/*
* 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 java.io.*;
-
import java.net.*;
-
import java.util.*;
-
import java.util.jar.*;
import javax.swing.*;
import org.exolab.castor.xml.*;
-
import jalview.schemabinding.version2.*;
-
-
-
+import jalview.schemes.*;
/**
* DOCUMENT ME!
String uniqueSetSuffix = "";
+ // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
+ public void SaveState(File statefile)
+ {
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
- public void SaveState(File statefile)
+ if (frames == null)
{
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-
- if (frames == null)
- {
- return;
- }
-
- try
- {
- FileOutputStream fos = new FileOutputStream(statefile);
- JarOutputStream jout = new JarOutputStream(fos);
-
- //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
- ////////////////////////////////////////////////////
- PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
- "UTF-8"));
+ return;
+ }
- Vector shortNames = new Vector();
+ try
+ {
+ FileOutputStream fos = new FileOutputStream(statefile);
+ JarOutputStream jout = new JarOutputStream(fos);
- //REVERSE ORDER
- for (int i = frames.length - 1; i > -1; i--)
- {
- if (frames[i] instanceof AlignFrame)
- {
- AlignFrame af = (AlignFrame) frames[i];
+ //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
+ ////////////////////////////////////////////////////
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
+ "UTF-8"));
- String shortName = af.getTitle();
+ Vector shortNames = new Vector();
- if (shortName.indexOf(File.separatorChar) > -1)
- {
- shortName = shortName.substring(shortName.lastIndexOf(
- File.separatorChar) + 1);
- }
+ //REVERSE ORDER
+ for (int i = frames.length - 1; i > -1; i--)
+ {
+ if (frames[i] instanceof AlignFrame)
+ {
+ AlignFrame af = (AlignFrame) frames[i];
- int count = 1;
+ String shortName = af.getTitle();
- while (shortNames.contains(shortName))
- {
- if (shortName.endsWith("_" + (count - 1)))
- {
- shortName = shortName.substring(0,
- shortName.lastIndexOf("_"));
- }
-
- shortName = shortName.concat("_" + count);
- count++;
- }
+ if (shortName.indexOf(File.separatorChar) > -1)
+ {
+ shortName = shortName.substring(shortName.lastIndexOf(
+ File.separatorChar) + 1);
+ }
- shortNames.addElement(shortName);
+ int count = 1;
- if (!shortName.endsWith(".xml"))
- {
- shortName = shortName + ".xml";
- }
+ while (shortNames.contains(shortName))
+ {
+ if (shortName.endsWith("_" + (count - 1)))
+ {
+ shortName = shortName.substring(0,
+ shortName.lastIndexOf("_"));
+ }
- int ap, apSize= af.alignPanels.size();
- for (ap = 0; ap < apSize; ap++)
- {
- AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.
- elementAt(ap);
+ shortName = shortName.concat("_" + count);
+ count++;
+ }
- SaveState(apanel,
- apSize == 1 ? shortName : ap+shortName,
- jout, out);
- }
- }
- }
+ shortNames.addElement(shortName);
- out.close();
- jout.close();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
+ if (!shortName.endsWith(".xml"))
+ {
+ shortName = shortName + ".xml";
+ }
- // 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);
- PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
- "UTF-8"));
- for( ap=0; ap<apSize; ap++)
+ int ap, apSize = af.alignPanels.size();
+ for (ap = 0; ap < apSize; ap++)
{
- AlignmentPanel apanel = (AlignmentPanel)af.alignPanels.elementAt(ap);
+ AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.
+ elementAt(ap);
SaveState(apanel,
- apSize==1?fileName:fileName+ap,
+ apSize == 1 ? shortName : ap + shortName,
jout, out);
}
-
- out.close();
- jout.close();
- return true;
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- return false;
}
+ }
+
+ out.close();
+ jout.close();
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @param af DOCUMENT ME!
- * @param timeStamp DOCUMENT ME!
- * @param fileName DOCUMENT ME!
- * @param jout DOCUMENT ME!
- * @param out DOCUMENT ME!
- */
- public JalviewModel SaveState(AlignmentPanel ap,
- String fileName,
- JarOutputStream jout,
- PrintWriter out)
+ // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
+ public boolean SaveAlignment(AlignFrame af, String jarFile,
+ String fileName)
+ {
+ try
{
- if (seqRefIds == null)
- seqRefIds = new Hashtable();
+ int ap, apSize = af.alignPanels.size();
+ FileOutputStream fos = new FileOutputStream(jarFile);
+ JarOutputStream jout = new JarOutputStream(fos);
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
+ "UTF-8"));
+ for (ap = 0; ap < apSize; ap++)
+ {
+ AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.elementAt(ap);
- Vector userColours = new Vector();
+ SaveState(apanel,
+ apSize == 1 ? fileName : fileName + ap,
+ jout, out);
+ }
+
+ out.close();
+ jout.close();
+ return true;
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ return false;
+ }
+ }
- AlignViewport av = ap.av;
+ /**
+ * DOCUMENT ME!
+ *
+ * @param af DOCUMENT ME!
+ * @param timeStamp DOCUMENT ME!
+ * @param fileName DOCUMENT ME!
+ * @param jout DOCUMENT ME!
+ * @param out DOCUMENT ME!
