From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 7 Jul 2006 13:34:14 +0000 (+0000)
Subject: Redundant Remove Redundancy Removed
X-Git-Tag: Release_2_1~294
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c16afbb4d0e2672fdc54d32778b6d53f09c5d86c;p=jalview.git

Redundant Remove Redundancy Removed
---

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index b1f625d..daae7c5 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -277,56 +277,6 @@ public class Alignment implements AlignmentI
         sequences.removeElementAt(i);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param threshold DOCUMENT ME!
-     * @param sel DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    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++)
-            {
-                // Only do the comparison if either have not been deleted
-                if (!del.contains((SequenceI) sel.elementAt(i)) ||
-                        !del.contains((SequenceI) sel.elementAt(j)))
-                {
-                    // use PID instead of Comparison (which is really not pleasant)
-                    float pid = Comparison.PID((SequenceI) sel.elementAt(j),
-                            (SequenceI) sel.elementAt(i));
-
-                    if (pid >= threshold)
-                    {
-                        // Delete the shortest one
-                        if (((SequenceI) sel.elementAt(j)).getSequence().length() > ((SequenceI) sel
-                                                                                         .elementAt(
-                                    i)).getSequence().length())
-                        {
-                            del.addElement(sel.elementAt(i));
-                        }
-                        else
-                        {
-                            del.addElement(sel.elementAt(i));
-                        }
-                    }
-                }
-            }
-        }
-
-        // Now delete the sequences
-        for (int i = 0; i < del.size(); i++)
-        {
-            deleteSequence((SequenceI) del.elementAt(i));
-        }
-
-        return del;
-    }
 
     /**    */
     public SequenceGroup findGroup(int i)
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index e14c1e9..19b5b1c 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -161,15 +161,6 @@ public interface AlignmentI
      */
     public void removeGaps();
 
-    /**
-     * Removes redundant sequences from alignment.
-     *
-     * @param threshold Remove all sequences above the given threshold.
-     * @param sel Set of sequences which will have redundant sequences removed from.
-     *
-     * @return All sequences below redundancy threshold.
-     */
-    public Vector removeRedundancy(float threshold, Vector sel);
 
     /**
      * Finds group that sequence at index i in alignment is part of.