X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSequenceIdMatcher.java;h=1efe4982810ecb2a79b57a85834178374108926a;hb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;hp=f7862434aeac77fd52c0471caca487a32fb7c29b;hpb=9257b8510c7354cbd7e43a3fc2817978cc8e4ae9;p=jalview.git

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index f786243..1efe498 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -1,139 +1,163 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program 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 this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.analysis;
 
-import jalview.datamodel.SequenceI;
-
-import java.util.Hashtable;
-import java.util.Vector;
-
-
-/**
- * <p>Title: </p>
- * SequenceIdMatcher
- * <p>Description: </p>
- * Routine which does approximate Sequence Id resolution by name using string containment rather than equivalence
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
+import java.util.*;
+
+import jalview.datamodel.*;
+
+/**
+ * <p>Title: </p>
+ * SequenceIdMatcher
+ * <p>Description: </p>
+ * Routine which does approximate Sequence Id resolution by name using string containment rather than equivalence
+ * <p>Copyright: Copyright (c) 2004</p>
+ *
+ * <p>Company: Dundee University</p>
+ *
+ * @author not attributable
+ * @version 1.0
  */
-public class SequenceIdMatcher {
-    private Hashtable names;
+public class SequenceIdMatcher
+{
+  private Hashtable names;
 
-    public SequenceIdMatcher(SequenceI[] seqs) {
-        names = new Hashtable();
+  public SequenceIdMatcher(SequenceI[] seqs)
+  {
+    names = new Hashtable();
 
-        for (int i = 0; i < seqs.length; i++) {
-            names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
-        }
+    for (int i = 0; i < seqs.length; i++)
+    {
+      names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
     }
+  }
 
-    SequenceI findIdMatch(SequenceI seq) {
-        SeqIdName nam = new SeqIdName(seq.getName());
+  SequenceI findIdMatch(SequenceI seq)
+  {
+    SeqIdName nam = new SeqIdName(seq.getName());
 
-        if (names.containsKey(nam)) {
-            return (SequenceI) names.get(nam);
-        }
-
-        return null;
+    if (names.containsKey(nam))
+    {
+      return (SequenceI) names.get(nam);
     }
 
-    SequenceI findIdMatch(String seqnam) {
-        SeqIdName nam = new SeqIdName(seqnam);
+    return null;
+  }
 
-        if (names.containsKey(nam)) {
-            return (SequenceI) names.get(nam);
-        }
+  SequenceI findIdMatch(String seqnam)
+  {
+    SeqIdName nam = new SeqIdName(seqnam);
 
-        return null;
+    if (names.containsKey(nam))
+    {
+      return (SequenceI) names.get(nam);
     }
 
-    /**
- * findIdMatch
- *
- * Return pointers to sequences (or sequence object containers)
- * which have same Id as a given set of different sequence objects
- *
- * @param seqs SequenceI[]
- * @return SequenceI[]
- */
-    SequenceI[] findIdMatch(SequenceI[] seqs) {
-        SequenceI[] namedseqs = new SequenceI[seqs.length];
-
-        int i = 0;
-        SeqIdName nam;
-
-        if (seqs.length > 0) {
-            do {
-                nam = new SeqIdName(seqs[i].getName());
-
-                if (names.containsKey(nam)) {
-                    namedseqs[i] = (SequenceI) names.get(nam);
-                } else {
-                    namedseqs[i] = null;
-                }
-            } while (i++ < seqs.length);
+    return null;
+  }
+
+  /**
+   * findIdMatch
+   *
+   * Return pointers to sequences (or sequence object containers)
+   * which have same Id as a given set of different sequence objects
+   *
+   * @param seqs SequenceI[]
+   * @return SequenceI[]
+   */
+  SequenceI[] findIdMatch(SequenceI[] seqs)
+  {
+    SequenceI[] namedseqs = new SequenceI[seqs.length];
+
+    int i = 0;
+    SeqIdName nam;
+
+    if (seqs.length > 0)
+    {
+      do
+      {
+        nam = new SeqIdName(seqs[i].getName());
+
+        if (names.containsKey(nam))
+        {
+          namedseqs[i] = (SequenceI) names.get(nam);
         }
-
-        return namedseqs;
+        else
+        {
+          namedseqs[i] = null;
+        }
+      }
+      while (i++ < seqs.length);
     }
 
-    private class SeqIdName {
-        String id;
+    return namedseqs;
+  }
 
-        SeqIdName(String s) {
-            id = new String(s);
-        }
+  private class SeqIdName
+  {
+    String id;
 
-        public int hashCode() {
-            return (id.substring(0, 4).hashCode());
-        }
+    SeqIdName(String s)
+    {
+      id = new String(s);
+    }
 
-        public boolean equals(Object s) {
-            if (s instanceof SeqIdName) {
-                return this.equals((SeqIdName) s);
-            } else {
-                if (s instanceof String) {
-                    return this.equals((String) s);
-                }
-            }
+    public int hashCode()
+    {
+      return (id.substring(0, 4).hashCode());
+    }
 
-            return false;
+    public boolean equals(Object s)
+    {
+      if (s instanceof SeqIdName)
+      {
+        return this.equals( (SeqIdName) s);
+      }
+      else
+      {
+        if (s instanceof String)
+        {
+          return this.equals( (String) s);
         }
+      }
 
-        public boolean equals(SeqIdName s) {
-            if (id.startsWith(s.id) || s.id.startsWith(id)) {
-                return true;
-            }
+      return false;
+    }
 
-            return false;
-        }
+    public boolean equals(SeqIdName s)
+    {
+      if (id.startsWith(s.id) || s.id.startsWith(id))
+      {
+        return true;
+      }
 
-        public boolean equals(String s) {
-            if (id.startsWith(s) || s.startsWith(id)) {
-                return true;
-            }
+      return false;
+    }
 
-            return false;
-        }
+    public boolean equals(String s)
+    {
+      if (id.startsWith(s) || s.startsWith(id))
+      {
+        return true;
+      }
+
+      return false;
     }
+  }
 }