Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::AnalysisResultI - Interface for analysis result objects

SYNOPSIS

       Bio::AnalysisResultI defines an interface that must be implemented by a subclass. So you
       cannot create Bio::AnalysisResultI objects, only objects that inherit from
       Bio::AnalysisResultI.

DESCRIPTION

       The AnalysisResultI module provides an interface for modules encapsulating the result of
       an analysis that was carried out with a query sequence and an optional subject dataset.

       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 interface defines methods to access analysis result data and does not impose any
       constraints on how the analysis result data is acquired.

       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).

FEEDBACK

   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://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       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 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 the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Steve Chervitz, Hilmar Lapp

       Email sac@bioperl.org Email hlapp@gmx.net (author of Bio::Tools::AnalysisResult on which
       this module is based)

COPYRIGHT

       Copyright (c) 2001 Steve Chervitz. All Rights Reserved.

DISCLAIMER

       This software is provided "as is" without warranty of any kind.

APPENDIX

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

   analysis_query
        Usage     : $query_obj = $result->analysis_query();
        Purpose   : Get a Bio::PrimarySeqI-compatible object representing the entity
                    on which the analysis was performed. Lacks sequence information.
        Argument  : n/a
        Returns   : A Bio::PrimarySeqI-compatible object without sequence information.
                    The sequence will have display_id, description, moltype, and length data.

   analysis_subject
        Usage     : $obj = $result->analyis_subject();
        Purpose   : 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   : An object of a type the depends on the implementation
                    May also return undef for analyses that don\'t involve subjects.
        Argument  : n/a
        Comments  : Implementation of this method is optional.
                    AnalysisResultI provides a default behavior of returning undef.

   analysis_subject_version
        Usage     : $vers = $result->analyis_subject_version();
        Purpose   : Get the version string of the subject of the analysis.
        Returns   : String or undef for analyses that don\'t involve subjects.
        Argument  : n/a
        Comments  : Implementation of this method is optional.
                    AnalysisResultI provides a default behavior of returning undef.

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

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

   next_feature
        Title   : next_feature
        Usage   : $seqfeature = $obj->next_feature();
        Function: Returns the next feature available in the analysis result, or
                  undef if there are no more features.
        Example :
        Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
                  more features.
        Args    : none