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A

AbstractBuildAndEnvironmentInfo - Class in ch.systemsx.cisd.base.utilities
Abstract of all classes providing build and environment information.
AbstractBuildAndEnvironmentInfo(String) - Constructor for class ch.systemsx.cisd.base.utilities.AbstractBuildAndEnvironmentInfo
 
AbstractFileSystemTestCase - Class in ch.systemsx.cisd.base.tests
An abstract test case which accesses the file system.
AbstractFileSystemTestCase() - Constructor for class ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase
 
AbstractFileSystemTestCase(boolean) - Constructor for class ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase
 
adaptCapacityHyperRows() - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
 
adaptCapacityHyperRows() - Method in class ch.systemsx.cisd.base.mdarray.MDArray
 
adaptCapacityHyperRows() - Method in class ch.systemsx.cisd.base.mdarray.MDByteArray
 
adaptCapacityHyperRows() - Method in class ch.systemsx.cisd.base.mdarray.MDDoubleArray
 
adaptCapacityHyperRows() - Method in class ch.systemsx.cisd.base.mdarray.MDFloatArray
 
adaptCapacityHyperRows() - Method in class ch.systemsx.cisd.base.mdarray.MDIntArray
 
adaptCapacityHyperRows() - Method in class ch.systemsx.cisd.base.mdarray.MDLongArray
 
adaptCapacityHyperRows() - Method in class ch.systemsx.cisd.base.mdarray.MDShortArray
 
AdapterIInputStreamToInputStream - Class in ch.systemsx.cisd.base.io
An adapter for IInputStream that extends InputStream.
AdapterIInputStreamToInputStream(IInputStream) - Constructor for class ch.systemsx.cisd.base.io.AdapterIInputStreamToInputStream
 
AdapterInputStreamToIInputStream - Class in ch.systemsx.cisd.base.io
An adapter for InputStream that implements IInputStream.
AdapterInputStreamToIInputStream(InputStream) - Constructor for class ch.systemsx.cisd.base.io.AdapterInputStreamToIInputStream
 
AdapterIOutputStreamToOutputStream - Class in ch.systemsx.cisd.base.io
An adapter for IOutputStream that extends OutputStream.
AdapterIOutputStreamToOutputStream(IOutputStream) - Constructor for class ch.systemsx.cisd.base.io.AdapterIOutputStreamToOutputStream
 
AdapterOutputStreamToIOutputStream - Class in ch.systemsx.cisd.base.io
An adapter for OutputStream that implements IOutputStream.
AdapterOutputStreamToIOutputStream(OutputStream) - Constructor for class ch.systemsx.cisd.base.io.AdapterOutputStreamToIOutputStream
 
addPoolName(boolean) - Method in class ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor
If addPoolName is true, the threads will contain the pool name as the first part of the thread names.
afterClass() - Method in class ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase
 
afterExecute(Runnable, Throwable) - Method in class ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor
 
available() - Method in class ch.systemsx.cisd.base.io.AdapterIInputStreamToInputStream
 
available() - Method in class ch.systemsx.cisd.base.io.AdapterInputStreamToIInputStream
 
available() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
available() - Method in interface ch.systemsx.cisd.base.io.IInputStream
 
available() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 

B

beforeExecute(Thread, Runnable) - Method in class ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor
 
BuildAndEnvironmentInfo - Class in ch.systemsx.cisd.base
The build and environment information for cisd-base.
ByteBufferRandomAccessFile - Class in ch.systemsx.cisd.base.io
An implementation of IRandomAccessFile based on a ByteBuffer.
ByteBufferRandomAccessFile(ByteBuffer, int) - Constructor for class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
Creates a IRandomAccessFile wrapper for the given buf.
ByteBufferRandomAccessFile(ByteBuffer) - Constructor for class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
Creates a IRandomAccessFile wrapper for the given buf.
ByteBufferRandomAccessFile(byte[], int) - Constructor for class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
Creates a IRandomAccessFile wrapper for the given array.
ByteBufferRandomAccessFile(byte[]) - Constructor for class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
Creates a IRandomAccessFile wrapper for the given array.
ByteBufferRandomAccessFile(int) - Constructor for class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
Creates a IRandomAccessFile wrapper for a ByteBuffer with capacity.
byteToChar(byte[], NativeData.ByteOrder, int, int) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a byte[] array into a char[] array.
byteToChar(byte[], NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a byte[] array into a char[] array.
byteToDouble(byte[], NativeData.ByteOrder, int, int) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a byte[] array into a double[] array.
byteToDouble(byte[], NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a byte[] array into a double[] array.
byteToFloat(byte[], NativeData.ByteOrder, int, int) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a byte[] array into a float[] array.
byteToFloat(byte[], NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a byte[] array into a float[] array.
byteToInt(byte[], NativeData.ByteOrder, int, int) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a byte[] array into an int[] array.
byteToInt(byte[], NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a byte[] array into an int[] array.
byteToLong(byte[], NativeData.ByteOrder, int, int) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a byte[] array into a long[] array.
byteToLong(byte[], NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a byte[] array into a long[] array.
byteToShort(byte[], NativeData.ByteOrder, int, int) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a byte[] array into a short[] array.
byteToShort(byte[], NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a byte[] array into a short[] array.

