NAME

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

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).

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Hilmar Lapp

Email hlapp-at-gmx.net

APPENDIX

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

_initialize_state

 Title   : _initialize_state
 Usage   : n/a; usually called by _initialize()
 Function: This method is for BioPerl B<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. B<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 L<new()|new> and L<_initialize()|_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_query

 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_subject

 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_date

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

analysis_method

 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_version

 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