import jalview.schemes.*;
-import jalview.gui.*;
-
import java.io.*;
import java.net.*;
*/
public class Jalview2XML
{
- // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
+
+ Hashtable seqRefIds;
+
+ /**
+ * This maintains a list of viewports, the key being the
+ * seqSetId. Important to set historyItem and redoList
+ * for multiple views
+ */
+ Hashtable viewportsAdded;
+
+ String uniqueSetSuffix = "";
+
+
+ // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
public void SaveState(File statefile)
{
- long creation = System.currentTimeMillis();
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
if (frames == null)
shortName = shortName + ".xml";
}
- SaveState(af, creation, shortName, jout, out);
+ int ap, apSize= af.alignPanels.size();
+ for (ap = 0; ap < apSize; ap++)
+ {
+ AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.
+ elementAt(ap);
+
+ SaveState(apanel,
+ apSize == 1 ? shortName : ap+shortName,
+ jout, out);
+ }
}
}
}
// USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
- public void SaveAlignment(AlignFrame af, String jarFile,
+ public boolean SaveAlignment(AlignFrame af, String jarFile,
String fileName)
{
try
{
- FileOutputStream fos = new FileOutputStream(jarFile);
- JarOutputStream jout = new JarOutputStream(fos);
+ 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);
- //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
- ////////////////////////////////////////////////////
- PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
- "UTF-8"));
+ SaveState(apanel,
+ apSize==1?fileName:fileName+ap,
+ jout, out);
+ }
- SaveState(af, System.currentTimeMillis(), fileName, jout, out);
- out.close();
- jout.close();
+ out.close();
+ jout.close();
+ return true;
}
catch (Exception ex)
{
ex.printStackTrace();
+ return false;
}
}
* @param jout DOCUMENT ME!
* @param out DOCUMENT ME!
*/
- public void SaveState(AlignFrame af, long timeStamp,
- String fileName, JarOutputStream jout, PrintWriter out)
+ public JalviewModel SaveState(AlignmentPanel ap,
+ String fileName,
+ JarOutputStream jout,
+ PrintWriter out)
{
- Vector seqids = new Vector();
+ if (seqRefIds == null)
+ seqRefIds = new Hashtable();
+
Vector userColours = new Vector();
- AlignViewport av = af.viewport;
+ AlignViewport av = ap.av;
JalviewModel object = new JalviewModel();
object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
- object.setCreationDate(new java.util.Date(timeStamp));
+ object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
- jalview.datamodel.AlignmentI jal = af.viewport.alignment;
- jalview.datamodel.AlignmentI jalhidden = null;
+ jalview.datamodel.AlignmentI jal = av.alignment;
if(av.hasHiddenRows)
{
- jalhidden = jal;
jal = jal.getHiddenSequences().getFullAlignment();
}
-
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++)
{
- 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());
-
- if(jal.getSequenceAt(i).getDatasetSequence().getDBRef()!=null)
+ jds = jal.getSequenceAt(i);
+ id = jds.hashCode();
+
+ if(seqRefIds.get(id+"")!=null)
{
- jalview.datamodel.DBRefEntry [] dbrefs =
- jal.getSequenceAt(i).getDatasetSequence().getDBRef();
- for(int d=0; d<dbrefs.length; d++)
+ }
+ else
+ {
+ vamsasSeq = new Sequence();
+ vamsasSeq.setId(id + "");
+ vamsasSeq.setName(jds.getName());
+ vamsasSeq.setSequence(jds.getSequenceAsString());
+ vamsasSeq.setDescription(jds.getDescription());
+
+ if (jds.getDatasetSequence().getDBRef() != null)
{
- DBRef dbref = new DBRef();
- dbref.setSource( dbrefs[d].getSource() );
- dbref.setVersion( dbrefs[d].getVersion());
- dbref.setAccessionId(dbrefs[d].getAccessionId());
- vamsasSeq.addDBRef(dbref);
+ jalview.datamodel.DBRefEntry[] dbrefs =
+ jds.getDatasetSequence().getDBRef();
+
+ 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);
+ }
}
+
+ vamsasSet.addSequence(vamsasSeq);
+ seqRefIds.put(id+"", jal.getSequenceAt(i));
}
jseq = new JSeq();
- jseq.setStart(jal.getSequenceAt(i).getStart());
- jseq.setEnd(jal.getSequenceAt(i).getEnd());
- jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
+ jseq.setStart(jds.getStart());
+ jseq.setEnd(jds.getEnd());
+ jseq.setColour( av.getSequenceColour(jds).getRGB());
