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.\" ========================================================================
.\"
.IX Title "Bio::Tools::pSW 3pm"
.TH Bio::Tools::pSW 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Tools::pSW \- pairwise Smith Waterman object
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 6
\&    use Bio::Tools::pSW;
\&    use Bio::AlignIO;
\&    my $factory = Bio::Tools::pSW\->new( \*(Aq\-matrix\*(Aq => \*(Aqblosum62.bla\*(Aq,
\&                                       \*(Aq\-gap\*(Aq => 12,
\&                                       \*(Aq\-ext\*(Aq => 2,
\&                                       );
\&
\&    #use the factory to make some output
\&
\&    $factory\->align_and_show($seq1,$seq2,STDOUT);
\&
\&    # make a Bio::SimpleAlign and do something with it
\&
\&    my $aln = $factory\->pairwise_alignment($seq1,$seq2);
\&    my $alnout = Bio::AlignIO\->new(\-format => \*(Aqmsf\*(Aq,
\&                                  \-fh     => \e*STDOUT);
\&
\&    $alnout\->write_aln($aln);
.Ve
.SH "INSTALLATION"
.IX Header "INSTALLATION"
This module is included with the central Bioperl distribution:
.PP
.Vb 2
\&   http://bio.perl.org/Core/Latest
\&   ftp://bio.perl.org/pub/DIST
.Ve
.PP
Follow the installation instructions included in the \s-1INSTALL\s0 file.
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
pSW is an Alignment Factory for protein sequences. It builds pairwise
alignments using the Smith-Waterman algorithm. The alignment algorithm is
implemented in C and added in using an \s-1XS\s0 extension. The \s-1XS\s0 extension basically
comes from the Wise2 package, but has been slimmed down to only be the
alignment part of that (this is a good thing!). The \s-1XS\s0 extension comes
from the bioperl-ext package which is distributed along with bioperl.
\&\fIWarning:\fR This package will not work if you have not compiled the
bioperl-ext package.
.PP
The mixture of C and Perl is ideal for this sort of 
problem. Here are some plus points for this strategy:
.IP "Speed and Memory" 2
.IX Item "Speed and Memory"
The algorithm is actually implemented in C, which means it is faster than
a pure perl implementation (I have never done one, so I have no idea
how faster) and will use considerably less memory, as it efficiently
assigns memory for the calculation.
.IP "Algorithm efficiency" 2
.IX Item "Algorithm efficiency"
The algorithm was written using Dynamite, and so contains an automatic
switch to the linear space divide-and-conquer method. This means you
could effectively align very large sequences without killing your machine
(it could take a while though!).
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
User feedback is an integral part of the evolution of this and other
Bioperl modules.  Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.
.SS "Reporting Bugs"
.IX Subsection "Reporting Bugs"
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Ewan Birney, birney\-at\-sanger.ac.uk or birney\-at\-ebi.ac.uk
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Jason Stajich, jason\-at\-bioperl.org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with an underscore \*(L"_\*(R".
.SS "pairwise_alignment"
.IX Subsection "pairwise_alignment"
.Vb 5
\& Title   : pairwise_alignment
\& Usage   : $aln = $factory\->pairwise_alignment($seq1,$seq2)
\& Function: Makes a SimpleAlign object from two sequences
\& Returns : A SimpleAlign object
\& Args    :
.Ve
.SS "align_and_show"
.IX Subsection "align_and_show"
.Vb 2
\& Title   : align_and_show
\& Usage   : $factory\->align_and_show($seq1,$seq2,STDOUT)
.Ve
.SS "matrix"
.IX Subsection "matrix"
.Vb 6
\& Title     : matrix()
\& Usage     : $factory\->matrix(\*(Aqblosum62.bla\*(Aq);
\& Function  : Reads in comparison matrix based on name
\&           :
\& Returns   : 
\& Argument  : comparison matrix
.Ve
.SS "gap"
.IX Subsection "gap"
.Vb 7
\& Title     : gap
\& Usage     : $gap = $factory\->gap() #get
\&           : $factory\->gap($value) #set
\& Function  : the set get for the gap penalty
\& Example   :
\& Returns   : gap value 
\& Arguments : new value
.Ve
.SS "ext"
.IX Subsection "ext"
.Vb 7
\& Title     : ext
\& Usage     : $ext = $factory\->ext() #get
\&           : $factory\->ext($value) #set
\& Function  : the set get for the ext penalty
\& Example   :
\& Returns   : ext value 
\& Arguments : new value
.Ve