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A

accept(ClassInfo, ClassFinder) - Method in class org.wikibrain.conf.ProviderFilter
 
add(File) - Method in class org.clapper.util.classutil.ClassFinder
Add a jar file, zip file or directory to the list of places to search for classes.
add(File[]) - Method in class org.clapper.util.classutil.ClassFinder
Add an array jar files, zip files and/or directories to the list of places to search for classes.
add(Collection<File>) - Method in class org.clapper.util.classutil.ClassFinder
Add a Collection of jar files, zip files and/or directories to the list of places to search for classes.
add(int) - Method in class org.wikibrain.utils.AtomicIntSet
Adds the specified value to the set.
add(long) - Method in class org.wikibrain.utils.AtomicLongSet
Adds the specified value to the set.
add(T, double) - Method in class org.wikibrain.utils.Scoreboard
 
add(double, double[], double[], double[]) - Static method in class org.wikibrain.utils.WbMathUtils
v1 <- alpha * v2 + v3
add(double, double[], double[], float[]) - Static method in class org.wikibrain.utils.WbMathUtils
v1 <- alpha * v2 + v3
add(double, double[], float[], float[]) - Static method in class org.wikibrain.utils.WbMathUtils
v1 <- alpha * v2 + v3
add(float, float[], float[], float[]) - Static method in class org.wikibrain.utils.WbMathUtils
v1 <- alpha * v2 + v3
addAndGet(int, int) - Method in class org.wikibrain.utils.AtomicByteArray
Atomically adds the given value to the element at index i.
addArguments(String[]) - Method in class org.wikibrain.utils.WbCommandLine
 
addClassPath() - Method in class org.clapper.util.classutil.ClassFinder
Add the contents of the system classpath for classes.
addMap(Map<T1, Double>) - Method in class org.wikibrain.utils.SummingHashMap
 
addValue(T1, Integer) - Method in class org.wikibrain.utils.SummingHashMap
 
addValue(T1, Double) - Method in class org.wikibrain.utils.SummingHashMap
 
appendBootClasspath(String) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
appendBootClasspath(File) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
appendBootClasspath() - Method in class org.wikibrain.utils.JavaProcessBuilder
 
arg(String) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
args() - Method in class org.wikibrain.utils.JavaProcessBuilder
 
Argument() - Constructor for class org.wikibrain.utils.WbCommandLine.Argument
 
AtomicByteArray - Class in org.wikibrain.utils
A byte array in which elements may be updated atomically.
AtomicByteArray(int) - Constructor for class org.wikibrain.utils.AtomicByteArray
Creates a new AtomicByteArray of the given length, with all elements initially zero.
AtomicIntSet - Class in org.wikibrain.utils
An implement of a set containing int that uses open addressing The implementation is threadsafe and almost entirely lock-free.
AtomicIntSet() - Constructor for class org.wikibrain.utils.AtomicIntSet
 
AtomicIntSet(int) - Constructor for class org.wikibrain.utils.AtomicIntSet
Create a new set with the specified capacity.
AtomicLongSet - Class in org.wikibrain.utils
An implement of a set containing longs that uses open addressing The implementation is threadsafe and almost entirely lock-free.
AtomicLongSet() - Constructor for class org.wikibrain.utils.AtomicLongSet
 
AtomicLongSet(int) - Constructor for class org.wikibrain.utils.AtomicLongSet
Create a new set with the specified capacity.

B

bootClasspath(String) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
bootClasspath(File) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
bootClasspath() - Method in class org.wikibrain.utils.JavaProcessBuilder
 
BoundedExecutor(Executor, int) - Constructor for class org.wikibrain.utils.ParallelForEach.BoundedExecutor
 
bytesAre(byte[], int, int, byte[]) - Method in class org.wikibrain.utils.SevenZipBuffer
 
bytesToObject(byte[]) - Static method in class org.wikibrain.utils.WpIOUtils
Deserialize an array of bytes into an object.

C

call(T) - Method in interface org.wikibrain.utils.Function
Call the function.
call(T) - Method in interface org.wikibrain.utils.Procedure
Call the function.
ClassFinder - Class in org.clapper.util.classutil
A ClassFinder object is used to find classes.
ClassFinder() - Constructor for class org.clapper.util.classutil.ClassFinder
Create a new ClassFinder that will search for classes using the default class loader.
classForShortName(String) - Static method in class org.wikibrain.utils.JvmUtils
Returns the first class in the classpath that has the specified short name.
classpath(String) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
classpath(File) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
classpath() - Method in class org.wikibrain.utils.JavaProcessBuilder
 
clear() - Method in class org.clapper.util.classutil.ClassFinder
Clear the finder's notion of where to search.
clear() - Method in class org.wikibrain.utils.AtomicIntSet
Removes all elements in the set.
clear() - Method in class org.wikibrain.utils.AtomicLongSet
Removes all elements in the set.
clear() - Method in class org.wikibrain.utils.WbCommandLine
Clear out the whole command line.
clearArgs() - Method in class org.wikibrain.utils.WbCommandLine
Clear out the arguments but leave the executable in place for another operation.
client() - Method in class org.wikibrain.utils.JavaProcessBuilder
 
