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AIIA-GMT
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lib/AIIA/GMT.pm  view on Meta::CPAN 

our $VERSION = '0.05';

require XSLoader;
XSLoader::load('AIIA::GMT', $VERSION);

# Preloaded methods go here.

# Autoload methods go after =cut, and are processed by the autosplit program.
my $SERVER_URL = 'http://bcsp1.iis.sinica.edu.tw:8080/aiiagmt/XmlRpcServlet';

sub pmid2entity {
    my $id = shift;
    die "Usage: &pmid2entity(\'PubMed Article ID\');\n" if ($id !~ /^\d+$/);
    return &submit($id);
}

sub text2entity {
    my $txt = shift;
    $txt =~ s/\n//g;
    my $num;
    map {$num++;} split(/\s/, $txt);
    die "Usage: &text2entity(\'less than 3000 words\');\n" if ($num > 3000);
    return &submit($txt);
}

sub submit {
    my @args = (shift);
    my $client = Frontier::Client->new(url => $SERVER_URL, debug => 0);
    my $ret = $client->call('Annotator.getAnnotation', @args);
    my @rep;
    map {push @rep, $_->{'offset'} . "\t" . $_->{'mention'};} @{$ret->{'mentions'}};
    @rep = sort @rep;
    return \@rep;
}

1;

ppport.h  view on Meta::CPAN 

PERL_MAGIC_overload|5.007002||p
PERL_MAGIC_pos|5.007002||p
PERL_MAGIC_qr|5.007002||p
PERL_MAGIC_regdata|5.007002||p
PERL_MAGIC_regdatum|5.007002||p
PERL_MAGIC_regex_global|5.007002||p
PERL_MAGIC_shared_scalar|5.007003||p
PERL_MAGIC_shared|5.007003||p
PERL_MAGIC_sigelem|5.007002||p
PERL_MAGIC_sig|5.007002||p
PERL_MAGIC_substr|5.007002||p
PERL_MAGIC_sv|5.007002||p
PERL_MAGIC_taint|5.007002||p
PERL_MAGIC_tiedelem|5.007002||p
PERL_MAGIC_tiedscalar|5.007002||p
PERL_MAGIC_tied|5.007002||p
PERL_MAGIC_utf8|5.008001||p
PERL_MAGIC_uvar_elem|5.007003||p
PERL_MAGIC_uvar|5.007002||p
PERL_MAGIC_vec|5.007002||p
PERL_MAGIC_vstring|5.008001||p

ppport.h  view on Meta::CPAN 

PERL_UINT_MIN|5.004000||p
PERL_ULONG_MAX|5.004000||p
PERL_ULONG_MIN|5.004000||p
PERL_UNUSED_DECL|5.007002||p
PERL_UQUAD_MAX|5.004000||p
PERL_UQUAD_MIN|5.004000||p
PERL_USHORT_MAX|5.004000||p
PERL_USHORT_MIN|5.004000||p
PERL_VERSION|5.006000||p
PL_DBsingle|||pn
PL_DBsub|||pn
PL_DBtrace|||n
PL_Sv|5.005000||p
PL_compiling|5.004050||p
PL_copline|5.005000||p
PL_curcop|5.004050||p
PL_curstash|5.004050||p
PL_debstash|5.004050||p
PL_defgv|5.004050||p
PL_diehook|5.004050||p
PL_dirty|5.004050||p

ppport.h  view on Meta::CPAN 

ck_retarget|||
ck_return|||
ck_rfun|||
ck_rvconst|||
ck_sassign|||
ck_select|||
ck_shift|||
ck_sort|||
ck_spair|||
ck_split|||
ck_subr|||
ck_substr|||
ck_svconst|||
ck_trunc|||
ck_unpack|||
cl_and|||
cl_anything|||
cl_init_zero|||
cl_init|||
cl_is_anything|||
cl_or|||
closest_cop|||