C

canDetectProcesses() - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns true, if process detection is available on this system.
capacity() - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Returns the capacity of elements in the array.
capacity() - Method in class ch.systemsx.cisd.base.mdarray.MDArray
 
capacity() - Method in class ch.systemsx.cisd.base.mdarray.MDByteArray
 
capacity() - Method in class ch.systemsx.cisd.base.mdarray.MDDoubleArray
 
capacity() - Method in class ch.systemsx.cisd.base.mdarray.MDFloatArray
 
capacity() - Method in class ch.systemsx.cisd.base.mdarray.MDIntArray
 
capacity() - Method in class ch.systemsx.cisd.base.mdarray.MDLongArray
 
capacity() - Method in class ch.systemsx.cisd.base.mdarray.MDShortArray
 
capacityHyperRows - Variable in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
 
ch.systemsx.cisd.base - package ch.systemsx.cisd.base
 
ch.systemsx.cisd.base.annotation - package ch.systemsx.cisd.base.annotation
 
ch.systemsx.cisd.base.convert - package ch.systemsx.cisd.base.convert
 
ch.systemsx.cisd.base.exceptions - package ch.systemsx.cisd.base.exceptions
This package provides basic exceptions thrown by CISD software.
ch.systemsx.cisd.base.image - package ch.systemsx.cisd.base.image
 
ch.systemsx.cisd.base.io - package ch.systemsx.cisd.base.io
 
ch.systemsx.cisd.base.mdarray - package ch.systemsx.cisd.base.mdarray
This package provides an implementation of multi-dimensional numerical arrays in Java.
ch.systemsx.cisd.base.namedthread - package ch.systemsx.cisd.base.namedthread
This package provides named pool threads when using an java.util.concurrent.ExecutorService.
ch.systemsx.cisd.base.tests - package ch.systemsx.cisd.base.tests
 
ch.systemsx.cisd.base.unix - package ch.systemsx.cisd.base.unix
This package provides some basic (POSIX-compliant) Unix system calls.
ch.systemsx.cisd.base.utilities - package ch.systemsx.cisd.base.utilities
This package provides some basic utility classes.
changeByteOrder(short) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Changes the byte order of the bytes constituting s.
changeByteOrder(char) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Changes the byte order of the bytes constituting c.
changeByteOrder(int) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Changes the byte order of the bytes constituting i.
changeByteOrder(float) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Changes the byte order of the bytes constituting f.
changeByteOrder(long) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Changes the byte order of the bytes constituting l.
changeByteOrder(double) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Changes the byte order of the bytes constituting d.
CHAR_SIZE - Static variable in class ch.systemsx.cisd.base.convert.NativeData
Size of a char value in bytes.
charToByte(char[], NativeData.ByteOrder, int, int) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a char[] array to a byte[] array.
charToByte(char[], NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a char[] array to a byte[] array.
check() - Static method in exception ch.systemsx.cisd.base.exceptions.InterruptedExceptionUnchecked
Checks whether the current thread has been interrupted and, if it has, throw a InterruptedExceptionUnchecked.
CheckedExceptionTunnel - Exception in ch.systemsx.cisd.base.exceptions
An exception for tunneling checked exception through code that doesn't expect it.
CheckedExceptionTunnel(Exception) - Constructor for exception ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel
Returns an unchecked exception from a checkedException.
CheckedExceptionTunnel(String) - Constructor for exception ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel
 
