Package ffx.utilities

Class StringUtils

java.lang.Object

ffx.utilities.StringUtils

public class StringUtils
extends Object

StringUtils class.

Since:

1.0

Author:

Michael Schnieders

Field Summary

Fields

Modifier and Type	Field	Description
static final String	STANDARD_WATER_NAME	Constant STANDARD_WATER_NAME="HOH"

Method Summary

Modifier and Type	Method	Description
static String	cifForID(String id)	cifForID
static List<int[]>	consecutiveInts(int[] set)	Finds consecutive subranges in an array of ints, and returns their mins and maxes.
static Reader	createGzipReader(File file)	Creates a reader from a Gzip file to text.
static Reader	createGzipReader(File file, Charset cs)	Creates a reader from a Gzip file to text.
static Writer	createGzipWriter(File file)	Creates a writer for text to a Gzip file.
static Writer	createGzipWriter(File file, Charset cs)	Creates a writer for text to a Gzip file.
static String	fwDec(double val, int width, int prec)	Prints a fixed-width decimal, similar to String.format(%width.precf, val), but ensuring the resulting string is never longer than width.
static String	fwFpDec(double val, int width, int prec)	Prints a fixed-width decimal using String.format conventions, throwing an error if the value cannot be formatted within that space.
static String	fwFpTrunc(double val, int width, int prec)	Prints a fixed-width decimal using String.format conventions, reducing the value if necessary to fit within the width.
static Map<String,String>	getIonNames()	Returns a Map from recognized ion names to standard ion names.
static List<String>	getWaterNames()	Returns a List of recognized water names (defensive copy).
static boolean	looksLikeIon(String name)	Checks if a String matches a known monoatomic ion name.
static boolean	looksLikeWater(String name)	Checks if a String matches a known water name.
static String	padLeft(String s, int n)	padLeft
static String	padRight(String s, int n)	padRight
static List<Integer>	parseAtomRange(String keyType, String atomRange, int nAtoms)	Parses a numerical argument for an atom-specific flag.
static List<Integer>	parseAtomRanges(String keyType, String atomRanges, int nAtoms)	Parses a list of atom ranges for a per atom flag.
static List<String>	parseResidueString(String keyType, String resString, int nResidues)	Parses a list of residue (ChainResid) for a per residue flag.
static String	pdbForID(String id)	pdbForID
static String	tryParseIon(String name)	Checks if a String looks like a known ion.
static String	tryParseWater(String name)	Checks if a String looks like a water molecule.
static String	writeAtomRanges(int[] atoms)	Write atoms ranges for a list of atom indices.

Methods inherited from class java.lang.Object

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

Field Details

STANDARD_WATER_NAME

public static final String STANDARD_WATER_NAME

Constant STANDARD_WATER_NAME="HOH"

See Also:

• Constant Field Values

Method Details

cifForID

public static String cifForID(String id)

cifForID

Parameters:

id - a String object.

Returns:

a String object.

consecutiveInts

public static List<int[]> consecutiveInts(int[] set)

Finds consecutive subranges in an array of ints, and returns their mins and maxes. This can include singletons.

Example: [4, 5, 6, 1, 1, 2, 5, 6, 7] would become [4,6],[1,1],[1,2],[5,7]

Parameters:

set - Array of ints to split into consecutive subranges.

Returns:

Consecutive subrange mins, maxes

createGzipReader

public static Reader createGzipReader(File file)
                               throws IOException

Creates a reader from a Gzip file to text.

Parameters:

file - Gzip file to read from.

Returns:

A Reader.

Throws:

IOException - Thrown if creation of the GZip Reader fails.

createGzipReader

public static Reader createGzipReader(File file,
 Charset cs)
                               throws IOException

Creates a reader from a Gzip file to text.

Parameters:

file - Gzip file to read from.

cs - Character set to use.

Returns:

A Reader.

Throws:

IOException - Thrown if creation of the GZip Reader fails.

createGzipWriter

public static Writer createGzipWriter(File file)
                               throws IOException

Creates a writer for text to a Gzip file.

Parameters:

file - Gzip file to write to.

Returns:

A Writer

Throws:

IOException - Thrown if creation of the GZip Writer fails.

createGzipWriter

public static Writer createGzipWriter(File file,
 Charset cs)
                               throws IOException

Creates a writer for text to a Gzip file.

Parameters:

file - Gzip file to write to.

cs - Character set to use.

