JAL-2349 javadoc dummy contact matrix

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 35ee8c4..b251a89 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -24,11 +24,13 @@ import jalview.analysis.AlignmentUtils;
 import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.io.FastaFile;
 import jalview.util.Comparison;
+import jalview.util.LinkedIdentityHashSet;
 import jalview.util.MessageManager;
 
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Enumeration;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.List;
@@ -660,7 +662,7 @@ public class Alignment implements AlignmentI
    * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
    */
   @Override
-  public int findIndex(SearchResults results)
+  public int findIndex(SearchResultsI results)
   {
     int i = 0;
 
@@ -1054,6 +1056,7 @@ public class Alignment implements AlignmentI
   private void resolveAndAddDatasetSeq(SequenceI currentSeq,
           Set<SequenceI> seqs, boolean createDatasetSequence)
   {
+    SequenceI alignedSeq = currentSeq;
     if (currentSeq.getDatasetSequence() != null)
     {
       currentSeq = currentSeq.getDatasetSequence();
@@ -1088,12 +1091,19 @@ public class Alignment implements AlignmentI
         {
           if (dbr.getMap() != null && dbr.getMap().getTo() != null)
           {
+            if (dbr.getMap().getTo() == alignedSeq)
+            {
+              /*
+               * update mapping to be to the newly created dataset sequence
+               */
+              dbr.getMap().setTo(currentSeq);
+            }
             if (dbr.getMap().getTo().getDatasetSequence() != null)
             {
-              throw new Error("Implementation error: Map.getTo() for dbref"
-                      + dbr + " is not a dataset sequence.");
-              // TODO: if this happens, could also rewrite the reference to
-              // point to new dataset sequence
+              throw new Error(
+                      "Implementation error: Map.getTo() for dbref " + dbr
+                              + " from " + curDs.getName()
+                              + " is not a dataset sequence.");
             }
             // we recurse to add all forward references to dataset sequences via
             // DBRefs/etc
@@ -1115,7 +1125,7 @@ public class Alignment implements AlignmentI
       return;
     }
     // try to avoid using SequenceI.equals at this stage, it will be expensive
-    Set<SequenceI> seqs = new jalview.util.LinkedIdentityHashSet<SequenceI>();
+    Set<SequenceI> seqs = new LinkedIdentityHashSet<SequenceI>();
 
     for (int i = 0; i < getHeight(); i++)
     {
@@ -1828,7 +1838,7 @@ public class Alignment implements AlignmentI
   @Override
   public String toString()
   {
-    return new FastaFile().print(getSequencesArray());
+    return new FastaFile().print(getSequencesArray(), true);
   }
 
   /**
@@ -1937,4 +1947,38 @@ public class Alignment implements AlignmentI
     }
     return new int[] { startPos, endPos };
   }
+
+  Map<Object, ContactMatrixI> contactmaps = new HashMap<Object, ContactMatrixI>();
+  @Override
+  public
+  ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
+  {
+    ContactMatrixI cm = contactmaps.get(_aa.annotationId);
+    if (cm == null)
+    {
+      return null;
+    }
+    return cm.getContactList(column);
+  }
+
+  @Override
+  public AlignmentAnnotation addContactList(ContactMatrixI cm)
+  {
+    Annotation _aa[] = new Annotation[getWidth()];
+    Annotation dummy = new Annotation(0.0f);
+    for (int i = 0; i < _aa.length; _aa[i++] = dummy)
+    {
+      ;
+    }
+    AlignmentAnnotation aa = new AlignmentAnnotation("Contact Matrix",
+            "Contact Matrix", _aa);
+    aa.graph = AlignmentAnnotation.CUSTOMRENDERER;
+    aa.graphMin = 0f;
+    aa.graphMax = 100f;
+    aa.editable = false;
+    // aa.autoCalculated = true;
+    contactmaps.put(aa.annotationId, cm);
+    addAnnotation(aa);
+    return aa;
+  }
 }