import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SeqCigar;
.intValue();
}
}
- alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
- // was
- // duplicated
- // earlier
+ // annotation was duplicated earlier
+ alignment.addAnnotation(sequences[i].getAnnotation()[a]);
+ // take care of contact matrix too
+ ContactMatrixI cm=sequences[i].getContactMatrixFor(sequences[i].getAnnotation()[a]);
+ if (cm!=null)
+ {
+ alignment.addContactListFor(sequences[i].getAnnotation()[a], cm);
+ }
+
alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
a);
}
}
public void showContactMapTree(AlignmentAnnotation aa,
- PAEContactMatrix cm)
+ ContactMatrixI cm)
{
int x = 4, y = 5;
int w = 400, h = 500;
{
NewickFile fin = new NewickFile(
new FileParse(cm.getNewick(), DataSourceType.PASTE));
- String title = "PAE Matrix Tree for "
- + cm.getReferenceSeq().getDisplayId(false);
+ String title = cm.getAnnotLabel() + " " + cm.getTreeMethod() + " tree"
+ + aa.sequenceRef != null
+ ? (" for " + aa.sequenceRef.getDisplayId(false))
+ : "";
showColumnWiseTree(fin, aa, title, w, h, x, y);
} catch (Throwable xx)