.\" -*- mode: troff; coding: utf-8 -*-
.\" Automatically generated by Pod::Man 5.01 (Pod::Simple 3.43)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" \*(C` and \*(C' are quotes in nroff, nothing in troff, for use with C<>.
.ie n \{\
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds C`
.    ds C'
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is >0, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.\"
.\" Avoid warning from groff about undefined register 'F'.
.de IX
..
.nr rF 0
.if \n(.g .if rF .nr rF 1
.if (\n(rF:(\n(.g==0)) \{\
.    if \nF \{\
.        de IX
.        tm Index:\\$1\t\\n%\t"\\$2"
..
.        if !\nF==2 \{\
.            nr % 0
.            nr F 2
.        \}
.    \}
.\}
.rr rF
.\" ========================================================================
.\"
.IX Title "Bio::Tools::Run::Prints 3pm"
.TH Bio::Tools::Run::Prints 3pm 2024-04-27 "perl v5.38.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH NAME
Bio::Tools::Run::Prints \- PRINTS fingerprint identification algorithm
.SH SYNOPSIS
.IX Header "SYNOPSIS"
.Vb 1
\&  Build a Prints factory
\&
\&  my @params = (\*(AqDB\*(Aq,$dbfile);
\&  my $factory = Bio::Tools::Run::Prints\->new($params);
\&
\&  # Pass the factory a Bio::Seq object
\&  # @feats is an array of Bio::SeqFeature::Generic objects
\&  my @feats = $factory\->run($seq);
.Ve
.SH DESCRIPTION
.IX Header "DESCRIPTION"
.Vb 2
\&  FingerPRINTScan II is a PRINTS fingerprint identification algorithm.
\&  Copyright (C) 1998,1999  Phil Scordis
.Ve
.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
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Bala"
.IX Header "AUTHOR - Bala"
.Vb 1
\& Email savikalpa@fugu\-sg.org
.Ve
.SH APPENDIX
.IX Header "APPENDIX"
.Vb 2
\& The rest of the documentation details each of the object
\& methods. Internal methods are usually preceded with a _
.Ve
.SS program_name
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $factory>program_name()
\& Function: holds the program name
\& Returns:  string
\& Args    : None
.Ve
.SS program_dir
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : $factory\->program_dir(@params)
\& Function: returns the program directory, obtained from ENV variable.
\& Returns:  string
\& Args    :
.Ve
.SS new
.IX Subsection "new"
.Vb 5
\& Title   : new
\& Usage   : $prints\->new(@params)
\& Function: creates a new Prints factory
\& Returns:  Bio::Tools::Run::Prints
\& Args    :
.Ve
.SS predict_protein_features
.IX Subsection "predict_protein_features"
.Vb 5
\& Title   :   predict_protein_features()
\& Usage   :   DEPRECATED. Use $obj\->run($seqFile) instead.
\& Function:   Runs Prints and creates an array of featrues
\& Returns :   An array of Bio::SeqFeature::Generic objects
\& Args    :   A Bio::PrimarySeqI
.Ve
.SS run
.IX Subsection "run"
.Vb 5
\& Title   :   run 
\& Usage   :   $obj\->run($seq)
\& Function:   Runs Prints 
\& Returns :   An array of Bio::SeqFeature::Generic objects
\& Args    :   A Bio::PrimarySeqI, or a Fasta file name
.Ve
.SS _input
.IX Subsection "_input"
.Vb 5
\& Title   :   _input
\& Usage   :   obj\->_input($seqFile)
\& Function:   Internal(not to be used directly)
\& Returns :
\& Args    :
.Ve
.SS _run
.IX Subsection "_run"
.Vb 5
\& Title   :   _run
\& Usage   :   $obj\->_run()
\& Function:   Internal(not to be used directly)
\& Returns :   An array of Bio::SeqFeature::Generic objects
\& Args    :
.Ve
.SS _writeSeqFile
.IX Subsection "_writeSeqFile"
.Vb 5
\& Title   :   _writeSeqFile
\& Usage   :   obj\->_writeSeqFile($seq)
\& Function:   Internal(not to be used directly)
\& Returns :
\& Args    :
.Ve