+ */
+ public JalviewModel SaveState(AlignmentPanel ap,
+ String fileName,
+ JarOutputStream jout,
+ PrintWriter out)
+ {
+ if (seqRefIds == null)
+ {
+ seqRefIds = new Hashtable();
+ }
- JalviewModel object = new JalviewModel();
- object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
+ Vector userColours = new Vector();
- object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
- object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
+ AlignViewport av = ap.av;
- jalview.datamodel.AlignmentI jal = av.alignment;
+ JalviewModel object = new JalviewModel();
+ object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
- if(av.hasHiddenRows)
- {
- jal = jal.getHiddenSequences().getFullAlignment();
- }
+ object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
+ object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
- SequenceSet vamsasSet = new SequenceSet();
- Sequence vamsasSeq;
- JalviewModelSequence jms = new JalviewModelSequence();
+ jalview.datamodel.AlignmentI jal = av.alignment;
- vamsasSet.setGapChar(jal.getGapCharacter() + "");
+ if (av.hasHiddenRows)
+ {
+ jal = jal.getHiddenSequences().getFullAlignment();
+ }
- JSeq jseq;
- Vector pdbfiles = null;
+ SequenceSet vamsasSet = new SequenceSet();
+ Sequence vamsasSeq;
+ JalviewModelSequence jms = new JalviewModelSequence();
- //SAVE SEQUENCES
- int id = 0;
- jalview.datamodel.SequenceI jds;
- for (int i = 0; i < jal.getHeight(); i++)
- {
- jds = jal.getSequenceAt(i);
- id = jds.hashCode();
+ vamsasSet.setGapChar(jal.getGapCharacter() + "");
- if(seqRefIds.get(id+"")!=null)
- {
+ JSeq jseq;
+ Vector pdbfiles = null;
- }
- else
- {
- vamsasSeq = new Sequence();
- vamsasSeq.setId(id + "");
- vamsasSeq.setName(jds.getName());
- vamsasSeq.setSequence(jds.getSequenceAsString());
- vamsasSeq.setDescription(jds.getDescription());
+ //SAVE SEQUENCES
+ int id = 0;
+ jalview.datamodel.SequenceI jds;
+ for (int i = 0; i < jal.getHeight(); i++)
+ {
+ jds = jal.getSequenceAt(i);
+ id = jds.hashCode();
- if (jds.getDatasetSequence().getDBRef() != null)
- {
- jalview.datamodel.DBRefEntry[] dbrefs =
- jds.getDatasetSequence().getDBRef();
+ if (seqRefIds.get(id + "") != 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());
- vamsasSeq.addDBRef(dbref);
- }
- }
+ }
+ else
+ {
+ vamsasSeq = new Sequence();
+ vamsasSeq.setId(id + "");
+ vamsasSeq.setName(jds.getName());
+ vamsasSeq.setSequence(jds.getSequenceAsString());
+ vamsasSeq.setDescription(jds.getDescription());
- vamsasSet.addSequence(vamsasSeq);
- seqRefIds.put(id+"", jal.getSequenceAt(i));
- }
+ if (jds.getDatasetSequence().getDBRef() != null)
+ {
+ jalview.datamodel.DBRefEntry[] dbrefs =
+ jds.getDatasetSequence().getDBRef();
- jseq = new JSeq();
- jseq.setStart(jds.getStart());
- jseq.setEnd(jds.getEnd());
- jseq.setColour( av.getSequenceColour(jds).getRGB());
+ 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);
+ }
+ }
- jseq.setId(id);
+ vamsasSet.addSequence(vamsasSeq);
+ seqRefIds.put(id + "", jal.getSequenceAt(i));
+ }
- if (av.hasHiddenRows)
- {
- jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
+ jseq = new JSeq();
+ jseq.setStart(jds.getStart());
+ jseq.setEnd(jds.getEnd());
+ jseq.setColour(av.getSequenceColour(jds).getRGB());
- if(av.hiddenRepSequences!=null
- && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
- {
- jalview.datamodel.SequenceI[] reps =
- ( (jalview.datamodel.SequenceGroup)
- av.hiddenRepSequences.get(
- jal.getSequenceAt(i))).getSequencesInOrder(jal);
+ jseq.setId(id);
- for(int h=0; h<reps.length; h++)
- {
- if (reps[h] != jal.getSequenceAt(i))
- jseq.addHiddenSequences(
- jal.findIndex(reps[h])
- );
- }
- }
- }
+ if (av.hasHiddenRows)
+ {
+ jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
+ if (av.hiddenRepSequences != null
+ && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
+ {
+ jalview.datamodel.SequenceI[] reps =
+ ( (jalview.datamodel.SequenceGroup)
+ av.hiddenRepSequences.get(
+ jal.getSequenceAt(i))).getSequencesInOrder(jal);
- if(jds.getDatasetSequence().getSequenceFeatures()!=null)
+ for (int h = 0; h < reps.length; h++)
+ {
+ if (reps[h] != jal.getSequenceAt(i))
{
- 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.addFeatures(features);
- index ++;
- }
+ jseq.addHiddenSequences(
+ jal.findIndex(reps[h])
+ );
}
+ }
+ }
+ }
- if(jds.getDatasetSequence().getPDBId()!=null)
+ 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++)
{
- Enumeration en = jds.getDatasetSequence().getPDBId().elements();
- while(en.hasMoreElements())
- {
- 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)
- {
- pdb.setFile(entry.getFile());
- 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() && jout!=null)
- {
- 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();
- }
- }
- }
-
-
- 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);
- }
+ 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);
+ }
+ }
- jms.addJSeq(jseq);
+ jseq.addFeatures(features);
+ index++;
}
+ }
- if(av.hasHiddenRows)
- jal = av.alignment;
+ 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();
+ pdb.setId(entry.getId());
+ pdb.setType(entry.getType());
- //SAVE TREES
- ///////////////////////////////////
- if (av.currentTree != null)
- {
- // FIND ANY ASSOCIATED TREES
- // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
- if (Desktop.desktop != null)
+ if (entry.getFile() != null)
{
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ pdb.setFile(entry.getFile());
+ if (pdbfiles == null)
+ {
+ pdbfiles = new Vector();
+ }
- for (int t = 0; t < frames.length; t++)
+ if (!pdbfiles.contains(entry.getId()))
{
- if (frames[t] instanceof TreePanel)
+ pdbfiles.addElement(entry.getId());
+ try
{
- TreePanel tp = (TreePanel) frames[t];
-
- if (tp.treeCanvas.av.alignment == jal)
+ File file = new File(entry.getFile());
+ if (file.exists() && jout != null)
{
- 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);
+ 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();
+ }
}
}
- }
- //SAVE ANNOTATIONS
- if (jal.getAlignmentAnnotation() != null)
- {
- jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
-
- for (int i = 0; i < aa.length; i++)
