Hashtable annotationIds = new Hashtable();
String uniqueSetSuffix = "";
+ /**
+ * List of pdbfiles added to Jar
+ */
+ Vector pdbfiles = null;
// SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
public void SaveState(File statefile)
vamsasSet.setGapChar(jal.getGapCharacter() + "");
+ if(jal.getProperties()!=null)
+ {
+ Enumeration en = jal.getProperties().keys();
+ while(en.hasMoreElements())
+ {
+ String key = en.nextElement().toString();
+ SequenceSetProperties ssp = new SequenceSetProperties();
+ ssp.setKey(key);
+ ssp.setValue(jal.getProperties().get(key).toString());
+ vamsasSet.addSequenceSetProperties(ssp);
+ }
+ }
+
JSeq jseq;
- Vector pdbfiles = null;
//SAVE SEQUENCES
int id = 0;
pdb.setId(entry.getId());
pdb.setType(entry.getType());
- AppJMol jmol;
+ AppJmol jmol;
//This must have been loaded, is it still visible?
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
for (int f = frames.length - 1; f > -1; f--)
{
- if (frames[f] instanceof AppJMol)
+ if (frames[f] instanceof AppJmol)
{
- jmol = (AppJMol) frames[f];
+ jmol = (AppJmol) frames[f];
if (!jmol.pdbentry.getId().equals(entry.getId()))
continue;
+
StructureState state = new StructureState();
state.setVisible(true);
state.setXpos(jmol.getX());
state.setWidth(jmol.getWidth());
state.setHeight(jmol.getHeight());
- state.setContent(jmol.viewer.getStateInfo().replaceAll("\n", ""));
-
+ String statestring = jmol.viewer.getStateInfo();
+ if(state!=null)
+ {
+ state.setContent(statestring.replaceAll("\n", ""));
+ }
for (int s = 0; s < jmol.sequence.length; s++)
{
if (jal.findIndex(jmol.sequence[s]) > -1)
continue;
}
+ an.setVisible(aa[i].visible);
+
an.setDescription(aa[i].description);
if (aa[i].sequenceRef != null)
}
an.setLabel(aa[i].label);
-
+ if (aa[i].hasScore())
+ {
+ an.setScore(aa[i].getScore());
+ }
AnnotationElement ae;
-
- for (int a = 0; a < aa[i].annotations.length; a++)
+ if (aa[i].annotations!=null)
{
- if ( (aa[i] == null) || (aa[i].annotations[a] == null))
+ an.setScoreOnly(false);
+ for (int a = 0; a < aa[i].annotations.length; a++)
{
- continue;
- }
+ if ((aa[i] == null) || (aa[i].annotations[a] == null))
+ {
+ continue;
+ }
- 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 +
- "");
+ ae = new AnnotationElement();
+ if (aa[i].annotations[a].description != null)
+ ae.setDescription(aa[i].annotations[a].description);
+ if(aa[i].annotations[a].displayCharacter!=null)
+ ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
- if (aa[i].annotations[a].colour != java.awt.Color.black)
- {
- ae.setColour(aa[i].annotations[a].colour.getRGB());
- }
+ if (!Float.isNaN(aa[i].annotations[a].value))
+ ae.setValue(aa[i].annotations[a].value);
- an.addAnnotationElement(ae);
- }
+ ae.setPosition(a);
+ if (aa[i].annotations[a].secondaryStructure != ' '
+ && aa[i].annotations[a].secondaryStructure != '\0')
+ ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
+ + "");
+
+ if (aa[i].annotations[a].colour!=null
+ && aa[i].annotations[a].colour != java.awt.Color.black)
+ {
+ ae.setColour(aa[i].annotations[a].colour.getRGB());
+ }
+ an.addAnnotationElement(ae);
+ }
+ } else {
+ an.setScoreOnly(true);
+ }
vamsasSet.addAnnotation(an);
}
}
fs.addSetting(setting);
settingsAdded.addElement(renderOrder[ro]);
}
-
+
//Make sure we save none displayed feature settings
Enumeration en =
ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
setting.setDisplay(false);
float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(key);
- if (rorder>-1)
+ if (rorder>-1)
{
setting.setOrder(rorder);
}
settingsAdded.addElement(key);
}
en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
- Vector groupsAdded=new Vector();
+ Vector groupsAdded=new Vector();
while (en.hasMoreElements())
{
String grp = en.nextElement().toString();
- if (groupsAdded.contains(grp))
+ if (groupsAdded.contains(grp))
{
continue;
}
Hashtable gatherToThisFrame = new Hashtable();
+ String errorMessage = null;
+
try
{
//UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
}
while (jarentry != null);
}
+ catch(java.io.FileNotFoundException ex)
+ {
+ ex.printStackTrace();
+ errorMessage = "Couldn't locate Jalview XML file : "+file;
+ System.err.println("Exception whilst loading jalview XML file : " +
+ ex + "\n");
+ }
catch (java.net.UnknownHostException ex)
{
ex.printStackTrace();
- System.err.println("Couldn't locate Jalview XML file : " +
+ errorMessage = "Couldn't locate Jalview XML file : " +file;
+ System.err.println("Exception whilst loading jalview XML file : " +
ex + "\n");
-
- 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)
{
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)
(AlignFrame) en.nextElement());
}
+ if(errorMessage!=null)
+ {
+ final String finalErrorMessage = errorMessage;
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ finalErrorMessage,
+ "Error loading Jalview file",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
+
return af;
}
jalview.datamodel.Alignment al =
new jalview.datamodel.Alignment(orderedSeqs);
+ for(int i=0; i<vamsasSet.getSequenceSetPropertiesCount(); i++ )
+ {
+ SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
+ al.setProperty(ssp.getKey(), ssp.getValue());
+ }
+
+
al.setDataset(null);
/////////////////////////////////
if (an[i].getId() != null
&& annotationIds.containsKey(an[i].getId()))
{
- al.addAnnotation(
+ jalview.datamodel.AlignmentAnnotation jda =
(jalview.datamodel.AlignmentAnnotation) annotationIds.get(an[i].