clone() - Method in class org.wikibrain.utils.WbCommandLine
 
close() - Method in class org.wikibrain.conf.Configurator
Tries to close all open components, clears the components map.
close() - Method in class org.wikibrain.utils.ObjectDb
Close and flush the concept database.
close() - Method in class org.wikibrain.utils.ObjectDb.KeyIterator
 
close() - Method in class org.wikibrain.utils.SevenZipBuffer
 
command() - Method in class org.wikibrain.utils.JavaProcessBuilder
Returns command with all its arguments
compare(K, K) - Method in class org.wikibrain.utils.MapValueComparator
 
compareAndSet(int, byte, byte) - Method in class org.wikibrain.utils.AtomicByteArray
Atomically sets the element at position i to the given updated value if the current value == the expected value.
Configuration - Class in org.wikibrain.conf
A generic configuration file.
Configuration() - Constructor for class org.wikibrain.conf.Configuration
Create a configuration file using default settings.
Configuration(File) - Constructor for class org.wikibrain.conf.Configuration
Creates a configuration file with the specified settings.
Configuration(Map<String, Object>, File...) - Constructor for class org.wikibrain.conf.Configuration
Creates a configuration using a specific chain of overrridden configurations.
ConfigurationException - Exception in org.wikibrain.conf
 
ConfigurationException(String, Exception) - Constructor for exception org.wikibrain.conf.ConfigurationException
 
ConfigurationException(Exception) - Constructor for exception org.wikibrain.conf.ConfigurationException
 
ConfigurationException(String) - Constructor for exception org.wikibrain.conf.ConfigurationException
 
Configurator - Class in org.wikibrain.conf
Binds together providers for a collection of components.
Configurator(Configuration) - Constructor for class org.wikibrain.conf.Configurator
Constructs a new configuration object with the specified configuration.
construct(Class<T>, String, Config, Map<String, String>) - Method in class org.wikibrain.conf.Configurator
Constructs an instance of the specified class with the passed in config.
contains(int) - Method in class org.wikibrain.utils.AtomicIntSet
Returns true iff the set contains the specified value.
contains(long) - Method in class org.wikibrain.utils.AtomicLongSet
Returns true iff the set contains the specified value.
create(char) - Method in class org.wikibrain.conf.DefaultOptionBuilder
Create an Option using the current settings and with the specified Option char.
create() - Method in class org.wikibrain.conf.DefaultOptionBuilder
Create an Option using the current settings
create(String) - Method in class org.wikibrain.conf.DefaultOptionBuilder
Create an Option using the current settings and with the specified Option char.
createArgument() - Method in class org.wikibrain.utils.WbCommandLine
Creates an argument object.
createArgument(boolean) - Method in class org.wikibrain.utils.WbCommandLine
Creates an argument object and adds it to our list of args.
createMarker() - Method in class org.wikibrain.utils.WbCommandLine
Return a marker.
createTempDirectory(String, boolean) - Static method in class org.wikibrain.utils.WpIOUtils
Creates a new temporary directory
createTempDirectory(String) - Static method in class org.wikibrain.utils.WpIOUtils
 

D

debugPort(int) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
debugPort() - Method in class org.wikibrain.utils.JavaProcessBuilder
 
debugSuspend(boolean) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
debugSuspend() - Method in class org.wikibrain.utils.JavaProcessBuilder
 
decrementAndGet(int) - Method in class org.wikibrain.utils.AtomicByteArray
Atomically decrements by one the element at index i.
DEFAULT_DIR - Static variable in class org.wikibrain.utils.ResourceInstaller
 
DEFAULT_RESOURCES - Static variable in class org.wikibrain.utils.ResourceInstaller
 
DefaultOptionBuilder - Class in org.wikibrain.conf
DefaultOptionBuilder is a non-static version of OptionBuilder that truly follows the builder pattern.
DefaultOptionBuilder() - Constructor for class org.wikibrain.conf.DefaultOptionBuilder
private constructor to prevent instances being created
describeArguments() - Method in class org.wikibrain.utils.WbCommandLine
Returns a String that describes the arguments suitable for verbose output before a call to Runtime.exec(String[])
describeArguments(WbCommandLine) - Static method in class org.wikibrain.utils.WbCommandLine
Returns a String that describes the arguments suitable for verbose output before a call to Runtime.exec(String[])
describeArguments(String[]) - Static method in class org.wikibrain.utils.WbCommandLine
Returns a String that describes the arguments suitable for verbose output before a call to Runtime.exec(String[])
describeArguments(String[], int) - Static method in class org.wikibrain.utils.WbCommandLine
Returns a String that describes the arguments suitable for verbose output before a call to Runtime.exec(String[])
describeCommand() - Method in class org.wikibrain.utils.WbCommandLine
Returns a String that describes the command and arguments suitable for verbose output before a call to Runtime.exec(String[])
describeCommand(WbCommandLine) - Static method in class org.wikibrain.utils.WbCommandLine
Returns a String that describes the command and arguments suitable for verbose output before a call to Runtime.exec(String[])
describeCommand(String[]) - Static method in class org.wikibrain.utils.WbCommandLine
Returns a String that describes the command and arguments suitable for verbose output before a call to Runtime.exec(String[]).
DISCLAIMER - Static variable in class org.wikibrain.utils.WbCommandLine
 
