merge from 2_4_Release branch

[jalview.git] / src / jalview / io / PfamFile.java

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index 2b0bf13..223e7a4 100755 (executable)
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
@@ -24,30 +24,29 @@ import java.util.*;
 import jalview.datamodel.*;
 import jalview.util.*;
 
-public class PfamFile
-    extends AlignFile
+public class PfamFile extends AlignFile
 {
 
   public PfamFile()
   {
   }
 
-  public PfamFile(String inFile, String type)
-      throws IOException
+  public PfamFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
+
   public PfamFile(FileParse source) throws IOException
   {
     super(source);
   }
+
   public void initData()
   {
     super.initData();
   }
 
-  public void parse()
-      throws IOException
+  public void parse() throws IOException
   {
     int i = 0;
     String line;
@@ -55,7 +54,7 @@ public class PfamFile
     Hashtable seqhash = new Hashtable();
     Vector headers = new Vector();
 
-    while ( (line = nextLine()) != null)
+    while ((line = nextLine()) != null)
     {
       if (line.indexOf(" ") != 0)
       {
@@ -80,7 +79,7 @@ public class PfamFile
               seqhash.put(id, tempseq);
             }
 
-            if (! (headers.contains(id)))
+            if (!(headers.contains(id)))
             {
               headers.addElement(id);
             }
@@ -103,21 +102,20 @@ public class PfamFile
       if (seqhash.get(headers.elementAt(i)) != null)
       {
         if (maxLength < seqhash.get(headers.elementAt(i)).toString()
-            .length())
+                .length())
         {
-          maxLength = seqhash.get(headers.elementAt(i)).toString()
-              .length();
+          maxLength = seqhash.get(headers.elementAt(i)).toString().length();
         }
 
         Sequence newSeq = parseId(headers.elementAt(i).toString());
-        newSeq.setSequence(seqhash.get(headers.elementAt(i).toString()).
-                           toString());
+        newSeq.setSequence(seqhash.get(headers.elementAt(i).toString())
+                .toString());
         seqs.addElement(newSeq);
       }
       else
       {
-        System.err.println("PFAM File reader: Can't find sequence for " +
-                           headers.elementAt(i));
+        System.err.println("PFAM File reader: Can't find sequence for "
+                + headers.elementAt(i));
       }
     }
   }
@@ -131,7 +129,7 @@ public class PfamFile
 
     int i = 0;
 
-    while ( (i < s.length) && (s[i] != null))
+    while ((i < s.length) && (s[i] != null))
     {
       String tmp = printId(s[i]);
 
@@ -155,7 +153,7 @@ public class PfamFile
 
     int j = 0;
 
-    while ( (j < s.length) && (s[j] != null))
+    while ((j < s.length) && (s[j] != null))
     {
       out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));