Returns:

A Writer

Throws:

IOException - Thrown if creation of the GZip Writer fails.

fwDec

public static String fwDec(double val,
 int width,
 int prec)
                    throws IllegalArgumentException

Prints a fixed-width decimal, similar to String.format(%width.precf, val), but ensuring the resulting string is never longer than width. If the result ends in a period (such as 14.), the method leaves off the decimal. An exception is thrown if the value cannot be formatted in the specified width.

Parameters:

val - Value to print

width - Width of field

prec - Number of decimal places

Returns:

Formatted string

Throws:

IllegalArgumentException - if any.

fwFpDec

public static String fwFpDec(double val,
 int width,
 int prec)
                      throws IllegalArgumentException

Prints a fixed-width decimal using String.format conventions, throwing an error if the value cannot be formatted within that space.

Parameters:

val - the value to print.

width - the width of the field.

prec - the number of decimal places.

Returns:

a String object.

Throws:

IllegalArgumentException - If the length of String is greater than the width.

fwFpTrunc

public static String fwFpTrunc(double val,
 int width,
 int prec)

Prints a fixed-width decimal using String.format conventions, reducing the value if necessary to fit within the width.

Parameters:

val - The value to print.

width - The width of the field.

prec - The number of decimal places.

Returns:

a String object.

getIonNames

public static Map<String,String> getIonNames()

Returns a Map from recognized ion names to standard ion names.

Returns:

Map from ion names to standardized ion names.

getWaterNames

public static List<String> getWaterNames()

Returns a List of recognized water names (defensive copy).

Returns:

List of water names.

looksLikeIon

public static boolean looksLikeIon(String name)

Checks if a String matches a known monoatomic ion name.

Parameters:

name - String to check.

Returns:

If it is the name of a monoatomic ion.

looksLikeWater

public static boolean looksLikeWater(String name)

Checks if a String matches a known water name.

Parameters:

name - String to check.

Returns:

If it is a water name.

padLeft

public static String padLeft(String s,
 int n)

padLeft

Parameters:

s - a String object.

n - The number of spaces to pad.

Returns:

a String object.

padRight

public static String padRight(String s,
 int n)

padRight

Parameters:

s - a String object.

n - The number of spaces to pad.

Returns:

a String object.

parseAtomRange

public static List<Integer> parseAtomRange(String keyType,
 String atomRange,
 int nAtoms)
                                    throws IllegalArgumentException

Parses a numerical argument for an atom-specific flag.

Parses, checks validity, and then returns the appropriate range.

Input should be 1-indexed (user end), output 0-indexed.

Parameters:

keyType - Type of key

atomRange - Input string

nAtoms - Number of atoms in the MolecularAssembly

Returns:

A List of selected atoms.

Throws:

IllegalArgumentException - if an invalid argument

parseAtomRanges

public static List<Integer> parseAtomRanges(String keyType,
 String atomRanges,
 int nAtoms)
                                     throws IllegalArgumentException

Parses a list of atom ranges for a per atom flag.

Parses, checks validity, and then returns a list with the index of selected atoms.

Input should be 1-indexed (user end) and the output 0-indexed.

Parameters:

keyType - Type of key

atomRanges - Input string

nAtoms - Number of atoms in the MolecularAssembly

Returns:

A List of selected atoms.

Throws:

IllegalArgumentException - if an invalid argument

parseResidueString

public static List<String> parseResidueString(String keyType,
 String resString,
 int nResidues)
                                       throws IllegalArgumentException

Parses a list of residue (ChainResid) for a per residue flag.

Parses, semi-checks validity, and then returns a list with alternating chain and numbers of selected residues.

Input should be a single character chain with a 1-indexed residue number.

Parameters:

keyType - Type of key

resString - Input string

nResidues - Number of residues in the MolecularAssembly

Returns:

A List of chain and residue numbers alternating.

Throws:

IllegalArgumentException - if an invalid argument

pdbForID

public static String pdbForID(String id)

pdbForID

Parameters:

id - a String object.

Returns:

a String object.

tryParseIon

public static String tryParseIon(String name)

Checks if a String looks like a known ion. Returns either its standardized name, or null if it doesn't look like an ion.

Parameters:

name - String to check.

Returns:

Standard ion name (matches) or null (no match).

tryParseWater

public static String tryParseWater(String name)

Checks if a String looks like a water molecule. Returns either a standardized water name, or null if it doesn't look like water.

Parameters:

name - String to check.

Returns:

Standard water name (matches) or null (no match).

writeAtomRanges

public static String writeAtomRanges(int[] atoms)

Write atoms ranges for a list of atom indices.

Parameters:

atoms - Atoms indices for which a comma separated list is desired.

Returns:

String of the atom list (comma separated, hyphens for large ranges).