X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=10e2766580e9b93626d49e15f965b50b379d717d;hb=1a6fbadeec90e7524075ed6e37bbe4b7bba97a94;hp=dd02bc12626f3b396b3109ee24a6a0aa92747c9d;hpb=2cf0e6316cf8b4e545bad1648966b02fad49017f;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index dd02bc1..10e2766 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -11,7 +11,12 @@ public class Alignment implements AlignmentI
 
   protected Vector      sequences;
   protected Vector      groups = new Vector();
-  protected char      gapCharacter = '-';
+  protected ArrayList   superGroup = new ArrayList();
+  protected char        gapCharacter = '-';
+  public AlignmentAnnotation [] annotations;
+  public Conservation conservation;
+
+  public boolean featuresAdded = false;
 
   /** Make an alignment from an array of Sequences.
   *
@@ -39,14 +44,11 @@ public class Alignment implements AlignmentI
   }
 
   /** Adds a sequence to the alignment.  Recalculates maxLength and size.
-   * Should put the new sequence in a sequence group!!!
    *
    * @param snew
    */
   public void addSequence(SequenceI snew) {
     sequences.addElement(snew);
-
-    ((SequenceGroup)groups.lastElement()).addSequence(snew);
   }
 
   public void addSequence(SequenceI[] seq) {
@@ -56,8 +58,7 @@ public class Alignment implements AlignmentI
   }
 
   /** Adds a sequence to the alignment.  Recalculates maxLength and size.
-   * Should put the new sequence in a sequence group!!!
-   *
+    *
    * @param snew
    */
   public void setSequenceAt(int i,SequenceI snew) {
@@ -65,8 +66,6 @@ public class Alignment implements AlignmentI
     deleteSequence(oldseq);
 
     sequences.setElementAt(snew,i);
-
-    ((SequenceGroup)groups.lastElement()).addSequence(snew);
   }
 
   public Vector getGroups() {
@@ -328,6 +327,7 @@ public class Alignment implements AlignmentI
     for (int i = 0; i < this.groups.size();i++)
     {
       SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
+
       if (sg.sequences.contains(s))
        temp.add(sg);
     }
@@ -356,17 +356,45 @@ public class Alignment implements AlignmentI
     }
   }
 
+  public void addSuperGroup(SuperGroup sg)
+  {
+    superGroup.add(sg);
+  }
+
+  public void removeSuperGroup(SuperGroup sg)
+  {
+    superGroup.remove(sg);
+  }
+
+  public SuperGroup     getSuperGroup(SequenceGroup sg)
+  {
+    for (int i = 0; i < this.superGroup.size(); i++)
+    {
+      SuperGroup temp = (SuperGroup) superGroup.get(i);
+      if (temp.sequenceGroups.contains(sg))
+        return temp;
+    }
+    return null;
+  }
+
   /**    */
   public void addGroup(SequenceGroup sg) {
     if(!groups.contains(sg))
       groups.addElement(sg);
   }
 
-  /**    */
-  public SequenceGroup addGroup() {
-    SequenceGroup sg = new SequenceGroup();
-    groups.addElement(sg);
-    return sg;
+  public void deleteAllGroups()
+  {
+    groups.clear();
+    superGroup.clear();
+   int i=0;
+    while (i < sequences.size()) {
+     SequenceI s = getSequenceAt(i);
+     s.setColor(java.awt.Color.white);
+     i++;
+   }
+
+
   }
 
   /**    */
@@ -470,6 +498,61 @@ public class Alignment implements AlignmentI
   {
     return AAFrequency.calculate(sequences, 0, getWidth());
   }
+
+  public boolean isAligned()
+  {
+    int width = getWidth();
+    for (int i = 0; i < sequences.size(); i++)
+      if (getSequenceAt(i).getLength() != width)
+        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;
+  }
+
 }