X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSequenceIdMatcher.java;h=c029ea970b26f2163a4ed1ae6090df6c8fb58416;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=1285f6c1355e6fa39701c444a4c5726e7cacd6b0;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 1285f6c..c029ea9 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -1,26 +1,33 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 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;
 
 /**
  * Routines for approximate Sequence Id resolution by name using string
@@ -30,27 +37,42 @@ import jalview.datamodel.*;
  */
 public class SequenceIdMatcher
 {
-  private Hashtable names;
+  private HashMap<SeqIdName, SequenceI> names;
 
-  public SequenceIdMatcher(SequenceI[] seqs)
+  public SequenceIdMatcher(List<SequenceI> seqs)
   {
-    names = new Hashtable();
-    for (int i = 0; i < seqs.length; i++)
+    names = new HashMap<SeqIdName, SequenceI>();
+    addAll(seqs);
+  }
+
+  /**
+   * add more sequences to this matcher - also used by the constructor
+   * 
+   * @param seqs
+   */
+  public void addAll(List<SequenceI> seqs)
+  {
+    for (SequenceI seq : seqs)
     {
       // 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]);
+      names.put(new SeqIdName(seq.getDisplayId(true)), seq);
+      SequenceI dbseq = seq;
+      while (dbseq.getDatasetSequence() != null)
+      {
+        dbseq = dbseq.getDatasetSequence();
+      }
       // add in any interesting identifiers
-      if (seqs[i].getDBRef() != null)
+      if (dbseq.getDBRef() != null)
       {
-        DBRefEntry dbr[] = seqs[i].getDBRef();
+        DBRefEntry dbr[] = dbseq.getDBRef();
         SeqIdName sid = null;
         for (int r = 0; r < dbr.length; r++)
         {
           sid = new SeqIdName(dbr[r].getAccessionId());
-          if (!names.contains(sid))
+          if (!names.containsKey(sid))
           {
-            names.put(sid, seqs[i]);
+            names.put(sid, seq);
           }
         }
       }
@@ -58,19 +80,30 @@ public class SequenceIdMatcher
   }
 
   /**
+   * 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[] st = pickbestMatches(candName, matches);
-    return st == null || st.length == 0 ? null : st[0];
+    List<SequenceI> st = pickbestMatches(candName, matches);
+    return st == null || st.size() == 0 ? null : st.get(0);
   }
 
   /**
@@ -84,16 +117,15 @@ public class SequenceIdMatcher
    * @return Object[] { SequenceI closest SequenceI to SeqIdName, SequenceI[]
    *         ties }
    */
-  private SequenceI[] pickbestMatches(SeqIdName candName, Vector matches)
+  private List<SequenceI> pickbestMatches(SeqIdName candName,
+          List<SequenceI> matches)
   {
-    ArrayList best = new ArrayList();
-    SequenceI match = null;
+    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();
@@ -101,8 +133,7 @@ public class SequenceIdMatcher
     while (matches.size() > 0)
     {
       // look through for a better one.
-      SequenceI cand = (SequenceI) matches.elementAt(0);
-      matches.remove(0);
+      SequenceI cand = matches.remove(0);
       names.put(new SeqIdName(cand.getName()), cand);
       int q, w, candlen = cand.getName().length();
       // keep the one with an id 'closer' to the given seqnam string
@@ -126,7 +157,7 @@ public class SequenceIdMatcher
       return null;
     }
     ;
-    return (SequenceI[]) best.toArray(new SequenceI[0]);
+    return best;
   }
 
   /**
@@ -153,12 +184,18 @@ public class SequenceIdMatcher
    * 
    * @param seqnam
    *          string to query Matcher with.
+   * @return a new array or (possibly) null
    */
   public SequenceI[] findAllIdMatches(String seqnam)
   {
 
     SeqIdName nam = new SeqIdName(seqnam);
-    return findAllIdMatches(nam);
+    List<SequenceI> m = findAllIdMatches(nam);
+    if (m != null)
+    {
+      return m.toArray(new SequenceI[m.size()]);
+    }
+    return null;
   }
 
   /**
@@ -223,15 +260,15 @@ public class SequenceIdMatcher
    *          SeqIdName
    * @return SequenceI[]
    */
-  private SequenceI[] findAllIdMatches(
+  private List<SequenceI> findAllIdMatches(
           jalview.analysis.SequenceIdMatcher.SeqIdName nam)
   {
-    Vector matches = new Vector();
+    ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
     while (names.containsKey(nam))
     {
-      matches.addElement(names.remove(nam));
+      matches.add(names.remove(nam));
     }
-    SequenceI[] r = pickbestMatches(nam, matches);
+    List<SequenceI> r = pickbestMatches(nam, matches);
     return r;
   }
 
@@ -251,14 +288,20 @@ public class SequenceIdMatcher
       }
     }
 
+    @Override
     public int 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);