NAME

 Bio::Prospect::SoapServer -- execute Prospect locally
 $Id: SoapServer.pm,v 1.10 2003/11/18 19:45:45 rkh Exp $

SYNOPSIS

 use Bio::Prospect::SoapServer;
 use Bio::Prospect::Options;
 my $p2options = new Bio::Prospect::Options;
 my $p2factory = new Bio::Prospect::SoapServer( {options=>$p2options} );
 my $xmlout = $p2factory->thread( $sequence );

DESCRIPTION

Bio::Prospect::SoapServer is runs Prospect remotely using SOAP as the protocol. Utilize a LocalClient object to actually run Prospect.

ROUTINES & METHODS

thread_summary()

 Name:      thread_summary()
 Purpose:   thread a sequence using Bio::Prospect::LocalClient
 Arguments: comma-separated list:
    0 - string containing sequence id
    1 - string, contains protein sequence (or '' if secondary structure is
        defined in #2)
    2 - string, contains secondary structure information in phd format
        (or '' if sequence is defined in #1)
    3 - string, one of 'scop', 'fssp', 'all' (or '' if templates is defined in #4)
        to define a template set
    4 - string, contains a space-separated list of templates (or '' if
        template set is defined in #3)
    5 - string, one of 'global' or 'global_local' for alignment type
    6 - string, either '0' (false) or '1' (true) for calculating zscores
 Returns:   XML string containing prospect results

thread()

 Name:      xml()
 Purpose:   thread a sequence using Bio::Prospect::LocalClient
 Arguments: comma-separated list:
    0 - string containing sequence id
    1 - string, contains protein sequence (or '' if secondary structure is
        defined in #2)
    2 - string, contains secondary structure information in phd format
        (or '' if sequence is defined in #1)
    3 - string, one of 'scop', 'fssp', 'all' (or '' if templates is defined in #4)
        to define a template set
    4 - string, contains a space-separated list of templates (or '' if
        template set is defined in #3)
    5 - string, one of 'global' or 'global_local' for alignment type
    6 - string, either '0' (false) or '1' (true) for calculating zscores
 Returns:   XML string containing prospect results

ping()

 Name:      ping()
 Purpose:   return whether alive or not
 Arguments: none
 Returns:   0 - dead, 1 - alive

INTERNAL METHODS & ROUTINES

The following functions are documented for developers' benefit. THESE SHOULD NOT BE CALLED OUTSIDE OF THIS MODULE. YOU'VE BEEN WARNED.

_parseOption()

 Name:      _parseOption()
 Purpose:   parse arguments to the thread, thread_summary, and xml() methods
 Arguments: comma-separated list:
    1 - string, one of 'scop', 'fssp', 'all' (or '' if templates is defined in #4)
        to define a template set
    2 - string, contains a space-separated list of templates (or '' if
        template set is defined in #3)
    3 - string, one of 'global' or 'global_local' for alignment type
    4 - string, either '0' (false) or '1' (true) for calculating zscores
 Returns:   Bio::Prospect::Options object