X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSequenceIdMatcher.java;h=0744937743bcba699e34bc0421f06133144b08ca;hb=d4b1e4d0c74b1c6d0f3c3556b10be91a6aaea475;hp=7c974e26873a4dc72bb95abd3f71100be68f9e6d;hpb=7ae574fd34bd7ffd1ea23be7602d6b3dc57aa49f;p=jalview.git

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 7c974e2..0744937 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, 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
@@ -49,6 +49,7 @@ public class SequenceIdMatcher
       names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
     }
   }
+
   /**
    * returns the closest SequenceI in matches to SeqIdName and returns all the matches
    * to the names hash.
@@ -56,22 +57,28 @@ public class SequenceIdMatcher
    * @param matches Vector of SequenceI objects
    * @return SequenceI closest SequenceI to SeqIdName
    */
-  private SequenceI pickbestMatch(SeqIdName candName, Vector matches) {
-    SequenceI match=null;
-    if (candName==null || matches==null || matches.size()==0)
+  private SequenceI pickbestMatch(SeqIdName candName, Vector matches)
+  {
+    SequenceI match = null;
+    if (candName == null || matches == null || matches.size() == 0)
+    {
       return null;
-    match=(SequenceI) matches.elementAt(0);
+    }
+    match = (SequenceI) matches.elementAt(0);
     matches.removeElementAt(0);
     names.put(new SeqIdName(match.getName()), match);
-    int matchlen=match.getName().length();
-    int namlen=candName.id.length();
-    while (matches.size()>0) {
+    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 = (SequenceI) matches.elementAt(0);
       names.put(new SeqIdName(cand.getName()), cand);
       int 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 (Math.abs(matchlen - namlen) > Math.abs(candlen - namlen) &&
+          candlen > matchlen)
+      {
         match = cand;
         matchlen = candlen;
       }
@@ -91,10 +98,11 @@ public class SequenceIdMatcher
   }
 
   SequenceI findIdMatch(String seqnam)
-    {
-      SeqIdName nam = new SeqIdName(seqnam);
-      return findIdMatch(nam);
+  {
+    SeqIdName nam = new SeqIdName(seqnam);
+    return findIdMatch(nam);
   }
+
   /**
    * findIdMatch
    *
@@ -140,7 +148,7 @@ public class SequenceIdMatcher
   private SequenceI findIdMatch(jalview.analysis.SequenceIdMatcher.SeqIdName
                                 nam)
   {
-    Vector matches=new Vector();
+    Vector matches = new Vector();
     while (names.containsKey(nam))
     {
       matches.addElement(names.remove(nam));
@@ -154,15 +162,19 @@ public class SequenceIdMatcher
 
     SeqIdName(String s)
     {
-      if (s!=null)
+      if (s != null)
+      {
         id = new String(s);
+      }
       else
+      {
         id = "";
+      }
     }
 
     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());
     }
 
     public boolean equals(Object s)
@@ -188,39 +200,47 @@ public class SequenceIdMatcher
      * JBPNote: This is a heuristic that will fail for arbritrarily extended sequence id's
      * (like portions of an aligned set of repeats from one sequence)
      */
-    private String WORD_SEP="~. |#\\/<>!\"£$%^*)}[@',?_";
-
-   /**
-    * matches if one ID properly contains another at a whitespace boundary.
-    * TODO: (JBPNote) These are not efficient. should use char[] for speed
-    * todo: (JBPNote) Set separator characters appropriately
-    * @param s SeqIdName
-    * @return boolean
-    */
+    private String WORD_SEP = "~. |#\\/<>!\"£$%^*)}[@',?_";
+
+    /**
+     * matches if one ID properly contains another at a whitespace boundary.
+     * TODO: (JBPNote) These are not efficient. should use char[] for speed
+     * todo: (JBPNote) Set separator characters appropriately
+     * @param s SeqIdName
+     * @return boolean
+     */
     public boolean equals(SeqIdName s)
     {
-      if (id.length()>s.id.length()) {
+      if (id.length() > s.id.length())
+      {
         return id.startsWith(s.id) ?
-            (WORD_SEP.indexOf(id.charAt(s.id.length()))>-1)
+            (WORD_SEP.indexOf(id.charAt(s.id.length())) > -1)
             : false;
-      } else
+      }
+      else
+      {
         return s.id.startsWith(id) ?
             (s.id.equals(id) ? true :
-             (WORD_SEP.indexOf(s.id.charAt(id.length()))>-1))
+             (WORD_SEP.indexOf(s.id.charAt(id.length())) > -1))
             : false;
+      }
     }
 
     public boolean equals(String s)
     {
-      if (id.length()>s.length()) {
+      if (id.length() > s.length())
+      {
         return id.startsWith(s) ?
-            (WORD_SEP.indexOf(id.charAt(s.length()))>-1)
+            (WORD_SEP.indexOf(id.charAt(s.length())) > -1)
             : false;
-      } else
+      }
+      else
+      {
         return s.startsWith(id) ?
             (s.equals(id) ? true :
-             (WORD_SEP.indexOf(s.charAt(id.length()))>-1))
+             (WORD_SEP.indexOf(s.charAt(id.length())) > -1))
             : false;
+      }
     }
   }
 }