X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBLCFile.java;h=a499f750f8187e1d91f95db282ed74ceb2788419;hb=0a5ce6145bb76fc7eb8a5cc2670e20453fbedd29;hp=4a07ac4e1a30b5fee81e29e17f7d848133da4f7b;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index 4a07ac4..a499f75 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 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* 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!
@@ -113,7 +116,9 @@ public class BLCFile extends AlignFile
{
line = nextLine();
if (line == null)
+ {
break;
+ }
// seek end of ids
if (line.indexOf("*") > -1)
{
@@ -148,7 +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()];
@@ -196,9 +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);
}
}