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lib/FAST/Bio/UnivAln.pm  view on Meta::CPAN

@ISA         = qw(Exporter);
@EXPORT      = qw();
@EXPORT_OK   = qw($VERSION %UnivAlnType @UnivAlnType
                  %UnivAlnForm @UnivAlnForm %UnivAlnAlphs @UnivAlnAlphs);
require 5.002;
use Carp;
#if ($] < 5.005) {carp "Not tested for Perl 5.002 or 5.003";}
use POSIX;
use File::Basename;

use vars qw($_NOFILE_FLAG $_GAP_SYMBOL $_UNKN_SYMBOL $_UNKN_SYMBOL2 $_NO_CONSENSUS_SYMBOL $_NaN $_MAX_SIZE_TAXANAME $_READSEQ $_CLUSTAL);
$_NOFILE_FLAG='_undef';
$_GAP_SYMBOL ='-';
$_UNKN_SYMBOL='\?'; # the backslash seems to be needed to be able to write
                    # ($str =~ /$_UNKN_SYMBOL/) ??!!
$_UNKN_SYMBOL2='N'; # ONLY USED IN UNDOCUMENTED FUNCTION special_free_seqs()
$_NO_CONSENSUS_SYMBOL='!';
$_NaN = POSIX::INT_MAX;   #anything better ?
$_MAX_SIZE_TAXANAME=20;
$_READSEQ = "";
$_CLUSTAL = "";
$ENV{READSEQ} = "readseq";
 # name of the readseq executable to be found in
 # $ENV{READSEQ_DIR} or "\.". Set this to "" if readseq is
 # installed, but shall be ignored
$ENV{CLUSTAL} = "clustal";
 # name of the clustal executable to be found in
 # $ENV{CLUSTAL_DIR} or "\.". Set this to "" if clustal is

lib/FAST/Bio/UnivAln.pm  view on Meta::CPAN

        delete $all_row_ids_hash{$row_id};
      } else {
        carp("Requested row named $row_id not found, or duplicate");
      }
    }
    $rowindices2 = \@rows;
  }

  if (ref($rowindices) eq 'CODE') {
    my $ctr = $firstindx - 1;
    $rowindices2 = [ grep {$_ != $_NaN}
                      # filter out $_NaN-value indexes, see next comment
                    map {($ctr++,$_) ? $ctr : $_NaN}
                      # convert list of function values into list of indices
                      # in canonical order, except that false values trigger an
                      # index of $_NaN, e.g. (1,$_NaN,3,$_NaN,5) is the result
                      # of map {($ctr++,$_) ? $ctr : $_NaN} ("A","","B",0,"C")
                      # note that the comma operator evaluates the first
                      # argument and throws the result away, and then
                      # evaluates the second argument; the side effect
                      # of the first evaluation is the increment of $ctr.
                    $self->map_r($rowindices) ];
  }

  my($ii);
  for $ii (0 .. $#{$rowindices2}) {
    if ($rowindices2->[$ii] < $firstindx) {

lib/FAST/Bio/UnivAln.pm  view on Meta::CPAN

    }
    my(@restkeys) = keys %col_ids_hash;
    if (scalar(@restkeys) > 0) {
      carp("Requested columns named @restkeys not found");
    }
    $colindices2 = \@cols;
  }

  if (ref($colindices) eq 'CODE') {
    my $ctr = $firstindx - 1;
    $colindices2 = [ grep {$_ != $_NaN}
                      # see _rowbounds()
                    map {($ctr++,$_) ? $ctr : $_NaN}
                    $self->map_c($colindices) ];
  }

  my($ii);
  for $ii (0 .. ($#{$colindices2})) {
    if ($colindices2->[$ii] < $firstindx) {
      carp "Requested column $colindices2->[$ii] of an alignment starting at $firstindx";
    }
    if (($colindices2->[$ii] - $firstindx + 1) > $width) {
      carp "Requested column $colindices2->[$ii] is beyond the end of the alignment";