formatting

[jalview.git] / src / jalview / analysis / SequenceIdMatcher.java

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 4b1900c..eb912c8 100755 (executable)
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -36,7 +36,8 @@ public class SequenceIdMatcher
     names = new Hashtable();
     for (int i = 0; i < seqs.length; i++)
     {
-      // TODO: deal with ID collisions - SequenceI should be appended to list associated with this key.
+      // 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)
@@ -67,9 +68,10 @@ public class SequenceIdMatcher
    */
   private SequenceI pickbestMatch(SeqIdName candName, Vector matches)
   {
-    SequenceI[] st= pickbestMatches(candName, matches);
-    return st==null || st.length==0 ? null : st[0];
+    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.
@@ -78,11 +80,12 @@ public class SequenceIdMatcher
    *          SeqIdName
    * @param matches
    *          Vector of SequenceI objects
-   * @return Object[] { SequenceI closest SequenceI to SeqIdName, SequenceI[] ties }
+   * @return Object[] { SequenceI closest SequenceI to SeqIdName, SequenceI[]
+   *         ties }
    */
   private SequenceI[] pickbestMatches(SeqIdName candName, Vector matches)
   {
-    ArrayList best=new ArrayList();
+    ArrayList best = new ArrayList();
     SequenceI match = null;
     if (candName == null || matches == null || matches.size() == 0)
     {
@@ -100,9 +103,10 @@ public class SequenceIdMatcher
       SequenceI cand = (SequenceI) matches.elementAt(0);
       matches.remove(0);
       names.put(new SeqIdName(cand.getName()), cand);
-      int q,w,candlen = cand.getName().length();
+      int q, w, candlen = cand.getName().length();
       // keep the one with an id 'closer' to the given seqnam string
-      if ((q=Math.abs(matchlen - namlen)) > (w=Math.abs(candlen - namlen))
+      if ((q = Math.abs(matchlen - namlen)) > (w = Math.abs(candlen
+              - namlen))
               && candlen > matchlen)
       {
         best.clear();
@@ -110,13 +114,17 @@ public class SequenceIdMatcher
         matchlen = candlen;
         best.add(match);
       }
-      if (q==w && candlen==matchlen)
+      if (q == w && candlen == matchlen)
       {
         // record any ties
         best.add(cand);
       }
     }
-    if (best.size()==0) { return null; };
+    if (best.size() == 0)
+    {
+      return null;
+    }
+    ;
     return (SequenceI[]) best.toArray(new SequenceI[0]);
   }
 
@@ -140,8 +148,10 @@ public class SequenceIdMatcher
   }
 
   /**
-   *  Find all matches for a given sequence name.
-   *  @param seqnam string to query Matcher with.
+   * Find all matches for a given sequence name.
+   * 
+   * @param seqnam
+   *          string to query Matcher with.
    */
   public SequenceI[] findAllIdMatches(String seqnam)
   {
@@ -204,6 +214,7 @@ public class SequenceIdMatcher
     }
     return pickbestMatch(nam, matches);
   }
+
   /**
    * core findIdMatch search method for finding all equivalent matches
    * 
@@ -219,11 +230,10 @@ public class SequenceIdMatcher
     {
       matches.addElement(names.remove(nam));
     }
-    SequenceI[] r=pickbestMatches(nam, matches);
+    SequenceI[] r = pickbestMatches(nam, matches);
     return r;
   }
 
-
   private class SeqIdName
   {
     String id;
@@ -269,7 +279,8 @@ public class SequenceIdMatcher
      * arbritrarily extended sequence id's (like portions of an aligned set of
      * repeats from one sequence)
      */
-    private String WORD_SEP = "~. |#\\/<>!\""+((char)0x00A4)+"$%^*)}[@',?_";
+    private String WORD_SEP = "~. |#\\/<>!\"" + ((char) 0x00A4)
+            + "$%^*)}[@',?_";
 
     /**
      * matches if one ID properly contains another at a whitespace boundary.
@@ -282,7 +293,8 @@ public class SequenceIdMatcher
      */
     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
+      // 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