AIIA-GMT
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# http://module-build.sourceforge.net/META-spec.html
#XXXXXXX This is a prototype!!! It will change in the future!!! XXXXX#
name: AIIA-GMT
version: 0.05
version_from: lib/AIIA/GMT.pm
installdirs: site
requires:
Frontier::Client: 0
distribution_type: module
generated_by: ExtUtils::MakeMaker version 6.30
To install this module type the following:
perl Makefile.PL
make
make test
make install
DEPENDENCIES
This module requires these other modules and libraries:
Frontier::Client
COPYRIGHT AND LICENCE
Copyright (c) 2008 by Cheng-Ju Kuo and the Institute of Information
Science, Academia Sinica, Taipei, Taiwan.
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.8.8 or,
lib/AIIA/GMT.pm view on Meta::CPAN
=head1 NAME
AIIA::GMT - a XML-RPC client of a web-service server, AIIA gene mention tagger, which provides the service to recognize named entities in the biomedical articles
=head1 SYNOPSIS
use YAML;
use AIIA::GMT;
$result = &text2entity('less than 3000 words');
print Dump $result;
=head1 DESCRIPTION
AIIA::GMT is a XML-RPC client of a web-service server, AIIA gene mention tagger, which provides the service to recognize named entities in the biomedical articles.
AIIA gene mention tagger, developed by Adaptive Internet Intelligent Agents Lab, Institute of Information Science, Academia Sinica, Taiwan and I-Fang Chung's Lab, Institute of Bioinformatics, National Yang-Ming University, Taiwan, is a named entity r...
This module is developed to help those who want to use this remote service with XML-RPC, rather than with its web interface. Finally, this module and service is released under a GPLv3 License. You're free to use it for both academic or personal use.
=head1 OPTIONS
=head2 --help
Display a brief usage summary.
=head2 --patch=I<file>
If this option is given, a single patch file will be created if
any changes are suggested. This requires a working diff program
to be installed on your system.
=head2 --copy=I<suffix>
If this option is given, a copy of each file will be saved with
the given suffix that contains the suggested changes. This does
not require any external programs.
If neither C<--patch> or C<--copy> are given, the default is to
simply print the diffs for each file. This requires either
C<Text::Diff> or a C<diff> program to be installed.
=head2 --diff=I<program>
Manually set the diff program and options to use. The default
is to use C<Text::Diff>, when installed, and output unified
context diffs.
=head2 --compat-version=I<version>
=head2 --list-unsupported
Lists the API elements that are known not to be supported by
F<ppport.h> and below which version of Perl they probably
won't be available or work.
=head2 --api-info=I<name>
Show portability information for API elements matching I<name>.
If I<name> is surrounded by slashes, it is interpreted as a regular
expression.
=head1 DESCRIPTION
In order for a Perl extension (XS) module to be as portable as possible
across differing versions of Perl itself, certain steps need to be taken.
=over 4
=item *
=item *
You should avoid using deprecated parts of the API. For example, using
global Perl variables without the C<PL_> prefix is deprecated. Also,
some API functions used to have a C<perl_> prefix. Using this form is
also deprecated. You can safely use the supported API, as F<ppport.h>
will provide wrappers for older Perl versions.
=item *
If you use one of a few functions that were not present in earlier
versions of Perl, and that can't be provided using a macro, you have
to explicitly request support for these functions by adding one or
more C<#define>s in your source code before the inclusion of F<ppport.h>.
These functions will be marked C<explicit> in the list shown by
C<--list-provided>.
Depending on whether you module has a single or multiple files that
use such functions, you want either C<static> or global variants.
=head1 EXAMPLES
To verify whether F<ppport.h> is needed for your module, whether you
should make any changes to your code, and whether any special defines
should be used, F<ppport.h> can be run as a Perl script to check your
source code. Simply say:
perl ppport.h
The result will usually be a list of patches suggesting changes
that should at least be acceptable, if not necessarily the most
efficient solution, or a fix for all possible problems.
If you know that your XS module uses features only available in
newer Perl releases, if you're aware that it uses C++ comments,
and if you want all suggestions as a single patch file, you could
use something like this:
perl ppport.h --compat-version=5.6.0 --cplusplus --patch=test.diff
If you only want your code to be scanned without any suggestions
for changes, use:
perl ppport.h --nochanges
perl ppport.h --diff='diff -C 10'
This would output context diffs with 10 lines of context.
