Algorithm-TrunkClassifier

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Algorithm/TrunkClassifier/ppport.h  view on Meta::CPAN

  --version                   show version

  --patch=file                write one patch file with changes
  --copy=suffix               write changed copies with suffix
  --diff=program              use diff program and options

  --compat-version=version    provide compatibility with Perl version
  --cplusplus                 accept C++ comments

  --quiet                     don't output anything except fatal errors
  --nodiag                    don't show diagnostics
  --nohints                   don't show hints
  --nochanges                 don't suggest changes
  --nofilter                  don't filter input files

  --strip                     strip all script and doc functionality from
                              ppport.h

  --list-provided             list provided API
  --list-unsupported          list unsupported API

Algorithm/TrunkClassifier/ppport.h  view on Meta::CPAN

=head2 --cplusplus

Usually, F<ppport.h> will detect C++ style comments and
replace them with C style comments for portability reasons.
Using this option instructs F<ppport.h> to leave C++
comments untouched.

=head2 --quiet

Be quiet. Don't print anything except fatal errors.

=head2 --nodiag

Don't output any diagnostic messages. Only portability
alerts will be printed.

=head2 --nohints

Don't output any hints. Hints often contain useful portability
notes. Warnings will still be displayed.

Algorithm/TrunkClassifier/ppport.h  view on Meta::CPAN

PUSHmortal|5.009002||p
PUSHn|||
PUSHp|||
PUSHs|||
PUSHu|5.004000||p
PUTBACK|||
PerlIO_clearerr||5.007003|
PerlIO_close||5.007003|
PerlIO_context_layers||5.009004|
PerlIO_eof||5.007003|
PerlIO_error||5.007003|
PerlIO_fileno||5.007003|
PerlIO_fill||5.007003|
PerlIO_flush||5.007003|
PerlIO_get_base||5.007003|
PerlIO_get_bufsiz||5.007003|
PerlIO_get_cnt||5.007003|
PerlIO_get_ptr||5.007003|
PerlIO_read||5.007003|
PerlIO_seek||5.007003|
PerlIO_set_cnt||5.007003|

Algorithm/TrunkClassifier/ppport.h  view on Meta::CPAN

ptr_table_free||5.009005|
ptr_table_new||5.009005|
ptr_table_split||5.009005|
ptr_table_store||5.009005|
push_scope|||
put_byte|||
pv_display||5.006000|
pv_escape||5.009004|
pv_pretty||5.009004|
pv_uni_display||5.007003|
qerror|||
qsortsvu|||
re_compile||5.009005|
re_croak2|||
re_dup|||
re_intuit_start||5.009005|
re_intuit_string||5.006000|
readpipe_override|||
realloc||5.007002|n
reentrant_free|||
reentrant_init|||

Algorithm/TrunkClassifier/ppport.h  view on Meta::CPAN

write_no_mem|||
write_to_stderr|||
xmldump_all|||
xmldump_attr|||
xmldump_eval|||
xmldump_form|||
xmldump_indent|||v
xmldump_packsubs|||
xmldump_sub|||
xmldump_vindent|||
yyerror|||
yylex|||
yyparse|||
yywarn|||
);

if (exists $opt{'list-unsupported'}) {
  my $f;
  for $f (sort { lc $a cmp lc $b } keys %API) {
    next unless $API{$f}{todo};
    print "$f ", '.'x(40-length($f)), " ", format_version($API{$f}{todo}), "\n";

Algorithm/TrunkClassifier/ppport.h  view on Meta::CPAN

  }

  my $s = $warnings != 1 ? 's' : '';
  my $warn = $warnings ? " ($warnings warning$s)" : '';
  info("Analysis completed$warn");

  if ($file{changes}) {
    if (exists $opt{copy}) {
      my $newfile = "$filename$opt{copy}";
      if (-e $newfile) {
        error("'$newfile' already exists, refusing to write copy of '$filename'");
      }
      else {
        local *F;
        if (open F, ">$newfile") {
          info("Writing copy of '$filename' with changes to '$newfile'");
          print F $c;
          close F;
        }
        else {
          error("Cannot open '$newfile' for writing: $!");
        }
      }
    }
    elsif (exists $opt{patch} || $opt{changes}) {
      if (exists $opt{patch}) {
        unless ($patch_opened) {
          if (open PATCH, ">$opt{patch}") {
            $patch_opened = 1;
          }
          else {
            error("Cannot open '$opt{patch}' for writing: $!");
            delete $opt{patch};
            $opt{changes} = 1;
            goto fallback;
          }
        }
        mydiff(\*PATCH, $filename, $c);
      }
      else {
fallback:
        info("Suggested changes:");

Algorithm/TrunkClassifier/ppport.h  view on Meta::CPAN

  if (!defined $diff) {
    $diff = run_diff('diff -u', $file, $str);
  }

  if (!defined $diff) {
    $diff = run_diff('diff', $file, $str);
  }

  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';

Algorithm/TrunkClassifier/ppport.h  view on Meta::CPAN

        $diff .= $_;
      }
      close F;
      unlink $tmp;
      return $diff;
    }

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

  return undef;
}

sub rec_depend
{
  my($func, $seen) = @_;
  return () unless exists $depends{$func};
  $seen = {%{$seen||{}}};

Algorithm/TrunkClassifier/ppport.h  view on Meta::CPAN

  $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;
my %given_warnings;
sub hint
{
  $opt{quiet} and return;
  my $func = shift;

Algorithm/TrunkClassifier/ppport.h  view on Meta::CPAN

#  endif
#endif

#define _dpppDEC2BCD(dec) ((((dec)/100)<<8)|((((dec)%100)/10)<<4)|((dec)%10))
#define PERL_BCDVERSION ((_dpppDEC2BCD(PERL_REVISION)<<24)|(_dpppDEC2BCD(PERL_VERSION)<<12)|_dpppDEC2BCD(PERL_SUBVERSION))

/* It is very unlikely that anyone will try to use this with Perl 6
   (or greater), but who knows.
 */
#if PERL_REVISION != 5
#  error ppport.h only works with Perl version 5
#endif /* PERL_REVISION != 5 */

#ifdef I_LIMITS
#  include <limits.h>
#endif

#ifndef PERL_UCHAR_MIN
#  define PERL_UCHAR_MIN ((unsigned char)0)
#endif

Algorithm/TrunkClassifier/ppport.h  view on Meta::CPAN

#ifndef PERL_LOADMOD_IMPORT_OPS
#  define PERL_LOADMOD_IMPORT_OPS        0x4
#endif

/* Replace: 0 */

/* Replace perl_eval_pv with eval_pv */

#ifndef eval_pv
#if defined(NEED_eval_pv)
static SV* DPPP_(my_eval_pv)(char *p, I32 croak_on_error);
static
#else
extern SV* DPPP_(my_eval_pv)(char *p, I32 croak_on_error);
#endif

#ifdef eval_pv
#  undef eval_pv
#endif
#define eval_pv(a,b) DPPP_(my_eval_pv)(aTHX_ a,b)
#define Perl_eval_pv DPPP_(my_eval_pv)

#if defined(NEED_eval_pv) || defined(NEED_eval_pv_GLOBAL)

SV*
DPPP_(my_eval_pv)(char *p, I32 croak_on_error)
{
    dSP;
    SV* sv = newSVpv(p, 0);

    PUSHMARK(sp);
    eval_sv(sv, G_SCALAR);
    SvREFCNT_dec(sv);

    SPAGAIN;
    sv = POPs;
    PUTBACK;

    if (croak_on_error && SvTRUE(GvSV(errgv)))
	croak(SvPVx(GvSV(errgv), na));

    return sv;
}

#endif
#endif

#ifndef vload_module
#if defined(NEED_vload_module)

pod/TrunkClassifier.pod  view on Meta::CPAN

By comparing the output files, differences can be seen in how many folds of LOOCV has
been carried out, and in what probes where selected for the decision trunks. The log
file will also reflect that a different classification variable was used. Accuracy will
be good when classifying TISSUE, because the healthy and tumor samples have sufficiently
different gene expression values. For GRADE, however, all tumor samples have the same mean
and standard deviation, so the algorithm is not able to separate them.

=head2 WARNINGS AND ERROR MESSAGES

If an invalid argument is given, or if there is something wrong with the input data file
or supplementary file, the algorithm will output a warning or error message. Warnings
will not prevent the algorithm from running, but errors will. Here is a list of all
warnings/errors and how to interpret them

=head3 WARNINGS

=over 4

=item No classification variable names found in supplementary file

Indicates that the supplementary file has less than two columns. The algorithm expects the
first column to contain sample names and the following columns to contain class labels of
samples. The first row in the file must contain the names of the columns. For column 2, 3