CheckedExceptionTunnel() - Constructor for exception ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel
 
cleanUpDirectoryBeforeTheTest(File) - Method in class ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase
Deletes, recreates and verifies that this is the empty directory
clearRunnableName() - Method in class ch.systemsx.cisd.base.namedthread.PoolNameThread
Clears the name of the runnable, setting the name of the thread to the pool name.
close() - Method in class ch.systemsx.cisd.base.io.AdapterIInputStreamToInputStream
 
close() - Method in class ch.systemsx.cisd.base.io.AdapterInputStreamToIInputStream
 
close() - Method in class ch.systemsx.cisd.base.io.AdapterIOutputStreamToOutputStream
 
close() - Method in class ch.systemsx.cisd.base.io.AdapterOutputStreamToIOutputStream
 
close() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
close() - Method in interface ch.systemsx.cisd.base.io.IInputStream
 
close() - Method in interface ch.systemsx.cisd.base.io.IOutputStream
 
close() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
computeHyperRowLength(int[]) - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
 
computeIndex(int...) - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Computes the linear index for the multi-dimensional indices provided.
computeIndex(int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Computes the linear index for the two-dimensional (indexX, indexY) provided.
computeIndex(int, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Computes the linear index for the three-dimensional (indexX, indexY, indexZ) provided.
computeReverseIndex(int) - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Computes the multi-dimensional index from the linearIndex.
copyByteToChar(byte[], int, char[], int, int, NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Copies a range from an array of byte into an array of char.
copyByteToDouble(byte[], int, double[], int, int, NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Copies a range from an array of byte into an array of double.
copyByteToFloat(byte[], int, float[], int, int, NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Copies a range from an array of byte into an array of float.
copyByteToInt(byte[], int, int[], int, int, NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Copies a range from an array of byte into an array of int.
copyByteToLong(byte[], int, long[], int, int, NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Copies a range from an array of byte into an array of long.
copyByteToShort(byte[], int, short[], int, int, NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Copies a range from an array of byte into an array of short.
copyCharToByte(char[], int, byte[], int, int, NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Copies a range from an array of char into an array of byte.
copyDoubleToByte(double[], int, byte[], int, int, NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Copies a range from an array of double into an array of byte.
copyFloatToByte(float[], int, byte[], int, int, NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Copies a range from an array of float into an array of byte.
copyIntToByte(int[], int, byte[], int, int, NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Copies a range from an array of int into an array of byte.
copyLongToByte(long[], int, byte[], int, int, NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Copies a range from an array of long into an array of byte.
copyResourceToFile(String, RandomAccessFile) - Static method in class ch.systemsx.cisd.base.utilities.ResourceUtilities
Copies the resource with the given name to a file on the file system..
copyResourceToTempFile(String, String, String) - Static method in class ch.systemsx.cisd.base.utilities.ResourceUtilities
Copies the resource with the given name to a temporary file.
copyResourceToTempFile(String, Path, String, String, boolean) - Static method in class ch.systemsx.cisd.base.utilities.ResourceUtilities
Copies the resource with the given name to a temporary file.
copyShortToByte(short[], int, byte[], int, int, NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Copies a range from an array of short into an array of byte.
corePoolSize(int) - Method in class ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor
Same as ThreadPoolExecutor.setCorePoolSize(int), but returns the object itself for chaining.
create(String) - Method in class ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase
Creates a File with name in the working directory.
createDirectoryInUnitTestRoot(String) - Method in class ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase
Creates a directory in the unit test root directory "targets/unit-test-wd"
createHardLink(String, String) - Static method in class ch.systemsx.cisd.base.unix.Unix
Creates a hard link linkName that points to fileName.
createSymbolicLink(String, String) - Static method in class ch.systemsx.cisd.base.unix.Unix
Creates a symbolic link linkName that points to fileName.
createTransformer() - Method in interface ch.systemsx.cisd.base.image.IImageTransformerFactory
Creates a transformer object based on the attributes of the factory.
createTransformer() - Method in interface ch.systemsx.cisd.base.image.IStreamingImageTransformerFactory
Creates a transformer object based on the attributes of the factory.

