NAME

ScanRegExp - ScanRegExp utilities.


SYNOPSIS

  # examples here
  use Dispatcher::Tool::ScanRegExp;


DESCRIPTION


VERSIONS

$Id: ScanRegExp.pm.html,v 1.1.1.1 2005/08/18 13:18:25 hunter Exp $

Copyright (c) European Bioinformatics Institute 2002


AUTHORS / ACKNOWLEDGEMENTS

Ville Silventoinen <vsi@ebi.ac.uk> Emmanuel Quevillon <tuco@ebi.ac.uk>

new

 Description: Constructor allocates an anonymous hash, which
              is tied to the class.
 Arguments:   $name        ScanRegExp tool name (optional). If given, sets
                           the Dispatcher::Config object automatically inside
                           the object. If not given, the Dispatcher::Config
                           must be set later with setConfig.
              $defaults    Default values for configuration, hash reference
                           (optional).
 Returns:     $self object

getCmdLine

 Description: Returns ScanRegExp command line.
 Arguments:   -
 Returns:     1, cmd on success
              0, msg on failure

parseResult

 Description: Reads a scanregexp result file and creates a hash table:
              'nhits' => '2',
              '1'     => { 'seqid'  => 'WAP_RAT',
                           'methid' => 'PS00317',
                           'psdesc' => '4_DISULFIDE_CORE',
                           'start'  => '48',
                           'end'    => '61',
                           'status' => '?' },
              '2'     => { ... }
              ...
 Arguments:   $href          Reference to a hash.
              $result        Path to a ScanRegExp result file.
 Returns:     1, ''  on success
              0, msg on failure

getRawResult

 Description: Returns raw formatted result string.
 Arguments:   $href      Reference to a result hash.
              $seqs      Sequence hash (see InterProScan::checkSequences).
              $iprscan   Reference to Dispatcher::Tool::InterProScan object.
                         Required for IPR fields and GO terms.
              $ipr       1: add IPR fields
                         0: no (default)
              $go        1: add GO terms
                         0: no (default)
 Returns:     1, str on success
              0, msg on failure