X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=15a1455c446cb5aa77501507279a88ad48d8e6a8;hb=5d2e589a842cf831e4fdeff6b8ed7e7ce6729fd5;hp=86d2c0e4e2ca02264b95132d26eedef5618ecb8a;hpb=cd1ded4a9a6f3478f3b704c9c97fd323ac5dbdd7;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 86d2c0e..15a1455 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -11,8 +11,11 @@ public class Alignment implements AlignmentI
 
   protected Vector      sequences;
   protected Vector      groups = new Vector();
-  protected ArrayList   superGroup = new ArrayList();
+  protected Vector   superGroup = new Vector();
   protected char        gapCharacter = '-';
+  public AlignmentAnnotation [] annotations;
+
+  public boolean featuresAdded = false;
 
   /** Make an alignment from an array of Sequences.
   *
@@ -318,18 +321,19 @@ public class Alignment implements AlignmentI
   public SequenceGroup [] findAllGroups(SequenceI s)
   {
 
-    ArrayList temp = new ArrayList();
+    Vector temp = new Vector();
 
     for (int i = 0; i < this.groups.size();i++)
     {
       SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
 
       if (sg.sequences.contains(s))
-       temp.add(sg);
+       temp.addElement(sg);
     }
 
     SequenceGroup [] ret = new SequenceGroup[temp.size()];
-    temp.toArray( ret );
+    for(int i=0; i<temp.size(); i++)
+      ret[i] = (SequenceGroup)temp.elementAt(i);
 
     return ret;
 
@@ -354,19 +358,19 @@ public class Alignment implements AlignmentI
 
   public void addSuperGroup(SuperGroup sg)
   {
-    superGroup.add(sg);
+    superGroup.addElement(sg);
   }
 
   public void removeSuperGroup(SuperGroup sg)
   {
-    superGroup.remove(sg);
+    superGroup.removeElement(sg);
   }
 
   public SuperGroup     getSuperGroup(SequenceGroup sg)
   {
     for (int i = 0; i < this.superGroup.size(); i++)
     {
-      SuperGroup temp = (SuperGroup) superGroup.get(i);
+      SuperGroup temp = (SuperGroup) superGroup.elementAt(i);
       if (temp.sequenceGroups.contains(sg))
         return temp;
     }
@@ -381,8 +385,8 @@ public class Alignment implements AlignmentI
 
   public void deleteAllGroups()
   {
-    groups.clear();
-    superGroup.clear();
+    groups.removeAllElements();
+    superGroup.removeAllElements();
    int i=0;
     while (i < sequences.size()) {
      SequenceI s = getSequenceAt(i);
@@ -477,12 +481,12 @@ public class Alignment implements AlignmentI
 
   public void setGapCharacter(char gc)
   {
-    char old = getGapCharacter();
     gapCharacter = gc;
     for (int i=0; i < sequences.size(); i++)
      {
        Sequence seq = (Sequence)sequences.elementAt(i);
-       seq.sequence = seq.sequence.replace(old, gc);
+       seq.sequence = seq.sequence.replace('.', gc);
+       seq.sequence = seq.sequence.replace('-', gc);
      }
   }
 
@@ -503,8 +507,52 @@ public class Alignment implements AlignmentI
         return false;
 
     return true;
+  }
+
+   public void deleteAnnotation(AlignmentAnnotation aa)
+   {
+     int aSize = 1;
+     if(annotations!=null)
+       aSize = annotations.length;
+
+     AlignmentAnnotation [] temp = new AlignmentAnnotation [aSize-1];
+
+     int tIndex = 0;
+     for (int i = 0; i < aSize; i++)
+      {
+        if(annotations[i]==aa)
+          continue;
+
+
+        temp[tIndex] = annotations[i];
+        tIndex++;
+      }
+
+     annotations = temp;
 
+   }
+
+  public void addAnnotation(AlignmentAnnotation aa)
+  {
+    int aSize = 1;
+    if(annotations!=null)
+      aSize = annotations.length+1;
+
+    AlignmentAnnotation [] temp = new AlignmentAnnotation [aSize];
+    int i=0;
+    if (aSize > 1)
+      for (i = 0; i < aSize-1; i++)
+        temp[i] = annotations[i];
+
+    temp[i] = aa;
+
+    annotations = temp;
   }
+  public AlignmentAnnotation[] getAlignmentAnnotation()
+  {
+    return annotations;
+  }
+
 }