+ if (entry.getProperty() != null)
+ {
+ PdbentryItem item = new PdbentryItem();
+ Hashtable properties = entry.getProperty();
+ Enumeration en2 = properties.keys();
+ while (en2.hasMoreElements())
{
- Annotation an = new Annotation();
-
- if(aa[i].annotationId!=null)
- {
- annotationIds.put(aa[i].annotationId, aa[i]);
- }
-
- an.setId(aa[i].annotationId);
-
- 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;
- }
-
-
- an.setDescription(aa[i].description);
-
- if(aa[i].sequenceRef!=null)
- {
- an.setSequenceRef(aa[i].sequenceRef.getName());
- }
-
- 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);
-
- an.setLabel(aa[i].label);
-
- AnnotationElement ae;
-
- for (int a = 0; a < aa[i].annotations.length; a++)
- {
- if ((aa[i] == null) || (aa[i].annotations[a] == null))
- {
- continue;
- }
+ Property prop = new Property();
+ String key = en2.nextElement().toString();
+ prop.setName(key);
+ prop.setValue(properties.get(key).toString());
+ item.addProperty(prop);
+ }
+ pdb.addPdbentryItem(item);
+ }
- 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 +
- "");
+ jseq.addPdbids(pdb);
+ }
+ }
- if(aa[i].annotations[a].colour!=java.awt.Color.black)
- ae.setColour(aa[i].annotations[a].colour.getRGB());
+ jms.addJSeq(jseq);
+ }
- an.addAnnotationElement(ae);
- }
+ if (av.hasHiddenRows)
+ {
+ jal = av.alignment;
+ }
- vamsasSet.addAnnotation(an);
- }
- }
+ //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();
- //SAVE GROUPS
- if (jal.getGroups() != null)
+ for (int t = 0; t < frames.length; t++)
{
- JGroup[] groups = new JGroup[jal.getGroups().size()];
+ if (frames[t] instanceof TreePanel)
+ {
+ TreePanel tp = (TreePanel) frames[t];
- for (int i = 0; i < groups.length; i++)
+ if (tp.treeCanvas.av.alignment == jal)
{
- 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());
-
- 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));
- }
-
- groups[i].setPidThreshold(sg.cs.getThreshold());
- }
-
- 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);
-
- for (int s = 0; s < sg.getSize(); s++)
- {
- jalview.datamodel.Sequence seq =
- (jalview.datamodel.Sequence) sg.getSequenceAt(s);
- groups[i].addSeq(seq.hashCode());
- }
+ 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);
}
-
- jms.setJGroup(groups);
+ }
}
+ }
+ }
+ //SAVE ANNOTATIONS
+ if (jal.getAlignmentAnnotation() != null)
+ {
+ jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
- ///////////SAVE VIEWPORT
- Viewport view = new Viewport();
- view.setTitle(ap.alignFrame.getTitle());
- view.setSequenceSetId(av.getSequenceSetId());
- view.setViewName(av.viewName);
- view.setGatheredViews(av.gatherViewsHere);
-
+ for (int i = 0; i < aa.length; i++)
+ {
+ Annotation an = new Annotation();
- 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
+ if (aa[i].annotationId != null)
{
- view.setXpos(ap.alignFrame.getBounds().x);
- view.setYpos(ap.alignFrame.getBounds().y);
- view.setWidth(ap.alignFrame.getBounds().width);
- view.setHeight(ap.alignFrame.getBounds().height);
+ annotationIds.put(aa[i].annotationId, aa[i]);
}
- view.setStartRes(av.startRes);
- view.setStartSeq(av.startSeq);
+ an.setId(aa[i].annotationId);
- if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
+ if (aa[i] == av.quality ||
+ aa[i] == av.conservation ||
+ aa[i] == av.consensus)
{
- view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
- userColours, jms));
+ an.setLabel(aa[i].label);
+ an.setGraph(true);
+ vamsasSet.addAnnotation(an);
+ continue;
}
- 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()));
- ac.setMaxColour(acg.getMaxColour().getRGB());
- ac.setMinColour(acg.getMinColour().getRGB());
- view.setAnnotationColours(ac);
- view.setBgColour("AnnotationColourGradient");
- }
- else
+ an.setDescription(aa[i].description);
+
+ if (aa[i].sequenceRef != null)
{
- view.setBgColour(ColourSchemeProperty.getColourName(
- av.getGlobalColourScheme()));
+ an.setSequenceRef(aa[i].sequenceRef.getName());
}
- ColourSchemeI cs = av.getGlobalColourScheme();
-
- if(cs!=null)
+ if (aa[i].graph > 0)
{
- if (cs.conservationApplied())
- {
- view.setConsThreshold(cs.getConservationInc());
- if (cs instanceof jalview.schemes.UserColourScheme)
- view.setBgColour(SetUserColourScheme(cs, userColours, jms));
- }
-
- if (cs instanceof ResidueColourScheme)
+ an.setGraph(true);
+ an.setGraphType(aa[i].graph);
+ an.setGraphGroup(aa[i].graphGroup);
+ if (aa[i].getThreshold() != null)
{
- view.setPidThreshold(cs.getThreshold());
+ 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);
}
}
-
- 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)
+ else
{
- jalview.schemabinding.version2.FeatureSettings fs
- = new jalview.schemabinding.version2.FeatureSettings();
-
- String [] renderOrder =
- ap.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(
- ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
- );
+ an.setGraph(false);
+ }
- setting.setDisplay(
- av.featuresDisplayed.containsKey(renderOrder[ro])
- );
+ an.setLabel(aa[i].label);
- fs.addSetting(setting);
- settingsAdded.addElement(renderOrder[ro]);
- }
+ AnnotationElement ae;
- //Make sure we save none displayed feature settings
- Enumeration en =
- ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
- while(en.hasMoreElements())
+ for (int a = 0; a < aa[i].annotations.length; a++)
+ {
+ if ( (aa[i] == null) || (aa[i].annotations[a] == null))
{
- String key = en.nextElement().toString();
- if(settingsAdded.contains(key))
- continue;
-
- Setting setting = new Setting();
- setting.setType(key);
- setting.setColour(
- ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
- );
-
- setting.setDisplay(false);
-
- fs.addSetting(setting);
- settingsAdded.addElement(key);
+ continue;
}
- jms.setFeatureSettings(fs);
-
- }
+ 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(av.hasHiddenColumns)
- {
- for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)
+ if (aa[i].annotations[a].colour != java.awt.Color.black)
{
- int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);
- HiddenColumns hc = new HiddenColumns();
- hc.setStart(region[0]);
- hc.setEnd(region[1]);
- view.addHiddenColumns(hc);
+ ae.setColour(aa[i].annotations[a].colour.getRGB());
