Bio::Tools AnalysisResult
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Summary
Bio::Tools::AnalysisResult - Base class for analysis result objects and parsers
Package variables
No package variables defined.
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
new
No description
Code
_initialize
No description
Code
_initialize_stateDescriptionCode
parse
No description
Code
analysis_queryDescriptionCode
analysis_subjectDescriptionCode
analysis_dateDescriptionCode
analysis_methodDescriptionCode
analysis_method_versionDescriptionCode
Methods description
_initialize_statecode    nextTop
 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. Note, however,
that this is potentially dangerous in a multi-threading
environment. In general, calling this method twice is discouraged
for this reason.
This method is supposed to reset the state such that any 'history' is lost. State information that does not change during object lifetime is not considered as history, e.g. parent, name, etc shall not be reset. An inheriting object should only be concerned with state information it introduces itself, and for everything else call SUPER::_initialize_state(@args). An example is parsing an input file: a state reset implies discarding any unread input, and the actual input itself, followed by setting the new input. The argument syntax is the same as for new() 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 :
analysis_querycodeprevnextTop
 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.
analysis_subjectcodeprevnextTop
 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 :
analysis_datecodeprevnextTop
 Usage     : $result->analysis_date();
Purpose : Set/Get the date on which the analysis was performed.
Returns : String
Argument :
Comments :
analysis_methodcodeprevnextTop
 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
analysis_method_versioncodeprevnextTop
 Usage     : $result->analysis_method_version();
Purpose : Set/Get the version string of the analysis program.
: (e.g., 1.4.9MP, 2.0a19MP-WashU).
Returns : String
Argument : n/a
Methods code
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    $self->_initialize(@args);
    return $self;
}
_initializedescriptionprevnextTop
sub _initialize {
  my($self,@args) = @_;

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

  $self->_initialize_state(@args);
  return $make; # success - we hope!
}
_initialize_statedescriptionprevnextTop
sub _initialize_state {
    my ($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
}
parsedescriptionprevnextTop
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 $method;
}
analysis_querydescriptionprevnextTop
sub analysis_query {
    my ($self, $obj) = @_;
    if($obj) {
	$self->{'_analysis_query'} = $obj;
    }
    return $self->{'_analysis_query'};
}
#--------
}
analysis_subjectdescriptionprevnextTop
sub analysis_subject {
#---------------
my ($self, $sbjct_obj) = @_; if($sbjct_obj) { $self->{'_analysis_sbjct'} = $sbjct_obj; } return $self->{'_analysis_sbjct'};
}
analysis_datedescriptionprevnextTop
sub analysis_date {
    my ($self, $date) = @_;
    if($date) {
	$self->{'_analysis_date'} = $date;
    }
    return $self->{'_analysis_date'};
}
#----------
}
analysis_methoddescriptionprevnextTop
sub analysis_method {
#-------------
my ($self, $method) = @_; if($method) { $self->{'_analysis_prog'} = $method; } return $self->{'_analysis_prog'};
}
analysis_method_versiondescriptionprevnextTop
sub analysis_method_version {
#---------------------
my ($self, $version) = @_; if($version) { $self->{'_analysis_progVersion'} = $version; } return $self->{'_analysis_progVersion'}; } 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar LappTop
Email hlapp-at-gmx.net
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _