X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=10e2766580e9b93626d49e15f965b50b379d717d;hb=c59fb56cb143b05c5643a71f5b39996ac1cd2fef;hp=abf48742bd3c8207cc3fdfc5e346b0bf63a2fd0a;hpb=5070eb1dd71c2f7d0f35bfac180326ab04b21a8b;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index abf4874..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() {
@@ -112,7 +111,7 @@ public class Alignment implements AlignmentI
         if (current.getLength() > i)
         {
 	    /* MC Should move this to a method somewhere */
-          if (current.getCharAt(i)!='-' && current.getCharAt(i)!='.' && current.getCharAt(i)!=' ')
+          if ( !jalview.util.Comparison.isGap(current.getCharAt(i)))
             delete = false;
 
         }
@@ -217,35 +216,34 @@ public class Alignment implements AlignmentI
   public Vector removeRedundancy(float threshold, Vector sel) {
     Vector del = new Vector();
 
-    for (int i=1; i < sel.size(); i++) {
-      for (int j = 0; j < i; j++) {
+    for (int i = 1; i < sel.size(); i++)
+    {
+      for (int j = 0; j < i; j++)
+      {
         // Only do the comparison if either have not been deleted
-        if (!del.contains((SequenceI)sel.elementAt(i)) ||
-            !del.contains((SequenceI)sel.elementAt(j))) {
+        if (!del.contains( (SequenceI) sel.elementAt(i)) ||
+            !del.contains( (SequenceI) sel.elementAt(j)))
+        {
 
-          float pid = Comparison.compare((SequenceI)sel.elementAt(j),
-                                         (SequenceI)sel.elementAt(i));
+          float pid = Comparison.compare( (SequenceI) sel.elementAt(j),
+                                         (SequenceI) sel.elementAt(i));
 
-          if (pid >= threshold) {
+          if (pid >= threshold)
+          {
             // Delete the shortest one
-            if (((SequenceI)sel.elementAt(j)).getSequence().length() >
-                ((SequenceI)sel.elementAt(i)).getSequence().length()) {
+            if ( ( (SequenceI) sel.elementAt(j)).getSequence().length() >
+                ( (SequenceI) sel.elementAt(i)).getSequence().length())
               del.addElement(sel.elementAt(i));
-              System.out.println("Deleting sequence " + ((SequenceI)sel.elementAt(i)).getName());
-            } else {
+            else
               del.addElement(sel.elementAt(i));
-              System.out.println("Deleting sequence " + ((SequenceI)sel.elementAt(i)).getName());
-            }
           }
         }
       }
     }
 
     // Now delete the sequences
-    for (int i=0; i < del.size(); i++) {
-      System.out.println("Deleting sequence " + ((SequenceI)del.elementAt(i)).getName());
+    for (int i=0; i < del.size(); i++)
       deleteSequence((SequenceI)del.elementAt(i));
-    }
 
     return del;
   }
@@ -319,6 +317,25 @@ public class Alignment implements AlignmentI
 
     }
     return null;
+  }
+
+  public SequenceGroup [] findAllGroups(SequenceI s)
+  {
+
+    ArrayList temp = new ArrayList();
+
+    for (int i = 0; i < this.groups.size();i++)
+    {
+      SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
+
+      if (sg.sequences.contains(s))
+       temp.add(sg);
+    }
+
+    SequenceGroup [] ret = new SequenceGroup[temp.size()];
+    temp.toArray( ret );
+
+    return ret;
 
   }
   /**    */
@@ -339,17 +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++;
+   }
+
+
   }
 
   /**    */
@@ -386,12 +431,14 @@ public class Alignment implements AlignmentI
   }
 
   /**    */
-  public int findIndex(SequenceI s) {
+  public int findIndex(SequenceI s)
+  {
     int i=0;
-    while (i < sequences.size()) {
-      if (s == getSequenceAt(i)) {
+    while (i < sequences.size())
+    {
+      if (s == getSequenceAt(i))
         return i;
-      }
+
       i++;
     }
     return -1;
@@ -451,6 +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;
+  }
+
 }