X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPileUpfile.java;h=2a902b44992e8f1a53bb4a777c75f95138d40edd;hb=227ee1c1c69c228b67d408a0a83ae51bf5811272;hp=d120ac38b89b753da44eeb4ce62a0e56df064c0c;hpb=c5677e9860106a821a3e6e0429b20ede7b9a732a;p=jalview.git

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index d120ac3..2a902b4 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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;
 
@@ -34,14 +37,6 @@ package jalview.io;
  */
 import java.io.*;
 
-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 jalview.datamodel.*;
 import jalview.util.*;
 
@@ -65,19 +60,13 @@ public class PileUpfile extends MSFfile
    * 
    * @throws IOException
    *           DOCUMENT ME!
- * @throws SAXException 
- * @throws ParserConfigurationException 
- * @throws ExceptionFileFormatOrSyntax 
- * @throws ExceptionLoadingFailed 
- * @throws ExceptionPermissionDenied 
- * @throws InterruptedException 
    */
-  public PileUpfile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+  public PileUpfile(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
 
-  public PileUpfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+  public PileUpfile(FileParse source) throws IOException
   {
     super(source);
   }
@@ -97,7 +86,7 @@ public class PileUpfile extends MSFfile
     StringBuffer out = new StringBuffer("PileUp");
     out.append(newline);
     out.append(newline);
-    
+
     int max = 0;
     int maxid = 0;
 
@@ -112,8 +101,7 @@ public class PileUpfile extends MSFfile
     }
 
     out.append("   MSF: " + s[0].getSequence().length
-            + "   Type: P    Check:  " + bigChecksum % 10000
-            + "   ..");
+            + "   Type: P    Check:  " + bigChecksum % 10000 + "   ..");
     out.append(newline);
     out.append(newline);
     out.append(newline);
@@ -145,8 +133,11 @@ public class PileUpfile extends MSFfile
     }
 
     maxid++;
-    out.append(newline);out.append(newline);out.append("//");
-    out.append(newline);out.append(newline);
+    out.append(newline);
+    out.append(newline);
+    out.append("//");
+    out.append(newline);
+    out.append(newline);
 
     int len = 50;