X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSequenceIdMatcher.java;h=3ec162d440b8c426ff052b9bc21f9ca7d5c6ad10;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=0046cf565ce82b82a4303ba12d03ab0d022e4fcc;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 0046cf5..3ec162d 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -1,113 +1,174 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * 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.
- * 
+ * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.analysis;
 
-import java.util.*;
+import java.util.Locale;
+
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Vector;
 
 /**
- * <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
 {
-  private Hashtable names;
+  private HashMap<SeqIdName, SequenceI> names;
 
-  public SequenceIdMatcher(SequenceI[] seqs)
+  public SequenceIdMatcher(List<SequenceI> seqs)
+  {
+    names = new HashMap<SeqIdName, SequenceI>();
+    addAll(seqs);
+  }
+
+  /**
+   * Adds sequences to this matcher
+   * 
+   * @param seqs
+   */
+  public void addAll(List<SequenceI> seqs)
   {
-    names = new Hashtable();
-    for (int i = 0; i < seqs.length; i++)
+    for (SequenceI seq : seqs)
+    {
+      add(seq);
+    }
+  }
+
+  /**
+   * Adds one sequence to this matcher
+   * 
+   * @param seq
+   */
+  public void add(SequenceI seq)
+  {
+    // TODO: deal with ID collisions - SequenceI should be appended to list
+    // associated with this key.
+    names.put(new SeqIdName(seq.getDisplayId(true)), seq);
+    SequenceI dbseq = seq;
+    while (dbseq.getDatasetSequence() != null)
+    {
+      dbseq = dbseq.getDatasetSequence();
+    }
+    // add in any interesting identifiers
+    List<DBRefEntry> dbr = dbseq.getDBRefs(); 
+    if (dbr != null)
     {
-      names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
-      // add in any interesting identifiers
-      if (seqs[i].getDBRef() != null)
+      SeqIdName sid = null;
+      for (int r = 0, nr = dbr.size(); r < nr; r++)
       {
-        DBRefEntry dbr[] = seqs[i].getDBRef();
-        SeqIdName sid = null;
-        for (int r = 0; r < dbr.length; r++)
+        sid = new SeqIdName(dbr.get(r).getAccessionId());
+        if (!names.containsKey(sid))
         {
-          sid = new SeqIdName(dbr[r].getAccessionId());
-          if (!names.contains(sid))
-          {
-            names.put(sid, seqs[i]);
-          }
+          names.put(sid, seq);
         }
       }
     }
   }
 
   /**
+   * convenience method to make a matcher from concrete array
+   * 
+   * @param sequences
+   */
+  public SequenceIdMatcher(SequenceI[] sequences)
+  {
+    this(Arrays.asList(sequences));
+  }
+
+  /**
    * 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
+   *          List of SequenceI objects
    * @return SequenceI closest SequenceI to SeqIdName
    */
-  private SequenceI pickbestMatch(SeqIdName candName, Vector matches)
+  private SequenceI pickbestMatch(SeqIdName candName,
+          List<SequenceI> matches)
   {
-    SequenceI match = null;
+    List<SequenceI> st = pickbestMatches(candName, matches);
+    return st == null || st.size() == 0 ? null : st.get(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 List<SequenceI> pickbestMatches(SeqIdName candName,
+          List<SequenceI> matches)
+  {
+    ArrayList<SequenceI> best = new ArrayList<SequenceI>();
     if (candName == null || matches == null || matches.size() == 0)
     {
       return null;
     }
-    match = (SequenceI) matches.elementAt(0);
-    matches.removeElementAt(0);
+    SequenceI match = matches.remove(0);
+    best.add(match);
     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);
+      SequenceI cand = 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)
-              && candlen > matchlen)
+      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);
+      }
+    }
+    if (best.size() == 0)
+    {
+      return null;
     }
-    return match;
+    ;
+    return best;
   }
 
