refined id matching to pick the closest match (by length) to the query and added...

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