org.mathIT.genes

Class DNA

java.lang.Object

org.mathIT.genes.DNA

All Implemented Interfaces:

Serializable

public class DNA
extends Object
implements Serializable

This class represents the DNA genome of a living organism. The genome is the entire genetic information of a cell. It specifies an algorithm for creating and maintaining the entire organism containing the cell. Gene regulatory proteins supply some of the switches turning specific instructions of the algorithm on and off. These are the start codon ATG and the stop codons TAA, TAG and TGA. For usual DNA sequences, the heap memory heap size has to be augmented. A DNA sequence consisting of some 30 million letters requires a heap memory of some 1 GB, which can be allocated by invoking the application via

java -ms1024m -mx1024m org.mathIT.genes.DNA

Version:

1.1

Author:

Andreas de Vries

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
DNA(String name, ArrayList<Character> sequence) Constructor of this genome.
DNA(String name, char[] sequence) Constructor of this genome.

Method Summary

Modifier and Type	Method and Description
String	asHTMLString() Returns a string representing this genome, with line breaks encoded by " " instead of '\n'.
static DNA	encode(String name, CharSequence string) Factory method producing a genome from a specified DNA base sequence of the letters A, C, G, T.
double	entropy() Returns the entropy of the frequency distribution of this genome.
TreeMap<Character,Integer>	getFrequency() Returns the frequency distribution of the 4 nucleobases.
String	getFrequencyAsHTMLGraph() Returns the frequency distribution of the 64 codons as HTML graph.
String	getFrequencyAsHTMLTable() Returns the frequency distribution of the 64 codons as HTML table.
String	getName() Returns the name of this genome.
StringBuilder	getSequence() Returns the nucleobase sequence of this genome.
ArrayList<Character>	getSequenceAsArrayList() Returns the nucleobase sequence of this genome.
static DNA	loadDNA() Returns a genome after opening a file in GNOM format, found by a file chooser dialog.
static DNA	loadFASTA() Returns a genome after opening a file in FASTA format, determined by a file chooser dialog.
double	p(char b) Returns the probability to obtain the specified nucleobase of this genome sequence.
void	save() Saves this genome in gnom format.
String	toString() Returns a string representing this genome.

Methods inherited from class java.lang.Object

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

Constructor Detail

DNA

public DNA(String name,
           ArrayList<Character> sequence)

Constructor of this genome.

Parameters:

name - the name of this genome

sequence - the sequence of nucleobases

DNA

public DNA(String name,
           char[] sequence)

Constructor of this genome.

Parameters:

name - the name of this genome

sequence - the sequence of nucleobases

Method Detail

getName

public String getName()

Returns the name of this genome.

Returns:

the name of this genome

getSequence

public StringBuilder getSequence()

Returns the nucleobase sequence of this genome.

Returns:

the nucleobase sequence of this genome

getSequenceAsArrayList

public ArrayList<Character> getSequenceAsArrayList()

Returns the nucleobase sequence of this genome.

Returns:

the nucleobase sequence of this genome

getFrequency

public TreeMap<Character,Integer> getFrequency()

Returns the frequency distribution of the 4 nucleobases. Each frequency is given in %.

Returns:

the frequency distribution [in %] of the 4 nucleobases

getFrequencyAsHTMLTable

public String getFrequencyAsHTMLTable()

Returns the frequency distribution of the 64 codons as HTML table. Each frequency is given in %.

Returns:

an HTML string representing the frequency distribution of the 64 codons

getFrequencyAsHTMLGraph

public String getFrequencyAsHTMLGraph()

Returns the frequency distribution of the 64 codons as HTML graph. Each frequency is given in %.

Returns:

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

p

public double p(char b)

Returns the probability to obtain the specified nucleobase of this genome sequence.

Parameters:

b - the specified nucleobase

Returns:

the probability of the nucleobase of this genome

entropy

public double entropy()

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

Returns:

the entropy of the frequency distribution of this genome

asHTMLString

public String asHTMLString()

Returns a string representing this genome, with line breaks encoded by "
" instead of '\n'.

Returns:

an HTML string representing this genome

toString

public String toString()

Returns a string representing this genome.

Overrides:

toString in class Object

Returns:

a string representing this genome

encode

public static DNA encode(String name,
                         CharSequence string)

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

Parameters:

name - the name of the generated genome

string - DNA base sequence

Returns:

the genome specified by the DNA sequence

loadFASTA

public static DNA loadFASTA()

Returns a genome after opening a file in FASTA format, determined by a file chooser dialog.

Returns:

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

save

public void save()

Saves this genome in gnom format.

loadDNA

public static DNA loadDNA()

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