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added aligned codon frames, and dataset reference ids for sequenceSet and sequences...
[jalview.git]
/
src
/
jalview
/
io
/
PfamFile.java
diff --git
a/src/jalview/io/PfamFile.java
b/src/jalview/io/PfamFile.java
index
1af7573
..
4c90bca
100755
(executable)
--- a/
src/jalview/io/PfamFile.java
+++ b/
src/jalview/io/PfamFile.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) 2007 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
@@
-43,7
+43,8
@@
public class PfamFile
super.initData();
\r
}
\r
\r
super.initData();
\r
}
\r
\r
- public void parse() throws IOException
\r
+ public void parse()
\r
+ throws IOException
\r
{
\r
int i = 0;
\r
String line;
\r
{
\r
int i = 0;
\r
String line;
\r
@@
-105,17
+106,10
@@
public class PfamFile
.length();
\r
}
\r
\r
.length();
\r
}
\r
\r
-
\r
Sequence newSeq = parseId(headers.elementAt(i).toString());
\r
Sequence newSeq = parseId(headers.elementAt(i).toString());
\r
- newSeq.setSequence( seqhash.get(headers.elementAt(i).toString()).toString());
\r
+ newSeq.setSequence(seqhash.get(headers.elementAt(i).toString()).
\r
+ toString());
\r
seqs.addElement(newSeq);
\r
seqs.addElement(newSeq);
\r
-
\r
- if (!isValidProteinSequence(newSeq.getSequence()))
\r
- {
\r
- throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
\r
- +" : "+ newSeq.getName()
\r
- +" : "+invalidCharacter);
\r
- }
\r
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
@@
-138,9
+132,9
@@
public class PfamFile
{
\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
@@
-160,9
+154,9
@@
public class PfamFile
\r
while ( (j < s.length) && (s[j] != null))
\r
{
\r
\r
while ( (j < s.length) && (s[j] != null))
\r
{
\r
- out.append(new Format("%-" + maxid + "s").form( printId(s[j])+" "));
\r
+ out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));
\r
\r
\r
- out.append(s[j].getSequence() + "\n");
\r
+ out.append(s[j].getSequenceAsString() + "\n");
\r
j++;
\r
}
\r
\r
j++;
\r
}
\r
\r