A B C D F G H I L M N P R S T V W 

A

add(E) - Method in class nextflow.util.ArrayTuple
 
add(int, E) - Method in class nextflow.util.ArrayTuple
 
addAll(Collection<? extends E>) - Method in class nextflow.util.ArrayTuple
 
addAll(int, Collection<? extends E>) - Method in class nextflow.util.ArrayTuple
 
ArrayTuple<E> - Class in nextflow.util
Provides a basic tuple implementation extending an ArrayList and not allowing any content change operation
ArrayTuple() - Constructor for class nextflow.util.ArrayTuple
 
ArrayTuple(Collection<E>) - Constructor for class nextflow.util.ArrayTuple
 
ArrayTuple(int) - Constructor for class nextflow.util.ArrayTuple
 
available() - Method in class nextflow.file.FastBufferedInputStream
Returns an estimate of the number of bytes that can be read (or skipped over) from this input stream without blocking by the next invocation of a method for this input stream.
available() - Method in class nextflow.file.FastByteArrayInputStream
Returns the number of remaining bytes that can be read (or skipped over) from this input stream.

B

buf - Variable in class nextflow.file.FastBufferedInputStream
The internal buffer array where the data is stored.
buf - Variable in class nextflow.file.FastBufferedOutputStream
The internal buffer where data is stored.
buf - Variable in class nextflow.file.FastByteArrayInputStream
An array of bytes that was provided by the creator of the stream.
buf - Variable in class nextflow.file.FastByteArrayOutputStream
The buffer where data is stored.

C

CacheHelper - Class in nextflow.util
Provide helper method to handle caching
CacheHelper() - Constructor for class nextflow.util.CacheHelper
 
CacheHelper.HashMode - Enum in nextflow.util
 
clear() - Method in class nextflow.util.ArrayTuple
 
close() - Method in class nextflow.file.FastBufferedInputStream
Closes this input stream and releases any system resources associated with the stream.
close() - Method in class nextflow.file.FastByteArrayInputStream
Closing a ByteArrayInputStream has no effect.
close() - Method in class nextflow.file.FastByteArrayOutputStream
Closing a ByteArrayOutputStream has no effect.
count - Variable in class nextflow.file.FastBufferedInputStream
The index one greater than the index of the last valid byte in the buffer.
count - Variable in class nextflow.file.FastBufferedOutputStream
The number of valid bytes in the buffer.
count - Variable in class nextflow.file.FastByteArrayInputStream
The index one greater than the last valid character in the input stream buffer.
count - Variable in class nextflow.file.FastByteArrayOutputStream
The number of valid bytes in the buffer.

D

defaultHasher() - Static method in class nextflow.util.CacheHelper
 

F

FastBufferedInputStream - Class in nextflow.file
A BufferedInputStream adds functionality to another input stream-namely, the ability to buffer the input and to support the mark and reset methods.
FastBufferedInputStream(InputStream) - Constructor for class nextflow.file.FastBufferedInputStream
Creates a BufferedInputStream and saves its argument, the input stream in, for later use.
FastBufferedInputStream(InputStream, int) - Constructor for class nextflow.file.FastBufferedInputStream
Creates a BufferedInputStream with the specified buffer size, and saves its argument, the input stream in, for later use.
FastBufferedInputStream(InputStream, byte[]) - Constructor for class nextflow.file.FastBufferedInputStream
 
FastBufferedOutputStream - Class in nextflow.file
The class implements a buffered output stream.
FastBufferedOutputStream(OutputStream) - Constructor for class nextflow.file.FastBufferedOutputStream
Creates a new buffered output stream to write data to the specified underlying output stream.
FastBufferedOutputStream(OutputStream, int) - Constructor for class nextflow.file.FastBufferedOutputStream
Creates a new buffered output stream to write data to the specified underlying output stream with the specified buffer size.
FastBufferedOutputStream(OutputStream, byte[]) - Constructor for class nextflow.file.FastBufferedOutputStream
 
FastByteArrayInputStream - Class in nextflow.file
A ByteArrayInputStream contains an internal buffer that contains bytes that may be read from the stream.
FastByteArrayInputStream(byte[]) - Constructor for class nextflow.file.FastByteArrayInputStream
Creates a ByteArrayInputStream so that it uses buf as its buffer array.
FastByteArrayInputStream(byte[], int, int) - Constructor for class nextflow.file.FastByteArrayInputStream
Creates ByteArrayInputStream that uses buf as its buffer array.
FastByteArrayOutputStream - Class in nextflow.file
This class implements an output stream in which the data is written into a byte array.
FastByteArrayOutputStream() - Constructor for class nextflow.file.FastByteArrayOutputStream
Creates a new byte array output stream.
FastByteArrayOutputStream(int) - Constructor for class nextflow.file.FastByteArrayOutputStream
Creates a new byte array output stream, with a buffer capacity of the specified size, in bytes.
flush() - Method in class nextflow.file.FastBufferedOutputStream
Flushes this buffered output stream.

G

Globs - Class in nextflow.file
 
Globs() - Constructor for class nextflow.file.Globs
 

H

hasher(Object) - Static method in class nextflow.util.CacheHelper
 
hasher(Object, CacheHelper.HashMode) - Static method in class nextflow.util.CacheHelper
 
hasher(HashFunction, Object, CacheHelper.HashMode) - Static method in class nextflow.util.CacheHelper
 
hasher(Hasher, Object, CacheHelper.HashMode) - Static method in class nextflow.util.CacheHelper
 

I

iterator() - Method in class nextflow.util.ArrayTuple
 
iterator() - Method in class nextflow.util.ServiceDiscover
Lazily loads the available providers of this loader's service.

