X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBLCFile.java;h=c0ecd580e2b3329ef3d1f172acdbf6bf1fcd8b11;hb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;hp=9b5b3e56ed095cc1a16d7a27f35ac8fb9ad33509;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index 9b5b3e5..c0ecd58 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -1,27 +1,30 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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!
@@ -44,16 +47,17 @@ public class BLCFile extends AlignFile
    * Creates a new BLCFile object.
    * 
    * @param inFile
-   *                DOCUMENT ME!
-   * @param type
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
+   * @param sourceType
+   *          DOCUMENT ME!
    * 
    * @throws IOException
-   *                 DOCUMENT ME!
+   *           DOCUMENT ME!
    */
-  public BLCFile(String inFile, String type) throws IOException
+  public BLCFile(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   public BLCFile(FileParse source) throws IOException
@@ -64,6 +68,7 @@ public class BLCFile extends AlignFile
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void initData()
   {
     super.initData();
@@ -86,6 +91,7 @@ public class BLCFile extends AlignFile
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void parse() throws IOException
   {
     StringBuffer headerLines = new StringBuffer();
@@ -113,7 +119,9 @@ public class BLCFile extends AlignFile
       {
         line = nextLine();
         if (line == null)
+        {
           break;
+        }
         // seek end of ids
         if (line.indexOf("*") > -1)
         {
@@ -143,12 +151,14 @@ 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()];
 
@@ -196,9 +206,11 @@ public class BLCFile extends AlignFile
     }
     if (seqs.size() > 0)
     {
-      if (headerLines.length() > 1 + numHeaderLines) // could see if buffer is
-                                                      // just whitespace or not.
+      if (headerLines.length() > 1 + numHeaderLines)
+      {
+        // just whitespace or not.
         setAlignmentProperty("Comments", headerLines.toString());
+      }
       setAlignmentProperty("iteration", "" + iterationCount);
     }
   }
@@ -208,6 +220,7 @@ public class BLCFile extends AlignFile
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public String print()
   {
     return print(getSeqsAsArray());
@@ -217,7 +230,7 @@ public class BLCFile extends AlignFile
    * DOCUMENT ME!
    * 
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -241,7 +254,7 @@ public class BLCFile extends AlignFile
         out.append(" " + s[i].getDescription());
       }
 
-      out.append("\n");
+      out.append(newline);
 
       if (s[i].getSequence().length > max)
       {
@@ -251,7 +264,8 @@ 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++)
     {
@@ -271,10 +285,11 @@ public class BLCFile extends AlignFile
         i++;
       }
 
-      out.append("\n");
+      out.append(newline);
     }
 
-    out.append("*\n");
+    out.append("*");
+    out.append(newline);
 
     return out.toString();
   }