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added description of alignment quality scores and separated
[jalview.git]
/
src
/
jalview
/
io
/
PfamFile.java
diff --git
a/src/jalview/io/PfamFile.java
b/src/jalview/io/PfamFile.java
index
ec52bac
..
8056f38
100755
(executable)
--- a/
src/jalview/io/PfamFile.java
+++ b/
src/jalview/io/PfamFile.java
@@
-48,8
+48,7
@@
public class PfamFile
super.initData();
\r
}
\r
\r
super.initData();
\r
}
\r
\r
- public void parse()
\r
- throws IOException
\r
+ public void parse() throws IOException
\r
{
\r
int i = 0;
\r
String line;
\r
{
\r
int i = 0;
\r
String line;
\r
@@
-118,8
+117,9
@@
public class PfamFile
\r
if (!isValidProteinSequence(newSeq.getSequence()))
\r
{
\r
\r
if (!isValidProteinSequence(newSeq.getSequence()))
\r
{
\r
- throw new IOException(
\r
- "Not a valid protein sequence - (PFAM input)");
\r
+ throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
\r
+ +" : "+ newSeq.getName()
\r
+ +" : "+invalidCharacter);
\r
}
\r
}
\r
else
\r
}
\r
}
\r
else
\r