D

daemonize() - Method in class ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor
Sets the thread factory of this pool executor to daemon creation mode.
dealWithError(Throwable) - Method in interface ch.systemsx.cisd.base.exceptions.IErrorStrategy
Called when an exception ex has occurred.
decNumberOfHyperRows(int) - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Decrease the number of hyper-rows by count.
DEFAULT_ERROR_STRATEGY - Static variable in interface ch.systemsx.cisd.base.exceptions.IErrorStrategy
The default error strategy, just re-throws the exception.
DEFAULT_KEEP_ALIVE_TIME_MILLIS - Static variable in class ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor
The default time (in milli-seconds) to keep threads alive that are above the core pool size.
dimensions - Variable in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
 
dimensions() - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Returns a copy of the dimensions of the multi-dimensional array.
DOUBLE_SIZE - Static variable in class ch.systemsx.cisd.base.convert.NativeData
Size of a double value in bytes.
doubleToByte(double[], NativeData.ByteOrder, int, int) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a double[] array to a byte[] array.
doubleToByte(double[], NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a double[] array to a byte[] array.

E

ensureNativeLibIsLoaded() - Static method in class ch.systemsx.cisd.base.convert.NativeData
Call to ensure that the native library is loaded.
equals(Object) - Method in class ch.systemsx.cisd.base.io.AdapterIInputStreamToInputStream
 
equals(Object) - Method in class ch.systemsx.cisd.base.io.AdapterInputStreamToIInputStream
 
equals(Object) - Method in class ch.systemsx.cisd.base.io.AdapterIOutputStreamToOutputStream
 
equals(Object) - Method in class ch.systemsx.cisd.base.io.AdapterOutputStreamToIOutputStream
 
equals(Object) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
equals(Object) - Method in class ch.systemsx.cisd.base.mdarray.MDArray
 
equals(Object) - Method in class ch.systemsx.cisd.base.mdarray.MDByteArray
 
equals(Object) - Method in class ch.systemsx.cisd.base.mdarray.MDDoubleArray
 
equals(Object) - Method in class ch.systemsx.cisd.base.mdarray.MDFloatArray
 
equals(Object) - Method in class ch.systemsx.cisd.base.mdarray.MDIntArray
 
equals(Object) - Method in class ch.systemsx.cisd.base.mdarray.MDLongArray
 
equals(Object) - Method in class ch.systemsx.cisd.base.mdarray.MDShortArray
 
executableExists(String) - Static method in class ch.systemsx.cisd.base.utilities.OSUtilities
 
executableExists(File) - Static method in class ch.systemsx.cisd.base.utilities.OSUtilities
 

F

FileLinkType - Enum in ch.systemsx.cisd.base.unix
The type of a link in the file system.
findExecutable(String) - Static method in class ch.systemsx.cisd.base.utilities.OSUtilities
Search for the binary program with name binaryName in the operating system path..
findExecutable(String, Set<String>) - Static method in class ch.systemsx.cisd.base.utilities.OSUtilities
Search for the binary program with name binaryName in the set of paths denoted by pathSet.
FLOAT_SIZE - Static variable in class ch.systemsx.cisd.base.convert.NativeData
Size of a float value in bytes.
floatToByte(float[], NativeData.ByteOrder, int, int) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a float[] array to a byte[] array.
floatToByte(float[], NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a float[] array to a byte[] array.
flush() - Method in class ch.systemsx.cisd.base.io.AdapterIOutputStreamToOutputStream
 
flush() - Method in class ch.systemsx.cisd.base.io.AdapterOutputStreamToIOutputStream
 
flush() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
flush() - Method in interface ch.systemsx.cisd.base.io.IOutputStream
 
