X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBLCFile.java;h=c7cf2d68f7056967bb26857fceeb5b8deddaeed2;hb=3412b273e964fb1a9d22564b04a5f0c827ec2461;hp=71c95b50c1c2d434008949a9bda17b12ab0109a7;hpb=1a8f953dd71a9e319e910261927f269d69b4692c;p=jalview.git

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index 71c95b5..c7cf2d6 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -1,35 +1,30 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-
-import jalview.datamodel.*;
+import java.io.IOException;
+import java.util.Vector;
 
 /**
  * DOCUMENT ME!
@@ -55,14 +50,16 @@ public class BLCFile extends AlignFile
    *          DOCUMENT ME!
    * @param type
    *          DOCUMENT ME!
- * @throws Exception 
+   * 
+   * @throws IOException
+   *           DOCUMENT ME!
    */
-  public BLCFile(String inFile, String type) throws Exception
+  public BLCFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
 
-  public BLCFile(FileParse source) throws Exception
+  public BLCFile(FileParse source) throws IOException
   {
     super(source);
   }
@@ -119,7 +116,9 @@ public class BLCFile extends AlignFile
       {
         line = nextLine();
         if (line == null)
+        {
           break;
+        }
         // seek end of ids
         if (line.indexOf("*") > -1)
         {
@@ -154,7 +153,9 @@ public class BLCFile extends AlignFile
         }
       } while (!idsFound);
       if (line == null)
+       {
         break; // end of file.
+      }
       int starCol = line.indexOf("*");
       seqstrings = new StringBuffer[seqs.size()];
 
@@ -202,9 +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);
     }
   }