org.mathIT.genes

Class Utils

java.lang.Object

org.mathIT.genes.Utils

public class Utils
extends Object

This class provides static utility methods for the gene library package.

Version:

1.0

Author:

Andreas de Vries

Method Summary

Modifier and Type	Method and Description
static TreeMap<String,Integer>	computeTupleFrequencies(File[] files, int n) Loads a FASTA file and returns the n-tuple frequencies of its letters.
static TreeMap<String,Integer>	computeTupleFrequencies(File file, int n, char[] base) Loads a FASTA file and returns the n-tuple frequencies of its letters.
static TreeMap<String,Integer>	computeTupleFrequencies(int n) Loads a FASTA file and returns the n-tuple frequencies of its letters.
static TreeMap<String,Integer>	computeTupleFrequencies(int n, char[] base) Asks the user to select a FASTA file, loads it and returns the n-tuple frequencies of its letters.
static String	getAsCSVTable(Map<String,Integer> map) Returns the specified map as a CSV data table string, with data aligned in columns.
static String	getAsCSVTable(Map<String,Integer> map, int minimum) Returns the specified map as a CSV data table string, with data aligned in columns.
protected static String	getAsCSVTableRows(Map<String,Integer> map) Returns the specified map as a CSV data table string, with data aligned in rows.
static String	getFrequenciesAsHTMLGraph(Map<String,Integer> frequencies) Returns the frequency distribution of amino acid triplets as HTML graph.
static void	save(String fileName, CharSequence string) Saves the specified character sequence.
static void	saveOccurrencesAsText(String fileName, TreeMap<String,Integer> distribution, int frequency) Saves those occurrences of a frequency distribution which have the specified frequency into a text file.
static void	saveOccurrencesAsText(String fileName, TreeMap<String,Integer> distribution, int frequency, char[] ignore) Saves those occurrences of a frequency distribution which have the specified frequency into a text file.
static void	saveWordFrequenciesAsCSV() This method asks the user to select a list of files, computes the word frequencies and saves them in a CSV file.
static File[]	selectFASTAFiles() Asks the user to select a directory and returns a list of FASTA files.

Methods inherited from class java.lang.Object

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

Method Detail

getAsCSVTable

public static String getAsCSVTable(Map<String,Integer> map)

Returns the specified map as a CSV data table string, with data aligned in columns. The data separator is the tabulator sign '\t'.

Parameters:

map - the map to be saved

Returns:

CSV data table string

getAsCSVTable

public static String getAsCSVTable(Map<String,Integer> map,
                                   int minimum)

Returns the specified map as a CSV data table string, with data aligned in columns. The data separator is the tabulator sign '\t'.

Parameters:

map - the map to be saved

minimum - the minimum frequency number to be saved

Returns:

CSV data table string

getAsCSVTableRows

protected static String getAsCSVTableRows(Map<String,Integer> map)

Returns the specified map as a CSV data table string, with data aligned in rows. The data separator is the tabulator sign '\t'.

Parameters:

map - a map of data

Returns:

CSV data table string

getFrequenciesAsHTMLGraph

public static String getFrequenciesAsHTMLGraph(Map<String,Integer> frequencies)

Returns the frequency distribution of amino acid triplets as HTML graph.

Parameters:

frequencies - frequency distribution

Returns:

a graphical HTML string representing the frequency distribution of the amino acid triplets

computeTupleFrequencies

public static TreeMap<String,Integer> computeTupleFrequencies(int n)

Loads a FASTA file and returns the n-tuple frequencies of its letters.

Parameters:

n - the tuple size

Returns:

the frequency distribution of n-tuples over the base alphabet

computeTupleFrequencies

public static TreeMap<String,Integer> computeTupleFrequencies(int n,
                                                              char[] base)

Asks the user to select a FASTA file, loads it and returns the n-tuple frequencies of its letters.

Parameters:

n - the tuple size

base - the base alphabet (important for finding zero occurrences)

Returns:

the frequency distribution of n-tuples over the base alphabet

selectFASTAFiles

public static File[] selectFASTAFiles()

Asks the user to select a directory and returns a list of FASTA files.

Returns:

a list of FASTA files

computeTupleFrequencies

public static TreeMap<String,Integer> computeTupleFrequencies(File[] files,
                                                              int n)

Loads a FASTA file and returns the n-tuple frequencies of its letters.

Parameters:

files - an array of FASTA file

n - the tuple size

Returns:

the frequency distribution of n-tuples over the base alphabet

computeTupleFrequencies

public static TreeMap<String,Integer> computeTupleFrequencies(File file,
                                                              int n,
                                                              char[] base)

Loads a FASTA file and returns the n-tuple frequencies of its letters.

Parameters:

file - a FASTA file

n - the tuple size

base - the base alphabet (important for finding zero occurrences)

Returns:

the frequency distribution of n-tuples over the base alphabet

saveOccurrencesAsText

public static void saveOccurrencesAsText(String fileName,
                                         TreeMap<String,Integer> distribution,
                                         int frequency)

Saves those occurrences of a frequency distribution which have the specified frequency into a text file.

Parameters:

fileName - the file name (without extension) in which the text is stored

distribution - the frequency distribution

frequency - the frequency which filters the occurrences

saveOccurrencesAsText

public static void saveOccurrencesAsText(String fileName,
                                         TreeMap<String,Integer> distribution,
                                         int frequency,
                                         char[] ignore)

Saves those occurrences of a frequency distribution which have the specified frequency into a text file.

Parameters:

fileName - the file name (without extension) in which the text is stored

distribution - the frequency distribution

frequency - the frequency which filters the occurrences

ignore - list of characters to be ignored

saveWordFrequenciesAsCSV

public static void saveWordFrequenciesAsCSV()

This method asks the user to select a list of files, computes the word frequencies and saves them in a CSV file. Note that the first line of each input file is ignored. Comma and space are condidered as separator symbols.

save

public static void save(String fileName,
                        CharSequence string)

Saves the specified character sequence.

Parameters:

fileName - name of the file

string - a sequence of characters