To display portability information for the C<newSVpvn> function,
use:
perl ppport.h --api-info=newSVpvn
Since the argument to C<--api-info> can be a regular expression,
you can use
perl ppport.h --api-info=/_nomg$/
to display portability information for all C<_nomg> functions or
perl ppport.h --api-info=/./
to display information for all known API elements.
mg_length||5.005000|
mg_localize|||
mg_magical|||
mg_set|||
mg_size||5.005000|
mini_mktime||5.007002|
missingterm|||
mode_from_discipline|||
modkids|||
mod|||
moreswitches|||
mul128|||
mulexp10|||n
my_atof2||5.007002|
my_atof||5.006000|
my_attrs|||
my_bcopy|||n
my_betoh16|||n
my_betoh32|||n
my_betoh64|||n
my_betohi|||n
pad_block_start|||
pad_check_dup|||
pad_compname_type|||
pad_findlex|||
pad_findmy|||
pad_fixup_inner_anons|||
pad_free|||
pad_leavemy|||
pad_new|||
pad_push|||
pad_reset|||
pad_setsv|||
pad_sv|||
pad_swipe|||
pad_tidy|||
pad_undef|||
parse_body|||
parse_unicode_opts|||
path_is_absolute|||
peep|||
pending_ident|||
regtry|||
reguni|||
regwhite|||
reg|||
repeatcpy|||
report_evil_fh|||
report_uninit|||
require_errno|||
require_pv||5.006000|
rninstr|||
rsignal_restore|||
rsignal_save|||
rsignal_state||5.004000|
rsignal||5.004000|
run_body|||
runops_debug||5.005000|
runops_standard||5.005000|
rvpv_dup|||
rxres_free|||
rxres_restore|||
rxres_save|||
safesyscalloc||5.006000|n
safesysfree||5.006000|n
safesysmalloc||5.006000|n
safesysrealloc||5.006000|n
same_dirent|||
save_I16||5.004000|
save_I32|||
save_I8||5.006000|
save_aelem||5.004050|
save_alloc||5.006000|
strnEQ|||
strnNE|||
study_chunk|||
sub_crush_depth|||
sublex_done|||
sublex_push|||
sublex_start|||
sv_2bool|||
sv_2cv|||
sv_2io|||
sv_2iuv_non_preserve|||
sv_2iv_flags||5.009001|
sv_2iv|||
sv_2mortal|||
sv_2nv|||
sv_2pv_flags||5.007002|
sv_2pv_nolen|5.006000||p
sv_2pvbyte_nolen|||
sv_2pvbyte|5.006000||p
sv_2pvutf8_nolen||5.006000|
sv_2pvutf8||5.006000|
sv_pvutf8n_force||5.006000|
sv_pvutf8n||5.006000|
sv_pvutf8||5.006000|
sv_pv||5.006000|
sv_recode_to_utf8||5.007003|
sv_reftype|||
sv_release_COW|||
sv_release_IVX|||
sv_replace|||
sv_report_used|||
sv_reset|||
sv_rvweaken||5.006000|
sv_setiv_mg|5.006000||p
sv_setiv|||
sv_setnv_mg|5.006000||p
sv_setnv|||
sv_setpv_mg|5.006000||p
sv_setpvf_mg_nocontext|||pvn
sv_setpvf_mg|5.006000|5.004000|pv
sv_setpvf_nocontext|||vn
sv_setpvf||5.004000|v
# Scan for possible replacement candidates
my(%replace, %need, %hints, %depends);
my $replace = 0;
my $hint = '';
while (<DATA>) {
if ($hint) {
if (m{^\s*\*\s(.*?)\s*$}) {
$hints{$hint} ||= ''; # suppress warning with older perls
$hints{$hint} .= "$1\n";
}
else {
$hint = '';
}
}
$hint = $1 if m{^\s*$rccs\sHint:\s+(\w+)\s*$};
$replace = $1 if m{^\s*$rccs\s+Replace:\s+(\d+)\s+$rcce\s*$};
$replace{$2} = $1 if $replace and m{^\s*#\s*define\s+(\w+)(?:\([^)]*\))?\s+(\w+)};
for (qw(uses needs uses_todo needed_global needed_static)) {
for $func (keys %{$file{$_}}) {
push @{$global{$_}{$func}}, $filename;
}
}
$files{$filename} = \%file;
}
# Globally resolve NEED_'s
my $need;
for $need (keys %{$global{needs}}) {
if (@{$global{needs}{$need}} > 1) {
my @targets = @{$global{needs}{$need}};
my @t = grep $files{$_}{needed_global}{$need}, @targets;
@targets = @t if @t;
@t = grep /\.xs$/i, @targets;
@targets = @t if @t;
my $target = shift @targets;
$files{$target}{needs}{$need} = 'global';
# define ERRSV get_sv("@",FALSE)
#endif
#ifndef newSVpvn
# define newSVpvn(data,len) ((data) \
? ((len) ? newSVpv((data), (len)) : newSVpv("", 0)) \
: newSV(0))
#endif
/* Hint: gv_stashpvn
* This function's backport doesn't support the length parameter, but
* rather ignores it. Portability can only be ensured if the length
* parameter is used for speed reasons, but the length can always be
* correctly computed from the string argument.
