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Wait for response from server before next sequence
[jalview.git]
/
src
/
jalview
/
io
/
ClustalFile.java
diff --git
a/src/jalview/io/ClustalFile.java
b/src/jalview/io/ClustalFile.java
index
e72e0df
..
e3f83ee
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
@@
-48,7
+43,7
@@
public class ClustalFile
super.initData();
\r
}
\r
\r
super.initData();
\r
}
\r
\r
- public void parse()
\r
+ public void parse() throws IOException
\r
{
\r
int i = 0;
\r
boolean flag = false;
\r
{
\r
int i = 0;
\r
boolean flag = false;
\r
@@
-131,6
+126,14
@@
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