X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=34cc78febab20e05262abdb28bebdc41e9bc2f99;hb=9ca6b95ab67df6eaeea56765cc293133da436e76;hp=ddb58c3870ffaa3ae246aeaf7d9bf67ae0348e75;hpb=c39e588784c0fbb64c7dabfcae8db4faedde10e6;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index ddb58c3..34cc78f 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -40,6 +40,8 @@ public class Alignment
 
   HiddenSequences hiddenSequences = new HiddenSequences(this);
 
+  public Hashtable alignmentProperties;
+
   private void initAlignment(SequenceI[] seqs)
   {
     int i = 0;
@@ -139,25 +141,26 @@ public class Alignment
   {
     if (dataset != null)
     {
+      // maintain dataset integrity
       if (snew.getDatasetSequence() != null)
       {
         getDataset().addSequence(snew.getDatasetSequence());
       }
       else
       {
-        Sequence ds = new Sequence(snew.getName(),
-                                   AlignSeq.extractGaps("-. ",
-            snew.getSequenceAsString()),
-                                   snew.getStart(),
-                                   snew.getEnd());
-
-        snew.setDatasetSequence(ds);
-        getDataset().addSequence(ds);
+        // derive new sequence
+        SequenceI adding = snew.deriveSequence();
+        getDataset().addSequence(adding.getDatasetSequence());
+        snew = adding;
       }
     }
-    sequences.addElement(snew);
-
-    hiddenSequences.adjustHeightSequenceAdded();
+    if (sequences==null) {
+      initAlignment(new SequenceI[] { snew });
+    } else {
+      sequences.addElement(snew);
+    }
+    if (hiddenSequences!=null)
+      hiddenSequences.adjustHeightSequenceAdded();
   }
 
   /** Adds a sequence to the alignment.  Recalculates maxLength and size.
@@ -182,10 +185,10 @@ public class Alignment
     return groups;
   }
 
-  public void destroyAlignment()
+  public void finalize()
   {
     if(getDataset()!=null)
-      getDataset().destroyAlignment();
+      getDataset().finalize();
 
     dataset = null;
     sequences = null;
@@ -465,6 +468,9 @@ public class Alignment
    */
   public void deleteAnnotation(AlignmentAnnotation aa)
   {
+    if(aa.sequenceRef!=null)
+      aa.sequenceRef.removeAlignmentAnnotation(aa);
+
     int aSize = 1;
 
     if (annotations != null)
@@ -698,4 +704,21 @@ public class Alignment
     return cal;
   }
 
+  public void setProperty(Object key, Object value)
+  {
+    if(alignmentProperties==null)
+      alignmentProperties = new Hashtable();
+
+    alignmentProperties.put(key,value);
+  }
+
+  public Object getProperty(Object key)
+  {
+    if(alignmentProperties!=null)
+      return alignmentProperties.get(key);
+    else
+      return null;
+  }
+
+
 }