jseq.setId(id);
if (av.hasHiddenRows)
{
- jseq.setHidden(jalhidden.getHiddenSequences().isHidden(
- jal.getSequenceAt(i)));
+ jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
if(jal.getSequenceAt(i).getHiddenSequences()!=null)
{
}
- if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)
+ if(jds.getDatasetSequence().getSequenceFeatures()!=null)
{
jalview.datamodel.SequenceFeature[] sf
- = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
+ = jds.getDatasetSequence().getSequenceFeatures();
int index = 0;
while(index < sf.length)
{
}
}
- if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)
+ if(jds.getDatasetSequence().getPDBId()!=null)
{
- Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();
+ Enumeration en = jds.getDatasetSequence().getPDBId().elements();
while(en.hasMoreElements())
{
Pdbids pdb = new Pdbids();
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())
+ if(file.exists() && jout!=null)
{
byte[] data = new byte[ (int) file.length()];
jout.putNextEntry(new JarEntry(entry.getId()));
}
jms.addJSeq(jseq);
- vamsasSet.addSequence(vamsasSeq);
- id++;
}
+ if(av.hasHiddenRows)
+ jal = av.alignment;
+
+
//SAVE TREES
///////////////////////////////////
- if (af.viewport.currentTree != null)
+ if (av.currentTree != null)
{
// FIND ANY ASSOCIATED TREES
// NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
{
Tree tree = new Tree();
tree.setTitle(tp.getTitle());
- tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));
+ tree.setCurrentTree( (av.currentTree == tp.getTree()));
tree.setNewick(tp.getTree().toString());
tree.setThreshold(tp.treeCanvas.threshold);
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(false); s++)
{
- jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);
- int index = seqids.indexOf(seq);
- groups[i].addSeq(index);
+ jalview.datamodel.Sequence seq =
+ (jalview.datamodel.Sequence) sg.getSequenceAt(s);
+ groups[i].addSeq(seq.hashCode());
}
}
///////////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.setTitle(ap.alignFrame.getTitle());
+ view.setSequenceSetId(av.getSequenceSetId());
+ view.setViewName(av.viewName);
+ view.setGatheredViews(av.gatherViewsHere);
+
+
+ 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);
+ }
+
view.setStartRes(av.startRes);
view.setStartSeq(av.startSeq);
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.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)
{
= new jalview.schemabinding.version2.FeatureSettings();
String [] renderOrder =
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().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(
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
+ ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
);
setting.setDisplay(
//Make sure we save none displayed feature settings
Enumeration en =
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
+ ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
while(en.hasMoreElements())
{
String key = en.nextElement().toString();
Setting setting = new Setting();
setting.setType(key);
setting.setColour(
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
+ ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
);
setting.setDisplay(false);
object.setJalviewModelSequence(jms);
object.getVamsasModel().addSequenceSet(vamsasSet);
- try
+ 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"))
{
- fileName = fileName + ".xml";
+ fileName = fileName + ".xml";
}
JarEntry entry = new JarEntry(fileName);
jout.putNextEntry(entry);
object.marshal(out);
- }
- catch (Exception ex)
- {
+ }
+ catch (Exception ex)
+ {
ex.printStackTrace();
+ }
}
+ return object;
}
String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
return ucs;
}
+
/**
* 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();
+
try
{
//UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
unmar.setValidation(false);
object = (JalviewModel) unmar.unmarshal( in );
- af = LoadFromObject(object, file);
+ af = LoadFromObject(object, file, true);
+ if(af.viewport.gatherViewsHere)
+ {
+ gatherToThisFrame.add(af);
+ }
entryCount++;
}
else if (jarentry != null)
}
catch (Exception ex)
{
-
//Is Version 1 Jar file?