}
- }
- jms.addViewport(view);
+ an.addAnnotationElement(ae);
+ }
+ vamsasSet.addAnnotation(an);
+ }
+ }
- object.setJalviewModelSequence(jms);
- object.getVamsasModel().addSequenceSet(vamsasSet);
+ //SAVE GROUPS
+ if (jal.getGroups() != null)
+ {
+ JGroup[] groups = new JGroup[jal.getGroups().size()];
- if(out!=null)
+ 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)
{
- //We may not want to right the object to disk,
- //eg we can copy the alignViewport to a new view object
- //using save and then load
- try
+ if (sg.cs.conservationApplied())
{
- if (!fileName.endsWith(".xml"))
+ groups[i].setConsThreshold(sg.cs.getConservationInc());
+
+ if (sg.cs instanceof jalview.schemes.UserColourScheme)
{
- fileName = fileName + ".xml";
+ groups[i].setColour(SetUserColourScheme(sg.cs,
+ userColours,
+ jms));
}
-
- JarEntry entry = new JarEntry(fileName);
- jout.putNextEntry(entry);
-
- object.marshal(out);
+ 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()));
}
- catch (Exception ex)
+ else if (sg.cs instanceof jalview.schemes.UserColourScheme)
{
- ex.printStackTrace();
+ groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
+ jms));
}
+ else
+ {
+ groups[i].setColour(ColourSchemeProperty.getColourName(
+ sg.cs));
+ }
+
+ groups[i].setPidThreshold(sg.cs.getThreshold());
}
- return object;
- }
- String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
- Vector userColours, JalviewModelSequence jms)
- {
- String id = null;
- jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
+ 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);
- if (!userColours.contains(ucs))
+ for (int s = 0; s < sg.getSize(); s++)
{
- 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++)
- {
- 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);
- }
- }
-
- id = "ucs" + userColours.indexOf(ucs);
- uc.setId(id);
- uc.setUserColourScheme(jbucs);
- jms.addUserColours(uc);
+ jalview.datamodel.Sequence seq =
+ (jalview.datamodel.Sequence) sg.getSequenceAt(s);
+ groups[i].addSeq(seq.hashCode());
}
+ }
- return id;
+ jms.setJGroup(groups);
}
- jalview.schemes.UserColourScheme GetUserColourScheme(
- JalviewModelSequence jms, String id)
- {
- UserColours[] uc = jms.getUserColours();
- UserColours colours = null;
+ ///////////SAVE VIEWPORT
+ Viewport view = new Viewport();
+ view.setTitle(ap.alignFrame.getTitle());
+ view.setSequenceSetId(av.getSequenceSetId());
+ view.setViewName(av.viewName);
+ view.setGatheredViews(av.gatherViewsHere);
- for (int i = 0; i < uc.length; i++)
- {
- if (uc[i].getId().equals(id))
- {
- colours = uc[i];
+ 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);
+ }
- break;
- }
- }
+ view.setStartRes(av.startRes);
+ view.setStartSeq(av.startSeq);
- java.awt.Color[] newColours = new java.awt.Color[24];
+ 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()));
+ }
- for (int i = 0; i < 24; i++)
- {
- newColours[i] = new java.awt.Color(Integer.parseInt(
- colours.getUserColourScheme().getColour(i).getRGB(), 16));
- }
+ ac.setMaxColour(acg.getMaxColour().getRGB());
+ ac.setMinColour(acg.getMinColour().getRGB());
+ view.setAnnotationColours(ac);
+ view.setBgColour("AnnotationColourGradient");
+ }
+ else
+ {
+ view.setBgColour(ColourSchemeProperty.getColourName(
+ av.getGlobalColourScheme()));
+ }
- jalview.schemes.UserColourScheme ucs =
- new jalview.schemes.UserColourScheme(newColours);
+ ColourSchemeI cs = av.getGlobalColourScheme();
- if (colours.getUserColourScheme().getColourCount() > 24)
+ if (cs != null)
+ {
+ if (cs.conservationApplied())
+ {
+ view.setConsThreshold(cs.getConservationInc());
+ if (cs instanceof jalview.schemes.UserColourScheme)
{
- 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);
+ view.setBgColour(SetUserColourScheme(cs, userColours, jms));
}
+ }
- return ucs;
+ if (cs instanceof ResidueColourScheme)
+ {
+ view.setPidThreshold(cs.getThreshold());
+ }
}
-
- /**
- * DOCUMENT ME!
- *
- * @param file DOCUMENT ME!
- */
- public AlignFrame LoadJalviewAlign(final String file)
+ 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)
{
- uniqueSetSuffix = System.currentTimeMillis()%100000 +"";
-
- jalview.gui.AlignFrame af = null;
+ jalview.schemabinding.version2.FeatureSettings fs
+ = new jalview.schemabinding.version2.FeatureSettings();
- seqRefIds = new Hashtable();
- viewportsAdded = new Hashtable();
+ String[] renderOrder =
+ ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
- Vector gatherToThisFrame= new Vector();
+ 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])
+ );
+
+ fs.addSetting(setting);
+ settingsAdded.addElement(renderOrder[ro]);
+ }
- try
+ //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))
{
- //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
- URL url = null;
+ continue;
+ }
- if (file.startsWith("http://"))
- {
- url = new URL(file);
- }
+ Setting setting = new Setting();
+ setting.setType(key);
+ setting.setColour(
+ ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
+ );
- JarInputStream jin = null;
- JarEntry jarentry = null;
- int entryCount = 1;
+ setting.setDisplay(false);
- do
- {
- if (url != null)
- {
- jin = new JarInputStream(url.openStream());
- }
- else
- {
- jin = new JarInputStream(new FileInputStream(file));
- }
+ fs.addSetting(setting);
+ settingsAdded.addElement(key);
+ }
- for (int i = 0; i < entryCount; i++)
- {
- jarentry = jin.getNextJarEntry();
- }
+ jms.setFeatureSettings(fs);
- 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 );
+ if (av.hasHiddenColumns)
+ {
+ 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);
+ }
+ }
- af = LoadFromObject(object, file, true);
- if(af.viewport.gatherViewsHere)
- {
- gatherToThisFrame.add(af);
- }
- 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");
+ jms.addViewport(view);
- 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)
+ object.setJalviewModelSequence(jms);
+ object.getVamsasModel().addSequenceSet(vamsasSet);
+
+ if (out != null)
+ {
+ //We may not want to right the object to disk,
+ //eg we can copy the alignViewport to a new view object
+ //using save and then load
+ try
+ {
+ if (!fileName.endsWith(".xml"))
{
- //Is Version 1 Jar file?
