merge from 2_4_Release branch

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

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index b18b8f4..4c10abe 100755 (executable)
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.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
@@ -23,38 +23,37 @@ import java.util.*;
 
 import jalview.datamodel.*;
 
-public class PIRFile
-    extends AlignFile
+public class PIRFile extends AlignFile
 {
   public static boolean useModellerOutput = false;
 
-  Vector words = new Vector(); //Stores the words in a line after splitting
+  Vector words = new Vector(); // Stores the words in a line after splitting
 
   public PIRFile()
   {
   }
 
-  public PIRFile(String inFile, String type)
-      throws IOException
+  public PIRFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
+
   public PIRFile(FileParse source) throws IOException
   {
     super(source);
   }
-  public void parse()
-      throws IOException
+
+  public void parse() throws IOException
   {
     StringBuffer sequence;
     String line = null;
     ModellerDescription md;
 
-    while ( (line = nextLine()) != null)
+    while ((line = nextLine()) != null)
     {
       if (line.length() == 0)
       {
-        //System.out.println("blank line");
+        // System.out.println("blank line");
         continue;
       }
       if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)
@@ -92,8 +91,7 @@ public class PIRFile
 
         seqs.addElement(newSeq);
 
-        md = new ModellerDescription(newSeq.
-                                     getDescription());
+        md = new ModellerDescription(newSeq.getDescription());
         md.updateSequenceI(newSeq);
       }
     }
@@ -112,7 +110,7 @@ public class PIRFile
     int i = 0;
     ModellerDescription md;
 
-    while ( (i < s.length) && (s[i] != null))
+    while ((i < s.length) && (s[i] != null))
     {
       String seq = s[i].getSequenceAsString();
       seq = seq + "*";
@@ -133,8 +131,8 @@ public class PIRFile
         out.append(">N1;" + s[i].getName() + "\n");
         if (s[i].getDescription() == null)
         {
-          out.append(s[i].getName() + " " +
-                     (s[i].getEnd() - s[i].getStart() + 1));
+          out.append(s[i].getName() + " "
+                  + (s[i].getEnd() - s[i].getStart() + 1));
           out.append(is_NA ? " bases\n" : " residues\n");
         }
         else
@@ -160,9 +158,10 @@ public class PIRFile
           }
           else
           {
-            out.append(s[i].getName() + " "
-                       + (s[i].getEnd() - s[i].getStart() + 1)
-                       + " residues\n");
+            out
+                    .append(s[i].getName() + " "
+                            + (s[i].getEnd() - s[i].getStart() + 1)
+                            + " residues\n");
           }
         }
       }