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Watch out for - symbol lin jnet files
[jalview.git]
/
src
/
jalview
/
io
/
BLCFile.java
diff --git
a/src/jalview/io/BLCFile.java
b/src/jalview/io/BLCFile.java
index
56d40f9
..
4a9e777
100755
(executable)
--- a/
src/jalview/io/BLCFile.java
+++ b/
src/jalview/io/BLCFile.java
@@
-1,6
+1,6
@@
/*
\r
* Jalview - A Sequence Alignment Editor and Viewer
\r
/*
\r
* Jalview - A Sequence Alignment Editor and Viewer
\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
*
\r
* This program is free software; you can redistribute it and/or
\r
* modify it under the terms of the GNU General Public License
\r
*
\r
* This program is free software; you can redistribute it and/or
\r
* modify it under the terms of the GNU General Public License
\r
@@
-42,15
+42,6
@@
public class BLCFile extends AlignFile
{
\r
}
\r
\r
{
\r
}
\r
\r
- /**
\r
- * Creates a new BLCFile object.
\r
- *
\r
- * @param inStr DOCUMENT ME!
\r
- */
\r
- public BLCFile(String inStr)
\r
- {
\r
- super(inStr);
\r
- }
\r
\r
/**
\r
* Creates a new BLCFile object.
\r
\r
/**
\r
* Creates a new BLCFile object.
\r
@@
-197,9
+188,9
@@
public class BLCFile extends AlignFile
{
\r
out.append(">" + printId(s[i]) +"\n");
\r
\r
{
\r
out.append(">" + printId(s[i]) +"\n");
\r
\r
- if (s[i].getSequence().length() > max)
\r
+ if (s[i].getSequence().length > max)
\r
{
\r
{
\r
- max = s[i].getSequence().length();
\r
+ max = s[i].getSequence().length;
\r
}
\r
\r
i++;
\r
}
\r
\r
i++;
\r
@@
-213,9
+204,9
@@
public class BLCFile extends AlignFile
\r
while ((i < s.length) && (s[i] != null))
\r
{
\r
\r
while ((i < s.length) && (s[i] != null))
\r
{
\r
- if (s[i].getSequence().length() > j)
\r
+ if (s[i].getSequence().length > j)
\r
{
\r
{
\r
- out.append(s[i].getSequence().substring(j, j + 1));
\r
+ out.append(s[i].getSequenceAsString(j, j + 1));
\r
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r