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fix regex for annotation subtype to use non-whitespace presence rather than word...
author
jprocter
<Jim Procter>
Mon, 21 Jan 2008 16:57:16 +0000
(16:57 +0000)
committer
jprocter
<Jim Procter>
Mon, 21 Jan 2008 16:57:16 +0000
(16:57 +0000)
src/jalview/io/StockholmFile.java
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diff --git
a/src/jalview/io/StockholmFile.java
b/src/jalview/io/StockholmFile.java
index
e7b1c6e
..
bac1916
100644
(file)
--- a/
src/jalview/io/StockholmFile.java
+++ b/
src/jalview/io/StockholmFile.java
@@
-97,7
+97,7
@@
public class StockholmFile extends AlignFile
rend = new Regex("\\/\\/"); // Find the end of an alignment
\r
p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
\r
// id/from/to
\r
rend = new Regex("\\/\\/"); // Find the end of an alignment
\r
p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
\r
// id/from/to
\r
- s = new Regex("(\\S+)\\s+(\\w{2})\\s+(.*)"); // Parses annotation subtype
\r
+ s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype
\r
r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
\r
x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence
\r
\r
r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
\r
x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence
\r
\r
@@
-432,7
+432,8
@@
public class StockholmFile extends AlignFile
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
- throw new IOException("Error parsing " + line);
\r
+ System.err.println("Warning - couldn't parse sequence annotation row line:\n"+line);
\r
+ // throw new IOException("Error parsing " + line);
\r
}
\r
}
\r
else
\r
}
\r
}
\r
else
\r