X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FMSFfile.java;h=c3ee382a004d9e8577b8d06e872644d27e26821d;hb=28787d9646cca5dd77190930f59b7ff32cf995b4;hp=6b584a80f16363d2cc452db9dca1e6853049eee1;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 6b584a8..c3ee382 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -1,13 +1,13 @@
 /*
- * 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)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * 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.
- * 
+ *  
  * 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 
@@ -20,6 +20,15 @@ package jalview.io;
 import java.io.*;
 import java.util.*;
 
+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 jalview.util.*;
 
@@ -49,13 +58,20 @@ public class MSFfile extends AlignFile
    * 
    * @throws IOException
    *           DOCUMENT ME!
+ * @throws SAXException 
+ * @throws ParserConfigurationException 
+ * @throws ExceptionFileFormatOrSyntax 
+ * @throws ExceptionLoadingFailed 
+ * @throws ExceptionPermissionDenied 
+ * @throws InterruptedException 
+ * @throws ExceptionUnmatchedClosingParentheses 
    */
-  public MSFfile(String inFile, String type) throws IOException
+  public MSFfile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     super(inFile, type);
   }
 
-  public MSFfile(FileParse source) throws IOException
+  public MSFfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     super(source);
   }
@@ -217,7 +233,7 @@ public class MSFfile extends AlignFile
 
     StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA")
             + "_MULTIPLE_ALIGNMENT 1.0");
-     // TODO: JBPNote : Jalview doesn't remember NA or AA yet.
+    // TODO: JBPNote : Jalview doesn't remember NA or AA yet.
     out.append(newline);
     out.append(newline);
     int max = 0;
@@ -228,7 +244,7 @@ public class MSFfile extends AlignFile
     {
       // Replace all internal gaps with . and external spaces with ~
       s[i] = new Sequence(seqs[i].getName(), seqs[i].getSequenceAsString()
-              .replace('-', '.'), seqs[i].getStart(),seqs[i].getEnd());
+              .replace('-', '.'), seqs[i].getStart(), seqs[i].getEnd());
 
       StringBuffer sb = new StringBuffer();
       sb.append(s[i].getSequence());
@@ -301,7 +317,7 @@ public class MSFfile extends AlignFile
 
       idBlock[i] = new String("Len: "
               + maxLenpad.form(s[i].getSequence().length) + "  Check: "
-              + maxChkpad.form(checksums[i]) + "  Weight: 1.00"+newline);
+              + maxChkpad.form(checksums[i]) + "  Weight: 1.00" + newline);
 
       if (s[i].getName().length() > maxid)
       {
@@ -335,7 +351,8 @@ public class MSFfile extends AlignFile
 
     maxid++;
     out.append(newline);
-    out.append(newline);out.append("//");
+    out.append(newline);
+    out.append("//");
     out.append(newline);
     out.append(newline);
     int len = 50;