flush() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 

G

get(int...) - Method in class ch.systemsx.cisd.base.mdarray.MDArray
Returns the value of array at the position defined by indices.
get(int) - Method in class ch.systemsx.cisd.base.mdarray.MDArray
Returns the value of a one-dimensional array at the position defined by index.
get(int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDArray
Returns the value of a two-dimensional array at the position defined by indexX and indexY.
get(int, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDArray
Returns the value of a three-dimensional array at the position defined by indexX, indexY and indexZ.
get(int...) - Method in class ch.systemsx.cisd.base.mdarray.MDByteArray
Returns the value of array at the position defined by indices.
get(int) - Method in class ch.systemsx.cisd.base.mdarray.MDByteArray
Returns the value of a one-dimensional array at the position defined by index.
get(int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDByteArray
Returns the value of a two-dimensional array at the position defined by indexX and indexY.
get(int, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDByteArray
Returns the value of a three-dimensional array at the position defined by indexX, indexY and indexZ.
get(int...) - Method in class ch.systemsx.cisd.base.mdarray.MDDoubleArray
Returns the value of array at the position defined by indices.
get(int) - Method in class ch.systemsx.cisd.base.mdarray.MDDoubleArray
Returns the value of a one-dimensional array at the position defined by index.
get(int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDDoubleArray
Returns the value of a two-dimensional array at the position defined by indexX and indexY.
get(int, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDDoubleArray
Returns the value of a three-dimensional array at the position defined by indexX, indexY and indexZ.
get(int...) - Method in class ch.systemsx.cisd.base.mdarray.MDFloatArray
Returns the value of array at the position defined by indices.
get(int) - Method in class ch.systemsx.cisd.base.mdarray.MDFloatArray
Returns the value of a one-dimensional array at the position defined by index.
get(int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDFloatArray
Returns the value of a two-dimensional array at the position defined by indexX and indexY.
get(int, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDFloatArray
Returns the value of a three-dimensional array at the position defined by indexX, indexY and indexZ.
get(int...) - Method in class ch.systemsx.cisd.base.mdarray.MDIntArray
Returns the value of array at the position defined by indices.
get(int) - Method in class ch.systemsx.cisd.base.mdarray.MDIntArray
Returns the value of a one-dimensional array at the position defined by index.
get(int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDIntArray
Returns the value of a two-dimensional array at the position defined by indexX and indexY.
get(int, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDIntArray
Returns the value of a three-dimensional array at the position defined by indexX, indexY and indexZ.
get(int...) - Method in class ch.systemsx.cisd.base.mdarray.MDLongArray
Returns the value of array at the position defined by indices.
get(int) - Method in class ch.systemsx.cisd.base.mdarray.MDLongArray
Returns the value of a one-dimensional array at the position defined by index.
get(int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDLongArray
Returns the value of a two-dimensional array at the position defined by indexX and indexY.
get(int, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDLongArray
Returns the value of a three-dimensional array at the position defined by indexX, indexY and indexZ.
get(int...) - Method in class ch.systemsx.cisd.base.mdarray.MDShortArray
Returns the value of array at the position defined by indices.
get(int) - Method in class ch.systemsx.cisd.base.mdarray.MDShortArray
Returns the value of a one-dimensional array at the position defined by index.
get(int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDShortArray
Returns the value of a two-dimensional array at the position defined by indexX and indexY.
get(int, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDShortArray
Returns the value of a three-dimensional array at the position defined by indexX, indexY and indexZ.
getApplicationName() - Method in class ch.systemsx.cisd.base.utilities.AbstractBuildAndEnvironmentInfo
 
getAsFlatArray() - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Returns the array in flattened form.
getAsFlatArray() - Method in class ch.systemsx.cisd.base.mdarray.MDArray
 
getAsFlatArray() - Method in class ch.systemsx.cisd.base.mdarray.MDByteArray
 
getAsFlatArray() - Method in class ch.systemsx.cisd.base.mdarray.MDDoubleArray
 
getAsFlatArray() - Method in class ch.systemsx.cisd.base.mdarray.MDFloatArray
 
getAsFlatArray() - Method in class ch.systemsx.cisd.base.mdarray.MDIntArray
 
getAsFlatArray() - Method in class ch.systemsx.cisd.base.mdarray.MDLongArray
 
getAsFlatArray() - Method in class ch.systemsx.cisd.base.mdarray.MDShortArray
 
getAsObject(int) - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Return an object which has the same value as the element of the array specified by linearIndex.
getAsObject(int...) - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Return an object which has the same value as the element of the array specified by indices.
getAsObject(int...) - Method in class ch.systemsx.cisd.base.mdarray.MDArray
 
getAsObject(int) - Method in class ch.systemsx.cisd.base.mdarray.MDArray
 
getAsObject(int...) - Method in class ch.systemsx.cisd.base.mdarray.MDByteArray
 
getAsObject(int) - Method in class ch.systemsx.cisd.base.mdarray.MDByteArray
 
getAsObject(int...) - Method in class ch.systemsx.cisd.base.mdarray.MDDoubleArray
 
