NAME

Coils - Coils utilities.


SYNOPSIS

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


DESCRIPTION


VERSIONS

$Id: Coils.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        Coils 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 Coils command line.
 Arguments:   -
 Returns:     1, cmd on success
              0, msg on failure

parseResult

 Description: Reads a coils result file and creates a hash table:
              'nhits' => '2',
              '1'     => { 'seqid'   => '1srya',
                           'seqdesc' => 'SERYL-TRNA SYNTHETASE (E.C.6.1.1.11)  (THERMUS THERMOPHILUS, STRAIN HB27)',
                           'start'   => '30',
                           'end'     => '58'
                         },
              '2'     => { 'seqid'   => '1srya',
                           'seqdesc' => 'SERYL-TRNA SYNTHETASE (E.C.6.1.1.11)  (THERMUS THERMOPHILUS, STRAIN HB27)',
                           'start'   => '66',
                           'end'     => '101'
                         }
 Arguments:   $href          Reference to a hash.
              $result        Path to a Coils 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