L

listIterator(int) - Method in class nextflow.util.ArrayTuple
 
load(Class<S>, ClassLoader) - Static method in class nextflow.util.ServiceDiscover
Creates a new service loader for the given service type and class loader.
load(Class<S>) - Static method in class nextflow.util.ServiceDiscover
Creates a new service loader for the given service type, using the current thread's context class loader.
loadInstalled(Class<S>) - Static method in class nextflow.util.ServiceDiscover
Creates a new service loader for the given service type, using the extension class loader.

M

mark(int) - Method in class nextflow.file.FastBufferedInputStream
See the general contract of the mark method of InputStream.
mark - Variable in class nextflow.file.FastByteArrayInputStream
The currently marked position in the stream.
mark(int) - Method in class nextflow.file.FastByteArrayInputStream
Set the current marked position in the stream.
marklimit - Variable in class nextflow.file.FastBufferedInputStream
The maximum read ahead allowed after a call to the mark method before subsequent calls to the reset method fail.
markpos - Variable in class nextflow.file.FastBufferedInputStream
The value of the pos field at the time the last mark method was called.
markSupported() - Method in class nextflow.file.FastBufferedInputStream
Tests if this input stream supports the mark and reset methods.
markSupported() - Method in class nextflow.file.FastByteArrayInputStream
Tests if this InputStream supports mark/reset.

N

nextflow.file - package nextflow.file
 
nextflow.util - package nextflow.util
 

P

pos - Variable in class nextflow.file.FastBufferedInputStream
The current position in the buffer.
pos - Variable in class nextflow.file.FastByteArrayInputStream
The index of the next character to read from the input stream buffer.

R

read() - Method in class nextflow.file.FastBufferedInputStream
See the general contract of the read method of InputStream.
read(byte[], int, int) - Method in class nextflow.file.FastBufferedInputStream
Reads bytes from this byte-input stream into the specified byte array, starting at the given offset.
read() - Method in class nextflow.file.FastByteArrayInputStream
Reads the next byte of data from this input stream.
read(byte[], int, int) - Method in class nextflow.file.FastByteArrayInputStream
Reads up to len bytes of data into an array of bytes from this input stream.
reload() - Method in class nextflow.util.ServiceDiscover
Clear this loader's provider cache so that all providers will be reloaded.
remove(Object) - Method in class nextflow.util.ArrayTuple
 
remove(int) - Method in class nextflow.util.ArrayTuple
 
removeAll(Collection<?>) - Method in class nextflow.util.ArrayTuple
 
reset() - Method in class nextflow.file.FastBufferedInputStream
See the general contract of the reset method of InputStream.
reset() - Method in class nextflow.file.FastByteArrayInputStream
Resets the buffer to the marked position.
reset() - Method in class nextflow.file.FastByteArrayOutputStream
Resets the count field of this byte array output stream to zero, so that all currently accumulated output in the output stream is discarded.
retainAll(Collection<?>) - Method in class nextflow.util.ArrayTuple
 

S

ServiceDiscover<S> - Class in nextflow.util
A simple service-provider loading facility.
set(int, E) - Method in class nextflow.util.ArrayTuple
 
size() - Method in class nextflow.file.FastByteArrayOutputStream
Returns the current size of the buffer.
skip(long) - Method in class nextflow.file.FastBufferedInputStream
See the general contract of the skip method of InputStream.
skip(long) - Method in class nextflow.file.FastByteArrayInputStream
Skips n bytes of input from this input stream.
subList(int, int) - Method in class nextflow.util.ArrayTuple
 

T

toByteArray() - Method in class nextflow.file.FastByteArrayOutputStream
Creates a newly allocated byte array.
toString() - Method in class nextflow.file.FastByteArrayOutputStream
Converts the buffer's contents into a string decoding bytes using the platform's default character set.
toString(String) - Method in class nextflow.file.FastByteArrayOutputStream
Converts the buffer's contents into a string by decoding the bytes using the specified charsetName.
toString(int) - Method in class nextflow.file.FastByteArrayOutputStream
Deprecated.
This method does not properly convert bytes into characters. As of JDK 1.1, the preferred way to do this is via the toString(String enc) method, which takes an encoding-name argument, or the toString() method, which uses the platform's default character encoding.
toString() - Method in class nextflow.util.ServiceDiscover
Returns a string describing this service.

V

valueOf(String) - Static method in enum nextflow.util.CacheHelper.HashMode
Returns the enum constant of this type with the specified name.
values() - Static method in enum nextflow.util.CacheHelper.HashMode
Returns an array containing the constants of this enum type, in the order they are declared.

W

write(int) - Method in class nextflow.file.FastBufferedOutputStream
Writes the specified byte to this buffered output stream.
write(byte[], int, int) - Method in class nextflow.file.FastBufferedOutputStream
Writes len bytes from the specified byte array starting at offset off to this buffered output stream.
write(int) - Method in class nextflow.file.FastByteArrayOutputStream
Writes the specified byte to this byte array output stream.
write(byte[], int, int) - Method in class nextflow.file.FastByteArrayOutputStream
Writes len bytes from the specified byte array starting at offset off to this byte array output stream.
writeTo(OutputStream) - Method in class nextflow.file.FastByteArrayOutputStream
Writes the complete contents of this byte array output stream to the specified output stream argument, as if by calling the output stream's write method using out.write(buf, 0, count).
A B C D F G H I L M N P R S T V W