Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch

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

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index 2b0bf13..f4d61bc 100755 (executable)
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -1,53 +1,53 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * 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
- * 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 (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
 import java.io.*;
 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;
@@ -55,12 +55,14 @@ public class PfamFile
     Hashtable seqhash = new Hashtable();
     Vector headers = new Vector();
 
-    while ( (line = nextLine()) != null)
+    while ((line = nextLine()) != null)
     {
       if (line.indexOf(" ") != 0)
       {
         if (line.indexOf("#") != 0)
         {
+          // TODO: verify pfam format requires spaces and not tab characters -
+          // if not upgrade to use stevesoft regex and look for whitespace.
           StringTokenizer str = new StringTokenizer(line, " ");
           String id = "";
 
@@ -80,12 +82,14 @@ public class PfamFile
               seqhash.put(id, tempseq);
             }
 
-            if (! (headers.contains(id)))
+            if (!(headers.contains(id)))
             {
               headers.addElement(id);
             }
-
-            tempseq.append(str.nextToken());
+            if (str.hasMoreTokens())
+            {
+              tempseq.append(str.nextToken());
+            }
           }
         }
       }
@@ -103,21 +107,20 @@ 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 +134,7 @@ 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]);
 
@@ -155,15 +158,16 @@ 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]) + " "));
 
-      out.append(s[j].getSequenceAsString() + "\n");
+      out.append(s[j].getSequenceAsString());
+      out.append(newline);
       j++;
     }
 
-    out.append("\n");
+    out.append(newline);
 
     return out.toString();
   }