X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=3a79ac60c5eaa2136a42dd659ce6df699766bb07;hb=ceba202c97c435a5a0f70307961ba74316bd8312;hp=1956df7f10be8f6664575bbf5d92b8f94ca124c0;hpb=97761a98a97b49dcdf65e574aeff21f62f8a70b7;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 1956df7..3a79ac6 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -47,7 +47,7 @@ import java.util.Vector;
  * @author JimP
  * 
  */
-public class Alignment implements AlignmentI
+public class Alignment implements AlignmentI, AutoCloseable
 {
   private Alignment dataset;
 
@@ -292,6 +292,32 @@ public class Alignment implements AlignmentI
   }
 
   /**
+   * Inserts a sequence at a point in the alignment.
+   * 
+   * @param i
+   *          the index of the position the sequence is to be inserted in.
+   */
+  @Override
+  public void insertSequenceAt(int i, SequenceI snew)
+  {
+    synchronized (sequences)
+    {
+      if (sequences.size() > i)
+      {
+        sequences.add(i, snew);
+        return;
+
+      }
+      else
+      {
+        sequences.add(snew);
+        hiddenSequences.adjustHeightSequenceAdded();
+      }
+      return;
+    }
+  }
+
+  /**
    * DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
@@ -303,15 +329,20 @@ 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();
   }
 
   /**
@@ -586,7 +617,8 @@ public class Alignment implements AlignmentI
   @Override
   public SequenceI findName(SequenceI startAfter, String token, boolean b)
   {
-
+    if (token == null)
+      return null;
     int i = 0;
     SequenceI sq = null;
     String sqname = null;
@@ -1600,34 +1632,50 @@ public class Alignment implements AlignmentI
           String calcId, boolean autoCalc, SequenceI seqRef,
           SequenceGroup groupRef)
   {
-    if (annotations != null)
+    AlignmentAnnotation annot = annotations == null ? null
+            : AlignmentAnnotation.findFirstAnnotation(
+              Arrays.asList(getAlignmentAnnotation()), name, calcId,
+              autoCalc, seqRef, groupRef);
+
+    if (annot == null)
     {
-      for (AlignmentAnnotation annot : getAlignmentAnnotation())
+
+      annot = new AlignmentAnnotation(name, name, new Annotation[1], 0f, 0f,
+              AlignmentAnnotation.BAR_GRAPH);
+      annot.hasText = false;
+      if (calcId != null)
       {
-        if (annot.autoCalculated == autoCalc && (name.equals(annot.label))
-                && (calcId == null || annot.getCalcId().equals(calcId))
-                && annot.sequenceRef == seqRef
-                && annot.groupRef == groupRef)
-        {
-          return annot;
-        }
+        annot.setCalcId(calcId);
+      }
+      annot.autoCalculated = autoCalc;
+      if (seqRef != null)
+      {
+        annot.setSequenceRef(seqRef);
       }
+      annot.groupRef = groupRef;
+      addAnnotation(annot);
     }
-    AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
-            new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
-    annot.hasText = false;
-    if (calcId != null)
+    return annot;
+  }
+
+
+  @Override
+  public AlignmentAnnotation updateFromOrCopyAnnotation(
+          AlignmentAnnotation ala)
+  {
+    AlignmentAnnotation annot = AlignmentAnnotation.findFirstAnnotation(
+            Arrays.asList(getAlignmentAnnotation()), ala.label, ala.calcId,
+            ala.autoCalculated, ala.sequenceRef, ala.groupRef);
+    if (annot == null)
     {
-      annot.setCalcId(new String(calcId));
+      annot = new AlignmentAnnotation(ala);
+      addAnnotation(annot);
     }
-    annot.autoCalculated = autoCalc;
-    if (seqRef != null)
+    else
     {
-      annot.setSequenceRef(seqRef);
+      annot.updateAlignmentAnnotationFrom(ala);
     }
-    annot.groupRef = groupRef;
-    addAnnotation(annot);
-
+    validateAnnotation(annot);
     return annot;
   }
 
@@ -2027,4 +2075,18 @@ public class Alignment implements AlignmentI
     }
   }
 
+  @Override
+  public List<SequenceI> getHmmSequences()
+  {
+    List<SequenceI> result = new ArrayList<>();
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      SequenceI seq = sequences.get(i);
+      if (seq.hasHMMProfile())
+      {
+        result.add(seq);
+      }
+    }
+    return result;
+  }
 }