Bio::Prospect::SoapServer -- execute Prospect locally $Id: SoapServer.pm,v 1.10 2003/11/18 19:45:45 rkh Exp $
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 );
Bio::Prospect::SoapServer is runs Prospect remotely using SOAP as the protocol. Utilize a LocalClient object to actually run Prospect.
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
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
Name: ping() Purpose: return whether alive or not Arguments: none Returns: 0 - dead, 1 - alive
The following functions are documented for developers' benefit. THESE SHOULD NOT BE CALLED OUTSIDE OF THIS MODULE. YOU'VE BEEN WARNED.
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
To install Bio::Prospect::File, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Prospect::File
CPAN shell
perl -MCPAN -e shell install Bio::Prospect::File
For more information on module installation, please visit the detailed CPAN module installation guide.