X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBLCFile.java;h=a499f750f8187e1d91f95db282ed74ceb2788419;hb=1b4069135fa518efcb11d9cb729e5031347b8fe0;hp=d0eb80ec8ee94db11ee41bb014bba76efed83fe8;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index d0eb80e..a499f75 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -1,26 +1,30 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- * 
+ * 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/>.
+ * 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.Sequence;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.io.IOException;
+import java.util.Vector;
 
 /**
  * DOCUMENT ME!
@@ -112,7 +116,9 @@ public class BLCFile extends AlignFile
       {
         line = nextLine();
         if (line == null)
+        {
           break;
+        }
         // seek end of ids
         if (line.indexOf("*") > -1)
         {
@@ -142,12 +148,14 @@ public class BLCFile extends AlignFile
         {
           // header lines - keep them for the alignment comments.
           headerLines.append(line);
-          headerLines.append("\n");
+          headerLines.append(newline);
           numHeaderLines++;
         }
       } while (!idsFound);
       if (line == null)
+      {
         break; // end of file.
+      }
       int starCol = line.indexOf("*");
       seqstrings = new StringBuffer[seqs.size()];
 
@@ -195,9 +203,11 @@ public class BLCFile extends AlignFile
     }
     if (seqs.size() > 0)
     {
-      if (headerLines.length() > 1 + numHeaderLines) // could see if buffer is
+      if (headerLines.length() > 1 + numHeaderLines)
+      {
         // just whitespace or not.
         setAlignmentProperty("Comments", headerLines.toString());
+      }
       setAlignmentProperty("iteration", "" + iterationCount);
     }
   }
@@ -240,7 +250,7 @@ public class BLCFile extends AlignFile
         out.append(" " + s[i].getDescription());
       }
 
-      out.append("\n");
+      out.append(newline);
 
       if (s[i].getSequence().length > max)
       {
@@ -250,7 +260,8 @@ public class BLCFile extends AlignFile
       i++;
     }
 
-    out.append("* iteration 1\n");
+    out.append("* iteration 1");
+    out.append(newline);
 
     for (int j = 0; j < max; j++)
     {
@@ -270,10 +281,11 @@ public class BLCFile extends AlignFile
         i++;
       }
 
-      out.append("\n");
+      out.append(newline);
     }
 
-    out.append("*\n");
+    out.append("*");
+    out.append(newline);
 
     return out.toString();
   }