Docs For Class Bio

Description

Bio.php Bio::PHP base class.

author: Mark Brooks <markabrooks@users.sourceforge.net>
version: 0.8.2
copyright: 2004-2008 Mark Brooks <markabrooks@users.sourceforge.net>
link: http://plasmidb.sf.net/
license: GPL

Located in /Root/Bio.php (line 47)

PEAR
   |
   --Bio

Direct descendents

Class	Description
Atom	class Atom
Molecule	Molecule
PeriodicTableData	PeriodicTableData
IUPACData	IUPACData
LetterConversionData	LetterConversionData
RestrictionEnzymeData	RestrictionEnzymeData
AlphabetEncoder	AlphabetEncoder
Translator	Translator
Aligner	Aligner
Factory	Factory
Str	String.php
Dictionary	Dictionary
RestrictionDigester	RestrictionDigester Contains definition of Restriction (restriction endonucleases) class.
RestrictionEnzyme	RestrictionEnzyme.php
Transcriber	Transcriber Takes a Dna Seq object and transcribes it.

Class Constant Summary

NEWLINE = "<BR>\n"

Variable Summary

static mixed $bWarnings

Method Summary

$this __construct (none 0)

void printWithNl (string $string, [string $nl = "<BR>\n"])

Variables

static mixed $bWarnings = TRUE (line 51)

access: public

Methods

Constructor __construct (line 61)

function Bio ()

$this __construct (none 0)

none 0

Redefined in descendants as:

Atom::__construct() : function __construct (constructor)
Molecule::__construct() : function __construct
IUPACData::__construct() : function __construct
Alphabet::__construct() : function Alphabet
SingleLetterAlphabet::__construct() : function __construct
ProteinAlphabet::__construct() : function __construct
IUPACProtein::__construct() : function __construct
ExtendedIUPACProtein::__construct() : function __construct
NucleotideAlphabet::__construct() : function __construct
DnaAlphabet::__construct() : function __construct
IUPACAmbiguousDna::__construct() : function __construct
IUPACUnambiguousDna::__construct() : function __construct
ExtendedIUPACDna::__construct() : function __construct
RnaAlphabet::__construct() : function __construct
IUPACAmbiguousRna::__construct() : function __construct
IUPACUnambiguousRna::__construct() : function __construct
ExtendedIUPACRna::__construct() : function __construct
SecondaryStructure::__construct() : function __construct
ThreeLetterProtein::__construct() : function __construct
AlphabetEncoder::__construct() : function __construct
Gapped::__construct() : function __construct
HasStopCodon::__construct() : function __construct
Translator::__construct() : function __construct
Aligner::__construct() : function __construct
AlphabetFactory::__construct() : function __construct
SeqFactory::__construct() : function __construct
Str::__construct() : function __construct
Seq::__construct() : function __construct
Protein::__construct() : function __construct
NucAcid::__construct() : __construct
Dna::__construct() : function __construct
Rna::__construct() : function __construct
Dictionary::__construct() : function __construct
NcbiTableDictionary::__construct() : function __construct
RestrictionEnzymeDictionary::__construct() : function __construct
RestrictionDigester::__construct() : function __construct Is the constructor method for the Restriction class. It creates a new RestrictionEnzyme object and initializes its properties accordingly.
RestrictionEnzyme::__construct() : function __construct Is the constructor method for the Restriction class. It creates a new RestrictionEnzyme object and initializes its properties accordingly.
Transcriber::__construct() : __construct

printWithNl (line 82)

function printWithNl

access: public

void printWithNl (string $string, [string $nl = "<BR>\n"])

string $nl: newline characters
string $string: to print

Class Constants

NEWLINE = "<BR>\n" (line 49)