distance(double[], double[]) - Static method in class org.wikibrain.utils.WbMathUtils
 
divideBy(double) - Method in class org.wikibrain.utils.SummingHashMap
 
dot(float[], float[]) - Static method in class org.wikibrain.utils.WbMathUtils
 
dot(double[], float[]) - Static method in class org.wikibrain.utils.WbMathUtils
 
dot(double[], double[]) - Static method in class org.wikibrain.utils.WbMathUtils
 
double2Float(double[]) - Static method in class org.wikibrain.utils.WbMathUtils
 

E

endorsedDir(String) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
endorsedDir(File) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
endorsedDirs() - Method in class org.wikibrain.utils.JavaProcessBuilder
 
extDir(String) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
extDir(File) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
extDirs() - Method in class org.wikibrain.utils.JavaProcessBuilder
 

F

findAllInterfaces(ClassInfo, Map<String, ClassInfo>) - Method in class org.clapper.util.classutil.ClassFinder
Intended to be called only from a ClassFilter object's accept() method, this method attempts to find all the interfaces implemented by given class (directly and indirectly), by checking all the currently-loaded class data.
findAllSuperClasses(ClassInfo, Map<String, ClassInfo>) - Method in class org.clapper.util.classutil.ClassFinder
Intended to be called only from a ClassFilter object's accept() method, this method attempts to find all the superclasses (except java.lang.Objectfor a given class, by checking all the currently-loaded class data.
findClasses(Collection<ClassInfo>) - Method in class org.clapper.util.classutil.ClassFinder
Find all classes in the search areas, implicitly accepting all of them.
findClasses(Collection<ClassInfo>, ClassFilter) - Method in class org.clapper.util.classutil.ClassFinder
Search all classes in the search areas, keeping only those that pass the specified filter.
findColinearColumns(double[][], double) - Static method in class org.wikibrain.utils.WbMathUtils
Find colinear columns in a matrix.
findColinearColumns(double[][]) - Static method in class org.wikibrain.utils.WbMathUtils
 
flush() - Method in class org.wikibrain.utils.ObjectDb
 
Function<T,R> - Interface in org.wikibrain.utils
Interface for a function that takes a single argument of type T and returns a value of type R.

G

get() - Method in class org.wikibrain.conf.Configuration
Returns the sub config object.
get(Class<T>, String) - Method in class org.wikibrain.conf.Configurator
 
get(Class<T>, String, String, String) - Method in class org.wikibrain.conf.Configurator
Get a component with a single runtime parameter
get(Class<T>, String, Map<String, String>) - Method in class org.wikibrain.conf.Configurator
Get a specific named instance of the component with the specified class.
get(Class<T>) - Method in class org.wikibrain.conf.Configurator
Get a specific named instance of the component with the specified class.
get(String, Config, Map<String, String>) - Method in class org.wikibrain.conf.Provider
Should return a configured instance of the requested class, or null if it cannot be created by this provider.
get(int) - Method in class org.wikibrain.utils.AtomicByteArray
Gets the current value at position i.
get(String) - Method in class org.wikibrain.utils.ObjectDb
Returns the value associated with the key, or null if none exists.
get(String) - Static method in enum org.wikibrain.utils.OS
 
get() - Static method in enum org.wikibrain.utils.OS
 
getAndAdd(int, int) - Method in class org.wikibrain.utils.AtomicByteArray
Atomically adds the given value to the element at index i.
getAndDecrement(int) - Method in class org.wikibrain.utils.AtomicByteArray
Atomically decrements by one the element at index i.
getAndIncrement(int) - Method in class org.wikibrain.utils.AtomicByteArray
Atomically increments by one the element at index i.
getArguments() - Method in class org.wikibrain.utils.WbCommandLine
Returns all arguments defined by addLine, addValue or the argument object.
getBoolean(String...) - Method in class org.wikibrain.conf.Configuration
 
getClassPath() - Static method in class org.wikibrain.utils.JvmUtils
Returns a carefully constructed classpath matching the current process.
getClassPathAsList() - Static method in class org.wikibrain.utils.JvmUtils
 
getCommandline() - Method in class org.wikibrain.utils.WbCommandLine
Returns the executable and all defined arguments.
getConf() - Method in class org.wikibrain.conf.Configurator
 
getConfig(String...) - Method in class org.wikibrain.conf.Configuration
 
getConfig(Class, String) - Method in class org.wikibrain.conf.Configurator
Returns the config object associated with the given class and name.
getConfig() - Method in class org.wikibrain.conf.Provider
 
