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Summary

Bio::Tools::AnalysisResult - Base class for analysis result objects and parsers

Package variables

Included modules

Inherit

Bio::AnalysisResultI Bio::Root::IO Bio::Root::Root Bio::SeqAnalysisParserI

Synopsis

    # obtain a AnalysisResult derived object somehow
    print "Method ", $result->analysis_method(),
          ", version " $result->analysis_method_version(), 
          ", performed on ", $result->analysis_date(), "\n";
    # annotate a sequence utilizing SeqAnalysisParserI methods
    while($feat = $result->next_feature()) {
	$seq->add_SeqFeature($feat);
    }
    $result->close();
    # query object, e.g. a Bio::SeqI implementing object
    $queryseq = $result->analysis_query();
    # Subject of the analysis -- may be undefined. Refer to derived module
    # to find out what is returned.
    $subject = $result->analysis_subject();

Description

The AnalysisResult module is supposed to be the base class for modules
encapsulating parsers and interpreters for the result of a analysis that was
carried out with a query sequence.
The notion of an analysis represented by this base class is that of a unary or
binary operator, taking either one query or a query and a subject and producing
a result. The query is e.g. a sequence, and a subject is either a sequence,
too, or a database of sequences.
This module also implements the Bio::SeqAnalysisParserI interface, and thus
can be used wherever such an object fits.
See Bio::SeqAnalysisParserI.
Developers will find a ready-to-use parse() method, but need to implement
next_feature() in an inheriting class. Support for initialization with input
file names and reading from streams is also ready to use.
Note that this module does not provide support for running an analysis.
Rather, it is positioned in the subsequent parsing step (concerned with
turning raw results into BioPerl objects).

Methods

Methods description

 Title   : _initialize_state
 Usage   : n/a; usually called by _initialize()
 Function: This method is for BioPerl developers only, as indicated by the
           leading underscore in its name.

           Performs initialization or reset of the state of this object. The
           difference to _initialize() is that it may be called at any time,
           and repeatedly within the lifetime of this object. Bnew() and _initialize(),
           i.e., named parameters following the -name=>$value convention.
           The following parameters are dealt with by the implementation
           provided here:
              -INPUT, -FH, -FILE
           (tags are case-insensitive).
 Example :
 Returns :
 Args    :

 Usage     : $result->analysis_date();
 Purpose   : Set/Get the date on which the analysis was performed.
 Returns   : String
 Argument  : 
 Comments  :

 Usage     : $result->analysis_method();
 Purpose   : Set/Get the name of the sequence analysis method that was used
             to produce this result (BLASTP, FASTA, etc.). May also be the
             actual name of a program.
 Returns   : String
 Argument  : n/a

 Usage     : $result->analysis_method_version();
 Purpose   : Set/Get the version string of the analysis program.
           : (e.g., 1.4.9MP, 2.0a19MP-WashU).
 Returns   : String
 Argument  : n/a

 Usage     : $query_obj = $result->analysis_query();
 Purpose   : Set/Get the name of the query used to generate the result, that
             is, the entity on which the analysis was performed. Will mostly
             be a sequence object (Bio::PrimarySeq compatible).
 Argument  : 
 Returns   : The object set before. Mostly a Bio::PrimarySeq compatible object.

 Usage     : $result->analyis_subject();
 Purpose   : Set/Get the subject of the analysis against which it was
             performed. For similarity searches it will probably be a database,
             and for sequence feature predictions (exons, promoters, etc) it
             may be a collection of models or homologous sequences that were
             used, or undefined.
 Returns   : The object that was set before, or undef.
 Argument  :

Methods code

sub _initialize {

  my($self,@args) = @_;

  my $make = $self->SUPER::_initialize(@args);

  $self->_initialize_state(@args);
  return $make; # success - we hope!

}

sub _initialize_state {

    my ($self,@args) = @_;

    $self->close();
    $self->_initialize_io(@args);

    $self->{'_analysis_sbjct'} = undef;
    $self->{'_analysis_query'} = undef;
    $self->{'_analysis_prog'} = undef;
    $self->{'_analysis_progVersion'} = undef;
    $self->{'_analysis_date'} = undef;

    return 1;
}

#  =head2 parse
#
#   Title   : parse
#   Usage   : $obj->parse(-input=>$inputobj, [ -params=>[@params] ],
#  		       [ -method => $method ] )
#   Function: Sets up parsing for feature retrieval from an analysis file, 
#             or object.
#
#             This method was originally required by SeqAnalysisParserI, but
#             is now discouraged due to potential problems in a multi-
#             threading environment (CORBA!). If called only once, it doesn't
#             add any functionality to calling new() with the same
#             parameters.
#
#             The implementation provided here calls automatically
#             _initialize_state() and passes on -input=>$inputobj and
#             @params as final arguments.
#   Example :
#   Returns : void
#   Args    : B<input>  - object/file where analysis are coming from
#  	   B<params> - parameter to use when parsing/running analysis
#  	   B<method> - method of analysis
#
#  =cut

}

sub analysis_date {

    my ($self, $date) = @_;
    if($date) {
	$self->{'_analysis_date'} = $date;
    }
    return $self->{'_analysis_date'};
}
#----------

}

sub analysis_method {

 #-------------
    my ($self, $method) = @_;  
    if($method) {
	$self->{'_analysis_prog'} = $method;
    }
    return $self->{'_analysis_prog'};

}

sub analysis_method_version {

#---------------------
    my ($self, $version) = @_; 
    if($version) {
	$self->{'_analysis_progVersion'} = $version;
    }
    return $self->{'_analysis_progVersion'}; 
}


1;

}

sub analysis_query {

    my ($self, $obj) = @_;
    if($obj) {
	$self->{'_analysis_query'} = $obj;
    }
    return $self->{'_analysis_query'};
}
#--------

}

sub analysis_subject {

 #---------------
    my ($self, $sbjct_obj) = @_; 
    if($sbjct_obj) {
	$self->{'_analysis_sbjct'} = $sbjct_obj;
    }
    return $self->{'_analysis_sbjct'};

}

sub new {

    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    $self->_initialize(@args);
    return $self;

}

sub parse {

    my ($self, @args) = @_;

    my ($input, $params, $method) = 
	$self->_rearrange([qw(INPUT
			      PARAMS
			      METHOD
			      )],
			  @args);

    # initialize with new input
    if($params) {
	$self->_initialize_state('-input' => $input, @$params);
    } else {
	$self->_initialize_state('-input' => $input);
    }
    $self->analysis_method($method) if $method;

}

General documentation

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
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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/

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Describe contact details here

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