ppport.h  view on Meta::CPAN 

dofile|||
dofindlabel|||
doform|||
doing_taint||5.008001|n
dooneliner|||
doopen_pm|||
doparseform|||
dopoptoeval|||
dopoptolabel|||
dopoptoloop|||
dopoptosub_at|||
dopoptosub|||
dounwind|||
dowantarray|||
dump_all||5.006000|
dump_eval||5.006000|
dump_fds|||
dump_form||5.006000|
dump_indent||5.006000|v
dump_mstats|||
dump_packsubs||5.006000|
dump_sub||5.006000|
dump_vindent||5.006000|
dumpuntil|||
dup_attrlist|||
emulate_eaccess|||
eval_pv|5.006000||p
eval_sv|5.006000||p
expect_number|||
fbm_compile||5.005000|
fbm_instr||5.005000|
fd_on_nosuid_fs|||

ppport.h  view on Meta::CPAN 

form||5.004000|v
fp_dup|||
fprintf_nocontext|||vn
free_global_struct|||
free_tied_hv_pool|||
free_tmps|||
gen_constant_list|||
get_av|5.006000||p
get_context||5.006000|n
get_cv|5.006000||p
get_db_sub|||
get_debug_opts|||
get_hash_seed|||
get_hv|5.006000||p
get_mstats|||
get_no_modify|||
get_num|||
get_op_descs||5.005000|
get_op_names||5.005000|
get_opargs|||
get_ppaddr||5.006000|

ppport.h  view on Meta::CPAN 

isALPHA|||
isDIGIT|||
isLOWER|||
isSPACE|||
isUPPER|||
is_an_int|||
is_gv_magical_sv|||
is_gv_magical|||
is_handle_constructor|||
is_list_assignment|||
is_lvalue_sub||5.007001|
is_uni_alnum_lc||5.006000|
is_uni_alnumc_lc||5.006000|
is_uni_alnumc||5.006000|
is_uni_alnum||5.006000|
is_uni_alpha_lc||5.006000|
is_uni_alpha||5.006000|
is_uni_ascii_lc||5.006000|
is_uni_ascii||5.006000|
is_uni_cntrl_lc||5.006000|
is_uni_cntrl||5.006000|

ppport.h  view on Meta::CPAN 

magic_freearylen_p|||
magic_freeovrld|||
magic_freeregexp|||
magic_getarylen|||
magic_getdefelem|||
magic_getglob|||
magic_getnkeys|||
magic_getpack|||
magic_getpos|||
magic_getsig|||
magic_getsubstr|||
magic_gettaint|||
magic_getuvar|||
magic_getvec|||
magic_get|||
magic_killbackrefs|||
magic_len|||
magic_methcall|||
magic_methpack|||
magic_nextpack|||
magic_regdata_cnt|||

ppport.h  view on Meta::CPAN 

magic_setenv|||
magic_setfm|||
magic_setglob|||
magic_setisa|||
magic_setmglob|||
magic_setnkeys|||
magic_setpack|||
magic_setpos|||
magic_setregexp|||
magic_setsig|||
magic_setsubstr|||
magic_settaint|||
magic_setutf8|||
magic_setuvar|||
magic_setvec|||
magic_set|||
magic_sizepack|||
magic_wipepack|||
magicname|||
make_trie|||
malloced_size|||n

ppport.h  view on Meta::CPAN 

scan_const|||
scan_formline|||
scan_heredoc|||
scan_hex|||
scan_ident|||
scan_inputsymbol|||
scan_num||5.007001|
scan_oct|||
scan_pat|||
scan_str|||
scan_subst|||
scan_trans|||
scan_version||5.009001|
scan_vstring||5.008001|
scan_word|||
scope|||
screaminstr||5.005000|
seed|||
set_context||5.006000|n
set_csh|||
set_numeric_local||5.006000|

ppport.h  view on Meta::CPAN 

share_hek_flags|||
share_hek|||
si_dup|||
sighandler|||n
simplify_sort|||
skipspace|||
sortsv||5.007003|
ss_dup|||
stack_grow|||
start_glob|||
start_subparse||5.004000|
stashpv_hvname_match||5.009003|
stdize_locale|||
strEQ|||
strGE|||
strGT|||
strLE|||
strLT|||
strNE|||
str_to_version||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

