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;
//SAVE SEQUENCES
}
an.setLabel(aa[i].label);
- if (!Float.isNaN(aa[i].score))
+ if (aa[i].hasScore())
{
an.setScore(aa[i].getScore());
}
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);
/////////////////////////////////
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()==null ? ' ' :
+ (ae[aa].getSecondaryStructure()==null || ae[aa].getSecondaryStructure().length() == 0) ? ' ' :
ae[aa].getSecondaryStructure().charAt(0),
ae[aa].getValue()
else if(comp!=null)
{
StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, pdbFile,
+ .setMapping(seq, null, pdbFile,
jalview.io.AppletFormatAdapter.FILE);
( (AppJMol) comp).addSequence(seq);