Bio::Tools::AnalysisReUser(Contributed Perl DocumBio::Tools::AnalysisResult(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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
perl v5.14.1 2011-07-22 Bio::Tools::AnalysisResult(3)
