I am trying to replace and increment a lot of TEST_FONC_1 entries in my file with TEST_FONC_2 then TEST_FONC_3.....
I'm trying to use replace regexp but it doesn't work
I have tried
replace
_+
with
_\,(1+ \#&)
but it doesn't work. it find the entries but it replace it with the text... (4 Replies)
Hi all! I am new to this forum. I have recently installed Cygwin and XEmacs on my
laptop running Windows Vista. I am studing at the moment and the code I am creating is mainly for that purpose.
I am trying to create the algorithm of Insertion sort. When I compile my code in XEmacs i get some... (1 Reply)
Folks,
I am hoping someone out there can help me. I have been writing code for in-excess of 10 years. Throughout all this time I have used Xemacs. I have picked up bits of customizations here and there over the years, but would not profess to be anything of an expert in Lisp (or have a heavily... (3 Replies)
Hi all ,
I would like to have a new binding so that if im having the cursur on a word, one shortcut click (say f3) whould find the next occurrence of the word in the text and so one.
what is the right bind for it ?
I tried but its wrong.
thanks !
Zvika (1 Reply)
I need some help configuring xemacs to enable buffer tabs.
please, anybody, could walk me through on how to configure xemacs for this.
Thank You. (1 Reply)
How I can get the current make-file name in a make-file
So, if I run make with specified file:make -f target.mak
is it possible to have the 'target' inside of the that 'target.mak' from the file name? (2 Replies)
Sorry, this has probably been posted before, but my searches turn up nothing, and I have tried.
using a cygwin distro of xemacs
The default is NOT to display CR characters (I expect to see them as ^M). I want to change this so they do show up.
Can you tell me please, what command to issue?... (0 Replies)
xemacs uses default colors for coloring C files
how can I change those colors. I could only manage the default background and foreground colors and that too using .Xdefaults file changes. (2 Replies)
Hi guys
What is the difference between Xemacs and emacs. I assumed Xemacs runs only in X11.
What about in Linux on KDE? Am I running Xemacs or emacs. Well it says emacs though.
What is the advantage of one over other?
What can I run on OS X ?
SS (5 Replies)
Hi Folks,
Would like to download the xemacs editor for C. I searched the xemacs site but i donno the exact place of download.
Can any one pass the URL or way to go thru and download the editor?
Thanks in Advance,
Nisha (4 Replies)
Bio::Root::Exception(3pm) User Contributed Perl Documentation Bio::Root::Exception(3pm)NAME
Bio::Root::Exception - Generic exception objects for Bioperl
SYNOPSIS
Throwing exceptions using Error.pm throw:
use Bio::Root::Exception;
use Error;
# Set Error::Debug to include stack trace data in the error messages
$Error::Debug = 1;
$file = shift;
open (IN, $file) ||
throw Bio::Root::FileOpenException ( "Can't open file $file for reading", $!);
Throwing exceptions using Bioperl throw:
# Here we have an object that ISA Bio::Root::Root, so it inherits throw().
open (IN, $file) ||
$object->throw(-class => 'Bio::Root::FileOpenException',
-text => "Can't open file $file for reading",
-value => $!);
Catching and handling exceptions using Error.pm try:
use Bio::Root::Exception;
use Error qw(:try);
# Note that we need to import the 'try' tag from Error.pm
# Set Error::Debug to include stack trace data in the error messages
$Error::Debug = 1;
$file = shift;
try {
open (IN, $file) ||
throw Bio::Root::FileOpenException ( "Can't open file $file for reading", $!);
}
catch Bio::Root::FileOpenException with {
my $err = shift;
print STDERR "Using default input file: $default_file
";
open (IN, $default_file) || die "Can't open $default_file";
}
otherwise {
my $err = shift;
print STDERR "An unexpected exception occurred:
$err";
# By placing an the error object reference within double quotes,
# you're invoking its stringify() method.
}
finally {
# Any code that you want to execute regardless of whether or not
# an exception occurred.
};
# the ending semicolon is essential!
Defining a new Exception type as a subclass of Bio::Root::Exception:
@Bio::TestException::ISA = qw( Bio::Root::Exception );
DESCRIPTION
Exceptions defined in Bio::Root::Exception
These are generic exceptions for typical problem situations that could arise in any module or script.
Bio::Root::Exception()
Bio::Root::NotImplemented()
Bio::Root::IOException()
Bio::Root::FileOpenException()
Bio::Root::SystemException()
Bio::Root::BadParameter()
Bio::Root::OutOfRange()
Bio::Root::NoSuchThing()
Using defined exception classes like these is a good idea because it indicates the basic nature of what went wrong in a convenient,
computable way.
