Package htsjdk.samtools.util

Class StringUtil

java.lang.Object

htsjdk.samtools.util.StringUtil

public class StringUtil
extends Object

Grab-bag of stateless String-oriented utilities.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	EMPTY_STRING	Returns Object.toString() of the provided value if it isn't null; "" otherwise.

Constructor Summary

Constructors

Constructor	Description
StringUtil()

Method Summary

Modifier and Type	Method	Description
static String	asEmptyIfNull(Object string)
static String	assertCharactersNotInString(String illegalChars, char... chars)	Checks that a String doesn't contain one or more characters of interest.
static String	bytesToHexString(byte[] data)	Convert a byte array into a String hex representation.
static String	bytesToString(byte[] data)
static String	bytesToString(byte[] buffer, int offset, int length)
static char	byteToChar(byte b)	Convert ASCII byte to ASCII char.
static void	charsToBytes(char[] chars, int charOffset, int length, byte[] bytes, int byteOffset)	Convert chars to bytes merely by casting
static byte	charToByte(char c)	Convert ASCII char to byte.
static int	fromHexDigit(char c)
static int	hammingDistance(String s1, String s2)	Calculates the Hamming distance (number of character mismatches) between two strings s1 and s2.
static byte[]	hexStringToBytes(String s)	Convert a String containing hex characters into an array of bytes with the binary representation of the hex string
static String	humanReadableByteCount(long bytes)	Takes a long value representing the number of bytes and produces a human readable byte count.
static String	intValuesToString(int[] intVals)
static String	intValuesToString(short[] shortVals)
static boolean	isBlank(String str)	Checks if a String is whitespace, empty ("") or null.
static boolean	isWithinHammingDistance(String s1, String s2, int maxHammingDistance)	Determines if two strings s1 and s2 are within maxHammingDistance of each other using the Hamming distance metric.
static <T> String	join(String separator, Collection<T> objs)
static <T> String	join(String separator, T... objs)
static int	levenshteinDistance(String string1, String string2, int swap, int substitution, int insertion, int deletion)
static String	readNullTerminatedString(BinaryCodec binaryCodec)
static String	repeatCharNTimes(char c, int repeatNumber)
static String	reverseString(String s)	Reverse the given string.
static int	split(String aString, String[] tokens, char delim)	Split the string into tokens separated by the given delimiter.
static int	splitConcatenateExcessTokens(String aString, String[] tokens, char delim)	Split the string into tokens separated by the given delimiter.
static byte[]	stringToBytes(String s)
static byte[]	stringToBytes(String s, int offset, int length)
static char	toHexDigit(int value)
static byte	toLowerCase(byte b)
static byte	toUpperCase(byte b)
static void	toUpperCase(byte[] bytes)	Converts in place all lower case letters to upper case in the byte array provided.
static String	wordWrap(String s, int maxLineLength)	Return input string with newlines inserted to ensure that all lines have length <= maxLineLength.
static String	wordWrapSingleLine(String s, int maxLineLength)

Methods inherited from class java.lang.Object

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

Field Details

EMPTY_STRING

public static final String EMPTY_STRING

Returns Object.toString() of the provided value if it isn't null; "" otherwise.

See Also:

• Constant Field Values

Constructor Details

StringUtil

public StringUtil()

Method Details

join

public static <T> String join(String separator,
 Collection<T> objs)

Parameters:

separator - String to interject between each string in strings arg

objs - List of objs to be joined

Returns:

String that concatenates the result of each item's to String method for all items in objs, with separator between each of them.

join

public static <T> String join(String separator,
 T... objs)

split

public static int split(String aString,
 String[] tokens,
 char delim)

Split the string into tokens separated by the given delimiter. Profiling has revealed that the standard string.split() method typically takes > 1/2 the total time when used for parsing ascii files. Note that if tokens arg is not large enough to all the tokens in the string, excess tokens are discarded.

Parameters:

aString - the string to split

tokens - an array to hold the parsed tokens

delim - character that delimits tokens

Returns:

the number of tokens parsed

splitConcatenateExcessTokens

public static int splitConcatenateExcessTokens(String aString,
 String[] tokens,
 char delim)

Split the string into tokens separated by the given delimiter. Profiling has revealed that the standard string.split() method typically takes > 1/2 the total time when used for parsing ascii files. Note that the string is split into no more elements than tokens arg will hold, so the final tokenized element may contain delimiter chars.

Parameters:

aString - the string to split

tokens - an array to hold the parsed tokens

delim - character that delimits tokens

Returns:

the number of tokens parsed

toLowerCase

public static byte toLowerCase(byte b)

Parameters:

b - ASCII character

Returns:

lowercase version of arg if it was uppercase, otherwise returns arg

toUpperCase

public static byte toUpperCase(byte b)

Parameters:

b - ASCII character

Returns:

uppercase version of arg if it was lowercase, otherwise returns arg

toUpperCase

public static void toUpperCase(byte[] bytes)

Converts in place all lower case letters to upper case in the byte array provided.

assertCharactersNotInString

public static String assertCharactersNotInString(String illegalChars,
 char... chars)

Checks that a String doesn't contain one or more characters of interest.

