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[jalview.git]
/
src
/
jalview
/
io
/
ClustalFile.java
diff --git
a/src/jalview/io/ClustalFile.java
b/src/jalview/io/ClustalFile.java
index
2ea1d2f
..
90c22f9
100755
(executable)
--- a/
src/jalview/io/ClustalFile.java
+++ b/
src/jalview/io/ClustalFile.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
@@
-32,11
+32,6
@@
public class ClustalFile
{
\r
}
\r
\r
{
\r
}
\r
\r
- public ClustalFile(String inStr)
\r
- {
\r
- super(inStr);
\r
- }
\r
-
\r
public ClustalFile(String inFile, String type)
\r
throws IOException
\r
{
\r
public ClustalFile(String inFile, String type)
\r
throws IOException
\r
{
\r
@@
-131,14
+126,6
@@
public class ClustalFile
Sequence newSeq = parseId(headers.elementAt(i).toString());
\r
newSeq.setSequence( seqhash.get(headers.elementAt(i).toString()).toString() );
\r
\r
Sequence newSeq = parseId(headers.elementAt(i).toString());
\r
newSeq.setSequence( seqhash.get(headers.elementAt(i).toString()).toString() );
\r
\r
- if (!isValidProteinSequence(newSeq.getSequence()))
\r
- {
\r
- throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
\r
- + " : " + newSeq.getName()
\r
- + " : " + invalidCharacter);
\r
- }
\r
-
\r
-
\r
seqs.addElement(newSeq);
\r
}
\r
else
\r
seqs.addElement(newSeq);
\r
}
\r
else
\r
@@
-169,9
+156,9
@@
public class ClustalFile
{
\r
String tmp = printId(s[i]);
\r
\r
{
\r
String tmp = printId(s[i]);
\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
if (tmp.length() > maxid)
\r
}
\r
\r
if (tmp.length() > maxid)
\r
@@
-203,16
+190,16
@@
public class ClustalFile
int start = i * len;
\r
int end = start + len;
\r
\r
int start = i * len;
\r
int end = start + len;
\r
\r
- if ( (end < s[j].getSequence().length()) &&
\r
- (start < s[j].getSequence().length()))
\r
+ if ( (end < s[j].getSequence().length) &&
\r
+ (start < s[j].getSequence().length))
\r
{
\r
{
\r
- out.append(s[j].getSequence().substring(start, end));
\r
+ out.append(s[j].getSequenceAsString(start, end));
\r
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
- if (start < s[j].getSequence().length())
\r
+ if (start < s[j].getSequence().length)
\r
{
\r
{
\r
- out.append(s[j].getSequence().substring(start));
\r
+ out.append(s[j].getSequenceAsString().substring(start));
\r
}
\r
}
\r
\r
}
\r
}
\r
\r