Class Sequence

Sequence is an envelope holding information about one specific sequence

Namespace: DispatchModule
Located at DispatchModule/Sequence.php

Methods summary
`public`	# `loadData( array $data, $object = null )` Loads data from array into properties Loads data from array into properties Parameters `$data` array containing values indexed by attributes (properties) name `$object`
`protected mixed`	# `addOrdinal( mixed $data )` Adds preformated value - date/array/formated string Adds preformated value - date/array/formated string Parameters `$data` Returns mixed
`protected string`	# `formatString( string $string )` Formats string for displaying (newlines, etc) Formats string for displaying (newlines, etc) Parameters `$string` Returns string
`public array`	# `convertIntoOneDimensionalArray( )` Converts Sequence object into one dimensional array Converts Sequence object into one dimensional array Returns array One dimensional array
`public static array`	# `loadSequenceInfo( DispatchModule\SearchParser $searchParser, string $accession, integer $start = null, integer $stop = null )` Gets all info about sequence from database Gets all info about sequence from database Parameters `$searchParser` instance of search parser `$accession` accession number `$start` (optional) start position `$stop` (optional) stop position Returns array sequence data Throws `BaseModule\Exceptions\NotFoundException`
`public static string`	# `getPredictionFromGroup( array $predictions, integer $prediction_id )` Gets prediction structure from all sequence predictions Gets prediction structure from all sequence predictions Parameters `$predictions` array containing info about all structure predictions `$prediction_id` id of prediction to get Returns string prediction structure Throws `BaseModule\Exceptions\NotFoundException`
`public static string`	# `makeSimplePrediction( string $complexPrediction )` Simplifies the prediction - converts pseudoknots to ordinary knots ({}, [] -> ()) Simplifies the prediction - converts pseudoknots to ordinary knots ({}, [] -> ()) Parameters `$complexPrediction` prediction including curly braces/brackets Returns string simple dot-paren string suitable for use in ViennaRNA package

Properties summary
`public string`	`$sequence` String of nucleotide sequence String of nucleotide sequence	#
`public array`	`$matches` Statistics from similarity search Statistics from similarity search	# `array()`
`public string`	`$accession` Biological identifier Biological identifier	#
`public integer`	`$startPosition` Sequence region start Sequence region start	#
`public integer`	`$stopPosition` Sequence region stop Sequence region stop	#
`public integer`	`$regionLength` Length of sequence Length of sequence	#
`public string`	`$dataset` Source dataset Source dataset	#
`public float`	`$sequenceQuality` SILVA quality indicator (combination of ambig./homopol./vec.contam.) SILVA quality indicator (combination of ambig./homopol./vec.contam.)	#
`public float`	`$ambiguities` % of ambiguously sequenced nucleotides % of ambiguously sequenced nucleotides	#
`public float`	`$homopolymers` % of homopolymers longer than 4 nt. % of homopolymers longer than 4 nt.	#
`public float`	`$vectorContamination` % of sequence contaminated by vector % of sequence contaminated by vector	#
`public float`	`$alignmentQuality` Conservancy indicator Conservancy indicator	#
`public integer`	`$basePairScore` SILVA-specific: possible base pairs in common with SILVA ref. structure SILVA-specific: possible base pairs in common with SILVA ref. structure	#
`public integer`	`$alignedBases` Number of seq. bases aligned to within rRNA gene Number of seq. bases aligned to within rRNA gene	#
`public integer`	`$pintailQuality` Confidence that sequence is not anomalous Confidence that sequence is not anomalous	#
`public string`	`$description` Often contains 16S/23S/... info Often contains 16S/23S/... info	#
`public string`	`$moleculeType` Sequence source molecule type (rRNA, mRNA, DNA, etc.) Sequence source molecule type (rRNA, mRNA, DNA, etc.)	#
`public string`	`$dataClass` ENA data class annotation ENA data class annotation	#
`public string`	`$taxonomicDivision` ENA taxonomic division annotation ENA taxonomic division annotation	#
`public integer`	`$version` Version of the record in ENA database Version of the record in ENA database	#
`public timestamp`	`$firstPublic` Date when it was first published Date when it was first published	#
`public timestamp`	`$lastUpdated` Date of the last update Date of the last update	#
`public string`	`$lastUpdatedRelease` Identifier of the last release within this record has been updated Identifier of the last release within this record has been updated	#
`public string`	`$comment` Author’s comment Author’s comment	#
`public string`	`$name` Name of current specie Name of current specie	#
`public string`	`$pathName`	#
`public string`	`$annotationSource` Contains names of all of node’s ancestors recursively from the root. By default separated by a semicolon. Contains names of all of node’s ancestors recursively from the root. By default separated by a semicolon.	#
`public integer`	`$state` Allows to classify items Allows to classify items	#
`public array`	`$references` Contains information about references (ie. an article, paper,...) Contains information about references (ie. an article, paper,...)	#
`public array`	`$features` Unions some properties of a region of a nucleotide sequence (part of a gene) Unions some properties of a region of a nucleotide sequence (part of a gene)	#
`public array`	`$xrefs` Contains data about references (links) to external databases. Reference can be stored for annotaion (reference to a DB) or annotation reference (journal, webpage) as well Contains data about references (links) to external databases. Reference can be stored for annotaion (reference to a DB) or annotation reference (journal, webpage) as well	#
`public array`	`$predictions` Contains information about secondary structure prediction Contains information about secondary structure prediction	#

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Classes

Class Sequence

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