getAsObject(int) - Method in class ch.systemsx.cisd.base.mdarray.MDDoubleArray
 
getAsObject(int...) - Method in class ch.systemsx.cisd.base.mdarray.MDFloatArray
 
getAsObject(int) - Method in class ch.systemsx.cisd.base.mdarray.MDFloatArray
 
getAsObject(int...) - Method in class ch.systemsx.cisd.base.mdarray.MDIntArray
 
getAsObject(int) - Method in class ch.systemsx.cisd.base.mdarray.MDIntArray
 
getAsObject(int...) - Method in class ch.systemsx.cisd.base.mdarray.MDLongArray
 
getAsObject(int) - Method in class ch.systemsx.cisd.base.mdarray.MDLongArray
 
getAsObject(int...) - Method in class ch.systemsx.cisd.base.mdarray.MDShortArray
 
getAsObject(int) - Method in class ch.systemsx.cisd.base.mdarray.MDShortArray
 
getBlockSize() - Method in class ch.systemsx.cisd.base.unix.Unix.Stat
 
getByteOrder() - Method in enum ch.systemsx.cisd.base.convert.NativeArrayEncoding
Returns the byte order of the array.
getByteOrder() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
getByteOrder() - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
Gets the byte-order (endiness) of the random access file.
getByteOrder() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
getCallableName() - Method in interface ch.systemsx.cisd.base.namedthread.ICallableNameProvider
Returns the name to be used for the thread name.
getCause() - Method in exception ch.systemsx.cisd.base.exceptions.InterruptedExceptionUnchecked
 
getCause() - Method in exception ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked
 
getCause() - Method in exception ch.systemsx.cisd.base.exceptions.TimeoutExceptionUnchecked
 
getChannel() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
getCompatibleComputerPlatform() - Static method in class ch.systemsx.cisd.base.utilities.OSUtilities
 
getComponentClass() - Method in class ch.systemsx.cisd.base.mdarray.MDArray
Returns the component type of this array.
getComputerPlatform() - Static method in class ch.systemsx.cisd.base.utilities.OSUtilities
 
getCopyAsFlatArray() - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Returns a copy of the array in flattened form.
getCopyAsFlatArray() - Method in class ch.systemsx.cisd.base.mdarray.MDArray
 
getCopyAsFlatArray() - Method in class ch.systemsx.cisd.base.mdarray.MDByteArray
 
getCopyAsFlatArray() - Method in class ch.systemsx.cisd.base.mdarray.MDDoubleArray
 
getCopyAsFlatArray() - Method in class ch.systemsx.cisd.base.mdarray.MDFloatArray
 
getCopyAsFlatArray() - Method in class ch.systemsx.cisd.base.mdarray.MDIntArray
 
getCopyAsFlatArray() - Method in class ch.systemsx.cisd.base.mdarray.MDLongArray
 
getCopyAsFlatArray() - Method in class ch.systemsx.cisd.base.mdarray.MDShortArray
 
getCPUArchitecture() - Method in class ch.systemsx.cisd.base.utilities.AbstractBuildAndEnvironmentInfo
 
getCPUArchitecture() - Static method in class ch.systemsx.cisd.base.utilities.OSUtilities
 
getDeviceId() - Method in class ch.systemsx.cisd.base.unix.Unix.Stat
 
getDimensions() - Method in class ch.systemsx.cisd.base.convert.NativeTaggedArray.NativeArrayTag
Resurns the dimensions of the array.
getEgid() - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the effective gid that determines the permissions of this process.
getEncoding() - Method in class ch.systemsx.cisd.base.convert.NativeTaggedArray.NativeArrayTag
Returns the NativeArrayEncoding of the array.
getEnvironmentInfo() - Method in class ch.systemsx.cisd.base.utilities.AbstractBuildAndEnvironmentInfo
Returns version, build number, Java VM, and OS as a List with four entries.
getErrorString(int) - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the error string for the given errnum.
getEuid() - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the effective uid that determines the permissions of this process.
getFD() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
getFileInfo(String) - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the information about fileName.
getFilePointer() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
getFilePointer() - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
Returns the current offset in this file.
getFilePointer() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
getFullVersion() - Method in class ch.systemsx.cisd.base.utilities.AbstractBuildAndEnvironmentInfo
Returns the version accompanied by the build number of the software (if known).
getGid() - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the gid of the user that started this process.
getGid() - Method in class ch.systemsx.cisd.base.unix.Unix.Group
 
