import jalview.schemes.*;
-import jalview.gui.*;
-
import java.io.*;
import java.net.*;
*/
public class Jalview2XML
{
+
+ 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)
{
AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.
elementAt(ap);
- if (apanel.av.explodedPosition == null)
- apanel.av.explodedPosition = af.getBounds();
-
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
{
AlignmentPanel apanel = (AlignmentPanel)af.alignPanels.elementAt(ap);
- if (apanel.av.explodedPosition == null)
- apanel.av.explodedPosition = af.getBounds();
-
SaveState(apanel,
apSize==1?fileName:fileName+ap,
jout, out);
out.close();
jout.close();
+ return true;
}
catch (Exception ex)
{
ex.printStackTrace();
+ return false;
}
}
* @param jout DOCUMENT ME!
* @param out DOCUMENT ME!
*/
- public void SaveState(AlignmentPanel ap,
+ public JalviewModel SaveState(AlignmentPanel ap,
String fileName,
JarOutputStream jout,
PrintWriter out)
//SAVE SEQUENCES
int id = 0;
+ jalview.datamodel.SequenceI jds;
for (int i = 0; i < jal.getHeight(); i++)
{
- id = jal.getSequenceAt(i).hashCode();
+ jds = jal.getSequenceAt(i);
+ id = jds.hashCode();
if(seqRefIds.get(id+"")!=null)
{
{
vamsasSeq = new Sequence();
vamsasSeq.setId(id + "");
- vamsasSeq.setName(jal.getSequenceAt(i).getName());
- vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
- vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());
+ vamsasSeq.setName(jds.getName());
+ vamsasSeq.setSequence(jds.getSequenceAsString());
+ vamsasSeq.setDescription(jds.getDescription());
- if (jal.getSequenceAt(i).getDatasetSequence().getDBRef() != null)
+ if (jds.getDatasetSequence().getDBRef() != null)
{
jalview.datamodel.DBRefEntry[] dbrefs =
- jal.getSequenceAt(i).getDatasetSequence().getDBRef();
+ jds.getDatasetSequence().getDBRef();
for (int d = 0; d < dbrefs.length; d++)
{
}
vamsasSet.addSequence(vamsasSeq);
- seqRefIds.put(id+"", 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(av.alignment.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()));
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++)
{
view.setViewName(av.viewName);
view.setGatheredViews(av.gatherViewsHere);
- view.setXpos(av.explodedPosition.x);
- view.setYpos(av.explodedPosition.y);
- view.setWidth(av.explodedPosition.width);
- view.setHeight(av.explodedPosition.height);
+
+ 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.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)
{
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;
}
- Hashtable seqRefIds;
/**
* 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
unmar.setValidation(false);
object = (JalviewModel) unmar.unmarshal( in );
- af = LoadFromObject(object, file);
+ af = LoadFromObject(object, file, true);
if(af.viewport.gatherViewsHere)
{
gatherToThisFrame.add(af);
String loadPDBFile(String file, String pdbId)
{
+ System.out.println(file +" "+pdbId);
try
{
JarInputStream jin = null;
}
- AlignFrame LoadFromObject(JalviewModel object, String file)
+ AlignFrame LoadFromObject(JalviewModel object,
+ String file,
+ boolean loadTrees )
{
SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
Sequence[] vamsasSeq = vamsasSet.getSequence();
JalviewModelSequence jms = object.getJalviewModelSequence();
- Viewport[] views = jms.getViewport();
- Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
+ Viewport view = jms.getViewport(0);
//////////////////////////////////
//LOAD SEQUENCES
ArrayList tmpseqs = new ArrayList();
-
boolean multipleView = false;
JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
jseq.setDescription(vamsasSeq[i].getDescription());
jseq.setStart(JSEQ[i].getStart());
jseq.setEnd(JSEQ[i].getEnd());
- jseq.setColor(new java.awt.Color(JSEQ[i].getColour()));
seqRefIds.put(vamsasSeq[i].getId(), jseq);
tmpseqs.add( jseq );
}
+
if (JSEQ[i].getHidden())
{
if (hiddenSeqs == null)
}
}
-
- // af.changeColour() );
/////////////////////////
//LOAD GROUPS
if (jms.getJGroupCount() > 0)
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",
view.getWidth(),
view.getHeight() );
- af.viewport.sequenceSetID = view.getSequenceSetId();
+ af.setFileName(file, "Jalview");
+
+ for (int i = 0; i < JSEQ.length; i++)
+ {
+ af.viewport.setSequenceColour(
+ af.viewport.alignment.getSequenceAt(i),
+ new java.awt.Color(
+ JSEQ[i].getColour()));
+ }
+
+ //If we just load in the same jar file again, the sequenceSetId
+ //will be the same, and we end up with multiple references
+ //to the same sequenceSet. We must modify this id on load
+ //so that each load of the file gives a unique id
+ String uniqueSeqSetId = view.getSequenceSetId()+uniqueSetSuffix;
af.viewport.gatherViewsHere = view.getGatheredViews();
if (view.getSequenceSetId() != null)
- PaintRefresher.Register(af.alignPanel, view.getSequenceSetId());
+ {
+ 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++)
af.alignPanel.adjustAnnotationHeight();
}
- af.viewport.viewName = view.getViewName();
+ 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 = !hideConservation;
- af.viewport.showQuality = !hideQuality;
- af.viewport.showIdentity = !hideConsensus;
+ af.viewport.setShowAnnotation(view.getShowAnnotation());
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;
}
}
- 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