getConfigurator() - Method in class org.wikibrain.conf.Provider
 
getCopy() - Method in class org.wikibrain.utils.SummingHashMap
 
getDb() - Method in class org.wikibrain.utils.ObjectDb
Gets the underlying database.
getDouble(String...) - Method in class org.wikibrain.conf.Configuration
 
getDoubleList(String...) - Method in class org.wikibrain.conf.Configuration
 
getElement(int) - Method in class org.wikibrain.utils.Scoreboard
 
getEnvironment() - Method in class org.wikibrain.utils.ObjectDb
Gets the underlying database environment.
getExecutable() - Method in class org.wikibrain.utils.WbCommandLine
 
getFile(String...) - Method in class org.wikibrain.conf.Configuration
 
getFullClassName(String) - Static method in class org.wikibrain.utils.JvmUtils
Returns the first element in the classpath that has the specified short name.
getInt(String...) - Method in class org.wikibrain.conf.Configuration
 
getLastModifiedfromDir(File) - Static method in class org.wikibrain.utils.WpIOUtils
Return the most recent tstamp among files in a diretory.
getMaximum() - Method in class org.wikibrain.utils.SummingHashMap
 
getMaxThreads() - Static method in class org.wikibrain.utils.WpThreadUtils
 
getParts() - Method in class org.wikibrain.utils.WbCommandLine.Argument
Returns the parts this Argument consists of.
getPath() - Method in class org.wikibrain.conf.Provider
Returns the path in the configuration file for the components.
getPercentCompleted() - Method in class org.wikibrain.utils.SevenZipBuffer
 
getPosition() - Method in class org.wikibrain.utils.WbCommandLine.Marker
Return the number of arguments that preceeded this marker.
getRelativePath(File, File) - Static method in class org.wikibrain.utils.WpIOUtils
Gets the path relative to a specified directory.
getScope() - Method in class org.wikibrain.conf.Provider
Returns the scope of the
getScore(int) - Method in class org.wikibrain.utils.Scoreboard
 
getString(String...) - Method in class org.wikibrain.conf.Configuration
 
getStringList(String...) - Method in class org.wikibrain.conf.Configuration
 
getSum() - Method in class org.wikibrain.utils.SummingHashMap
 
getTotalBytes() - Method in class org.wikibrain.utils.SevenZipBuffer
 
getType() - Method in class org.wikibrain.conf.Provider
Returns the base class or interface that the class provides.
grow(int[], int) - Static method in class org.wikibrain.utils.WbArrayUtils
 
grow(String[], int) - Static method in class org.wikibrain.utils.WbArrayUtils
 

H

hasArg() - Method in class org.wikibrain.conf.DefaultOptionBuilder
The next Option created will require an argument value.
hasArg(boolean) - Method in class org.wikibrain.conf.DefaultOptionBuilder
The next Option created will require an argument value if hasArg is true.
hasArgs() - Method in class org.wikibrain.conf.DefaultOptionBuilder
The next Option created can have unlimited argument values.
hasArgs(int) - Method in class org.wikibrain.conf.DefaultOptionBuilder
The next Option created can have num argument values.
hash(int) - Static method in class org.wikibrain.utils.AtomicIntSet
From trove
hash(long) - Static method in class org.wikibrain.utils.AtomicLongSet
From trove
hash64(String) - Static method in class org.wikibrain.utils.MurmurHash
 
hash64(byte[], int) - Static method in class org.wikibrain.utils.MurmurHash
Generates 64 bit hash from byte array with default seed value.
hash64(byte[], int, int) - Static method in class org.wikibrain.utils.MurmurHash
Generates 64 bit hash from byte array of the given length and seed.
hasNext() - Method in class org.wikibrain.utils.IntRangeIterator
 
hasNext() - Method in class org.wikibrain.utils.ObjectDb.KeyIterator
 
hasOptionalArg() - Method in class org.wikibrain.conf.DefaultOptionBuilder
The next Option can have an optional argument.
hasOptionalArgs() - Method in class org.wikibrain.conf.DefaultOptionBuilder
The next Option can have an unlimited number of optional arguments.
hasOptionalArgs(int) - Method in class org.wikibrain.conf.DefaultOptionBuilder
The next Option can have the specified number of optional arguments.

I

increment(double[], double[]) - Static method in class org.wikibrain.utils.WbMathUtils
v1 += v2
increment(double[], float[]) - Static method in class org.wikibrain.utils.WbMathUtils
v1 += v2
increment(float[], float[]) - Static method in class org.wikibrain.utils.WbMathUtils
v1 += v2
incrementAndGet(int) - Method in class org.wikibrain.utils.AtomicByteArray
Atomically increments by one the element at index i.
incrementValue(T1) - Method in class org.wikibrain.utils.SummingHashMap
Increments the count for @code key by 1.
indexOf(TByteList, int, byte[]) - Method in class org.wikibrain.utils.SevenZipBuffer
 
indexOf(byte[], int, int, byte[]) - Method in class org.wikibrain.utils.SevenZipBuffer
 
initialHeap(int) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
initialHeap(String) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
initialHeap() - Method in class org.wikibrain.utils.JavaProcessBuilder
 
integrate(int) - Static method in class jnt.scimark2.MonteCarlo
 
IntRangeIterator - Class in org.wikibrain.utils
Based on http://stackoverflow.com/a/371043/141245, but threadsafe.
IntRangeIterator(int, int) - Constructor for class org.wikibrain.utils.IntRangeIterator
Creates an iterator for the range [min, max) (exclusive upper limit).
isEmpty() - Method in class org.wikibrain.utils.ObjectDb
 
isReal(double) - Static method in class org.wikibrain.utils.WbMathUtils
Returns true if the number is not NaN or infinite.
isRequired() - Method in class org.wikibrain.conf.DefaultOptionBuilder
The next Option created will be required.
isRequired(boolean) - Method in class org.wikibrain.conf.DefaultOptionBuilder
The next Option created will be required if required is true.
isSorted(Iterable<T>) - Static method in class org.wikibrain.utils.WpCollectionUtils
From http://stackoverflow.com/questions/3047051/how-to-determine-if-a-list-is-sorted-in-java
isUnix() - Method in enum org.wikibrain.utils.OS
 
isWindows() - Method in enum org.wikibrain.utils.OS
 
iterate(Iterator<T>, Procedure<T>, int) - Static method in class org.wikibrain.utils.ParallelForEach
 
iterate(Iterator<T>, Procedure<T>) - Static method in class org.wikibrain.utils.ParallelForEach
 
iterate(Iterator<T>, int, int, Procedure<T>, int) - Static method in class org.wikibrain.utils.ParallelForEach
 
iterator() - Method in class org.wikibrain.utils.ObjectDb
Iterate over key / value pairs.

J

javaHome(File) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
javaHome() - Method in class org.wikibrain.utils.JavaProcessBuilder
 
JavaProcessBuilder - Class in org.wikibrain.utils
Similar to ProcessBuilder, this class makes the java process creation easier.
JavaProcessBuilder() - Constructor for class org.wikibrain.utils.JavaProcessBuilder
 
jnt.scimark2 - package jnt.scimark2
 
jvmArg(String) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
jvmArgs() - Method in class org.wikibrain.utils.JavaProcessBuilder
 
JvmUtils - Class in org.wikibrain.utils
 
JvmUtils() - Constructor for class org.wikibrain.utils.JvmUtils
 

K

keyIterator() - Method in class org.wikibrain.utils.ObjectDb
 
KeyIterator() - Constructor for class org.wikibrain.utils.ObjectDb.KeyIterator
 

L

launch(OutputStream, OutputStream) - Method in class org.wikibrain.utils.JavaProcessBuilder
launches jvm with current configuration.
launch(Class, String[]) - Static method in class org.wikibrain.utils.JvmUtils
Launches a new java program that uses the running configuration settings.
launch(Class, String[], OutputStream, OutputStream, String) - Static method in class org.wikibrain.utils.JvmUtils
Launches a new java program that uses the running configuration settings.
length() - Method in class org.wikibrain.utils.AtomicByteArray
Returns the length of the array.
libraryPath(String) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
libraryPath(File) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
libraryPath() - Method in class org.wikibrain.utils.JavaProcessBuilder
 
LOG - Static variable in class org.wikibrain.utils.ParallelForEach
 
longHashCode(String) - Static method in class org.wikibrain.utils.WpStringUtils
 
longHashCode2(String) - Static method in class org.wikibrain.utils.WpStringUtils
This is much faster...
loop(Collection<T>, int, Function<T, R>) - Static method in class org.wikibrain.utils.ParallelForEach
 
loop(Collection<T>, Function<T, R>) - Static method in class org.wikibrain.utils.ParallelForEach
 
loop(Collection<T>, Procedure<T>) - Static method in class org.wikibrain.utils.ParallelForEach
 
loop(Collection<T>, int, Procedure<T>) - Static method in class org.wikibrain.utils.ParallelForEach
 
loop(Collection<T>, int, Procedure<T>, int) - Static method in class org.wikibrain.utils.ParallelForEach
 
loop(Collection<T>, Procedure<T>, int) - Static method in class org.wikibrain.utils.ParallelForEach
 
loop(Collection<T>, Function<T, R>, int) - Static method in class org.wikibrain.utils.ParallelForEach
 
loop(Collection<T>, int, Function<T, R>, int) - Static method in class org.wikibrain.utils.ParallelForEach
 

M

main(String[]) - Static method in class org.wikibrain.utils.ResourceInstaller
 
mainClass(String) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
mainClass() - Method in class org.wikibrain.utils.JavaProcessBuilder
 
makeMonotonicIncreasing(double[], double) - Static method in class org.wikibrain.utils.WbMathUtils
Make an array monotonically increasing by epsilon.
makeMonotonicIncreasing(TDoubleList, double) - Static method in class org.wikibrain.utils.WbMathUtils
 
MapValueComparator<K> - Class in org.wikibrain.utils
 
MapValueComparator(Map<K, Comparable>) - Constructor for class org.wikibrain.utils.MapValueComparator
 