Parameters:

illegalChars - the String to check

chars - the characters to check for

Returns:

String the input String for convenience

Throws:

IllegalArgumentException - if the String contains one or more of the characters

wordWrap

public static String wordWrap(String s,
 int maxLineLength)

Return input string with newlines inserted to ensure that all lines have length <= maxLineLength. if a word is too long, it is simply broken at maxLineLength. Does not handle tabs intelligently (due to implementer laziness).

wordWrapSingleLine

public static String wordWrapSingleLine(String s,
 int maxLineLength)

intValuesToString

public static String intValuesToString(int[] intVals)

intValuesToString

public static String intValuesToString(short[] shortVals)

bytesToString

public static String bytesToString(byte[] data)

bytesToString

public static String bytesToString(byte[] buffer,
 int offset,
 int length)

stringToBytes

public static byte[] stringToBytes(String s)

stringToBytes

public static byte[] stringToBytes(String s,
 int offset,
 int length)

readNullTerminatedString

public static String readNullTerminatedString(BinaryCodec binaryCodec)

charsToBytes

public static void charsToBytes(char[] chars,
 int charOffset,
 int length,
 byte[] bytes,
 int byteOffset)

Convert chars to bytes merely by casting

Parameters:

chars - input chars

charOffset - where to start converting from chars array

length - how many chars to convert

bytes - where to put the converted output

byteOffset - where to start writing the converted output.

charToByte

public static byte charToByte(char c)

Convert ASCII char to byte.

byteToChar

public static char byteToChar(byte b)

Convert ASCII byte to ASCII char.

bytesToHexString

public static String bytesToHexString(byte[] data)

Convert a byte array into a String hex representation.

Parameters:

data - Input to be converted.

Returns:

String twice as long as data.length with hex representation of data.

hexStringToBytes

public static byte[] hexStringToBytes(String s)
                               throws NumberFormatException

Convert a String containing hex characters into an array of bytes with the binary representation of the hex string

Parameters:

s - Hex string. Length must be even because each pair of hex chars is converted into a byte.

Returns:

byte array with binary representation of hex string.

Throws:

NumberFormatException

toHexDigit

public static char toHexDigit(int value)

fromHexDigit

public static int fromHexDigit(char c)
                        throws NumberFormatException

Throws:

NumberFormatException

reverseString

public static String reverseString(String s)

Reverse the given string. Does not check for null.

Parameters:

s - String to be reversed.

Returns:

New string that is the reverse of the input string.

isBlank

public static boolean isBlank(String str)

Checks if a String is whitespace, empty ("") or null.

 StringUtils.isBlank(null)      = true
 StringUtils.isBlank("")        = true
 StringUtils.isBlank(" ")       = true
 StringUtils.isBlank("sam")     = false
 StringUtils.isBlank("  sam  ") = false
 

Parameters:

str - the String to check, may be null

Returns:

true if the String is null, empty or whitespace

repeatCharNTimes

public static String repeatCharNTimes(char c,
 int repeatNumber)

asEmptyIfNull

public static String asEmptyIfNull(Object string)

levenshteinDistance

public static int levenshteinDistance(String string1,
 String string2,
 int swap,
 int substitution,
 int insertion,
 int deletion)

hammingDistance

public static int hammingDistance(String s1,
 String s2)

Calculates the Hamming distance (number of character mismatches) between two strings s1 and s2. Since Hamming distance is not defined for strings of differing lengths, we throw an exception if the two strings are of different lengths. Hamming distance is case sensitive and does not have any special treatment for DNA.

Parameters:

s1 - The first string to compare

s2 - The second string to compare, note that if s1 and s2 are swapped the value returned will be identical.

Returns:

Hamming distance between s1 and s2.

Throws:

IllegalArgumentException - If the two strings have differing lengths.

isWithinHammingDistance

public static boolean isWithinHammingDistance(String s1,
 String s2,
 int maxHammingDistance)

Determines if two strings s1 and s2 are within maxHammingDistance of each other using the Hamming distance metric. Since Hamming distance is not defined for strings of differing lengths, we throw an exception if the two strings are of different lengths. Hamming distance is case sensitive and does not have any special treatment for DNA.

Parameters:

s1 - The first string to compare

s2 - The second string to compare, note that if s1 and s2 are swapped the value returned will be identical.

maxHammingDistance - The largest Hamming distance the strings can have for this function to return true.

Returns:

true if the two strings are within maxHammingDistance of each other, false otherwise.

Throws:

IllegalArgumentException - If the two strings have differing lengths.

humanReadableByteCount

public static String humanReadableByteCount(long bytes)

Takes a long value representing the number of bytes and produces a human readable byte count.

Parameters:

bytes - The number of bytes to create a human readable string for.

Returns:

A human readable string of the number of bytes given.