*/
#ifndef gv_stashpvn
# define gv_stashpvn(str,len,create) gv_stashpv(str,create)
#endif
/* Replace: 1 */
#ifndef get_cv
# define get_cv perl_get_cv
}
#endif
#endif
/*
* Boilerplate macros for initializing and accessing interpreter-local
* data from C. All statics in extensions should be reworked to use
* this, if you want to make the extension thread-safe. See ext/re/re.xs
* for an example of the use of these macros.
*
* Code that uses these macros is responsible for the following:
* 1. #define MY_CXT_KEY to a unique string, e.g. "DynaLoader_guts"
* 2. Declare a typedef named my_cxt_t that is a structure that contains
* all the data that needs to be interpreter-local.
* 3. Use the START_MY_CXT macro after the declaration of my_cxt_t.
* 4. Use the MY_CXT_INIT macro such that it is called exactly once
* (typically put in the BOOT: section).
* 5. Use the members of the my_cxt_t structure everywhere as
* MY_CXT.member.
* 6. Use the dMY_CXT macro (a declaration) in all the functions that
* access MY_CXT.
#endif
/*
* The grok_* routines have been modified to use warn() instead of
* Perl_warner(). Also, 'hexdigit' was the former name of PL_hexdigit,
* which is why the stack variable has been renamed to 'xdigit'.
*/
#ifndef grok_bin
#if defined(NEED_grok_bin)
static UV DPPP_(my_grok_bin)(pTHX_ char *start, STRLEN *len_p, I32 *flags, NV *result);
static
#else
extern UV DPPP_(my_grok_bin)(pTHX_ char *start, STRLEN *len_p, I32 *flags, NV *result);
#endif
#ifdef grok_bin
# undef grok_bin
#endif
#define grok_bin(a,b,c,d) DPPP_(my_grok_bin)(aTHX_ a,b,c,d)
#define Perl_grok_bin DPPP_(my_grok_bin)
#if defined(NEED_grok_bin) || defined(NEED_grok_bin_GLOBAL)
UV
DPPP_(my_grok_bin)(pTHX_ char *start, STRLEN *len_p, I32 *flags, NV *result)
{
const char *s = start;
STRLEN len = *len_p;
UV value = 0;
NV value_nv = 0;
const UV max_div_2 = UV_MAX / 2;
bool allow_underscores = *flags & PERL_SCAN_ALLOW_UNDERSCORES;
bool overflowed = FALSE;
if (!(*flags & PERL_SCAN_DISALLOW_PREFIX)) {
/* strip off leading b or 0b.
for compatibility silently suffer "b" and "0b" as valid binary
numbers. */
if (len >= 1) {
if (s[0] == 'b') {
s++;
len--;
value = (value << 1) | (bit - '0');
continue;
}
/* Bah. We're just overflowed. */
warn("Integer overflow in binary number");
overflowed = TRUE;
value_nv = (NV) value;
}
value_nv *= 2.0;
/* If an NV has not enough bits in its mantissa to
* represent a UV this summing of small low-order numbers
* is a waste of time (because the NV cannot preserve
* the low-order bits anyway): we could just remember when
* did we overflow and in the end just multiply value_nv by the
* right amount. */
value_nv += (NV)(bit - '0');
continue;
}
if (bit == '_' && len && allow_underscores && (bit = s[1])
&& (bit == '0' || bit == '1'))
{
--len;
++s;
goto redo;
}
if (!(*flags & PERL_SCAN_SILENT_ILLDIGIT))
warn("Illegal binary digit '%c' ignored", *s);
break;
}
#endif
) {
warn("Binary number > 0b11111111111111111111111111111111 non-portable");
}
*len_p = s - start;
if (!overflowed) {
*flags = 0;
return value;
}
*flags = PERL_SCAN_GREATER_THAN_UV_MAX;
if (result)
*result = value_nv;
return UV_MAX;
}
#endif
#endif
#ifndef grok_hex
#if defined(NEED_grok_hex)
static UV DPPP_(my_grok_hex)(pTHX_ char *start, STRLEN *len_p, I32 *flags, NV *result);
static
#else
extern UV DPPP_(my_grok_hex)(pTHX_ char *start, STRLEN *len_p, I32 *flags, NV *result);
#endif
#ifdef grok_hex
# undef grok_hex
#endif
#define grok_hex(a,b,c,d) DPPP_(my_grok_hex)(aTHX_ a,b,c,d)
#define Perl_grok_hex DPPP_(my_grok_hex)
#if defined(NEED_grok_hex) || defined(NEED_grok_hex_GLOBAL)
UV
DPPP_(my_grok_hex)(pTHX_ char *start, STRLEN *len_p, I32 *flags, NV *result)
{
const char *s = start;
STRLEN len = *len_p;
UV value = 0;
NV value_nv = 0;
const UV max_div_16 = UV_MAX / 16;
bool allow_underscores = *flags & PERL_SCAN_ALLOW_UNDERSCORES;
bool overflowed = FALSE;
const char *xdigit;
if (!(*flags & PERL_SCAN_DISALLOW_PREFIX)) {
/* strip off leading x or 0x.
for compatibility silently suffer "x" and "0x" as valid hex numbers.
