Garbage Band Bio

Bio::NEXUS::WeightSet is a Perl module that represents column weights in alignment ( for each character). SYNOPSIS new Bio::NEXUS::WeightSet($name, @weights, $iswt); A module representing column weights in alignment (for each character) METHODS new Title : new Usage : $node = new...

Bio::NEXUS::HistoryBlock is a Perl module that represents a HISTORY block of a NEXUS file. SYNOPSIS $block_object = new Bio::NEXUS::HistoryBlock(history, $block, $verbose); This is a class representing a history block in NEXUS file METHODS new Title : new Usage : block_object = new...

Bio::Ontology::Relationship is a relationship for an ontology. SYNOPSIS $rel = Bio::Ontology::Relationship->new( -identifier => "16847", -subject_term => $subj, -object_term => $obj, -predicate_term => $pred ); This is a basic implementation of Bio::Ontology::RelationshipI. The...


Platforms: *nix

Bio::Ontology::GOterm is a representation of GO terms. SYNOPSIS $term = Bio::Ontology::GOterm->new ( -go_id => "GO:0016847", -name => "1-aminocyclopropane-1-carboxylate synthase", -definition => "Catalysis of ...", -is_obsolete => 0, -comment => "" ); $term->add_definition_references(...


Platforms: *nix

Bio::ConnectDots::ConnectDots is a top level class for connect-the-dots. SYNOPSIS use Bio::ConnectDots::DB; use Bio::ConnectDots::ConnectDots; my $db=new Bio::ConnectDots::DB(-database=>test, -host=>computername, -user=>usename, -password=>secret); my $cd=my $cd=new...


Platforms: *nix

Bio::AnnotationCollectionI is a Perl interface for annotation collections. SYNOPSIS # get an AnnotationCollectionI somehow, eg $ac = $seq->annotation(); foreach $key ( $ac->get_all_annotation_keys() ) { @values = $ac->get_Annotations($key); foreach $value ( @values ) { # value is an...


Platforms: *nix

Bio::Seq is a sequence object, with features. SYNOPSIS # This is the main sequence object in Bioperl # gets a sequence from a file $seqio = Bio::SeqIO->new( -format => embl , -file => myfile.dat); $seqobj = $seqio->next_seq(); # SeqIO can both read and write sequences; see Bio::SeqIO #...


Platforms: *nix

Bio::PrimarySeqI is a Perl Interface definition for a Bio::PrimarySeq. SYNOPSIS # Bio::PrimarySeqI is the interface class for sequences. # If you are a newcomer to bioperl, you should # start with Bio::Seq documentation. This # documentation is mainly for developers using # Bioperl. #...


Platforms: *nix

Bio::Index::Swissprot is a Perl Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format). SYNOPSIS # Complete code for making an index for several # Swissprot files use Bio::Index::Swissprot; use strict; my $Index_File_Name = shift; my $inx =...


Platforms: *nix

Band Saw is a syslog monitoring program for the GNOME desktop. Band Saw project allows the user to setup filters that define which messages should generate alerts. Combined with syslogs remote logging functionality it provides a scalable and easily deployed monitoring solution. How does it...


Platforms: *nix

The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new. Boehm-Demers-Weiser Conservative Garbage Collector allows you to allocate memory basically as you normally would, without explicitly deallocating memory that is no...


Platforms: *nix

Bio::Tools::CodonTable is a bioperl codon table object. SYNOPSIS # This is a read-only class for all known codon tables. The IDs are # the ones used by nucleotide sequence databases. All common IUPAC # ambiguity codes for DNA, RNA and animo acids are recognized. # to use use...


Platforms: *nix

Bio::Map::CytoMap is a Bio::MapI compliant map implementation handling cytogenic bands. SYNOPSIS use Bio::Map::CytoMap; my $map = new Bio::Map::CytoMap(-name => human1, -species => $human); foreach my $marker ( @markers ) { # get a list of markers somewhere $map->add_element($marker); }...


Platforms: *nix

Bio::Biblio::Patent is a representation of a patent. SYNOPSIS $obj = new Bio::Biblio::Patent (-doc_number => 1-2-3-4-5); #--- OR --- $obj = new Bio::Biblio::Patent; $obj->doc_number (1-2-3-4-5); A storage object for a patent. See its place in the class hierarchy in...


Platforms: *nix

Bio::Ontology::Ontology is a standard implementation of an Ontology. SYNOPSIS use Bio::Ontology::Ontology; # create ontology object my $ont = Bio::Ontology::Ontology->new(-name => "OBF"); # add terms, relationships ... my $bp = Bio::Ontology::Term->new(-name => "Bioperl"); my $obf =...


Platforms: *nix

Bio::Factory::SeqAnalysisParserFactoryI is a Perl interface describing objects capable of creating SeqAnalysisParserI compliant parsers. SYNOPSIS # initialize an object implementing this interface, e.g. $factory = Bio::Factory::SeqAnalysisParserFactory->new(); # obtain a parser object...


Platforms: *nix

Bio::Location::CoordinatePolicyI is an abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location. SYNOPSIS # get a location, e.g., from a SeqFeature $location = $feature->location(); # examine its coordinate computation policy print...


Platforms: *nix

Bio::Tools::Run::PiseApplication::freak is a Perl module. Bio::Tools::Run::PiseApplication::freak Bioperl class for: FREAK Residue/base frequency table or plot (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/freak.html for available values): freak...


Platforms: *nix

Bio::MAGE::Protocol::SoftwareApplication is a Perl module. SYNOPSIS use Bio::MAGE::Protocol::SoftwareApplication; # creating an empty instance my $softwareapplication = Bio::MAGE::Protocol::SoftwareApplication->new(); # creating an already populated instance my $softwareapplication =...


Platforms: *nix

Bio::MAGE::Protocol::Software - Software represents the software used. SYNOPSIS use Bio::MAGE::Protocol::Software; # creating an empty instance my $software = Bio::MAGE::Protocol::Software->new(); # creating an already populated instance my $software =...


Platforms: *nix