refactored to use SequenceI

[jalview.git] / src / jalview / analysis / SequenceIdMatcher.java

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 240f9cf..f878a09 100755 (executable)
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.analysis;
 
@@ -55,6 +54,20 @@ public class SequenceIdMatcher
     for (int i = 0; i < seqs.length; i++)
     {
       names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
+      // add in any interesting identifiers
+      if (seqs[i].getDBRef() != null)
+      {
+        DBRefEntry dbr[] = seqs[i].getDBRef();
+        SeqIdName sid = null;
+        for (int r = 0; r < dbr.length; r++)
+        {
+          sid = new SeqIdName(dbr[r].getAccessionId());
+          if (!names.contains(sid))
+          {
+            names.put(sid, seqs[i]);
+          }
+        }
+      }
     }
   }
 
@@ -63,9 +76,9 @@ public class SequenceIdMatcher
    * matches to the names hash.
    * 
    * @param candName
-   *                SeqIdName
+   *          SeqIdName
    * @param matches
-   *                Vector of SequenceI objects
+   *          Vector of SequenceI objects
    * @return SequenceI closest SequenceI to SeqIdName
    */
   private SequenceI pickbestMatch(SeqIdName candName, Vector matches)
@@ -101,16 +114,16 @@ public class SequenceIdMatcher
    * get SequenceI with closest SequenceI.getName() to seq.getName()
    * 
    * @param seq
-   *                SequenceI
+   *          SequenceI
    * @return SequenceI
    */
-  SequenceI findIdMatch(SequenceI seq)
+  public SequenceI findIdMatch(SequenceI seq)
   {
     SeqIdName nam = new SeqIdName(seq.getName());
     return findIdMatch(nam);
   }
 
-  SequenceI findIdMatch(String seqnam)
+  public SequenceI findIdMatch(String seqnam)
   {
     SeqIdName nam = new SeqIdName(seqnam);
     return findIdMatch(nam);
@@ -123,10 +136,10 @@ public class SequenceIdMatcher
    * same Id as a given set of different sequence objects
    * 
    * @param seqs
-   *                SequenceI[]
+   *          SequenceI[]
    * @return SequenceI[]
    */
-  SequenceI[] findIdMatch(SequenceI[] seqs)
+  public SequenceI[] findIdMatch(SequenceI[] seqs)
   {
     SequenceI[] namedseqs = null;
     int i = 0;
@@ -157,7 +170,7 @@ public class SequenceIdMatcher
    * core findIdMatch search method
    * 
    * @param nam
-   *                SeqIdName
+   *          SeqIdName
    * @return SequenceI
    */
   private SequenceI findIdMatch(
@@ -224,7 +237,7 @@ public class SequenceIdMatcher
      * todo: (JBPNote) Set separator characters appropriately
      * 
      * @param s
-     *                SeqIdName
+     *          SeqIdName
      * @return boolean
      */
     public boolean equals(SeqIdName s)