X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=95f578051e5b41c685feb674b683b077c3df8317;hb=85299bc2db43c8b108169661ebc1c4d9b2d3d2e5;hp=ea04361d94d261f98f9109520f21b8e69a77d788;hpb=4548727494c3bf521eeec90a07e3bc6c0bdfb64e;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index ea04361..95f5780 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -23,9 +23,9 @@ package jalview.datamodel;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.BitSet;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.Enumeration;
-import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.Iterator;
@@ -1653,8 +1653,10 @@ public class Alignment implements AlignmentI, AutoCloseable
   public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
           String calcId, String label)
   {
-    return AlignmentAnnotation.findAnnotations(
-            Arrays.asList(getAlignmentAnnotation()), seq, calcId, label);
+    return annotations == null ? null
+            : AlignmentAnnotation.findAnnotations(
+                    Arrays.asList(getAlignmentAnnotation()), seq, calcId,
+                    label);
   }
 
   @Override
@@ -1828,7 +1830,13 @@ public class Alignment implements AlignmentI, AutoCloseable
     {
       return AlignmentUtils.alignCdsAsProtein(this, al);
     }
-    return AlignmentUtils.alignAs(this, al);
+    else if (thatIsProtein && !thisIsNucleotide)
+    {
+    	// honour sense we were called - align this according to al 
+    	return AlignmentUtils.alignAs(this, al);
+    }
+    // otherwise doing a DNA to DNA alignment - so use legacy obverse sense
+    return AlignmentUtils.alignAs(this,al);    
   }
 
   /**
@@ -2033,42 +2041,91 @@ public class Alignment implements AlignmentI, AutoCloseable
     }
   }
 
-  Map<Object, ContactMatrixI> contactmaps = new HashMap<>();
+  ////
+  //// Contact Matrix Holder Boilerplate
+  ////
+  ContactMapHolder cmholder = new ContactMapHolder();
+
+  @Override
+  public Collection<ContactMatrixI> getContactMaps()
+  {
+    return cmholder.getContactMaps();
+  }
+
+  @Override
+  public ContactMatrixI getContactMatrixFor(AlignmentAnnotation _aa)
+  {
+    ContactMatrixI cm = cmholder.getContactMatrixFor(_aa);
+    if (cm == null && _aa.groupRef != null)
+    {
+      cm = _aa.groupRef.getContactMatrixFor(_aa);
+    }
+    if (cm == null && _aa.sequenceRef != null)
+    {
+      cm = _aa.sequenceRef.getContactMatrixFor(_aa);
+      if (cm == null && _aa.sequenceRef.getDatasetSequence() != null)
+      {
+        // TODO fix up this logic and unify with getContactListFor
+        cm = _aa.sequenceRef.getDatasetSequence().getContactMatrixFor(_aa);
+      }
+    }
+    return cm;
+  }
+
   @Override
   public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
   {
-    ContactMatrixI cm = contactmaps.get(_aa.annotationId);
-    if (cm == null)
+    if (_aa.annotations == null || column >= _aa.annotations.length
+            || column < 0)
     {
       return null;
     }
-    return cm.getContactList(column);
+    ContactListI cl = cmholder.getContactListFor(_aa, column);
+    if (cl == null && _aa.groupRef != null)
+    {
+      cl = _aa.groupRef.getContactListFor(_aa, column);
+    }
+    if (cl == null && _aa.sequenceRef != null)
+    {
+      if (_aa.annotations[column] != null)
+      {
+        // sequence associated
+        cl = _aa.sequenceRef.getContactListFor(_aa, column);
+        if (cl == null && _aa.sequenceRef.getDatasetSequence() != null)
+        {
+          int spos = _aa.sequenceRef.findPosition(column);
+          if (spos >= _aa.sequenceRef.getStart()
+                  && spos <= 1 + _aa.sequenceRef.getEnd())
+          {
+            cl = _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa,
+                    spos - _aa.sequenceRef.getStart());
+          }
+        }
+      }
+    }
+    return cl;
   }
 
   @Override
   public AlignmentAnnotation addContactList(ContactMatrixI cm)
   {
+    AlignmentAnnotation aa = cmholder.addContactList(cm);
+
     Annotation _aa[] = new Annotation[getWidth()];
-    Annotation dummy = new Annotation(0.0f);
-    for (int i = 0; i < _aa.length; _aa[i++] = dummy)
+    for (int i = 0; i < _aa.length; _aa[i++] = new Annotation(0.0f))
     {
       ;
     }
-    AlignmentAnnotation aa = new AlignmentAnnotation("Contact Matrix",
-            "Contact Matrix", _aa);
-    aa.graph = AlignmentAnnotation.CUSTOMRENDERER;
-    aa.graphMin = cm.getMin();
-    aa.graphMax = cm.getMax();
-    aa.editable = false;
-    // aa.autoCalculated = true;
-    contactmaps.put(aa.annotationId, cm);
-    // TODO: contact matrices could be intra or inter - more than one refseq
-    // possible!
-    if (cm.hasReferenceSeq())
-    {
-      aa.setSequenceRef(cm.getReferenceSeq());
-    }
+    aa.annotations = _aa;
     addAnnotation(aa);
     return aa;
   }
+
+  @Override
+  public void addContactListFor(AlignmentAnnotation annotation,
+          ContactMatrixI cm)
+  {
+    cmholder.addContactListFor(annotation, cm);
+
+  }
 }