While searching for another (still unresolved) bug, I found 2 small
bugs in SRS 4.02 - 4.04
Here's a list of them, plus the way how I solved them. Possibly there are
better solutions
Jeroen
==========================================================================
1)
Description
-----------
'>' signs in the SWISSPROT feature table are not translated to '>'
e.g.
FT VARIANT 42 42 N -> K (IN RABSON-MENDENHALL SYNDROME).
FT VARIANT 55 55 V -> A (IN LEPRECHAUNISM VERONA-1).
FT VARIANT 58 58 G -> R (IN LEPRECHAUNISM HELMOND;
FT INHIBITS PROCESSING AND TRANSPORT).
This could generate problems with HTML parsing
Solution
--------
This conversion has to be made before adding hyperlinks
2 routines are used to print fields :
WwwEntryTextPrint (srswww.c)
WwwPrintBuff (srswww.c)
I added SmSwapS lines to both:
The resulting routines are:
....................
static void WwwPrintBuff (char *ln)
{
SmSwapS (ln, ">", ">"); /* JC */
SmSwapS (ln, "<", "<"); /* JC */
strcat (buff, ln);
}
.....................
static INT4 WwwEntryTextPrint (ENTRYo *entry)
{
SLBoFIELD *field;
INT4 rv;
rv = EntryOpenText (entry);
_ErrRet (rv);
entry->convertLn = SMxMIXCASE;
while ((field = EntryNextField (entry, 0, 1))) {
if (field != (SLBoFIELD*) 1L)
WwwPrintField (entry, 1);
else {
if (EntryIsEndLine (entry))
break;
SmSwapS (entry->file[0]->ln, "%", "%%");
SmSwapS (entry->file[0]->ln, ">", ">"); /* JC */
SmSwapS (entry->file[0]->ln, "<", "<"); /* JC */
WwwPrintF (entry->file[0]->ln);
FilURead (entry->file[0]);
}
}
/* print the data part of ...file per entry type entries (eg, pdb) */
if (ParGetNum ("printData") && LibIsFilePerEntry (entry->lib))
do {
WwwPrintF (entry->file[0]->ln);
rv = FilURead (entry->file[0]);
}
while (rv != e__eof);
return 1;
}
==========================================================================
2) Clicking on feature in swissprot entry generates error messages
FT VARIANT 42 42 N -> K (IN RABSON-MENDENHALL SYNDROME).
Clicking on VARIANT in the above feature returns a parsing error message
Solution
--------
in expression.sdl, the %SWISSPROT_FEATURE_PARSER does not define
'>' as a valid character in the comment
Changed rule
comment = ~A-Za-z0-9\-_/. ()'~.
to
comment = ~A-Za-z0-9\-_/. ()'>:,~.
Adding '>' ':' and ','
As I have seen these in Swissprot feature comments
Possibly other chars should be added.
The errors appear on several servers, but not in Heidelberg. So I guess
Thure made this change, but forgot to add the new expression.sdl to the
new release (or made the change after the last release)
--
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. O . Jeroen Coppieters
. O O o O . Software Support
O O O O *o O O Jeroen.Coppieters at embl-ebi.ac.uk
O O O O( *o )O O (or jecop at ebi.ac.uk)
)O O O O o* O O( ++44 1223 494422
O O O O( o* )O O
)O O O O *o O O( EMBL Outstation EBI
O O O O( *o )O O (European Bioinformatics Institute)
)O @ O O o* O O( Hinxton Hall
O O O( o* )O(' Hinxton
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` O ' UK
http://www.ebi.ac.uk
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