MapValueComparator(Map<K, Comparable>, boolean) - Constructor for class org.wikibrain.utils.MapValueComparator
 
max(Collection<T>) - Static method in class org.wikibrain.utils.WpCollectionUtils
 
MAX_FILE_SIZE - Static variable in class org.wikibrain.conf.Configurator
 
MAX_FILE_SIZE - Static variable in class org.wikibrain.utils.JvmUtils
 
MAX_THREADS - Static variable in class org.wikibrain.utils.WpThreadUtils
 
maxHeap(int) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
maxHeap(String) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
maxHeap() - Method in class org.wikibrain.utils.JavaProcessBuilder
 
mean(Collection<? extends Number>) - Static method in class org.wikibrain.utils.WbMathUtils
 
min(Collection<T>) - Static method in class org.wikibrain.utils.WpCollectionUtils
 
mkdirsQuietly(File) - Static method in class org.wikibrain.utils.WpIOUtils
 
MonteCarlo - Class in jnt.scimark2
Estimate Pi by approximating the area of a circle.
MonteCarlo() - Constructor for class jnt.scimark2.MonteCarlo
 
MurmurHash - Class in org.wikibrain.utils
Adapted from Clearspring's stream-lib https://github.com/addthis/stream-lib/ by Shilad Sen.
MurmurHash() - Constructor for class org.wikibrain.utils.MurmurHash
 

N

next() - Method in class org.wikibrain.utils.IntRangeIterator
 
next() - Method in class org.wikibrain.utils.ObjectDb.KeyIterator
 
normalize() - Method in class org.wikibrain.utils.SummingHashMap
 
normalize(float[]) - Static method in class org.wikibrain.utils.WbMathUtils
 
normalize(double[]) - Static method in class org.wikibrain.utils.WbMathUtils
 
normalize(String) - Static method in class org.wikibrain.utils.WpStringUtils
Replaces consecutive non alpha-numeric characters with a space Converts to lowercase Removes whitespace
num_flops(int) - Static method in class jnt.scimark2.MonteCarlo
 

O

ObjectDb<V extends Serializable> - Class in org.wikibrain.utils
A key / value database where keys are strings and objects are serializable.
ObjectDb(File) - Constructor for class org.wikibrain.utils.ObjectDb
 
ObjectDb(File, boolean) - Constructor for class org.wikibrain.utils.ObjectDb
Creates a new object database.
ObjectDb.KeyIterator - Class in org.wikibrain.utils
Iterate over keys The cursor is closed when all the pairs have been read or when there is an error.
objectToBytes(Serializable) - Static method in class org.wikibrain.utils.WpIOUtils
Serialize an object into bytes.
openBufferedReader(File) - Static method in class org.wikibrain.utils.WpIOUtils
Open a possibly compressed file and return a buffered reader for it.
openBZ2Writer(File) - Static method in class org.wikibrain.utils.WpIOUtils
 
openInputStream(File) - Static method in class org.wikibrain.utils.WpIOUtils
Opens a possibly compressed input stream.
openReader(File) - Static method in class org.wikibrain.utils.WpIOUtils
Open a possibly compressed file and return a reader for it.
openResource(String) - Static method in class org.wikibrain.utils.WpIOUtils
Opens a resource in the classpath as a buffered reader.
openWriter(File) - Static method in class org.wikibrain.utils.WpIOUtils
Opens a buffered writer that uses UTF-8 encoding.
openWriter(String) - Static method in class org.wikibrain.utils.WpIOUtils
 
openWriterForAppend(File) - Static method in class org.wikibrain.utils.WpIOUtils
Opens a buffered writer that uses UTF-8 encoding.
org.clapper.util.classutil - package org.clapper.util.classutil
 
org.wikibrain.conf - package org.wikibrain.conf
 
org.wikibrain.utils - package org.wikibrain.utils
 
OS - Enum in org.wikibrain.utils
This enum contains values for each type of OS.

P

ParallelForEach - Class in org.wikibrain.utils
 
ParallelForEach() - Constructor for class org.wikibrain.utils.ParallelForEach
 
ParallelForEach.BoundedExecutor - Class in org.wikibrain.utils
From
prependBootClasspath(String) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
prependBootClasspath(File) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
prependBootClasspath() - Method in class org.wikibrain.utils.JavaProcessBuilder
 
Procedure<T> - Interface in org.wikibrain.utils
Interface for a function that takes a single argument of type T and returns nothing.
Provider<T> - Class in org.wikibrain.conf
Generates some type of object using a configuration file
Provider(Configurator, Configuration) - Constructor for class org.wikibrain.conf.Provider
Creates a new provider instance.
Provider.Scope - Enum in org.wikibrain.conf
 
ProviderFilter - Class in org.wikibrain.conf
SubclassFilter should be able to do this, but it doesn't for me.
ProviderFilter() - Constructor for class org.wikibrain.conf.ProviderFilter
 
put(String, V) - Method in class org.wikibrain.utils.ObjectDb
Add or replace an entry in the object database.
put(T1, Double) - Method in class org.wikibrain.utils.SummingHashMap
 

Q

quoteArgument(String) - Static method in class org.wikibrain.utils.WbCommandLine
Put quotes around the given String if necessary.