If there is a type of exception that you want to throw that is not covered by the classes listed above, it is easy to define a new one that
fits your needs. Just write a line like the following in your module or script where you want to use it (or put it somewhere that is
accessible to your code):
@NoCanDoException::ISA = qw( Bio::Root::Exception );
All of the exceptions defined in this module inherit from a common base class exception, Bio::Root::Exception. This allows a user to write
a handler for all Bioperl-derived exceptions as follows:
use Bio::Whatever;
use Error qw(:try);
try {
# some code that depends on Bioperl
}
catch Bio::Root::Exception with {
my $err = shift;
print "A Bioperl exception occurred:
$err
";
};
So if you do create your own exceptions, just be sure they inherit from Bio::Root::Exception directly, or indirectly by inheriting from a
Bio::Root::Exception subclass.
The exceptions in Bio::Root::Exception are extensions of Graham Barr's Error module available from CPAN. Despite this dependency, the
Bio::Root::Exception module does not explicitly "require Error". This permits Bio::Root::Exception to be loaded even when Error.pm is not
available.
Throwing exceptions within Bioperl modules
Error.pm is not part of the Bioperl distibution, and may not be present within any given perl installation. So, when you want to throw an
exception in a Bioperl module, the safe way to throw it is to use "throw" in Bio::Root::Root which can use Error.pm when it's available.
See documentation in Bio::Root::Root for details.
SEE ALSO
See the "examples/exceptions" directory of the Bioperl distribution for working demo code.
"throw" in Bio::Root::Root for information about throwing Bio::Root::Exception-based exceptions.
Error (available from CPAN, author: GBARR)
Error.pm is helping to guide the design of exception handling in Perl 6. See these RFC's:
http://dev.perl.org/rfc/63.pod
http://dev.perl.org/rfc/88.pod
AUTHOR
Steve Chervitz <sac@bioperl.org>
COPYRIGHT
Copyright (c) 2001 Steve Chervitz. All Rights Reserved.
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
DISCLAIMER
This software is provided "as is" without warranty of any kind.
EXCEPTIONS
Bio::Root::Exception
Purpose : A generic base class for all BioPerl exceptions.
By including a "catch Bio::Root::Exception" block, you
should be able to trap all BioPerl exceptions.
Example : throw Bio::Root::Exception("A generic exception", $!);
Methods defined by Bio::Root::Exception
new
Purpose : Guarantees that -value is set properly before
calling Error::new().
Arguments: key-value style arguments same as for Error::new()
You can also specify plain arguments as ($message, $value)
where $value is optional.
-value, if defined, must be non-zero and not an empty string
in order for eval{}-based exception handlers to work.
These require that if($@) evaluates to true, which will not
be the case if the Error has no value (Error overloads
numeric operations to the Error::value() method).
It is OK to create Bio::Root::Exception objects without
specifying -value. In this case, an invisible dummy value is used.
If you happen to specify a -value of zero(0), it will
be replaced by the string "The number zero(0)".
If you happen to specify a -value of empty string (""), it will
be replaced by the string "An empty string ("")".
pretty_format()
Purpose : Get a nicely formatted string containing information about the
exception. Format is similar to that produced by
Bio::Root::Root::throw(), with the addition of the name of
the exception class in the EXCEPTION line and some other
data available via the Error object.
Example : print $error->pretty_format;
stringify()
Purpose : Overrides Error::stringify() to call pretty_format().
This is called automatically when an exception object
is placed between double quotes.
Example : catch Bio::Root::Exception with {
my $error = shift;
print "$error";
}
See Also: pretty_format()
Subclasses of Bio::Root::Exception
Bio::Root::NotImplemented
Purpose : Indicates that a method has not been implemented.
Example : throw Bio::Root::NotImplemented(
-text => "Method "foo" not implemented in module FooBar.",
-value => "foo" );
Bio::Root::IOException
Purpose : Indicates that some input/output-related trouble has occurred.
Example : throw Bio::Root::IOException(
-text => "Can't save data to file $file.",
-value => $! );
Bio::Root::FileOpenException
Purpose : Indicates that a file could not be opened.
Example : throw Bio::Root::FileOpenException(
-text => "Can't open file $file for reading.",
-value => $! );
Bio::Root::SystemException
Purpose : Indicates that a system call failed.
Example : unlink($file) or throw Bio::Root::SystemException(
-text => "Can't unlink file $file.",
-value => $! );
Bio::Root::BadParameter
Purpose : Indicates that one or more parameters supplied to a method
are invalid, unspecified, or conflicting.
Example : throw Bio::Root::BadParameter(
-text => "Required parameter "-foo" was not specified",
-value => "-foo" );
Bio::Root::OutOfRange
Purpose : Indicates that a specified (start,end) range or
an index to an array is outside the permitted range.
Example : throw Bio::Root::OutOfRange(
-text => "Start coordinate ($start) cannot be less than zero.",
-value => $start );
Bio::Root::NoSuchThing
Purpose : Indicates that a requested thing cannot be located
and therefore could possibly be bogus.
Example : throw Bio::Root::NoSuchThing(
-text => "Accession M000001 could not be found.",
-value => "M000001" );
perl v5.14.2 2012-03-02 Bio::Root::Exception(3pm)