From 204617b73ee07ba28dcec3ffdf6b8e8eb2062011 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Thu, 19 Feb 2015 15:00:03 +0000
Subject: [PATCH] JAL-1115 JAL-653 partial introduction of List interface for
 sequence matcher

---
 src/jalview/analysis/SequenceIdMatcher.java |   79 ++++++++++++++++++---------
 1 file changed, 53 insertions(+), 26 deletions(-)

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index e6a4853..5b812dd 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -24,7 +24,9 @@ import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
 
 import java.util.ArrayList;
-import java.util.Hashtable;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
 import java.util.Vector;
 
 /**
@@ -35,17 +37,27 @@ import java.util.Vector;
  */
 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]);
-      SequenceI dbseq = seqs[i];
+      names.put(new SeqIdName(seq.getDisplayId(true)), seq);
+      SequenceI dbseq = seq;
       while (dbseq.getDatasetSequence()!=null)
       {
         dbseq = dbseq.getDatasetSequence();
@@ -58,9 +70,9 @@ public class SequenceIdMatcher
         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);
           }
         }
       }
@@ -68,19 +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);
   }
 
   /**
@@ -94,16 +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();
@@ -111,8 +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
@@ -136,7 +157,7 @@ public class SequenceIdMatcher
       return null;
     }
     ;
-    return (SequenceI[]) best.toArray(new SequenceI[0]);
+    return best;
   }
 
   /**
@@ -163,12 +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;
   }
 
   /**
@@ -233,15 +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;
   }
 
-- 
1.7.10.2