ppport.h  view on Meta::CPAN 

swash_fetch||5.007002|
swash_init||5.006000|
sys_intern_clear|||
sys_intern_dup|||
sys_intern_init|||
taint_env|||
taint_proper|||
tmps_grow||5.006000|
toLOWER|||
toUPPER|||
to_byte_substr|||
to_uni_fold||5.007003|
to_uni_lower_lc||5.006000|
to_uni_lower||5.007003|
to_uni_title_lc||5.006000|
to_uni_title||5.007003|
to_uni_upper_lc||5.006000|
to_uni_upper||5.007003|
to_utf8_case||5.007003|
to_utf8_fold||5.007003|
to_utf8_lower||5.007003|
to_utf8_substr|||
to_utf8_title||5.007003|
to_utf8_upper||5.007003|
tokeq|||
tokereport|||
too_few_arguments|||
too_many_arguments|||
unlnk|||
unpack_rec|||
unpack_str||5.007003|
unpackstring||5.008001|

ppport.h  view on Meta::CPAN 

my @srcext = qw( xs c h cc cpp );
my $srcext = join '|', @srcext;

if (@ARGV) {
  my %seen;
  @files = grep { -f && !exists $seen{$_} } map { glob $_ } @ARGV;
}
else {
  eval {
    require File::Find;
    File::Find::find(sub {
      $File::Find::name =~ /\.($srcext)$/i
          and push @files, $File::Find::name;
    }, '.');
  };
  if ($@) {
    @files = map { glob "*.$_" } @srcext;
  }
}

if (!@ARGV || $opt{filter}) {

ppport.h  view on Meta::CPAN 

  else {
    info("Looks good");
  }
}

close PATCH if $patch_opened;

exit 0;


sub mydiff
{
  local *F = shift;
  my($file, $str) = @_;
  my $diff;

  if (exists $opt{diff}) {
    $diff = run_diff($opt{diff}, $file, $str);
  }

  if (!defined $diff and can_use('Text::Diff')) {

ppport.h  view on Meta::CPAN 


  if (!defined $diff) {
    error("Cannot generate a diff. Please install Text::Diff or use --copy.");
    return;
  }

  print F $diff;

}

sub run_diff
{
  my($prog, $file, $str) = @_;
  my $tmp = 'dppptemp';
  my $suf = 'aaa';
  my $diff = '';
  local *F;

  while (-e "$tmp.$suf") { $suf++ }
  $tmp = "$tmp.$suf";

ppport.h  view on Meta::CPAN 


    unlink $tmp;
  }
  else {
    error("Cannot open '$tmp' for writing: $!");
  }

  return undef;
}

sub can_use
{
  eval "use @_;";
  return $@ eq '';
}

sub rec_depend
{
  my $func = shift;
  my %seen;
  return () unless exists $depends{$func};
  grep !$seen{$_}++, map { ($_, rec_depend($_)) } @{$depends{$func}};
}

sub parse_version
{
  my $ver = shift;

  if ($ver =~ /^(\d+)\.(\d+)\.(\d+)$/) {
    return ($1, $2, $3);
  }
  elsif ($ver !~ /^\d+\.[\d_]+$/) {
    die "cannot parse version '$ver'\n";
  }

ppport.h  view on Meta::CPAN 


  if ($r < 5 || ($r == 5 && $v < 6)) {
    if ($s % 10) {
      die "cannot parse version '$ver'\n";
    }
  }

  return ($r, $v, $s);
}

sub format_version
{
  my $ver = shift;

  $ver =~ s/$/000000/;
  my($r,$v,$s) = $ver =~ /(\d+)\.(\d{3})(\d{3})/;

