# $Id: SimpleAnalysisBase.pm,v 1.5 2003/09/23 13:50:37 radams Exp $ # # BioPerl module for Bio::Tools::Analysis::SimpleAnalysisBase # # Cared for by Heikki Lehvaslaiho # # Copyright Richard Adams # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Analysis::SimpleAnalysisBase - abstact superclass for SimpleAnalysis implementations =head1 SYNOPSIS # no to be run directly =head1 DESCRIPTION This class is a generic implementation of SimpleAnalysisI and should be used as a base class for specific implementations. SimpleAnalysis implementing modules just need to provide a specific _run() result() and _init() methods, plus any get/set methods for parameter to the analysis program. =head1 SEE ALSO L, L =head1 FEEDBACK =head2 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. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists =head2 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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ =head1 AUTHORS Richard Adams, Richard.Adams@ed.ac.uk, Heikki Lehvaslaiho, heikki@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Analysis::SimpleAnalysisBase; use vars qw(@ISA); use strict; use Data::Dumper; use Bio::SimpleAnalysisI; use Bio::WebAgent; my $FLOAT = '[+-]?\d*\.\d*'; my %STATUS = map { $_ => 1 } qw(CREATED COMPLETED TERMINATED_BY_ERROR); @ISA = qw(Bio::WebAgent Bio::SimpleAnalysisI ); =head2 new Usage : $job->new(...) Returns : a new analysis object, Args : none (but an implementation may choose to add arguments representing parameters for the analysis program. Each key value of must have a method implemented for it in a subclass. A seq () method is provided here as this will probably be needed by all sequence analysis programs =cut sub new { my $class = shift; my $self = $class->SUPER::new(); #WebAGent new $self->_init; #this line has to be before the attributes are filled in while ( @_ ) { my $key = lc shift; $key =~ s/^-//; $self->$key(shift); } return $self; } =head2 seq Usage : $job->seq() Returns : a Bio::PrimarySeqI implementing sequence object, or void Args : None, or a Bio::PrimarySeqI implementing object =cut sub seq { my ($self,$value) = @_; if ( defined $value) { $self->throw("I need a Bio::PrimarySeqI, not [". $value. "]") unless $value->isa('Bio::PrimarySeqI'); $self->throw(" I need a PrimarySeq object, not a BioSeq object ") if $value->isa('Bio::SeqI'); my $mol_type = $self->analysis_spec->{'type'}; $self->throw("I need a [" . $mol_type . "] seq, not a [". $value->alphabet. "]") unless $value->alphabet =~/$mol_type/i; $self->{'_seq'} = $value; return $self; } return $self->{'_seq'} ; } =head2 analysis_name Useage : $analysis->analysis_name(); Returns : The analysis name Arguments: none =cut sub analysis_name { my $self = shift; return $self->{'_ANALYSIS_NAME'}; } =head2 analysis_spec Useage : $analysis->analysis_spec(); Returns : a hash reference to a hash of analysis parameters. See Bio::SimpleAnalysisI for a list of recommended key values. Arguments: none =cut sub analysis_spec { my $self = shift; return $self->{'_ANALYSIS_SPEC'}; } =head2 clear Usage :$analysis->clear(); Returns :true value on success Arguments :none Purpose :to remove raw results from a previous analysis so that an analysis can be repeated with different parameters. =cut sub clear { my $self= shift; if (defined($self->{'_result'})) { delete $self->{'_result'}; } if (defined ($self->{'_parsed'})) { delete $self->{'_parsed'}; } return 1; } =head2 input_spec Useage : $analysis->input_spec(); Returns : a reference to an array of hashes of analysis parameters. See Bio::SimpleAnalysisI for a list of recommended key values. Arguments: none =cut sub input_spec { my $self = shift; return $self->{'_INPUT_SPEC'}; } =head2 result_spec Useage : $analysis->result_spec(); Returns : a reference to a hashes of resultformats. See Bio::SimpleAnalysisI for a list of recommended key values. The key values can be used as parameters to the result() method, the values provide descriptions. Arguments: none =cut sub result_spec { my $self = shift; return $self->{'_RESULT_SPEC'}; } sub run { my ($self, $args) = @_; $self->_process_arguments ($args) if $args; # check input $self->throw("Need a sequence object as an input") unless $self->seq; $self->debug(Data::Dumper->Dump([$self],[$self])); # internal run() $self->_run; return $self; } sub wait_for { my ($self, $args) = @_; $self->run($args); } sub status { my ($self,$value) = @_; if( defined $value) { no strict 'refs'; my $class = ref($self); $self->throw("Not a valid status value [$value]\n". "Valid values are ". join(", ", keys %STATUS )) unless defined $STATUS{$value}; $self->{'_status'} = $value; use strict; } return $self->{'_status'} || 'CREATED' ; } sub _process_arguments { my ($self, $args) = @_; my %spec; map {$spec{ $_->{'name'} } = $_ } @{$self->input_spec}; $self->debug(Data::Dumper->Dump([\%spec, $args],[\%spec, $args])); foreach my $key (keys %$args) { my $value = $args->{$key}; $self->throw("Unknown argument [$key]") unless $spec{$key}; $self->$key($value); } foreach my $key (keys %spec) { $self->throw("Mandatory argument [$key] is not set") if $spec{$key}{'mandatory'} eq 'true' and not defined $self->$key; } } sub _run { shift->throw_not_implemented();}