halo.tools
Class Tools

java.lang.Object
  halo.tools.Tools

public class Tools
extends java.lang.Object

Class containing several tools used for HALO analyses

Author:

Stefanie Kaufmann

Field Summary

static java.lang.String	HOMEPAGE
static java.lang.String	HOMEPAGEDOC
static java.lang.String	LIBRARYNAME
static java.lang.String	VERSION

Constructor Summary

Tools()

Method Summary

static double	calculateMedianForHalfLives(double time, Data data) Calculates the average median over two available half-life calculation methods
static java.util.ArrayList<java.lang.String>	getColumnLabels(java.io.File file) Reads the header/description line of a given file and provides all column labels (columns separated by tabulator) as a list
static boolean	hasLineColumns(java.lang.String line, int columns) Checks whether a line consists of at least the given number of columns, whereas columns are separated through any whitespace sign
static boolean	isLineValid(java.lang.String line) Tests if a given line is composed of the letters a-z (case ignored), numbers or whitespace symbols like TAB
static boolean	testValidityForFile(java.io.File file, int columns, boolean permitUnusualLetters) Tests the correctness of a given file according to format (= minimal number of columns has to be correct) and letters (= are there any unusual letters present?)

Methods inherited from class java.lang.Object

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

Field Detail

LIBRARYNAME

public static final java.lang.String LIBRARYNAME

See Also:

Constant Field Values

VERSION

public static final java.lang.String VERSION

See Also:

Constant Field Values

HOMEPAGE

public static final java.lang.String HOMEPAGE

See Also:

Constant Field Values

HOMEPAGEDOC

public static final java.lang.String HOMEPAGEDOC

See Also:

Constant Field Values

Constructor Detail

Tools

public Tools()

Method Detail

getColumnLabels

public static java.util.ArrayList<java.lang.String> getColumnLabels(java.io.File file)

Reads the header/description line of a given file and provides all column labels (columns separated by tabulator) as a list

Parameters:

file - The file containing the expression data

Returns:

A list containing all column labels

isLineValid

public static boolean isLineValid(java.lang.String line)

Tests if a given line is composed of the letters a-z (case ignored), numbers or whitespace symbols like TAB

Parameters:

line - The line that will be tested

Returns:

TRUE if the line is valid, FALSE otherwise

hasLineColumns

public static boolean hasLineColumns(java.lang.String line,
                                     int columns)

Checks whether a line consists of at least the given number of columns, whereas columns are separated through any whitespace sign

Parameters:

line - The line that will be checked for validity

columns - The minimal number of columns that has to be in this line

Returns:

TRUE if the line consists of this many columns or more

testValidityForFile

public static boolean testValidityForFile(java.io.File file,
                                          int columns,
                                          boolean permitUnusualLetters)

Tests the correctness of a given file according to format (= minimal number of columns has to be correct) and letters (= are there any unusual letters present?) according to the first line after the commentary

Parameters:

file - The input file that will be tested

columns - The minimal number of columns that has to be present in the file

Returns:

TRUE if the file is valid

calculateMedianForHalfLives

public static double calculateMedianForHalfLives(double time,
                                                 Data data)

Calculates the average median over two available half-life calculation methods

Parameters:

time - The labeling time for the calculations

data - The data

Returns:

The average median