af = new Jalview2XML_V1().LoadJalviewAlign(file);
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()
}});
}
+ if (Desktop.instance != null)
+ Desktop.instance.stopLoading();
+
+ for (int i = 0; i < gatherToThisFrame.size(); i++)
+ {
+ Desktop.instance.gatherViews(
+ (AlignFrame) gatherToThisFrame.elementAt(i));
+ }
+
return af;
}
String loadPDBFile(String file, String pdbId)
{
- System.out.println("load file "+file);
+ System.out.println(file +" "+pdbId);
try
{
JarInputStream jin = null;
}
- AlignFrame LoadFromObject(JalviewModel object, String file)
+ AlignFrame LoadFromObject(JalviewModel object,
+ String file,
+ boolean loadTrees )
{
- Vector seqids = new Vector();
SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
Sequence[] vamsasSeq = vamsasSet.getSequence();
JalviewModelSequence jms = object.getJalviewModelSequence();
+ Viewport view = jms.getViewport(0);
+
//////////////////////////////////
//LOAD SEQUENCES
+
Vector hiddenSeqs = null;
- jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
+ jalview.datamodel.Sequence jseq;
+
+ ArrayList tmpseqs = new ArrayList();
+
+ boolean multipleView = false;
+
JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
- for (int i = 0; i < vamsasSeq.length; i++)
+ for (int i = 0; i < JSEQ.length; i++)
{
- jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
- vamsasSeq[i].getSequence());
- jseqs[i].setDescription( vamsasSeq[i].getDescription() );
+ 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();
+
+
+ hiddenSeqs.addElement(
+ (jalview.datamodel.Sequence) seqRefIds.get(seqId));
+ }
- 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]);
}
///SequenceFeatures are added to the DatasetSequence,
// so we must create the dataset before loading features
/////////////////////////////////
- jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
+
+
+ jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
+ tmpseqs.size()];
+
+ tmpseqs.toArray(orderedSeqs) ;
+
+
+ jalview.datamodel.Alignment al =
+ new jalview.datamodel.Alignment(orderedSeqs);
+
al.setDataset(null);
/////////////////////////////////
Hashtable pdbloaded = new Hashtable();
- for (int i = 0; i < vamsasSeq.length; i++)
+ if(!multipleView)
{
- 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"))
- sf.addLink(keyValue.getValue());
- else
- sf.setValue(keyValue.getKey(), keyValue.getValue());
+ 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);
+ al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
+ }
}
- }
- if (JSEQ[i].getPdbidsCount() > 0)
- {
- Pdbids[] ids = JSEQ[i].getPdbids();
- for (int p = 0; p < ids.length; p++)
+ if (JSEQ[i].getPdbidsCount() > 0)
{
- jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
- entry.setId(ids[p].getId());
- entry.setType(ids[p].getType());
- if (ids[p].getFile() != null)
+ Pdbids[] ids = JSEQ[i].getPdbids();
+ for (int p = 0; p < ids.length; p++)
{
- if (!pdbloaded.containsKey(ids[p].getFile()))
+ jalview.datamodel.PDBEntry entry = new jalview.datamodel.