- af = new Jalview2XML_V1().LoadJalviewAlign(file);
+ fileName = fileName + ".xml";
+ }
- if(af!=null)
- {
- System.out.println("Successfully loaded archive file");
- return af;
- }
- ex.printStackTrace();
+ JarEntry entry = new JarEntry(fileName);
+ jout.putNextEntry(entry);
- System.err.println("Exception whilst loading jalview XML file : " +
- ex + "\n");
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
+ object.marshal(out);
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ return object;
+ }
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Error loading " + file,
- "Error loading Jalview file",
- JOptionPane.WARNING_MESSAGE);
- }});
- }
+ 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))
+ {
+ userColours.add(ucs);
- if (Desktop.instance != null)
- Desktop.instance.stopLoading();
+ 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 < gatherToThisFrame.size(); i++)
+ 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++)
{
- Desktop.instance.gatherViews(
- (AlignFrame) gatherToThisFrame.elementAt(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);
}
+ }
- return af;
+ id = "ucs" + userColours.indexOf(ucs);
+ uc.setId(id);
+ uc.setUserColourScheme(jbucs);
+ jms.addUserColours(uc);
}
- String loadPDBFile(String file, String pdbId)
+ return id;
+ }
+
+ jalview.schemes.UserColourScheme GetUserColourScheme(
+ JalviewModelSequence jms, String id)
+ {
+ UserColours[] uc = jms.getUserColours();
+ UserColours colours = null;
+
+ for (int i = 0; i < uc.length; i++)
{
- System.out.println(file +" "+pdbId);
- try
+ if (uc[i].getId().equals(id))
+ {
+ colours = uc[i];
+
+ break;
+ }
+ }
+
+ java.awt.Color[] newColours = new java.awt.Color[24];
+
+ for (int i = 0; i < 24; i++)
+ {
+ newColours[i] = new java.awt.Color(Integer.parseInt(
+ colours.getUserColourScheme().getColour(i).getRGB(), 16));
+ }
+
+ jalview.schemes.UserColourScheme ucs =
+ new jalview.schemes.UserColourScheme(newColours);
+
+ if (colours.getUserColourScheme().getColourCount() > 24)
+ {
+ newColours = new java.awt.Color[23];
+ for (int i = 0; i < 23; i++)
{
- JarInputStream jin = null;
+ newColours[i] = new java.awt.Color(Integer.parseInt(
+ colours.getUserColourScheme().getColour(i + 24).getRGB(), 16));
+ }
+ ucs.setLowerCaseColours(newColours);
+ }
+
+ return ucs;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param file DOCUMENT ME!
+ */
+ public AlignFrame LoadJalviewAlign(final String file)
+ {
+ uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
+
+ jalview.gui.AlignFrame af = null;
+
+ seqRefIds = new Hashtable();
+ viewportsAdded = new Hashtable();
+
+ Vector gatherToThisFrame = new Vector();
- if (file.startsWith("http://"))
+ try
+ {
+ //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
+ URL url = null;
+
+ if (file.startsWith("http://"))
+ {
+ url = new URL(file);
+ }
+
+ JarInputStream jin = null;
+ JarEntry jarentry = null;
+ int entryCount = 1;
+
+ 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.add(af);
+ }
+ entryCount++;
+ }
+ else if (jarentry != null)
{
- out.println(data);
+ //Some other file here.
+ entryCount++;
}
- out.close();
- return outFile.getAbsolutePath();
-
}
- catch (Exception ex)
+ while (jarentry != null);
+ }
+ catch (java.net.UnknownHostException ex)
+ {
+ ex.printStackTrace();
+ System.err.println("Couldn't locate Jalview XML file : " +
+ ex + "\n");
+
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- ex.printStackTrace();
+ public void run()
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Couldn't locate " + file,
+ "URL not found",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
+ catch (Exception ex)
+ {
+ //Is Version 1 Jar file?
+ af = new Jalview2XML_V1().LoadJalviewAlign(file);
+
+ if (af != null)
+ {
+ System.out.println("Successfully loaded archive file");
+ return af;
}
+ ex.printStackTrace();
- return null;
+ System.err.println("Exception whilst loading jalview XML file : " +
+ ex + "\n");
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Error loading " + file,
+ "Error loading Jalview file",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ });
}
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
- AlignFrame LoadFromObject(JalviewModel object,
- String file,
- boolean loadTrees )
+ for (int i = 0; i < gatherToThisFrame.size(); i++)
{
- SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
- Sequence[] vamsasSeq = vamsasSet.getSequence();
+ Desktop.instance.gatherViews(
+ (AlignFrame) gatherToThisFrame.elementAt(i));
+ }
- JalviewModelSequence jms = object.getJalviewModelSequence();
+ return af;
+ }
- Viewport view = jms.getViewport(0);
+ String loadPDBFile(String file, String pdbId)
+ {
+ System.out.println(file + " " + pdbId);
+ try
+ {
+ JarInputStream jin = null;
- //////////////////////////////////
- //LOAD SEQUENCES
+ if (file.startsWith("http://"))
+ {
+ jin = new JarInputStream(new URL(file).openStream());
+ }
+ else
+ {
+ jin = new JarInputStream(new FileInputStream(file));
+ }
- Vector hiddenSeqs = null;
- jalview.datamodel.Sequence jseq;
+ JarEntry entry = null;
+ do
+ {
+ entry = jin.getNextJarEntry();
+ }
+ while (!entry.getName().equals(pdbId));
- ArrayList tmpseqs = new ArrayList();
+ 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;
- boolean multipleView = false;
+ while ( (data = in.readLine()) != null)
+ {
+ out.println(data);
+ }
+ out.close();
+ return outFile.getAbsolutePath();
- JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
- for (int i = 0; i < JSEQ.length; i++)
- {
- String seqId = JSEQ[i].getId() + "";
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
- if (seqRefIds.get(seqId) != null)
- {
- tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
- multipleView = true;
- }
- else
- {
- jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
- vamsasSeq[i].getSequence());
- jseq.setDescription(vamsasSeq[i].getDescription());
- jseq.setStart(JSEQ[i].getStart());
- jseq.setEnd(JSEQ[i].getEnd());
- seqRefIds.put(vamsasSeq[i].getId(), jseq);
- tmpseqs.add( jseq );
- }
+ return null;
+ }
+ AlignFrame LoadFromObject(JalviewModel object,
+ String file,
+ boolean loadTrees)
+ {
+ SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
+ Sequence[] vamsasSeq = vamsasSet.getSequence();
+ JalviewModelSequence jms = object.getJalviewModelSequence();
- if (JSEQ[i].getHidden())
- {
- if (hiddenSeqs == null)
- hiddenSeqs = new Vector();
+ Viewport view = jms.getViewport(0);
+ //////////////////////////////////
+ //LOAD SEQUENCES
- hiddenSeqs.addElement(
- (jalview.datamodel.Sequence) seqRefIds.get(seqId));
- }
+ Vector hiddenSeqs = null;
+ jalview.datamodel.Sequence jseq;
+ ArrayList tmpseqs = new ArrayList();
+
+ boolean multipleView = false;
+
+ JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
+ 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[i].getName(),
+ vamsasSeq[i].getSequence());
+ jseq.setDescription(vamsasSeq[i].getDescription());
+ jseq.setStart(JSEQ[i].getStart());
+ jseq.setEnd(JSEQ[i].getEnd());
+ seqRefIds.put(vamsasSeq[i].getId(), jseq);
+ tmpseqs.add(jseq);
+ }
+
+ if (JSEQ[i].getHidden())
+ {
+ if (hiddenSeqs == null)
+ {
+ hiddenSeqs = new Vector();
}
- ///SequenceFeatures are added to the DatasetSequence,
- // so we must create the dataset before loading features
- /////////////////////////////////
+ hiddenSeqs.addElement(
+ (jalview.datamodel.Sequence) seqRefIds.get(seqId));
+ }
+ }
- jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
- tmpseqs.size()];
+ ///SequenceFeatures are added to the DatasetSequence,
+ // so we must create the dataset before loading features
+ /////////////////////////////////
- tmpseqs.toArray(orderedSeqs) ;
+ jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
+ tmpseqs.size()];
- jalview.datamodel.Alignment al =
- new jalview.datamodel.Alignment(orderedSeqs);
+ tmpseqs.toArray(orderedSeqs);
- al.setDataset(null);
- /////////////////////////////////
+ jalview.datamodel.Alignment al =
+ new jalview.datamodel.Alignment(orderedSeqs);
+ al.setDataset(null);
+ /////////////////////////////////
- Hashtable pdbloaded = new Hashtable();
- if(!multipleView)
+
+ Hashtable pdbloaded = new Hashtable();
+ if (!multipleView)
+ {
+ for (int i = 0; i < vamsasSeq.length; i++)
+ {
+ if (JSEQ[i].getFeaturesCount() > 0)
{
- for (int i = 0; i < vamsasSeq.length; i++)
+ Features[] features = JSEQ[i].getFeatures();
+ for (int f = 0; f < features.length; f++)
{
- if (JSEQ[i].getFeaturesCount() > 0)
+ 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++)
{
- Features[] features = JSEQ[i].getFeatures();
- for (int f = 0; f < features.length; f++)
+ OtherData keyValue = features[f].getOtherData(od);
+ if (keyValue.getKey().startsWith("LINK"))
{
- 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.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
+ sf.addLink(keyValue.getValue());
}
- }
- if (JSEQ[i].getPdbidsCount() > 0)
- {
- Pdbids[] ids = JSEQ[i].getPdbids();
- for (int p = 0; p < ids.length; p++)
+ else
{
- 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());
- }
-
- al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+ sf.setValue(keyValue.getKey(), keyValue.getValue());
}
+
}
- if (vamsasSeq[i].getDBRefCount() > 0)
+
+ 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)
{
- for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
+ if (!pdbloaded.containsKey(ids[p].getFile()))
{
- 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);
+ 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());
}
-
}
+
+ 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);
+ }
+ }
+ }
+ }
- /////////////////////////////////
- //////////////////////////////////
- //LOAD ANNOTATIONS
- boolean hideQuality = true,
- hideConservation = true,
- hideConsensus = true;
-
- if (vamsasSet.getAnnotationCount()>0)
- {
- Annotation[] an = vamsasSet.getAnnotation();
+ /////////////////////////////////
+ //////////////////////////////////
+ //LOAD ANNOTATIONS
+ boolean hideQuality = true,
+ hideConservation = true,
+ hideConsensus = true;
- 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;
- }
-
- if (an[i].getId() != null
- && annotationIds.containsKey(an[i].getId()))
- {
- al.addAnnotation(
- (jalview.datamodel.AlignmentAnnotation)annotationIds.get(an[i].getId())
- );
-
- continue;
- }
+ if (vamsasSet.getAnnotationCount() > 0)
+ {
+ Annotation[] an = vamsasSet.getAnnotation();
- AnnotationElement[] ae = an[i].getAnnotationElement();
- jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
+ 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;
+ }
- for (int aa = 0; aa < ae.length && aa<anot.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() );
- }
+ if (an[i].getId() != null
+ && annotationIds.containsKey(an[i].getId()))
+ {
+ al.addAnnotation(
+ (jalview.datamodel.AlignmentAnnotation) annotationIds.get(an[i].
