merge from 2_4_Release branch

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

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index d62d185..f46e3ad 100755 (executable)
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.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 ClustalFile
-    extends AlignFile
+public class ClustalFile extends AlignFile
 {
 
   public ClustalFile()
   {
   }
 
-  public ClustalFile(String inFile, String type)
-      throws IOException
+  public ClustalFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
+
   public ClustalFile(FileParse source) throws IOException
   {
     super(source);
   }
+
   public void initData()
   {
     super.initData();
   }
 
-  public void parse()
-      throws IOException
+  public void parse() throws IOException
   {
     int i = 0;
     boolean flag = false;
@@ -60,7 +59,7 @@ public class ClustalFile
 
     try
     {
-      while ( (line = nextLine()) != null)
+      while ((line = nextLine()) != null)
       {
         if (line.indexOf(" ") != 0)
         {
@@ -88,7 +87,7 @@ public class ClustalFile
                   seqhash.put(id, tempseq);
                 }
 
-                if (! (headers.contains(id)))
+                if (!(headers.contains(id)))
                 {
                   headers.addElement(id);
                 }
@@ -106,8 +105,7 @@ public class ClustalFile
           }
         }
       }
-    }
-    catch (IOException e)
+    } catch (IOException e)
     {
       System.err.println("Exception parsing clustal file " + e);
       e.printStackTrace();
@@ -117,29 +115,29 @@ public class ClustalFile
     {
       this.noSeqs = headers.size();
 
-      //Add sequences to the hash
+      // Add sequences to the hash
       for (i = 0; i < headers.size(); i++)
       {
         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();
+                    .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(
-              "Clustal File Reader: Can't find sequence for " +
-              headers.elementAt(i));
+          System.err
+                  .println("Clustal File Reader: Can't find sequence for "
+                          + headers.elementAt(i));
         }
       }
     }
@@ -159,7 +157,7 @@ public class ClustalFile
 
     int i = 0;
 
-    while ( (i < s.length) && (s[i] != null))
+    while ((i < s.length) && (s[i] != null))
     {
       String tmp = printId(s[i]);
 
@@ -190,15 +188,17 @@ public class ClustalFile
     {
       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(new Format("%-" + maxid + "s").form(printId(s[j])
+                        + " "));
 
         int start = i * len;
         int end = start + len;
 
-        if ( (end < s[j].getSequence().length) &&
-            (start < s[j].getSequence().length))
+        if ((end < s[j].getSequence().length)
+                && (start < s[j].getSequence().length))
         {
           out.append(s[j].getSequenceAsString(start, end));
         }