+ PDBEntry();
+ entry.setId(ids[p].getId());
+ entry.setType(ids[p].getType());
+ if (ids[p].getFile() != null)
{
- String tmppdb = loadPDBFile(file, ids[p].getId());
- entry.setFile(tmppdb);
- pdbloaded.put(ids[p].getId(), tmppdb);
+ 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());
}
- else
- entry.setFile(pdbloaded.get(ids[p].getId()).toString());
- }
- al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+ al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+ }
}
- }
- if(vamsasSeq[i].getDBRefCount()>0)
- {
- for(int d=0; d<vamsasSeq[i].getDBRefCount(); d++)
+ if (vamsasSeq[i].getDBRefCount() > 0)
{
- 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);
- }
+ 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
hideConservation = true,
hideConsensus = true;
- if (vamsasSet.getAnnotation() != null)
+ if (vamsasSet.getAnnotationCount()>0)
{
Annotation[] an = vamsasSet.getAnnotation();
}
}
-
- // af.changeColour() );
/////////////////////////
//LOAD GROUPS
if (jms.getJGroupCount() > 0)
}
Vector seqs = new Vector();
- int[] ids = groups[i].getSeq();
- for (int s = 0; s < ids.length; s++)
+ for (int s = 0; s < groups[i].getSeqCount(); s++)
{
- seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(
- ids[s]));
+ String seqId = groups[i].getSeq(s)+"";
+ seqs.addElement((jalview.datamodel.SequenceI) seqRefIds.get(seqId));
}
jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
sg.setOutlineColour(new java.awt.Color(
groups[i].getOutlineColour()));
+ 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",
/////////////////////////////////
// LOAD VIEWPORT
- Viewport[] views = jms.getViewport();
- Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
+ 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();
- AlignFrame af = new AlignFrame(al);
+ 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++)
}
- if(hideConsensus || hideQuality || hideConservation)
+ if((hideConsensus || hideQuality || hideConservation)
+ && al.getAlignmentAnnotation()!=null)
{
int hSize = al.getAlignmentAnnotation().length;
for (int h = 0; 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.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());
+ af.viewport.setConservationSelected(view.getConservationSelected());
af.viewport.setShowJVSuffix(view.getShowFullId());
- af.seqLimits.setSelected(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.renderGapsMenuItem.setSelected(view.getRenderGaps());
-
af.viewport.setWrapAlignment(view.getWrapAlignment());
- af.wrapMenuItem.setSelected(view.getWrapAlignment());
-
af.alignPanel.setWrapAlignment(view.getWrapAlignment());
-
- af.annotationPanelMenuItem.setState(view.getShowAnnotation());
af.viewport.setShowAnnotation(view.getShowAnnotation());
af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
af.viewport.setShowBoxes(view.getShowBoxes());
- af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
+
af.viewport.setShowText(view.getShowText());
- af.viewTextMenuItem.setSelected(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(cs!=null)
{
cs.setThreshold(view.getPidThreshold(), true);
- cs.setConsensus(af.viewport.vconsensus);
+ cs.setConsensus(af.viewport.hconsensus);
}
}
- af.setColourSelected(view.getBgColour());
+
af.viewport.setGlobalColourScheme(cs);
af.viewport.setColourAppliesToAllGroups(false);
- af.changeColour(cs);
+
if (view.getConservationSelected() && cs!=null)
{
cs.setConservationInc(view.getConsThreshold());
}
+ af.changeColour(cs);
+
af.viewport.setColourAppliesToAllGroups(true);
+
+
if (view.getShowSequenceFeatures())
{
af.viewport.showSequenceFeatures = true;
- af.showSeqFeatures.setSelected(true);
}
if(jms.getFeatureSettings()!=null)
}
}
+ af.setMenusFromViewport(af.viewport);
+
Desktop.addInternalFrame(af, view.getTitle(),
view.getWidth(), view.getHeight());
//LOAD TREES
///////////////////////////////////////
- if (jms.getTreeCount() > 0)
+ if (loadTrees && jms.getTreeCount() > 0)
{
try
{
return af;
}
+
+ public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, boolean keepSeqRefs )
+ {
+ jalview.schemabinding.version2.JalviewModel jm
+ = SaveState(ap, null, null, null);
+
+ if (!keepSeqRefs)
+ {
+ seqRefIds.clear();
+ jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
+ }
+ else
+ uniqueSetSuffix = "";
+
+ viewportsAdded = new Hashtable();
+
+ AlignFrame af = LoadFromObject(jm, null, false);
+ af.alignPanels.clear();
+ af.closeMenuItem_actionPerformed(true);
+
+ return af.alignPanel;
+ }
}
git://source.jalview.org / jalview.git / blobdiff