R

range(int, int, int, Procedure<Integer>) - Static method in class org.wikibrain.utils.ParallelForEach
Construct a parallel loop on [from, to).
range(int, int, Procedure<Integer>) - Static method in class org.wikibrain.utils.ParallelForEach
 
range(int, int, int, Function<Integer, R>) - Static method in class org.wikibrain.utils.ParallelForEach
 
range(int, int, Function<Integer, R>) - Static method in class org.wikibrain.utils.ParallelForEach
 
readObjectFromFile(File) - Static method in class org.wikibrain.utils.WpIOUtils
 
readUntil(String...) - Method in class org.wikibrain.utils.SevenZipBuffer
 
remove() - Method in class org.wikibrain.utils.IntRangeIterator
 
remove() - Method in class org.wikibrain.utils.ObjectDb.KeyIterator
 
remove(String) - Method in class org.wikibrain.utils.ObjectDb
 
removeNotNumberPoints(double[], double[]) - Static method in class org.wikibrain.utils.WbMathUtils
Given two parallel arrays of doubles representing x,y pairs remove all pairs that are NaN or Infinite, and return the result.
removeNotNumberPoints(TDoubleList, TDoubleList) - Static method in class org.wikibrain.utils.WbMathUtils
 
resolveComponentName(Class, String) - Method in class org.wikibrain.conf.Configurator
If the component name is "default" or null, return the name of the default implementation of the compoenent.
ResourceInstaller - Class in org.wikibrain.utils
 
ResourceInstaller() - Constructor for class org.wikibrain.utils.ResourceInstaller
 
resourceToString(String) - Static method in class org.wikibrain.utils.WpIOUtils
Reads a resource on the classpath into a string and returns it.
robustMean(double[]) - Static method in class org.wikibrain.utils.WbMathUtils
Calculates the weighted mean, where the weight is based on the rank difference from the median and normally distributed.

S

Scoreboard<T> - Class in org.wikibrain.utils
Priority queue that stores the largest or smallest n scores.
Scoreboard(int) - Constructor for class org.wikibrain.utils.Scoreboard
 
Scoreboard(int, Scoreboard.Order) - Constructor for class org.wikibrain.utils.Scoreboard
 
Scoreboard.Order - Enum in org.wikibrain.utils
 
server() - Method in class org.wikibrain.utils.JavaProcessBuilder
 
set(int, byte) - Method in class org.wikibrain.utils.AtomicByteArray
Sets the element at position i to the given value.
setExecutable(String) - Method in class org.wikibrain.utils.WbCommandLine
Sets the executable to run.
setFile(File) - Method in class org.wikibrain.utils.WbCommandLine.Argument
Sets a single commandline argument to the absolute filename of the given file.
setLine(String) - Method in class org.wikibrain.utils.WbCommandLine.Argument
Line to split into several commandline arguments.
setMaxThreads(int) - Static method in class org.wikibrain.utils.WpThreadUtils
 
setValue(String) - Method in class org.wikibrain.utils.WbCommandLine.Argument
Sets a single commandline argument.
setWikiBrainClassPattern(Pattern, Pattern) - Static method in class org.wikibrain.utils.JvmUtils
 
SevenZipBuffer - Class in org.wikibrain.utils
 
SevenZipBuffer(File) - Constructor for class org.wikibrain.utils.SevenZipBuffer
 
size() - Method in class org.wikibrain.utils.AtomicIntSet
Returns the number of elements stored in the set.
size() - Method in class org.wikibrain.utils.AtomicLongSet
Returns the number of elements stored in the set.
size() - Method in class org.wikibrain.utils.Scoreboard
 
size() - Method in class org.wikibrain.utils.WbCommandLine
 
skipUntil(String...) - Method in class org.wikibrain.utils.SevenZipBuffer
 
smooth(double[], double[], int, int) - Static method in class org.wikibrain.utils.WbMathUtils
Smooths the function specified by the X, Y pairs.
sortMap(Map<K, V>) - Static method in class org.wikibrain.utils.WpCollectionUtils
 
sortMap(Map<K, V>, boolean) - Static method in class org.wikibrain.utils.WpCollectionUtils
 
sortMapKeys(Map<K, V>, boolean) - Static method in class org.wikibrain.utils.WpCollectionUtils
 
sortMapKeys(Map<K, V>) - Static method in class org.wikibrain.utils.WpCollectionUtils
 
sortMapKeys(TIntFloatMap, boolean) - Static method in class org.wikibrain.utils.WpCollectionUtils
 
sortMapKeys(TIntDoubleMap, boolean) - Static method in class org.wikibrain.utils.WpCollectionUtils
 
sortMapKeys(TIntIntMap) - Static method in class org.wikibrain.utils.WpCollectionUtils
 
sortMapKeys(TIntIntMap, boolean) - Static method in class org.wikibrain.utils.WpCollectionUtils
 
submitTask(Runnable) - Method in class org.wikibrain.utils.ParallelForEach.BoundedExecutor
 
