X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=73ccdc53966e03e5303dabfa0072ed0cea2350e9;hb=HEAD;hp=1956df7f10be8f6664575bbf5d92b8f94ca124c0;hpb=97761a98a97b49dcdf65e574aeff21f62f8a70b7;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 1956df7..73ccdc5 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -20,16 +20,10 @@
  */
 package jalview.datamodel;
 
-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.Arrays;
 import java.util.BitSet;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashSet;
@@ -40,6 +34,13 @@ import java.util.Map;
 import java.util.Set;
 import java.util.Vector;
 
+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;
+
 /**
  * Data structure to hold and manipulate a multiple sequence alignment
  */
@@ -47,7 +48,7 @@ import java.util.Vector;
  * @author JimP
  * 
  */
-public class Alignment implements AlignmentI
+public class Alignment implements AlignmentI, AutoCloseable
 {
   private Alignment dataset;
 
@@ -195,7 +196,7 @@ public class Alignment implements AlignmentI
   {
     synchronized (sequences)
     {
-    
+
       if (i > -1 && i < sequences.size())
       {
         return sequences.get(i);
@@ -303,15 +304,20 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public void finalize() throws Throwable
+  public void close()
   {
     if (getDataset() != null)
     {
-      getDataset().removeAlignmentRef();
+      try
+      {
+        getDataset().removeAlignmentRef();
+      } catch (Throwable e)
+      {
+        e.printStackTrace();
+      }
     }
 
     nullReferences();
-    super.finalize();
   }
 
   /**
@@ -711,7 +717,7 @@ public class Alignment implements AlignmentI
   public int getWidth()
   {
     int maxLength = -1;
-  
+
     for (int i = 0; i < sequences.size(); i++)
     {
       maxLength = Math.max(maxLength, getSequenceAt(i).getLength());
@@ -1647,8 +1653,10 @@ public class Alignment implements AlignmentI
   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
@@ -2027,4 +2035,91 @@ public class Alignment implements AlignmentI
     }
   }
 
+  ////
+  //// 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)
+  {
+    if (_aa.annotations == null || column >= _aa.annotations.length
+            || column < 0)
+    {
+      return null;
+    }
+    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()];
+    for (int i = 0; i < _aa.length; _aa[i++] = new Annotation(0.0f))
+    {
+      ;
+    }
+    aa.annotations = _aa;
+    addAnnotation(aa);
+    return aa;
+  }
+
+  @Override
+  public void addContactListFor(AlignmentAnnotation annotation,
+          ContactMatrixI cm)
+  {
+    cmholder.addContactListFor(annotation, cm);
+
+  }
 }