From: jprocter <Jim Procter>
Date: Tue, 10 Oct 2006 16:01:58 +0000 (+0000)
Subject: refined id matching to pick the closest match (by length) to the query and added... 
X-Git-Tag: Release_2_2~286
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7ae574fd34bd7ffd1ea23be7602d6b3dc57aa49f;p=jalview.git

refined id matching to pick the closest match (by length) to the query and added '_' to the list of word separators
---

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index ed90422..7c974e2 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -27,7 +27,9 @@ import jalview.datamodel.*;
  * SequenceIdMatcher
  * <p>Description: </p>
  * Routine which does approximate Sequence Id resolution by name using
- * string containment (on word boundaries) rather than equivalence
+ * string containment (on word boundaries) rather than equivalence. It also
+ * attempts to resolve ties where no exact match is available by picking the
+ * the id closest to the query.
  * <p>Copyright: Copyright (c) 2004</p>
  *
  * <p>Company: Dundee University</p>
@@ -47,31 +49,52 @@ public class SequenceIdMatcher
       names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
     }
   }
+  /**
+   * returns the closest SequenceI in matches to SeqIdName and returns all the matches
+   * to the names hash.
+   * @param candName SeqIdName
+   * @param matches Vector of SequenceI objects
+   * @return SequenceI closest SequenceI to SeqIdName
+   */
+  private SequenceI pickbestMatch(SeqIdName candName, Vector matches) {
+    SequenceI match=null;
+    if (candName==null || matches==null || matches.size()==0)
+      return null;
+    match=(SequenceI) matches.elementAt(0);
+    matches.removeElementAt(0);
+    names.put(new SeqIdName(match.getName()), match);
+    int matchlen=match.getName().length();
+    int namlen=candName.id.length();
+    while (matches.size()>0) {
+      // look through for a better one.
+      SequenceI cand=(SequenceI) matches.elementAt(0);
+      names.put(new SeqIdName(cand.getName()), cand);
+      int candlen = cand.getName().length();
+      // keep the one with an id 'closer' to the given seqnam string
+      if (Math.abs(matchlen-namlen)>Math.abs(candlen-namlen) && candlen>matchlen) {
+        match = cand;
+        matchlen = candlen;
+      }
+    }
+    return match;
+  }
 
+  /**
+   * get SequenceI with closest SequenceI.getName() to seq.getName()
+   * @param seq SequenceI
+   * @return SequenceI
+   */
   SequenceI findIdMatch(SequenceI seq)
   {
     SeqIdName nam = new SeqIdName(seq.getName());
-
-    if (names.containsKey(nam))
-    {
-      return (SequenceI) names.get(nam);
-    }
-
-    return null;
+    return findIdMatch(nam);
   }
 
   SequenceI findIdMatch(String seqnam)
-  {
-    SeqIdName nam = new SeqIdName(seqnam);
-
-    if (names.containsKey(nam))
     {
-      return (SequenceI) names.get(nam);
-    }
-
-    return null;
+      SeqIdName nam = new SeqIdName(seqnam);
+      return findIdMatch(nam);
   }
-
   /**
    * findIdMatch
    *
@@ -96,7 +119,7 @@ public class SequenceIdMatcher
 
         if (names.containsKey(nam))
         {
-          namedseqs[i] = (SequenceI) names.get(nam);
+          namedseqs[i] = findIdMatch(nam);
         }
         else
         {
@@ -109,6 +132,22 @@ public class SequenceIdMatcher
     return namedseqs;
   }
 
+  /**
+   * core findIdMatch search method
+   * @param nam SeqIdName
+   * @return SequenceI
+   */
+  private SequenceI findIdMatch(jalview.analysis.SequenceIdMatcher.SeqIdName
+                                nam)
+  {
+    Vector matches=new Vector();
+    while (names.containsKey(nam))
+    {
+      matches.addElement(names.remove(nam));
+    }
+    return pickbestMatch(nam, matches);
+  }
+
   private class SeqIdName
   {
     String id;
@@ -149,7 +188,7 @@ public class SequenceIdMatcher
      * JBPNote: This is a heuristic that will fail for arbritrarily extended sequence id's
      * (like portions of an aligned set of repeats from one sequence)
      */
-    private String WORD_SEP="~. |#\\/<>!\"£$%^*)}[@',?";
+    private String WORD_SEP="~. |#\\/<>!\"£$%^*)}[@',?_";
 
    /**
     * matches if one ID properly contains another at a whitespace boundary.