Merge branch 'develop' into menard

[jalview.git] / src / jalview / io / MSFfile.java

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 616c90b..c3ee382 100755 (executable)
--- 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 
@@ -27,6 +27,7 @@ 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.*;
@@ -63,13 +64,14 @@ public class MSFfile extends AlignFile
  * @throws ExceptionLoadingFailed 
  * @throws ExceptionPermissionDenied 
  * @throws InterruptedException 
+ * @throws ExceptionUnmatchedClosingParentheses 
    */
-  public MSFfile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+  public MSFfile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     super(inFile, type);
   }
 
-  public MSFfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+  public MSFfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     super(source);
   }
@@ -231,7 +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;
@@ -242,7 +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());
@@ -315,7 +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)
       {
@@ -349,7 +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;