*/
if (len >= 1) {
if (s[0] == 'x') {
s++;
if (value <= max_div_16) {
value = (value << 4) | ((xdigit - PL_hexdigit) & 15);
continue;
}
warn("Integer overflow in hexadecimal number");
overflowed = TRUE;
value_nv = (NV) value;
}
value_nv *= 16.0;
/* If an NV has not enough bits in its mantissa to
* represent a UV this summing of small low-order numbers
* is a waste of time (because the NV cannot preserve
* the low-order bits anyway): we could just remember when
* did we overflow and in the end just multiply value_nv by the
* right amount of 16-tuples. */
value_nv += (NV)((xdigit - PL_hexdigit) & 15);
continue;
}
if (*s == '_' && len && allow_underscores && s[1]
&& (xdigit = strchr((char *) PL_hexdigit, s[1])))
{
--len;
++s;
goto redo;
}
if (!(*flags & PERL_SCAN_SILENT_ILLDIGIT))
warn("Illegal hexadecimal digit '%c' ignored", *s);
break;
}
#endif
) {
warn("Hexadecimal number > 0xffffffff non-portable");
}
*len_p = s - start;
if (!overflowed) {
*flags = 0;
return value;
}
*flags = PERL_SCAN_GREATER_THAN_UV_MAX;
if (result)
*result = value_nv;
return UV_MAX;
}
#endif
#endif
#ifndef grok_oct
#if defined(NEED_grok_oct)
static UV DPPP_(my_grok_oct)(pTHX_ char *start, STRLEN *len_p, I32 *flags, NV *result);
static
#else
extern UV DPPP_(my_grok_oct)(pTHX_ char *start, STRLEN *len_p, I32 *flags, NV *result);
#endif
#ifdef grok_oct
# undef grok_oct
#endif
#define grok_oct(a,b,c,d) DPPP_(my_grok_oct)(aTHX_ a,b,c,d)
#define Perl_grok_oct DPPP_(my_grok_oct)
#if defined(NEED_grok_oct) || defined(NEED_grok_oct_GLOBAL)
UV
DPPP_(my_grok_oct)(pTHX_ char *start, STRLEN *len_p, I32 *flags, NV *result)
{
const char *s = start;
STRLEN len = *len_p;
UV value = 0;
NV value_nv = 0;
const UV max_div_8 = UV_MAX / 8;
bool allow_underscores = *flags & PERL_SCAN_ALLOW_UNDERSCORES;
bool overflowed = FALSE;
for (; len-- && *s; s++) {
/* gcc 2.95 optimiser not smart enough to figure that this subtraction
out front allows slicker code. */
int digit = *s - '0';
if (digit >= 0 && digit <= 7) {
/* Write it in this wonky order with a goto to attempt to get the
compiler to make the common case integer-only loop pretty tight.
*/
value = (value << 3) | digit;
continue;
}
/* Bah. We're just overflowed. */
warn("Integer overflow in octal number");
overflowed = TRUE;
value_nv = (NV) value;
}
value_nv *= 8.0;
/* If an NV has not enough bits in its mantissa to
* represent a UV this summing of small low-order numbers
* is a waste of time (because the NV cannot preserve
* the low-order bits anyway): we could just remember when
* did we overflow and in the end just multiply value_nv by the
* right amount of 8-tuples. */
value_nv += (NV)digit;
continue;
}
if (digit == ('_' - '0') && len && allow_underscores
&& (digit = s[1] - '0') && (digit >= 0 && digit <= 7))
{
--len;
++s;
goto redo;
}
/* Allow \octal to work the DWIM way (that is, stop scanning
* as soon as non-octal characters are seen, complain only iff
* someone seems to want to use the digits eight and nine). */
if (digit == 8 || digit == 9) {
#endif
) {
warn("Octal number > 037777777777 non-portable");
}
*len_p = s - start;
if (!overflowed) {
*flags = 0;
return value;
}
*flags = PERL_SCAN_GREATER_THAN_UV_MAX;
if (result)
*result = value_nv;
return UV_MAX;
}
#endif
#endif
#ifdef NO_XSLOCKS
# ifdef dJMPENV
# define dXCPT dJMPENV; int rEtV = 0
# define XCPT_TRY_START JMPENV_PUSH(rEtV); if (rEtV == 0)
# define XCPT_TRY_END JMPENV_POP;
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