From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 10 May 2006 12:56:02 +0000 (+0000)
Subject: addAnnotation with seqRef
X-Git-Tag: Release_2_1~434
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=601989c95175f5ad883e73c4aa07a76713510d1f;p=jalview.git

addAnnotation with seqRef
---

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index b0b04ca..c62d707 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -31,7 +31,6 @@ public class Alignment implements AlignmentI
     protected Alignment dataset;
     protected Vector sequences;
     protected Vector groups = new Vector();
-    protected Vector superGroup = new Vector();
     protected char gapCharacter = '-';
     protected int type = NUCLEOTIDE;
     public static final int PROTEIN = 0;
@@ -61,19 +60,7 @@ public class Alignment implements AlignmentI
         for (i = 0; i < seqs.length; i++)
         {
             sequences.addElement(seqs[i]);
-
-            if(seqs[i].getDatasetSequence()!=null
-            && seqs[i].getDatasetSequence().getAnnotation()!=null)
-            {
-
-              for(int a=0; a<seqs[i].getDatasetSequence().getAnnotation().length; a++)
-              {
-                       this.addAnnotation(seqs[i].getDatasetSequence().getAnnotation()[a], seqs[i]);
-              }
-            }
         }
-
-        getWidth();
     }
 
     /**
@@ -409,7 +396,6 @@ public class Alignment implements AlignmentI
     public void deleteAllGroups()
     {
         groups.removeAllElements();
-        superGroup.removeAllElements();
 
         int i = 0;
 
@@ -614,70 +600,6 @@ public class Alignment implements AlignmentI
         annotations = temp;
     }
 
-    /**
-     *
-     * @param aa AlignmentAnnotation
-     * @param seqRef The sequence to associate this annotation with
-     * @return The adjusted AlignmentAnnotation, with dataset sequence and annotation added
-     */
-    public AlignmentAnnotation addAnnotation(AlignmentAnnotation aa, SequenceI seqRef)
-    {
-      if(seqRef!=null)
-      {
-          //We can only add Annotations to the dataset sequences
-           if(seqRef.getDatasetSequence()==null)
-           {
-                  setDataset(null);
-            }
-
-        AlignmentAnnotation []  old = seqRef.getDatasetSequence().getAnnotation();
-
-        //First check if this is a new annotation or not. If it is new,
-        //we must add the annotation to the dataset
-        boolean newAnnotation = true;
-        if(seqRef.getDatasetSequence().getAnnotation()!=null)
-        {
-          for(int a=0; a<old.length; a++)
-          {
-            if(old[a] == aa)
-            {
-
-              newAnnotation = false;
-              break;
-            }
-          }
-        }
-
-        if(newAnnotation)
-         {
-           seqRef.getDatasetSequence().addAlignmentAnnotation(aa);
-         }
-
-          AlignmentAnnotation copy = null;
-          if (aa.graph > 0)
-            copy = new AlignmentAnnotation(
-                aa.label, aa.description, aa.annotations, aa.graphMin,
-                aa.graphMax, aa.graph
-                );
-          else
-            copy = new AlignmentAnnotation(
-                aa.label, aa.description, aa.annotations
-                );
-
-         copy.datasetAnnotation = aa;
-
-         addAnnotation(copy);
-
-         copy.sequenceRef = seqRef;
-
-         return copy;
-      }
-      else
-      {
-        addAnnotation(aa);
-        return aa;
-      }
-    }
 
     public void adjustSequenceAnnotations()
     {
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 7fe4627..ebfb0ce 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -225,11 +225,6 @@ public interface AlignmentI
      */
     public void addAnnotation(AlignmentAnnotation aa);
 
-    /**
-     * Adds a new AlignmentAnnotation to this alignment,
-     *  associated to Sequence starting at sequence index
-     */
-    public AlignmentAnnotation addAnnotation(AlignmentAnnotation aa, SequenceI seqRef);
 
     public void setAnnotationIndex(AlignmentAnnotation aa, int index);