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Bio::NEXUS::DistancesBlock 0.67

  Date Added: July 08, 2010  |  Visits: 685

Bio::NEXUS::DistancesBlock

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Bio::NEXUS::DistancesBlock is a Perl module that represents DISTANCES block in NEXUS file. The DistancesBlock class represents a NEXUS Distances Block and provides methods for reading, writing, and accessing data within these blocks. Distances Blocks contain distance matrices, or a table of calculated distances between each possible pair of taxa. METHODS new Title : new Usage : block_object = new Bio::NEXUS::DistancesBlock($block_type, $commands, $verbose, $taxa); Function: Creates a new Bio::NEXUS::DistancesBlock object Returns : Bio::NEXUS::DistancesBlock object Args : type (string), the commands/comments to parse (array ref), and a verbose flag (0 or 1) get_matrix Title : get_matrix Usage : $matrix = $self->get_matrix(); Function: Retrieves the entire distance matrix Returns : a hashref of hashrefs Args : none Note : Distance values may be retrieved by specifying the row and column keys, e.g. $dist = $matrix->{$row_taxon}{$col_taxon} get_distances_for Title : get_distances_for Usage : %taxon1_distances = %{ $self->get_distances_for($first_taxon) }; Function: Retrieves a row of the distance matrix Returns : Args : the row label (a taxlabel) for the row desired (string) get_distance_between Title : get_distance_between Usage : $distance = $self->get_distance_between($row_taxon, $column_taxon); Function: Retrieves a cell from the matrix Returns : A scalar (number) Args : the row and column labels (both taxa) for the cell desired Note : Generally get_distance_between($A, $B) == get_distance_between($B, $A); however, this need not be true if the distance matrix is not symmetric. Make sure you are asking for the distance you want..

Requirements: No special requirements
Platforms: Linux
Keyword: Bionexusdistancesblock Block Distance Distancesblock Libraries Matrix Nexus Perl Module Programming Represents Row Taxon
Users rating: 0/10

License: Freeware Size: 153.6 KB
BIO::NEXUS::DISTANCESBLOCK RELATED
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Bio::NEXUS::DataBlock is a Perl module that represents the deprecated DATA Block in NEXUS file. SYNOPSIS $block_object = new Bio::NEXUS::DataBlock($type, $block, $verbose, $taxlabels_ref); The DataBlock class represents the deprecated Data...
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Libraries  -  Bio::NEXUS::TaxaBlock 0.67
Bio::NEXUS::TaxaBlock is a Perl module that represents TAXA block of a NEXUS file. SYNOPSIS if ( $type =~ /taxa/i ) { $block_object = new Bio::NEXUS::TaxaBlock($type, $block, $verbose); } If a NEXUS block is a taxa block, this module...
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Libraries  -  Bio::NEXUS::TreesBlock 0.67
Bio::NEXUS::TreesBlock is a Perl module that represents TREES block of a NEXUS file. SYNOPSIS if ( $type =~ /trees/i ) { $block_object = new Bio::NEXUS::TreesBlock( $block_type, $block, $verbose ); } If a NEXUS block is a Trees Block, this...
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Libraries  -  Bio::NEXUS::HistoryBlock 0.67
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...
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Bio::NEXUS::CodonsBlock is a Perl module that represents CODONS block in NEXUS file. METHODS new Title : new Usage : block_object = new Bio::NEXUS::CodonsBlock(); Function: Creates a new Bio::NEXUS::CodonsBlock object Returns :...
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Libraries  -  Bio::NEXUS::UnalignedBlock 0.67
Bio::NEXUS::UnalignedBlock is a Perl module that represents an UNALIGNED block of a NEXUS file. SYNOPSIS if ( $type =~ /unaligned/i ) { $block_object = new Bio::NEXUS::UnalignedBlock($type, $block, $verbose); } This is a class representing...
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Bio::NEXUS::SetsBlock is a Perl module that represents SETS block of a NEXUS file. SYNOPSIS $block_object = new Bio::NEXUS::SetsBlock($block_type, $block, $verbose); Parses Sets block of NEXUS file and stores Sets data. METHODS new...
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