+ getId())
+ );
- jalview.datamodel.AlignmentAnnotation jaa = null;
+ continue;
+ }
- if (an[i].getGraph())
- {
- jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
- an[i].getDescription(), anot, 0, 0,
- an[i].getGraphType());
+ AnnotationElement[] ae = an[i].getAnnotationElement();
+ jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[
+ al.getWidth()];
- jaa.graphGroup = an[i].getGraphGroup();
+ for (int aa = 0; aa < ae.length && aa < anot.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());
+ }
- 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()))
- );
+ 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());
- }
- else
- {
- jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
- an[i].getDescription(), anot);
- }
+ jaa.graphGroup = an[i].getGraphGroup();
- if(an[i].getId()!=null)
- {
- annotationIds.put(an[i].getId(), jaa);
- jaa.annotationId = an[i].getId();
- }
+ 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()))
+ );
- if(an[i].getSequenceRef()!=null)
- {
- jaa.createSequenceMapping(
- al.findName(an[i].getSequenceRef()), 1, true
- );
- al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
- }
+ }
- al.addAnnotation(jaa);
- }
}
-
- /////////////////////////
- //LOAD GROUPS
- if (jms.getJGroupCount() > 0)
+ else
{
- JGroup[] groups = jms.getJGroup();
-
- for (int i = 0; i < groups.length; i++)
- {
- ColourSchemeI cs = null;
-
- 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());
- }
+ jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+ an[i].getDescription(), anot);
+ }
- if(cs!=null)
- cs.setThreshold(groups[i].getPidThreshold(), true);
- }
+ if (an[i].getId() != null)
+ {
+ annotationIds.put(an[i].getId(), jaa);
+ jaa.annotationId = an[i].getId();
+ }
- Vector seqs = new Vector();
+ if (an[i].getSequenceRef() != null)
+ {
+ jaa.createSequenceMapping(
+ al.findName(an[i].getSequenceRef()), 1, true
+ );
+ al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
+ }
- 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);
+ al.addAnnotation(jaa);
+ }
+ }
- if (ts != null)
- seqs.addElement(ts);
- }
+ /////////////////////////
+ //LOAD GROUPS
+ if (jms.getJGroupCount() > 0)
+ {
+ JGroup[] groups = jms.getJGroup();
- if(seqs.size()<1)
- continue;
+ for (int i = 0; i < groups.length; i++)
+ {
+ ColourSchemeI cs = null;
- 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());
+ 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());
+ }
- sg.setOutlineColour(new java.awt.Color(
- groups[i].getOutlineColour()));
+ if (cs != null)
+ {
+ cs.setThreshold(groups[i].getPidThreshold(), true);
+ }
+ }
- sg.textColour = new java.awt.Color(groups[i].getTextCol1());
- sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
- sg.thresholdTextColour = groups[i].getTextColThreshold();
+ Vector seqs = new Vector();
- 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);
- }
+ 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);
- al.addGroup(sg);
- }
+ if (ts != null)
+ {
+ seqs.addElement(ts);
+ }
}
+ if (seqs.size() < 1)
+ {
+ continue;
+ }
- /////////////////////////////////
- // LOAD VIEWPORT
+ 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());
- AlignFrame af = new AlignFrame(al,
- view.getWidth(),
- view.getHeight() );
+ sg.setOutlineColour(new java.awt.Color(
+ groups[i].getOutlineColour()));
- af.setFileName(file, "Jalview");
+ sg.textColour = new java.awt.Color(groups[i].getTextCol1());
+ sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
+ sg.thresholdTextColour = groups[i].getTextColThreshold();
- for (int i = 0; i < JSEQ.length; i++)
+ if (groups[i].getConsThreshold() != 0)
{
- af.viewport.setSequenceColour(
- af.viewport.alignment.getSequenceAt(i),
- new java.awt.Color(
- JSEQ[i].getColour()));
+ 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);
}
- //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;
+ al.addGroup(sg);
+ }
+ }
- af.viewport.gatherViewsHere = view.getGatheredViews();
+ /////////////////////////////////
+ // LOAD VIEWPORT
- if (view.getSequenceSetId() != null)
- {
- jalview.gui.AlignViewport av =
- (jalview.gui.AlignViewport)
- viewportsAdded.get(uniqueSeqSetId);
+ AlignFrame af = new AlignFrame(al,
+ view.getWidth(),
+ view.getHeight());
- af.viewport.sequenceSetID = uniqueSeqSetId;
- if(av!=null)
- {
+ af.setFileName(file, "Jalview");
- af.viewport.historyList = av.historyList;
- af.viewport.redoList = av.redoList;
- }
- else
- {
- viewportsAdded.put(uniqueSeqSetId, af.viewport);
- }
+ for (int i = 0; i < JSEQ.length; i++)
+ {
+ af.viewport.setSequenceColour(
+ af.viewport.alignment.getSequenceAt(i),
+ new java.awt.Color(
+ JSEQ[i].getColour()));
+ }
- PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
- }
- if(hiddenSeqs!=null)
- {
- for(int s=0; s<JSEQ.length; s++)
- {
- jalview.datamodel.SequenceGroup hidden =
- new jalview.datamodel.SequenceGroup();
+ //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;
- 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);
- }
+ af.viewport.gatherViewsHere = view.getGatheredViews();
- 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);
+ if (view.getSequenceSetId() != null)
+ {
+ jalview.gui.AlignViewport av =
+ (jalview.gui.AlignViewport)
+ viewportsAdded.get(uniqueSeqSetId);
- af.viewport.hideSequence( hseqs );
+ 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();
- if((hideConsensus || hideQuality || hideConservation)
- && al.getAlignmentAnnotation()!=null)
+ for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
{
- 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();
+ 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()];
- if(view.getViewName()!=null)
+ 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")))
{
- af.viewport.viewName = view.getViewName();
- af.setInitialTabVisible();
+ al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
+ hSize--;
+ h--;
}
- af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
- view.getHeight());
+ }
+ af.alignPanel.adjustAnnotationHeight();
+ }
- af.viewport.setShowAnnotation(view.getShowAnnotation());
- af.viewport.setAbovePIDThreshold(view.getPidSelected());
+ if (view.getViewName() != null)
+ {
+ af.viewport.viewName = view.getViewName();
+ af.setInitialTabVisible();
+ }
+ af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
+ view.getHeight());
- af.viewport.setColourText(view.getShowColourText());
+ af.viewport.setShowAnnotation(view.getShowAnnotation());
+ af.viewport.setAbovePIDThreshold(view.getPidSelected());
- 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.setColourText(view.getShowColourText());
- af.viewport.setShowBoxes(view.getShowBoxes());
+ 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.setShowText(view.getShowText());
+ af.viewport.setShowBoxes(view.getShowBoxes());
- 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.setShowText(view.getShowText());
- af.viewport.setStartRes(view.getStartRes());
- af.viewport.setStartSeq(view.getStartSeq());
+ af.viewport.textColour = new java.awt.Color(view.getTextCol1());
+ af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
+ af.viewport.thresholdTextColour = view.getTextColThreshold();
- ColourSchemeI cs = null;
+ af.viewport.setStartRes(view.getStartRes());
+ af.viewport.setStartSeq(view.getStartSeq());
+
+ ColourSchemeI cs = null;
- if (view.getBgColour() != 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 (view.getBgColour().startsWith("ucs"))
+ if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
+ equals(view.getAnnotationColours().getAnnotation()))
+ {
+ if (af.viewport.alignment.getAlignmentAnnotation()[i].