- getId())
- );
+ getId());
+ if (an[i].hasVisible())
+ jda.visible = an[i].getVisible();
+
+ al.addAnnotation(jda);
continue;
}
AnnotationElement[] ae = an[i].getAnnotationElement();
- jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[
- al.getWidth()];
+ jalview.datamodel.Annotation[] anot = null;
- for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
+ if (!an[i].getScoreOnly())
{
- 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());
- }
+ anot = new jalview.datamodel.Annotation[
+ al.getWidth()];
+ for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
+ {
+ if(ae[aa].getPosition()>=anot.length)
+ continue;
+
+ anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
+
+ ae[aa].getDisplayCharacter(),
+ ae[aa].getDescription(),
+ (ae[aa].getSecondaryStructure()==null || ae[aa].getSecondaryStructure().length() == 0) ? ' ' :
+ ae[aa].getSecondaryStructure().charAt(0),
+ ae[aa].getValue()
+
+ );
+
+
+ anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa].
+ getColour());
+ }
+ }
jalview.datamodel.AlignmentAnnotation jaa = null;
if (an[i].getGraph())
if (an[i].getSequenceRef() != null)
{
- jaa.createSequenceMapping(
- al.findName(an[i].getSequenceRef()), 1, true
- );
- al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
+ if (al.findName(an[i].getSequenceRef()) != null)
+ {
+ jaa.createSequenceMapping(
+ al.findName(an[i].getSequenceRef()), 1, true
+ );
+ al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
+ }
+ }
+ if (an[i].hasScore())
+ {
+ jaa.setScore(an[i].getScore());
}
+ if(an[i].hasVisible())
+ jaa.visible = an[i].getVisible();
+
al.addAnnotation(jaa);
}
}
renderOrder;
Hashtable fgtable;
af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable=new Hashtable();
- for (int gs=0;gs<jms.getFeatureSettings().getGroupCount(); gs++)
+ for (int gs=0;gs<jms.getFeatureSettings().getGroupCount(); gs++)
{
Group grp = jms.getFeatureSettings().getGroup(gs);
fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
}
}
-
+
if (view.getHiddenColumnsCount() > 0)
{
for (int c = 0; c < view.getHiddenColumnsCount(); c++)
int width = ids[p].getStructureState(s).getWidth();
int height = ids[p].getStructureState(s).getHeight();
- java.awt.Component comp = Desktop.desktop.getComponentAt(x, y);
+ java.awt.Component comp = null;
+
+ JInternalFrame [] frames = Desktop.desktop.getAllFrames();
+ for(int f=0; f<frames.length; f++)
+ {
+ if(frames[f] instanceof AppJmol)
+ {
+ if (frames[f].getX() == x && frames[f].getY() == y
+ && frames[f].getHeight() == height
+ && frames[f].getWidth() == width)
+ {
+ comp = frames[f];
+ break;
+ }
+ }
+ }
+
+
+ Desktop.desktop.getComponentAt(x, y);
String pdbFile = loadPDBFile(file, ids[p].getId());
- jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
+ jalview.datamodel.SequenceI[] seq = new jalview.datamodel.
+ SequenceI[]
{
- al.getSequenceAt(i)};
+ (jalview.datamodel.SequenceI)
+ seqRefIds.get(JSEQ[i].getId()+"")};
+
- if (comp == null ||
- (comp.getWidth() != width && comp.getHeight() != height))
+ if (comp == null)
{
String state = ids[p].getStructureState(s).getContent();
newFileLoc.append(state.substring(
state.indexOf("\"", state.indexOf("load \"") + 6)));
- new AppJMol(pdbFile,
+ new AppJmol(pdbFile,
ids[p].getId(),
seq,
af.alignPanel,
else if(comp!=null)
{
StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, pdbFile,
+ .setMapping(seq, null, pdbFile,
jalview.io.AppletFormatAdapter.FILE);
- ( (AppJMol) comp).addSequence(seq);
+ ( (AppJmol) comp).addSequence(seq);
}
}
}
git://source.jalview.org / jalview.git / blobdiff