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

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

diff --git a/src/jalview/datamodel/ContactMapHolder.java b/src/jalview/datamodel/ContactMapHolder.java
new file mode 100644 (file)
index 0000000..45c0d18
--- /dev/null
+++ b/src/jalview/datamodel/ContactMapHolder.java
@@ -0,0 +1,99 @@
+package jalview.datamodel;
+
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+
+import jalview.ws.datamodel.MappableContactMatrixI;
+
+public class ContactMapHolder implements ContactMapHolderI
+{
+
+  Map<Object, ContactMatrixI> contactmaps = new HashMap<>();
+
+  @Override
+  public Collection<ContactMatrixI> getContactMaps()
+  {
+    if (contactmaps != null && contactmaps.size() > 0)
+    {
+      // defensive copy, and return non redundant set of ContactMatrixI
+      // instances
+      return new HashSet<ContactMatrixI>(contactmaps.values());
+    }
+    return Collections.EMPTY_LIST;
+  }
+
+  @Override
+  public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
+  {
+    ContactMatrixI cm = contactmaps.get(_aa.annotationId);
+    if (cm == null)
+    {
+      return null;
+    }
+    if (cm instanceof MappableContactMatrixI)
+    {
+      if (_aa.sequenceRef != null)
+      {
+        return ((MappableContactMatrixI) cm)
+                .getMappableContactList(_aa.sequenceRef, column);
+      }
+    }
+    // TODO: could resolve sequence position to column position here
+    // TODO: what about for complexes - where contactMatrix may involve two or
+    // more sequences
+    return cm.getContactList(column);
+  }
+
+  @Override
+  public AlignmentAnnotation addContactList(ContactMatrixI cm)
+  {
+
+    AlignmentAnnotation aa = new AlignmentAnnotation(cm.getAnnotLabel(),
+            cm.getAnnotDescr(), new Annotation[0]);
+    aa.graph = AlignmentAnnotation.CONTACT_MAP;
+    aa.graphMin = cm.getMin();
+    aa.graphMax = cm.getMax();
+    aa.editable = false;
+    aa.calcId = cm.getType();
+
+    contactmaps.put(aa.annotationId, cm);
+    // TODO: contact matrices could be intra or inter - more than one refseq
+    // possible!
+    if (cm instanceof MappableContactMatrixI)
+    {
+      aa.setSequenceRef(((MappableContactMatrixI) cm).getReferenceSeq());
+    }
+    return aa;
+  }
+
+  @Override
+  public ContactMatrixI getContactMatrixFor(AlignmentAnnotation ann)
+  {
+    return contactmaps == null ? null : contactmaps.get(ann.annotationId);
+  }
+
+  @Override
+  public void addContactListFor(AlignmentAnnotation annotation,
+          ContactMatrixI cm)
+  {
+    // update annotation with data from contact map
+    annotation.graphMin = cm.getMin();
+    annotation.graphMax = cm.getMax();
+    annotation.editable = false;
+    annotation.graph = AlignmentAnnotation.CONTACT_MAP;
+    annotation.calcId = cm.getType();
+    if (annotation.label == null || "".equals(annotation.label))
+    {
+      annotation.label = cm.getAnnotLabel();
+
+    }
+    if (annotation.description == null || "".equals(annotation.description))
+    {
+      annotation.description = cm.getAnnotDescr();
+    }
+    contactmaps.put(annotation.annotationId, cm);
+  }
+}