X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=33c8ac507a26d9272855907c12c76b054fc1d92b;hb=beb2fee66dde629e3bbb7febb38d0116e1a64df2;hp=d52e0497aa7f52b5a3c7092328c53c134cc93aa5;hpb=2eaab3084d84daa55785c0c288592d2a7f603742;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index d52e049..33c8ac5 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -20,17 +20,10 @@
  */
 package jalview.datamodel;
 
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.features.SequenceFeatures;
-import jalview.datamodel.features.SequenceFeaturesI;
-import jalview.util.Comparison;
-import jalview.util.DBRefUtils;
-import jalview.util.MapList;
-import jalview.util.StringUtils;
-
 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.Iterator;
@@ -39,6 +32,14 @@ import java.util.ListIterator;
 import java.util.Vector;
 
 import fr.orsay.lri.varna.models.rna.RNA;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.Comparison;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
+import jalview.util.StringUtils;
+import jalview.ws.datamodel.alphafold.MappableContactMatrix;
 
 /**
  * 
@@ -1415,6 +1416,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void addDBRef(DBRefEntry entry)
   {
+    // TODO JAL-3980 maintain as sorted list
     if (datasetSequence != null)
     {
       datasetSequence.addDBRef(entry);
@@ -1425,6 +1427,7 @@ public class Sequence extends ASequence implements SequenceI
     {
       dbrefs = new DBModList<>();
     }
+    // TODO JAL-3979 LOOK UP RATHER THAN SWEEP FOR EFFICIENCY
 
     for (int ib = 0, nb = dbrefs.size(); ib < nb; ib++)
     {
@@ -1623,6 +1626,13 @@ public class Sequence extends ASequence implements SequenceI
           _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);
+          }
         }
       }
     }
@@ -2105,4 +2115,57 @@ public class Sequence extends ASequence implements SequenceI
     // otherwise, sequence was completely hidden
     return 0;
   }
+
+  ////
+  //// Contact Matrix Holder Boilerplate
+  ////
+  ContactMapHolderI cmholder = new ContactMapHolder();
+
+  @Override
+  public Collection<ContactMatrixI> getContactMaps()
+  {
+    return cmholder.getContactMaps();
+  }
+
+  @Override
+  public ContactMatrixI getContactMatrixFor(AlignmentAnnotation ann)
+  {
+    return cmholder.getContactMatrixFor(ann);
+  }
+
+  @Override
+  public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
+  {
+    return cmholder.getContactListFor(_aa, column);
+  }
+
+  @Override
+  public AlignmentAnnotation addContactList(ContactMatrixI cm)
+  {
+    AlignmentAnnotation aa = cmholder.addContactList(cm);
+
+    Annotation _aa[] = new Annotation[getLength()];
+
+    for (int i = 0; i < _aa.length; _aa[i++] = new Annotation(0.0f))
+    {
+      ;
+    }
+    aa.annotations = _aa;
+    aa.setSequenceRef(this);
+    if (cm instanceof MappableContactMatrix
+            && !((MappableContactMatrix) cm).hasReferenceSeq())
+    {
+      ((MappableContactMatrix) cm).setRefSeq(this);
+    }
+    aa.createSequenceMapping(this, getStart(), false);
+    addAlignmentAnnotation(aa);
+    return aa;
+  }
+
+  @Override
+  public void addContactListFor(AlignmentAnnotation annotation,
+          ContactMatrixI cm)
+  {
+    cmholder.addContactListFor(annotation, cm);
+  }
 }