org.biojava.nbio.aaproperties

Class Utils

java.lang.Object

org.biojava.nbio.aaproperties.Utils

public class Utils
extends Object

This is a utility class that contains utility methods which will facilitates the coding of other methods

Since:

3.0.2

Version:

2011.08.22

Author:

kohchuanhock

Constructor Summary

Constructors

Constructor and Description
Utils()

Method Summary

Modifier and Type	Method and Description
static String	checkSequence(String sequence) Checks if the sequence contains invalid characters.
static String	checkSequence(String sequence, Set<Character> cSet) Checks if the sequence contains invalid characters.
static String	cleanSequence(String sequence, Set<Character> cSet) Returns a new sequence with all invalid characters being replaced by '-'.
static boolean	doesSequenceContainInvalidChar(String sequence, Set<Character> cSet) Checks if given sequence contains invalid characters.
static int	getNumberOfInvalidChar(String sequence, Set<Character> cSet, boolean ignoreCase) Return the number of invalid characters in sequence.
static double	roundToDecimals(double d, int c) Returns a value with the desired number of decimal places.

Methods inherited from class java.lang.Object

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

Constructor Detail

Utils

public Utils()

Method Detail

roundToDecimals

public static final double roundToDecimals(double d,
                                           int c)

Returns a value with the desired number of decimal places.

Parameters:

d - value to round

c - number of decimal places desired. Must be greater or equal to zero, otherwise, the given value d would be returned without any modification.

Returns:

a value with the given number of decimal places.

doesSequenceContainInvalidChar

public static final boolean doesSequenceContainInvalidChar(String sequence,
                                                           Set<Character> cSet)

Checks if given sequence contains invalid characters. Returns true if invalid characters are found, else return false. Note that any characters are deemed as valid only if it is found in cSet.

Parameters:

sequence - protein sequence to be check.

cSet - the set of characters that are deemed valid.

Returns:

true if invalid characters are found, else return false.

getNumberOfInvalidChar

public static final int getNumberOfInvalidChar(String sequence,
                                               Set<Character> cSet,
                                               boolean ignoreCase)

Return the number of invalid characters in sequence.

Parameters:

sequence - protein sequence to count for invalid characters.

cSet - the set of characters that are deemed valid.

ignoreCase - indicates if cases should be ignored

Returns:

the number of invalid characters in sequence.

cleanSequence

public static final String cleanSequence(String sequence,
                                         Set<Character> cSet)

Returns a new sequence with all invalid characters being replaced by '-'. Note that any character outside of the 20 standard protein amino acid codes are considered as invalid.

Parameters:

sequence - protein sequence to be clean

cSet - user defined characters that are valid. Can be null. If null, then 20 standard protein amino acid codes will be considered as valid.

Returns:

a new sequence with all invalid characters being replaced by '-'.

checkSequence

public static final String checkSequence(String sequence)

Checks if the sequence contains invalid characters. Note that any character outside of the 20 standard protein amino acid codes are considered as invalid. If yes, it will return a new sequence where invalid characters are replaced with '-'. If no, it will simply return the input sequence.

Parameters:

sequence - protein sequence to be check for invalid characters.

Returns:

a sequence with no invalid characters.

checkSequence

public static final String checkSequence(String sequence,
                                         Set<Character> cSet)

Checks if the sequence contains invalid characters. Note that any character outside of the 20 standard protein amino acid codes are considered as invalid. If yes, it will return a new sequence where invalid characters are replaced with '-'. If no, it will simply return the input sequence.

Parameters:

sequence - protein sequence to be check for invalid characters.

cSet - character set which define the valid characters.

Returns:

a sequence with no invalid characters.