NAME
Bio::Tools::AnalysisResult - Base class for analysis result objects and parsers
SYNOPSIS
# obtain a AnalysisResult derived object somehow
"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
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:
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