  $v = int $v;
  $s = int $s;

  if ($r < 5 || ($r == 5 && $v < 6)) {

ppport.h  view on Meta::CPAN 


    $ver = sprintf "%d.%03d", $r, $v;
    $s > 0 and $ver .= sprintf "_%02d", $s;

    return $ver;
  }

  return sprintf "%d.%d.%d", $r, $v, $s;
}

sub info
{
  $opt{quiet} and return;
  print @_, "\n";
}

sub diag
{
  $opt{quiet} and return;
  $opt{diag} and print @_, "\n";
}

sub warning
{
  $opt{quiet} and return;
  print "*** ", @_, "\n";
}

sub error
{
  print "*** ERROR: ", @_, "\n";
}

my %given_hints;
sub hint
{
  $opt{quiet} and return;
  $opt{hints} or return;
  my $func = shift;
  exists $hints{$func} or return;
  $given_hints{$func}++ and return;
  my $hint = $hints{$func};
  $hint =~ s/^/   /mg;
  print "   --- hint for $func ---\n", $hint;
}

sub usage
{
  my($usage) = do { local(@ARGV,$/)=($0); <> } =~ /^=head\d$HS+SYNOPSIS\s*^(.*?)\s*^=/ms;
  my %M = ( 'I' => '*' );
  $usage =~ s/^\s*perl\s+\S+/$^X $0/;
  $usage =~ s/([A-Z])<([^>]+)>/$M{$1}$2$M{$1}/g;

  print <<ENDUSAGE;

Usage: $usage

ppport.h  view on Meta::CPAN 

#  define PUSHu(u)                       STMT_START { sv_setuv(TARG, (UV)(u)); PUSHTARG;  } STMT_END
#endif

#ifndef XPUSHu
#  define XPUSHu(u)                      STMT_START { sv_setuv(TARG, (UV)(u)); XPUSHTARG; } STMT_END
#endif

#if (PERL_VERSION < 4) || ((PERL_VERSION == 4) && (PERL_SUBVERSION <= 5))
/* Replace: 1 */
#  define PL_DBsingle               DBsingle
#  define PL_DBsub                  DBsub
#  define PL_Sv                     Sv
#  define PL_compiling              compiling
#  define PL_copline                copline
#  define PL_curcop                 curcop
#  define PL_curstash               curstash
#  define PL_debstash               debstash
#  define PL_defgv                  defgv
#  define PL_diehook                diehook
#  define PL_dirty                  dirty
#  define PL_dowarn                 dowarn

ppport.h  view on Meta::CPAN 

	line_t oldline = PL_curcop->cop_line;
	PL_curcop->cop_line = PL_copline;

	PL_hints &= ~HINT_BLOCK_SCOPE;
	if (stash)
		PL_curstash = PL_curcop->cop_stash = stash;

	newSUB(

#if   ((PERL_VERSION < 3) || ((PERL_VERSION == 3) && (PERL_SUBVERSION < 22)))
		start_subparse(),
#elif ((PERL_VERSION == 3) && (PERL_SUBVERSION == 22))
     		start_subparse(0),
#else  /* 5.003_23  onwards */
     		start_subparse(FALSE, 0),
#endif

		newSVOP(OP_CONST, 0, newSVpv(name,0)),
		newSVOP(OP_CONST, 0, &PL_sv_no),   /* SvPV(&PL_sv_no) == "" -- GMB */
		newSTATEOP(0, Nullch, newSVOP(OP_CONST, 0, sv))
	);

	PL_hints = oldhints;
	PL_curcop->cop_stash = old_cop_stash;
	PL_curstash = old_curstash;

ppport.h  view on Meta::CPAN 

#endif

#ifndef PERL_MAGIC_vec
#  define PERL_MAGIC_vec                 'v'
#endif

#ifndef PERL_MAGIC_utf8
#  define PERL_MAGIC_utf8                'w'
#endif

#ifndef PERL_MAGIC_substr
#  define PERL_MAGIC_substr              'x'
#endif

#ifndef PERL_MAGIC_defelem
#  define PERL_MAGIC_defelem             'y'
#endif

#ifndef PERL_MAGIC_glob
#  define PERL_MAGIC_glob                '*'
#endif

ppport.h  view on Meta::CPAN 

    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.
            */
          redo:
            if (!overflowed) {
                if (value <= max_div_8) {
                    value = (value << 3) | digit;



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