { mc.getDseqFor(), jmap });
+ }
+ }
+ else
+ {
+ /**
+ * local sequence definition
+ */
+ Sequence ms = mc.getSequence();
+ jalview.datamodel.Sequence djs=null;
+ String sqid = ms.getDsseqid();
+ if (sqid!=null && sqid.length()>0)
+ {
+ /*
+ * recover dataset sequence
+ */
+ djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
+ } else {
+ System.err.println("Warning - making up dataset sequence id for DbRef sequence map reference");
+ sqid = ((Object)ms).toString(); // make up a new hascode for undefined dataset sequence hash (unlikely to happen)
+ }
+
+ if (djs==null) {
+ /**
+ * make a new dataset sequence and add it to refIds hash
+ */
+ djs = new jalview.datamodel.Sequence(ms
+ .getName(), ms.getSequence());
+ djs.setStart(jmap.getMap().getToLowest());
+ djs.setEnd(jmap.getMap().getToHighest());
+ djs.setVamsasId(uniqueSetSuffix + sqid);
+ jmap.setTo(djs);
+ seqRefIds.put(sqid, djs);
+
+ }
+ jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
+ addDBRefs(djs, ms);
+
+ }
+ }
+ return (jmap);
+
+ }
+
+ public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
+ boolean keepSeqRefs)
+ {
+ jalview.schemabinding.version2.JalviewModel jm =
+ SaveState(ap, null, null);
+
+ if (!keepSeqRefs)
+ {
+ clearSeqRefs();
+ jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
+ }
+ else
+ {
+ uniqueSetSuffix = "";
+ }
+
+ viewportsAdded = new Hashtable();
+
+ AlignFrame af = LoadFromObject(jm, null, false);
+ af.alignPanels.clear();
+ af.closeMenuItem_actionPerformed(true);
+
+ /* if(ap.av.alignment.getAlignmentAnnotation()!=null)
+ {
+ for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length; i++)
+ {
+ if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated)
+ {
+ af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
+ ap.av.alignment.getAlignmentAnnotation()[i];
+ }
+ }
+ } */
+
+ return af.alignPanel;
+ }
+ /* (non-Javadoc)
+ * @see java.lang.Object#finalize()
+ */
+ protected void finalize() throws Throwable
+ {
+ // really make sure we have no buried refs left.
+ clearSeqRefs();
+ this.seqRefIds = null;
+ this.seqsToIds = null;
+ super.finalize();
+ }
+
+}