From a9570778f83fa5a2138205488da1d20049acdecf Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 5 Jan 2011 16:06:36 +0000
Subject: [PATCH] more robust calculation of partition from possibly
 overlapping groups, and check to ensure minimum group size
 is honoured

---
 .../ws/rest/params/SeqGroupIndexVector.java        |   97 ++++++++++++--------
 1 file changed, 61 insertions(+), 36 deletions(-)

diff --git a/src/jalview/ws/rest/params/SeqGroupIndexVector.java b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
index 37d2789..4e7026e 100644
--- a/src/jalview/ws/rest/params/SeqGroupIndexVector.java
+++ b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
@@ -17,25 +17,39 @@ import org.apache.http.entity.mime.content.ContentBody;
 import org.apache.http.entity.mime.content.StringBody;
 
 /**
- * Represents the partitions defined on the alignment as indices
- * e.g. for a partition (A,B,C),(D,E),(F)
- * The indices would be 3,2,1. Note, the alignment must be ordered so groups are contiguous before this input type can be used.
+ * Represents the partitions defined on the alignment as indices e.g. for a
+ * partition (A,B,C),(D,E),(F) The indices would be 3,2,1. Note, the alignment
+ * must be ordered so groups are contiguous before this input type can be used.
+ * 
  * @author JimP
- *
+ * 
  */
-public class SeqGroupIndexVector extends InputType implements AlignmentProcessor{
+public class SeqGroupIndexVector extends InputType implements
+        AlignmentProcessor
+{
   public SeqGroupIndexVector()
   {
-    super(new Class[] { AlignmentI.class} );
+    super(new Class[]
+    { AlignmentI.class });
   }
+
   /**
    * separator for list of sequence Indices - default is ','
    */
-  public String sep=",";
+  public String sep = ",";
+
+  /**
+   * min size of each partition
+   */
+  public int minsize = 1;
+
   molType type;
+
   /**
    * prepare the context alignment for this input
-   * @param al - alignment to be processed
+   * 
+   * @param al
+   *          - alignment to be processed
    * @return al or a new alignment with appropriate attributes/order for input
    */
   public AlignmentI prepareAlignment(AlignmentI al)
@@ -43,57 +57,68 @@ public class SeqGroupIndexVector extends InputType implements AlignmentProcessor
     jalview.analysis.AlignmentSorter.sortByGroup(al);
     return al;
   }
+
   @Override
-  public ContentBody formatForInput(RestJob rj) throws UnsupportedEncodingException, NoValidInputDataException
+  public ContentBody formatForInput(RestJob rj)
+          throws UnsupportedEncodingException, NoValidInputDataException
   {
     StringBuffer idvector = new StringBuffer();
-    boolean list=false;
+    boolean list = false;
     AlignmentI al = rj.getAlignmentForInput(token, type);
-    // assume that alignment is properly ordered so groups form consecutive blocks
+    // assume that alignment is properly ordered so groups form consecutive
+    // blocks
     ArrayList<int[]> gl = new ArrayList<int[]>();
-    for (SequenceGroup sg : (Vector<SequenceGroup>)al.getGroups())
+    for (SequenceGroup sg : (Vector<SequenceGroup>) al.getGroups())
     {
-      // TODO: refactor to sequenceGroup for efficiency - getAlignmentRowInterval(AlignmentI al)
-      int[] se=null;
-      for (SequenceI sq: sg.getSequencesInOrder(al))
+      if (sg.getSize()<minsize)
+      {
+        throw new NoValidInputDataException("Group contains less than "+minsize+" sequences.");
+      }
+      // TODO: refactor to sequenceGroup for efficiency -
+      // getAlignmentRowInterval(AlignmentI al)
+      int[] se = null;
+      for (SequenceI sq : sg.getSequencesInOrder(al))
       {
         int p = al.findIndex(sq);
-        if (se==null)
+        if (se == null)
         {
-          se=new int[] { p, p};
+          se = new int[]
+          { p, p };
         }
-        else {
-          if (p<se[0])
-            se[0]=p;
-          if (p>se[1])
-            se[1]=p;
+        else
+        {
+          if (p < se[0])
+            se[0] = p;
+          if (p > se[1])
+            se[1] = p;
         }
       }
-      if (se!=null)
+      if (se != null)
       {
         gl.add(se);
       }
     }
     int[][] vals = gl.toArray(new int[gl.size()][]);
     int[] srt = new int[gl.size()];
-    for (int i=0;i<vals.length;i++)
-      srt[i]=vals[i][0];
+    for (int i = 0; i < vals.length; i++)
+      srt[i] = vals[i][0];
     jalview.util.QuickSort.sort(srt, vals);
-    list=false;
-    int last=vals[0][0]-1;
-    for (int[] range:vals)
+    list = false;
+    int last = vals[0][0] - 1;
+    for (int[] range : vals)
     {
-      if (range[1]>last) {
-        if (list)
+      if (range[1] > last)
       {
-        idvector.append(sep);
-      }
-      idvector.append(range[1]-last);
-      last=range[1];
-      list=true;
+        if (list)
+        {
+          idvector.append(sep);
+        }
+        idvector.append(range[1] - last);
+        last = range[1];
+        list = true;
       }
     }
     return new StringBody(idvector.toString());
   }
-  
+
 }
\ No newline at end of file
-- 
1.7.10.2