Genome

java.lang.Object
- org.mathIT.genes.Genome

All Implemented Interfaces:

Serializable
```
public class Genome
extends Object
implements Serializable
```
This class represents a 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. 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.Genome

Version:

1.0

Author:

Andreas de Vries

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor and Description
`Genome(String name, ArrayList<Character> sequence)` Constructor of a genome with the specified name and the specified sequence of nucleobases, i.e., the letters A, C, G, T (or U for an RNA genome).
`Genome(String name, char[] sequence)` Constructor of a genome with the specified name and the specified sequence of nucleobases, i.e., the letters A, C, G, T (or U for an RNA genome).
`Genome(String name, CharSequence sequence)` Constructor of a genome with the specified name and the specified sequence of nucleobases, i.e., the letters A, C, G, T (or U for an RNA genome).

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`String`	`asHTMLString()` Returns a string representing this genome, with line breaks encoded by "<br>" instead of '\n'.
`double`	`entropy()` Returns the entropy of the frequency distribution of the nucleobases of this genome.
`protected static String`	`getAsCSVTable(Map<String,Integer> map)` Returns the specified map as a CSV data table string.
`TreeMap<Character,Integer>`	`getFrequencies()` Returns the absolute frequency distribution of the nucleobases.
`protected String`	`getFrequenciesAsCSVTable()` Returns the frequency distribution of this genome as a CSV data table string.
`String`	`getFrequenciesAsHTMLGraph()` Returns the frequency distribution of the nucleobases as HTML graph.
`String`	`getFrequenciesAsHTMLGraph2()` Returns the frequency distribution of the nucleobases as HTML graph in landscape format.
`String`	`getFrequenciesAsHTMLTable()` Returns the frequency distribution of the nucleobases as HTML table.
`String`	`getName()` Returns the name of this genome.
`TreeMap<String,Integer>`	`getPairFrequencies()` Returns the absolute frequency distribution of the nucleobase pairs.
`String`	`getPairFrequenciesAsHTMLGraph()` Returns the frequency distribution of nucleobase pairs as HTML graph.
`StringBuilder`	`getSequence()` Returns the nucleobase sequence of this genome.
`ArrayList<Character>`	`getSequenceAsArrayList()` Returns the nucleobase sequence of this genome.
`TreeMap<String,Integer>`	`getTripletFrequencies()` Returns the absolute frequency distribution of the nucleobase triplets.
`String`	`getTripletFrequenciesAsHTMLGraph()` Returns the frequency distribution of nucleobase triplets as HTML graph.
`static Genome`	`loadFASTA()` Returns a genome after opening a file in FASTA format, determined by a file chooser dialog.
`static Genome`	`loadGenome()` Returns a genome after opening a file in GNOM format, found 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.
`void`	`saveAsCSV()` Saves this genome as CSV file.
`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
  - Genome
```
public Genome(String name,
              ArrayList<Character> sequence)
```
    Constructor of a genome with the specified name and the specified sequence of nucleobases, i.e., the letters A, C, G, T (or U for an RNA genome). Also accepted are letters specified by the FASTA format, but all letters ≠ 'N' are stored as '?'
    
    Parameters:
    
    name - the name of the genome
    
    sequence - the sequence of nucleobases
  - Genome
```
public Genome(String name,
              char[] sequence)
```
    Constructor of a genome with the specified name and the specified sequence of nucleobases, i.e., the letters A, C, G, T (or U for an RNA genome).
    
    Parameters:
    
    name - the name of the genome
    
    sequence - the sequence of nucleobases
  - Genome
```
public Genome(String name,
              CharSequence sequence)
```
    Constructor of a genome with the specified name and the specified sequence of nucleobases, i.e., the letters A, C, G, T (or U for an RNA genome).
    
    Parameters:
    
    name - the name of the genome
    
    sequence - 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
  - getFrequencies
```
public TreeMap<Character,Integer> getFrequencies()
```
    Returns the absolute frequency distribution of the nucleobases.
    
    Returns:
    
    the frequency distribution of the nucleobases
  - getPairFrequencies
```
public TreeMap<String,Integer> getPairFrequencies()
```
    Returns the absolute frequency distribution of the nucleobase pairs.
    
    Returns:
    
    the frequency distribution of the nucleobase pairs
  - getTripletFrequencies
```
public TreeMap<String,Integer> getTripletFrequencies()
```
    Returns the absolute frequency distribution of the nucleobase triplets.
    
    Returns:
    
    the frequency distribution of the nucleobase triplets
  - getFrequenciesAsHTMLTable
```
public String getFrequenciesAsHTMLTable()
```
    Returns the frequency distribution of the nucleobases as HTML table.
    
    Returns:
    
    an HTML string representing the frequency distribution of the nucleobases
  - getFrequenciesAsCSVTable
```
protected String getFrequenciesAsCSVTable()
```
    Returns the frequency distribution of this genome as a CSV data table string. The data separator is the tabulator sign '\t'.
    
    Returns:
    
    CSV data table string
  - getAsCSVTable
```
protected static String getAsCSVTable(Map<String,Integer> map)
```
    Returns the specified map as a CSV data table string. The data separator is the tabulator sign '\t'.
    
    Parameters:
    
    map - a map
    
    Returns:
    
    CSV data table string
  - getFrequenciesAsHTMLGraph
```
public String getFrequenciesAsHTMLGraph()
```
    Returns the frequency distribution of the nucleobases as HTML graph.
    
    Returns:
    
    a graphical HTML string representing the frequency distribution of the nucleobases
  - getFrequenciesAsHTMLGraph2
```
public String getFrequenciesAsHTMLGraph2()
```
    Returns the frequency distribution of the nucleobases as HTML graph in landscape format.
    
    Returns:
    
    a graphical HTML string in landscape format representing the frequency distribution of the nucleobases
  - getPairFrequenciesAsHTMLGraph
```
public String getPairFrequenciesAsHTMLGraph()
```
    Returns the frequency distribution of nucleobase pairs as HTML graph.
    
    Returns:
    
    a graphical HTML string representing the frequency distribution of nucleobase pairs
  - getTripletFrequenciesAsHTMLGraph
```
public String getTripletFrequenciesAsHTMLGraph()
```
    Returns the frequency distribution of nucleobase triplets as HTML graph.
    
    Returns:
    
    a graphical HTML string representing the frequency distribution of the nucleobase triplets
  - 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 the nucleobases 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 "<br>" 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
  - loadFASTA
```
public static Genome 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.
  - saveAsCSV
```
public void saveAsCSV()
```
    Saves this genome as CSV file.
  - loadGenome
```
public static Genome loadGenome()
```
    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

Class Genome

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Genome

Genome

Genome

Method Detail

getName

getSequence

getSequenceAsArrayList

getFrequencies

getPairFrequencies

getTripletFrequencies

getFrequenciesAsHTMLTable

getFrequenciesAsCSVTable

getAsCSVTable

getFrequenciesAsHTMLGraph

getFrequenciesAsHTMLGraph2

getPairFrequenciesAsHTMLGraph

getTripletFrequenciesAsHTMLGraph

p

entropy

asHTMLString

toString

loadFASTA

save

saveAsCSV

loadGenome