Bio::Tools::AnalysisResult - Base class for analysis result objects and parsers # 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(); 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 the Bio::SeqAnalysisParserI manpage. Developers will find a ready-to-use the parse manpage() 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).

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://bio.perl.org/MailList.html - 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 email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ Email hlapp@gmx.net Describe contact details here 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 L<_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>() and L<_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