org.mathIT.genes

Class ORF

java.lang.Object

org.mathIT.genes.ORF

All Implemented Interfaces:

Serializable

public class ORF
extends Object
implements Serializable

This class represents an ORF (open reading frame), i.e., a possible gene (or part of a gene) of a living organism coding a particular protein. An ORF usually is opened with a start codon ATG and ended with one of the stop codons TAA, TAG and TGA.

Version:

1.0

Author:

Andreas de Vries

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
ORF(ArrayList<Codon> sequence) Constructor of this gene.
ORF(Codon[] sequence) Constructor of this gene.
ORF(String info, ArrayList<Codon> sequence) Constructor of this gene.
ORF(String info, CharSequence string) Constructor of this gene where sequence is a DNA sequence without start and stop codons.
ORF(TreeMap<Codon,Double> frequency) Constructor of this gene.

Method Summary

Modifier and Type	Method and Description
static ArrayList<ORF>	decode(CharSequence string) Factory method producing a list of genes from a specified DNA base sequence of the letters A, C, G, T.
static double	entropy(ArrayList<ORF> orfs) Returns the entropy of the frequency distribution of this gene.
static String	getFrequencyAsHTMLGraph(ArrayList<ORF> orfs) Returns the frequency distribution of the codons in the specified list of ORF's as HTML graph.
static String	getFrequencyAsHTMLTable(ArrayList<ORF> genes) Returns the frequency distribution of the codons in the specified list of genes as HTML table.
String	getInfo() Returns the info of this ORF.
ArrayList<Codon>	getSequence() Returns the codon sequence of this gene.
static ArrayList<ORF>	loadFASTA(boolean completeGenome) Returns a genome after opening a file in FASTA format, determined by a file chooser dialog.
static ArrayList<ORF>	loadORFs() Returns a genome after opening a file in GNOM format, found by a file chooser dialog.
static void	save(ArrayList<ORF> orfs) Saves this genome in GENE format.
String	toString() Returns a string representing this gene.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

ORF

public ORF(String info,
           CharSequence string)

Constructor of this gene where sequence is a DNA sequence without start and stop codons.

Parameters:

info - information about this ORF

string - a DNA sequence

ORF

public ORF(String info,
           ArrayList<Codon> sequence)

Constructor of this gene.

Parameters:

info - information about this ORF

sequence - a sequence of codons

ORF

public ORF(ArrayList<Codon> sequence)

Constructor of this gene.

Parameters:

sequence - a sequence of codons

ORF

public ORF(Codon[] sequence)

Constructor of this gene.

Parameters:

sequence - a sequence of codons

ORF

public ORF(TreeMap<Codon,Double> frequency)

Constructor of this gene.

Parameters:

frequency - the frequency distribution of the 64 codons

Method Detail

getInfo

public String getInfo()

Returns the info of this ORF.

Returns:

the info of this ORF

getSequence

public ArrayList<Codon> getSequence()

Returns the codon sequence of this gene.

Returns:

the codon sequence of this gene

getFrequencyAsHTMLTable

public static String getFrequencyAsHTMLTable(ArrayList<ORF> genes)

Returns the frequency distribution of the codons in the specified list of genes as HTML table. Each frequency is given in %.

Parameters:

genes - a list of genes

Returns:

an HTML string representing the frequency distribution of the codons in the specified list

getFrequencyAsHTMLGraph

public static String getFrequencyAsHTMLGraph(ArrayList<ORF> orfs)

Returns the frequency distribution of the codons in the specified list of ORF's as HTML graph. Each frequency is given in %.

Parameters:

orfs - a list of ORF's

Returns:

a graphical HTML string representing the frequency distribution of the 64 codons

entropy

public static double entropy(ArrayList<ORF> orfs)

Returns the entropy of the frequency distribution of this gene. The entropy is computed to the basis 2, i.e., H = - ∑ p_i log₂p_i.

Parameters:

orfs - a list of ORF's

Returns:

the entropy of the frequency distribution of this list of ORF's

toString

public String toString()

Returns a string representing this gene.

Overrides:

toString in class Object

Returns:

a string representing this gene

decode

public static ArrayList<ORF> decode(CharSequence string)

Factory method producing a list of genes from a specified DNA base sequence of the letters A, C, G, T.

Parameters:

string - DNA base sequence

Returns:

a list of genes decoded by the specified string

loadFASTA

public static ArrayList<ORF> loadFASTA(boolean completeGenome)

Returns a genome after opening a file in FASTA format, determined by a file chooser dialog. The method uses the flag completeGenome which specifies whether the file represents a complete genome or a single gene. In a complete genmome, the start codons and stop codons have to be recognized to identify the different genes. (???)

Parameters:

completeGenome - flag specifying whether the file represents a complete genome

Returns:

a genome determined by the FASTA file, or null if no file is selected

save

public static void save(ArrayList<ORF> orfs)

Saves this genome in GENE format.

Parameters:

orfs - a list of ORF's

loadORFs

public static ArrayList<ORF> loadORFs()

Returns a genome after opening a file in GNOM format, found by a file chooser dialog.

Returns:

a genome determined by the GNOM file, or null if no file is selected