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Bio/Search/HSP/BlastHSP.pm  view on Meta::CPAN

           :      -PROGRAM      => string ('TBLASTN', 'BLASTP', etc.).
           :      -QUERY_NAME   => string, id of query sequence
           :      -HIT_NAME     => string, id of hit sequence
           :
 Comments  : Having the raw data allows this object to do lazy parsing of
           : the raw HSP data (i.e., not parsed until needed).
           :
           : Note that there is a fair amount of basic parsing that is
           : currently performed in this module that would be more appropriate
           : to do within a separate factory object.
           : This parsing code will likely be relocated and more initialization
           : parameters will be added to new().
           :
See Also   : L<Bio::SeqFeature::SimilarityPair::new()>, L<Bio::SeqFeature::Similarity::new()>

=cut

#----------------
sub new {
#----------------
    my ($class, @args ) = @_;

Bio/Search/HSP/PsiBlastHSP.pm  view on Meta::CPAN

           :      -PROGRAM      => string ('TBLASTN', 'BLASTP', etc.).
           :      -QUERY_NAME   => string, id of query sequence
           :      -HIT_NAME     => string, id of hit sequence
           :
 Comments  : Having the raw data allows this object to do lazy parsing of
           : the raw HSP data (i.e., not parsed until needed).
           :
           : Note that there is a fair amount of basic parsing that is
           : currently performed in this module that would be more appropriate
           : to do within a separate factory object.
           : This parsing code will likely be relocated and more initialization
           : parameters will be added to new().
           :
See Also   : L<Bio::SeqFeature::SimilarityPair::new()>, L<Bio::SeqFeature::Similarity::new()>

=cut

#----------------
sub new {
#----------------
    my ($class, @args ) = @_;

maintenance/cvs2cl_by_file.pl  view on Meta::CPAN

#
# There's a bug in Text::Wrap, which affects cvs2cl.  This script
# reveals it:
#
#   #!/usr/bin/perl -w
#
#   use Text::Wrap;
#
#   my $test_text =
#   "This script demonstrates a bug in Text::Wrap.  The very long line
#   following this paragraph will be relocated relative to the surrounding
#   text:
#
#   ====================================================================
#
#   See?  When the bug happens, we'll get the line of equal signs below
#   this paragraph, even though it should be above.";
#
#
#   # Print out the test text with no wrapping:
#   print "$test_text";