   /**
@@ -117,19 +178,38 @@ public class SequenceIdMatcher
    *          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.
+   * @return a new array or (possibly) null
+   */
+  public SequenceI[] findAllIdMatches(String seqnam)
+  {
+
+    SeqIdName nam = new SeqIdName(seqnam);
+    List<SequenceI> m = findAllIdMatches(nam);
+    if (m != null)
+    {
+      return m.toArray(new SequenceI[m.size()]);
+    }
+    return null;
+  }
+
+  /**
    * findIdMatch
    * 
    * Return pointers to sequences (or sequence object containers) which have
@@ -139,7 +219,7 @@ public class SequenceIdMatcher
    *          SequenceI[]
    * @return SequenceI[]
    */
-  SequenceI[] findIdMatch(SequenceI[] seqs)
+  public SequenceI[] findIdMatch(SequenceI[] seqs)
   {
     SequenceI[] namedseqs = null;
     int i = 0;
@@ -184,7 +264,26 @@ public class SequenceIdMatcher
     return pickbestMatch(nam, matches);
   }
 
-  private class SeqIdName
+  /**
+   * core findIdMatch search method for finding all equivalent matches
+   * 
+   * @param nam
+   *          SeqIdName
+   * @return SequenceI[]
+   */
+  private List<SequenceI> findAllIdMatches(
+          jalview.analysis.SequenceIdMatcher.SeqIdName nam)
+  {
+    ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
+    while (names.containsKey(nam))
+    {
+      matches.add(names.remove(nam));
+    }
+    List<SequenceI> r = pickbestMatches(nam, matches);
+    return r;
+  }
+
+  class SeqIdName
   {
     String id;
 
@@ -192,7 +291,7 @@ public class SequenceIdMatcher
     {
       if (s != null)
       {
-        id = new String(s);
+        id = s.toLowerCase(Locale.ROOT);
       }
       else
       {
@@ -200,23 +299,29 @@ public class SequenceIdMatcher
       }
     }
 
+    @Override
     public int hashCode()
     {
-      return ((id.length() >= 4) ? id.substring(0, 4).hashCode() : id
-              .hashCode());
+      return ((id.length() >= 4) ? id.substring(0, 4).hashCode()
+              : id.hashCode());
     }
 
+    @Override
     public boolean equals(Object s)
     {
+      if (s == null)
+      {
+        return false;
+      }
       if (s instanceof SeqIdName)
       {
-        return this.equals((SeqIdName) s);
+        return this.stringequals(((SeqIdName) s).id);
       }
       else
       {
         if (s instanceof String)
         {
-          return this.equals((String) s);
+          return this.stringequals(((String) s).toLowerCase(Locale.ROOT));
         }
       }
 
@@ -229,7 +334,8 @@ 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.
@@ -237,35 +343,33 @@ public class SequenceIdMatcher
      * todo: (JBPNote) Set separator characters appropriately
      * 
      * @param s
-     *          SeqIdName
      * @return boolean
      */
-    public boolean equals(SeqIdName s)
+    private boolean stringequals(String s)
     {
-      if (id.length() > s.id.length())
+      if (id.length() > s.length())
       {
-        return id.startsWith(s.id) ? (WORD_SEP.indexOf(id.charAt(s.id
-                .length())) > -1) : false;
+        return id.startsWith(s)
+                ? (WORD_SEP.indexOf(id.charAt(s.length())) > -1)
+                : false;
       }
       else
       {
-        return s.id.startsWith(id) ? (s.id.equals(id) ? true : (WORD_SEP
-                .indexOf(s.id.charAt(id.length())) > -1)) : false;
+        return s.startsWith(id)
+                ? (s.equals(id) ? true
+                        : (WORD_SEP.indexOf(s.charAt(id.length())) > -1))
+                : false;
       }
     }
 
-    public boolean equals(String s)
+    /**
+     * toString method returns the wrapped sequence id. For debugging purposes
+     * only, behaviour not guaranteed not to change.
+     */
+    @Override
+    public String toString()
     {
-      if (id.length() > s.length())
-      {
-        return id.startsWith(s) ? (WORD_SEP.indexOf(id.charAt(s.length())) > -1)
-                : false;
-      }
-      else
-      {
-        return s.startsWith(id) ? (s.equals(id) ? true : (WORD_SEP
-                .indexOf(s.charAt(id.length())) > -1)) : false;
-      }
+      return id;
     }
   }
 }