SummingHashMap<T1> - Class in org.wikibrain.utils
Class that maintains counts when adding things to HashMaps.
SummingHashMap() - Constructor for class org.wikibrain.utils.SummingHashMap
 
systemProperties() - Method in class org.wikibrain.utils.JavaProcessBuilder
 
systemProperty(String, String) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
systemProperty(String) - Method in class org.wikibrain.utils.JavaProcessBuilder
 

T

toArray() - Method in class org.wikibrain.utils.AtomicIntSet
Returns the values in the set.
toArray() - Method in class org.wikibrain.utils.AtomicLongSet
Returns the values in the set.
toAsymptote(double, double, double, double) - Static method in class org.wikibrain.utils.WbMathUtils
Returns a value that approaches yInf from y0 as xDelta increases.
toList(int[]) - Static method in class org.wikibrain.utils.WbArrayUtils
 
toString() - Method in class org.wikibrain.utils.WbCommandLine
 
toString(String[]) - Static method in class org.wikibrain.utils.WbCommandLine
Quotes the parts of the given array in way that makes them usable as command line arguments.
toString(int[][]) - Static method in class org.wikibrain.utils.WbMathUtils
 
translateCommandline(String) - Static method in class org.wikibrain.utils.WbCommandLine
 
transpose(float[][]) - Static method in class org.wikibrain.utils.WbMathUtils
 

U

unzip(File, File) - Static method in class org.wikibrain.utils.ZipDir
 
usage() - Static method in class org.wikibrain.utils.ResourceInstaller
 

V

valueOf(String) - Static method in enum org.wikibrain.conf.Provider.Scope
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.wikibrain.utils.OS
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.wikibrain.utils.Scoreboard.Order
Returns the enum constant of this type with the specified name.
values() - Static method in enum org.wikibrain.conf.Provider.Scope
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.wikibrain.utils.OS
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.wikibrain.utils.Scoreboard.Order
Returns an array containing the constants of this enum type, in the order they are declared.
vmType() - Method in class org.wikibrain.utils.JavaProcessBuilder
 

W

WbArrayUtils - Class in org.wikibrain.utils
 
WbArrayUtils() - Constructor for class org.wikibrain.utils.WbArrayUtils
 
WbCommandLine - Class in org.wikibrain.utils
Commandline objects help handling command lines specifying processes to execute.
WbCommandLine(String) - Constructor for class org.wikibrain.utils.WbCommandLine
 
WbCommandLine() - Constructor for class org.wikibrain.utils.WbCommandLine
 
WbCommandLine.Argument - Class in org.wikibrain.utils
Used for nested xml command line definitions.
WbCommandLine.Marker - Class in org.wikibrain.utils
Class to keep track of the position of an Argument.
WbMathUtils - Class in org.wikibrain.utils
 
WbMathUtils() - Constructor for class org.wikibrain.utils.WbMathUtils
 
withArgName(String) - Method in class org.wikibrain.conf.DefaultOptionBuilder
The next Option created will have the specified argument value name.
withDescription(String) - Method in class org.wikibrain.conf.DefaultOptionBuilder
The next Option created will have the specified description
withLongOpt(String) - Method in class org.wikibrain.conf.DefaultOptionBuilder
The next Option created will have the following long option value.
withType(Class) - Method in class org.wikibrain.conf.DefaultOptionBuilder
The next Option created will have a value that will be an instance of type.
withValueSeparator(char) - Method in class org.wikibrain.conf.DefaultOptionBuilder
The next Option created uses sep as a means to separate argument values.
withValueSeparator() - Method in class org.wikibrain.conf.DefaultOptionBuilder
The next Option created uses '=' as a means to separate argument values.
workingDir(String) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
workingDir(File) - Method in class org.wikibrain.utils.JavaProcessBuilder
 
workingDir() - Method in class org.wikibrain.utils.JavaProcessBuilder
 
WpCollectionUtils - Class in org.wikibrain.utils
 
WpCollectionUtils() - Constructor for class org.wikibrain.utils.WpCollectionUtils
 
WpIOUtils - Class in org.wikibrain.utils
 
WpIOUtils() - Constructor for class org.wikibrain.utils.WpIOUtils
 
WpStringUtils - Class in org.wikibrain.utils
 
WpStringUtils() - Constructor for class org.wikibrain.utils.WpStringUtils
 
WpThreadUtils - Class in org.wikibrain.utils
 
WpThreadUtils() - Constructor for class org.wikibrain.utils.WpThreadUtils
 
writeObjectToFile(File, Object) - Static method in class org.wikibrain.utils.WpIOUtils
 

Z

zero(float[][]) - Static method in class org.wikibrain.utils.WbMathUtils
 
zero(double[][]) - Static method in class org.wikibrain.utils.WbMathUtils
 
zip(File, File) - Static method in class org.wikibrain.utils.ZipDir
 
ZipDir - Class in org.wikibrain.utils
Creates zipfiles for directories and extract them to directories.
ZipDir() - Constructor for class org.wikibrain.utils.ZipDir
 
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