Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

[jalview.git] / src / jalview / datamodel / ContactMapHolderI.java

diff --git a/src/jalview/datamodel/ContactMapHolderI.java b/src/jalview/datamodel/ContactMapHolderI.java
new file mode 100644 (file)
index 0000000..342abf8
--- /dev/null
+++ b/src/jalview/datamodel/ContactMapHolderI.java
@@ -0,0 +1,28 @@
+package jalview.datamodel;
+
+import java.util.Collection;
+
+public interface ContactMapHolderI
+{
+  /**
+   * resolve a contact list instance (if any) associated with the annotation row
+   * 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
+   *          - base 0 column index
+   * @return
+   */
+  ContactListI getContactListFor(AlignmentAnnotation _aa, int column);
+
+  AlignmentAnnotation addContactList(ContactMatrixI cm);
+
+  Collection<ContactMatrixI> getContactMaps();
+
+  public ContactMatrixI getContactMatrixFor(AlignmentAnnotation ann);
+
+  void addContactListFor(AlignmentAnnotation annotation, ContactMatrixI cm);
+
+}