+ getThreshold() == null)
{
- cs = GetUserColourScheme(jms, view.getBgColour());
+ af.viewport.alignment.getAlignmentAnnotation()[i].
+ setThreshold(
+ new jalview.datamodel.GraphLine(
+ view.getAnnotationColours().getThreshold(),
+ "Threshold", java.awt.Color.black)
+
+ );
}
- else if(view.getBgColour().startsWith("Annotation"))
+
+ 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
{
- //int find annotation
- for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
+ 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++)
{
- if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
- equals(view.getAnnotationColours().getAnnotation()))
+ jalview.datamodel.SequenceGroup sg
+ = (jalview.datamodel.SequenceGroup) al.getGroups().
+ elementAt(g);
+
+ if (sg.cs == null)
{
- 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 = 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()
- );
- }
+ 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());
}
-
-
- break;
+ else*/
+ {
+ sg.cs = new AnnotationColourGradient(
+ af.viewport.alignment.getAlignmentAnnotation()[i],
+ sg.cs,
+ view.getAnnotationColours().getAboveThreshold()
+ );
}
}
}
- else
- {
- cs = ColourSchemeProperty.getColour(al, view.getBgColour());
- }
- if(cs!=null)
- {
- cs.setThreshold(view.getPidThreshold(), true);
- cs.setConsensus(af.viewport.hconsensus);
- }
+ break;
+ }
+
}
+ }
+ else
+ {
+ cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+ }
+ if (cs != null)
+ {
+ cs.setThreshold(view.getPidThreshold(), true);
+ cs.setConsensus(af.viewport.hconsensus);
+ }
+ }
- af.viewport.setGlobalColourScheme(cs);
- af.viewport.setColourAppliesToAllGroups(false);
+ af.viewport.setGlobalColourScheme(cs);
+ af.viewport.setColourAppliesToAllGroups(false);
- if (view.getConservationSelected() && cs!=null)
- {
- cs.setConservationInc(view.getConsThreshold());
- }
+ if (view.getConservationSelected() && cs != null)
+ {
+ cs.setConservationInc(view.getConsThreshold());
+ }
- af.changeColour(cs);
+ af.changeColour(cs);
- af.viewport.setColourAppliesToAllGroups(true);
+ 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);
- if (view.getShowSequenceFeatures())
- {
- af.viewport.showSequenceFeatures = true;
- }
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.
+ getType(),
+ new java.awt.Color(setting.getColour()));
- 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.getDisplay())
- af.viewport.featuresDisplayed.put(
- setting.getType(), new Integer(setting.getColour()));
- }
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
- }
+ renderOrder[fs] = setting.getType();
- if (view.getHiddenColumnsCount() > 0)
+ if (setting.getDisplay())
{
- for (int c = 0; c < view.getHiddenColumnsCount(); c++)
- {
- af.viewport.hideColumns(
- view.getHiddenColumns(c).getStart(),
- view.getHiddenColumns(c).getEnd() //+1
- );
- }
+ af.viewport.featuresDisplayed.put(
+ setting.getType(), new Integer(setting.getColour()));
}
+ }
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder =
+ renderOrder;
+ }
- af.setMenusFromViewport(af.viewport);
+ 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());
+ Desktop.addInternalFrame(af, view.getTitle(),
+ view.getWidth(), view.getHeight());
- //LOAD TREES
- ///////////////////////////////////////
- if (loadTrees && jms.getTreeCount() > 0)
+ //LOAD TREES
+ ///////////////////////////////////////
+ if (loadTrees && jms.getTreeCount() > 0)
+ {
+ try
+ {
+ for (int t = 0; t < jms.getTreeCount(); t++)
{
- try
- {
- for (int t = 0; t < jms.getTreeCount(); t++)
- {
- Tree tree = jms.getTree(t);
+ Tree tree = jms.getTree(t);
- TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
- tree.getNewick()), tree.getTitle(),
- tree.getWidth(), tree.getHeight(),
- tree.getXpos(), tree.getYpos());
+ TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
+ tree.getNewick()), tree.getTitle(),
+ tree.getWidth(), tree.getHeight(),
+ tree.getXpos(), tree.getYpos());
- tp.fitToWindow.setState(tree.getFitToWindow());
- tp.fitToWindow_actionPerformed(null);
+ tp.fitToWindow.setState(tree.getFitToWindow());
+ tp.fitToWindow_actionPerformed(null);
- 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()));
-
- tp.showPlaceholders(tree.getMarkUnlinked());
- tp.showBootstrap(tree.getShowBootstrap());
- tp.showDistances(tree.getShowDistances());
-
- tp.treeCanvas.threshold = tree.getThreshold();
+ 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 (tree.getCurrentTree())
- af.viewport.setCurrentTree(tp.getTree());
- }
+ tp.showPlaceholders(tree.getMarkUnlinked());
+ tp.showBootstrap(tree.getShowBootstrap());
+ tp.showDistances(tree.getShowDistances());
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ tp.treeCanvas.threshold = tree.getThreshold();
+ if (tree.getCurrentTree())
+ {
+ af.viewport.setCurrentTree(tp.getTree());
+ }
}
- return af;
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
}
- public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, boolean keepSeqRefs )
- {
- jalview.schemabinding.version2.JalviewModel jm
- = SaveState(ap, null, null, null);
+ return af;
+ }
- if (!keepSeqRefs)
- {
- seqRefIds.clear();
- jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
- }
- else
- uniqueSetSuffix = "";
+ public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
+ boolean keepSeqRefs)
+ {
+ jalview.schemabinding.version2.JalviewModel jm
+ = SaveState(ap, null, null, null);
- viewportsAdded = new Hashtable();
+ if (!keepSeqRefs)
+ {
+ seqRefIds.clear();
+ jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
+ }
+ else
+ {
+ uniqueSetSuffix = "";
+ }
- AlignFrame af = LoadFromObject(jm, null, false);
- af.alignPanels.clear();
- af.closeMenuItem_actionPerformed(true);
+ viewportsAdded = new Hashtable();
+
+ AlignFrame af = LoadFromObject(jm, null, false);
+ af.alignPanels.clear();
+ af.closeMenuItem_actionPerformed(true);
/* if(ap.av.alignment.getAlignmentAnnotation()!=null)
{
}
} */
- return af.alignPanel;
- }
+ return af.alignPanel;
+ }
}
-
git://source.jalview.org / jalview.git / blobdiff