Summary

Bio::Tools::Analysis::SimpleAnalysisBase - abstact superclass for
SimpleAnalysis implementations

Package variables

Included modules

Inherit

Bio::SimpleAnalysisI Bio::WebAgent

Synopsis

  # no to be run directly

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.

Methods

Methods description

 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

 Usage   : $job->seq()
 Returns : a Bio::PrimarySeqI implementing sequence object, or void
 Args    : None, or a Bio::PrimarySeqI implementing object

    Useage   :  $analysis->analysis_name();
    Returns  :  The analysis name
    Arguments:  none

    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

    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.

    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

    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

Methods code

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;

}

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'} ;

}

sub analysis_name {

    my $self = shift;
    return $self->{'_ANALYSIS_NAME'};

}

sub analysis_spec {

    my $self = shift;
    return $self->{'_ANALYSIS_SPEC'};

}

sub clear {

	my $self= shift;
	if (defined($self->{'_result'})) {
		delete $self->{'_result'};
		}
	if (defined ($self->{'_parsed'})) {
		delete $self->{'_parsed'};
		}
	return 1;

}

sub input_spec {

    my $self = shift;
    return $self->{'_INPUT_SPEC'};

}

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();

}

General documentation

Bio::SimpleAnalysisI,
Bio::WebAgent

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

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/

Richard Adams, Richard.Adams@ed.ac.uk,
Heikki Lehvaslaiho, heikki@ebi.ac.uk

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _