X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSequenceIdMatcher.java;h=aec7fafa799f854663f798d85e23f427ed16a6fe;hb=47168f025aefdaa044802bd5f8f510ffe43a4808;hp=56b760a59da440099c38598ea4856019db640400;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 56b760a..aec7faf 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -1,20 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * 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.
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.analysis;
 
@@ -23,27 +25,10 @@ import java.util.*;
 import jalview.datamodel.*;
 
 /**
- * <p>
- * Title:
- * </p>
- * SequenceIdMatcher
- * <p>
- * Description:
- * </p>
- * Routine which does approximate Sequence Id resolution by name using string
+ * Routines for approximate Sequence Id resolution by name using 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>
- * 
- * @author not attributable
- * @version 1.0
  */
 public class SequenceIdMatcher
 {
@@ -54,13 +39,15 @@ public class SequenceIdMatcher
     names = new Hashtable();
     for (int i = 0; i < seqs.length; i++)
     {
-      names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
+      // TODO: deal with ID collisions - SequenceI should be appended to list
+      // associated with this key.
+      names.put(new SeqIdName(seqs[i].getDisplayId(true)), seqs[i]);
       // add in any interesting identifiers
-      if (seqs[i].getDBRef()!=null)
+      if (seqs[i].getDBRef() != null)
       {
         DBRefEntry dbr[] = seqs[i].getDBRef();
-        SeqIdName sid=null;
-        for (int r=0;r<dbr.length;r++)
+        SeqIdName sid = null;
+        for (int r = 0; r < dbr.length; r++)
         {
           sid = new SeqIdName(dbr[r].getAccessionId());
           if (!names.contains(sid))
@@ -77,13 +64,31 @@ 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)
   {
+    SequenceI[] st = pickbestMatches(candName, matches);
+    return st == null || st.length == 0 ? null : st[0];
+  }
+
+  /**
+   * 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 Object[] { SequenceI closest SequenceI to SeqIdName, SequenceI[]
+   *         ties }
+   */
+  private SequenceI[] pickbestMatches(SeqIdName candName, Vector matches)
+  {
+    ArrayList best = new ArrayList();
     SequenceI match = null;
     if (candName == null || matches == null || matches.size() == 0)
     {
@@ -91,6 +96,7 @@ public class SequenceIdMatcher
     }
     match = (SequenceI) matches.elementAt(0);
     matches.removeElementAt(0);
+    best.add(match);
     names.put(new SeqIdName(match.getName()), match);
     int matchlen = match.getName().length();
     int namlen = candName.id.length();
@@ -98,49 +104,76 @@ public class SequenceIdMatcher
     {
       // look through for a better one.
       SequenceI cand = (SequenceI) matches.elementAt(0);
+      matches.remove(0);
       names.put(new SeqIdName(cand.getName()), cand);
-      int candlen = cand.getName().length();
+      int q, w, 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)
+      if ((q = Math.abs(matchlen - namlen)) > (w = Math.abs(candlen
+              - namlen))
               && candlen > matchlen)
       {
+        best.clear();
         match = cand;
         matchlen = candlen;
+        best.add(match);
+      }
+      if (q == w && candlen == matchlen)
+      {
+        // record any ties
+        best.add(cand);
       }
     }
-    return match;
+    if (best.size() == 0)
+    {
+      return null;
+    }
+    ;
+    return (SequenceI[]) best.toArray(new SequenceI[0]);
   }
 
   /**
    * 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);
   }
 
   /**
+   * Find all matches for a given sequence name.
+   * 
+   * @param seqnam
+   *          string to query Matcher with.
+   */
+  public SequenceI[] findAllIdMatches(String seqnam)
+  {
+
+    SeqIdName nam = new SeqIdName(seqnam);
+    return findAllIdMatches(nam);
+  }
+
+  /**
    * findIdMatch
    * 
    * Return pointers to sequences (or sequence object containers) which have
    * 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;
@@ -171,7 +204,7 @@ public class SequenceIdMatcher
    * core findIdMatch search method
    * 
    * @param nam
-   *                SeqIdName
+   *          SeqIdName
    * @return SequenceI
    */
   private SequenceI findIdMatch(
@@ -185,6 +218,25 @@ public class SequenceIdMatcher
     return pickbestMatch(nam, matches);
   }
 
+  /**
+   * core findIdMatch search method for finding all equivalent matches
+   * 
+   * @param nam
+   *          SeqIdName
+   * @return SequenceI[]
+   */
+  private SequenceI[] findAllIdMatches(
+          jalview.analysis.SequenceIdMatcher.SeqIdName nam)
+  {
+    Vector matches = new Vector();
+    while (names.containsKey(nam))
+    {
+      matches.addElement(names.remove(nam));
+    }
+    SequenceI[] r = pickbestMatches(nam, matches);
+    return r;
+  }
+
   private class SeqIdName
   {
     String id;
@@ -230,7 +282,8 @@ public class SequenceIdMatcher
      * arbritrarily extended sequence id's (like portions of an aligned set of
      * repeats from one sequence)
      */
-    private String WORD_SEP = "~. |#\\/<>!\"£$%^*)}[@',?_";
+    private String WORD_SEP = "~. |#\\/<>!\"" + ((char) 0x00A4)
+            + "$%^*)}[@',?_";
 
     /**
      * matches if one ID properly contains another at a whitespace boundary.
@@ -238,11 +291,13 @@ public class SequenceIdMatcher
      * todo: (JBPNote) Set separator characters appropriately
      * 
      * @param s
-     *                SeqIdName
+     *          SeqIdName
      * @return boolean
      */
     public boolean equals(SeqIdName s)
     {
+      // TODO: JAL-732 patch for cases when name includes a list of IDs, and the
+      // match contains one ID flanked
       if (id.length() > s.id.length())
       {
         return id.startsWith(s.id) ? (WORD_SEP.indexOf(id.charAt(s.id