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JAL-2349 JAL-3855 Integrate pAE retrieval in StructureFile so it can be transferred...
[jalview.git]
/
src
/
jalview
/
datamodel
/
Sequence.java
diff --git
a/src/jalview/datamodel/Sequence.java
b/src/jalview/datamodel/Sequence.java
index
d62be17
..
5ae7195
100755
(executable)
--- a/
src/jalview/datamodel/Sequence.java
+++ b/
src/jalview/datamodel/Sequence.java
@@
-1625,6
+1625,13
@@
public class Sequence extends ASequence implements SequenceI
_aa.adjustForAlignment(); // uses annotation's own record of
// sequence-column mapping
datasetSequence.addAlignmentAnnotation(_aa);
_aa.adjustForAlignment(); // uses annotation's own record of
// sequence-column mapping
datasetSequence.addAlignmentAnnotation(_aa);
+
+ // transfer contact matrices
+ ContactMatrixI cm = getContactMatrixFor(aa);
+ if (cm != null)
+ {
+ datasetSequence.addContactListFor(_aa, cm);
+ }
}
}
}
}
}
}
@@
-2111,7
+2118,7
@@
public class Sequence extends ASequence implements SequenceI
////
//// Contact Matrix Holder Boilerplate
////
////
//// Contact Matrix Holder Boilerplate
////
- ContactMapHolder cmholder = new ContactMapHolder();
+ ContactMapHolderI cmholder = new ContactMapHolder();
@Override
public Collection<ContactMatrixI> getContactMaps()
@Override
public Collection<ContactMatrixI> getContactMaps()
@@
-2120,6
+2127,12
@@
public class Sequence extends ASequence implements SequenceI
}
@Override
}
@Override
+ public ContactMatrixI getContactMatrixFor(AlignmentAnnotation ann)
+ {
+ return cmholder.getContactMatrixFor(ann);
+ }
+
+ @Override
public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
{
return cmholder.getContactListFor(_aa, column);
public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
{
return cmholder.getContactListFor(_aa, column);
@@
-2137,8
+2150,16
@@
public class Sequence extends ASequence implements SequenceI
;
}
aa.annotations = _aa;
;
}
aa.annotations = _aa;
+ aa.setSequenceRef(this);
+ aa.createSequenceMapping(this, getStart(), false);
addAlignmentAnnotation(aa);
return aa;
}
addAlignmentAnnotation(aa);
return aa;
}
+ @Override
+ public void addContactListFor(AlignmentAnnotation annotation,
+ ContactMatrixI cm)
+ {
+ cmholder.addContactListFor(annotation, cm);
+ }
}
}