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Merge branch 'doc/JAL-4090_Release_2_11_3_0' into develop
[jalview.git]
/
src
/
jalview
/
datamodel
/
ContactMapHolderI.java
diff --git
a/src/jalview/datamodel/ContactMapHolderI.java
b/src/jalview/datamodel/ContactMapHolderI.java
index
624a03e
..
342abf8
100644
(file)
--- a/
src/jalview/datamodel/ContactMapHolderI.java
+++ b/
src/jalview/datamodel/ContactMapHolderI.java
@@
-6,10
+6,13
@@
public interface ContactMapHolderI
{
/**
* resolve a contact list instance (if any) associated with the annotation row
{
/**
* resolve a contact list instance (if any) associated with the annotation row
- * and column position
+ * and column position Columns of ContactMap are indexed relative to context
+ * object (columns of alignment, positions on sequence relative to
+ * sequence.getStart())
*
* @param _aa
* @param column
*
* @param _aa
* @param column
+ * - base 0 column index
* @return
*/
ContactListI getContactListFor(AlignmentAnnotation _aa, int column);
* @return
*/
ContactListI getContactListFor(AlignmentAnnotation _aa, int column);
@@
-18,4
+21,8
@@
public interface ContactMapHolderI
Collection<ContactMatrixI> getContactMaps();
Collection<ContactMatrixI> getContactMaps();
+ public ContactMatrixI getContactMatrixFor(AlignmentAnnotation ann);
+
+ void addContactListFor(AlignmentAnnotation annotation, ContactMatrixI cm);
+
}
}