getGid() - Method in class ch.systemsx.cisd.base.unix.Unix.Password
 
getGid() - Method in class ch.systemsx.cisd.base.unix.Unix.Stat
 
getGidForGroupName(String) - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the gid of the groupName, or -1, if no group with this name exists.
getGroupMembers() - Method in class ch.systemsx.cisd.base.unix.Unix.Group
 
getGroupName() - Method in class ch.systemsx.cisd.base.unix.Unix.Group
 
getGroupPasswordHash() - Method in class ch.systemsx.cisd.base.unix.Unix.Group
 
getHomeDirectory() - Method in class ch.systemsx.cisd.base.unix.Unix.Password
 
getIndex() - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray.ArrayEntry
The multi-dimensional index of this entry.
getInode(String) - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the inode for the fileName.
getInode() - Method in class ch.systemsx.cisd.base.unix.Unix.Stat
 
getJavaVM() - Method in class ch.systemsx.cisd.base.utilities.AbstractBuildAndEnvironmentInfo
 
getLastAccess() - Method in class ch.systemsx.cisd.base.unix.Unix.Stat
 
getLastError() - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the last error that occurred in this class.
getLastModified() - Method in class ch.systemsx.cisd.base.unix.Unix.Stat
 
getLastStatusChange() - Method in class ch.systemsx.cisd.base.unix.Unix.Stat
 
getLength(int[]) - Static method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Returns the one-dimensional length of the multi-dimensional array defined by dimensions.
getLength(int[], int) - Static method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Returns the one-dimensional length of the multi-dimensional array defined by dimensions.
getLength(long[]) - Static method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Returns the one-dimensional length of the multi-dimensional array defined by dimensions.
getLength(long[], long) - Static method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Returns the one-dimensional length of the multi-dimensional array defined by dimensions.
getLinearIndex() - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray.ArrayEntry
The linear index of this entry.
getLinkInfo(String) - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the information about linkName.
getLinkInfo(String, boolean) - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the information about linkName.
getLinkType() - Method in class ch.systemsx.cisd.base.unix.Unix.Stat
 
getMessage() - Method in exception ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel
 
getNativeByteOrder() - Static method in class ch.systemsx.cisd.base.convert.NativeData
Returns the native byte order of the host running this JRE.
getNumberOfBlocks() - Method in class ch.systemsx.cisd.base.unix.Unix.Stat
 
getNumberOfHardLinks(String) - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the number of hard links for the fileName.
getNumberOfHardLinks() - Method in class ch.systemsx.cisd.base.unix.Unix.Stat
 
getOS() - Method in class ch.systemsx.cisd.base.utilities.AbstractBuildAndEnvironmentInfo
 
getOSName() - Static method in class ch.systemsx.cisd.base.utilities.OSUtilities
 
getOSPath() - Static method in class ch.systemsx.cisd.base.utilities.OSUtilities
 
getPasswordHash() - Method in class ch.systemsx.cisd.base.unix.Unix.Password
 
getPermissions() - Method in class ch.systemsx.cisd.base.unix.Unix.Stat
 
getPid() - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the process identifier of the current process.
getRevision() - Method in class ch.systemsx.cisd.base.utilities.AbstractBuildAndEnvironmentInfo
 
getRunnableName() - Method in interface ch.systemsx.cisd.base.namedthread.IRunnableNameProvider
Returns the name to be used for the thread name.
getSafeOSPath(boolean) - Static method in class ch.systemsx.cisd.base.utilities.OSUtilities
 
getSafeOSPath() - Static method in class ch.systemsx.cisd.base.utilities.OSUtilities
Convenience method for OSUtilities.getSafeOSPath(boolean) with root=false.
getShell() - Method in class ch.systemsx.cisd.base.unix.Unix.Password
 
getSize() - Method in class ch.systemsx.cisd.base.unix.Unix.Stat
 
getSizeInBytes() - Method in enum ch.systemsx.cisd.base.convert.NativeArrayEncoding
Returns the size of one element in bytes.
getThreadCount() - Method in class ch.systemsx.cisd.base.namedthread.NamingThreadFactory
 
getThreadFactory() - Method in class ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor
 
getUid() - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the uid of the user that started this process.
getUid() - Method in class ch.systemsx.cisd.base.unix.Unix.Password
 
getUid() - Method in class ch.systemsx.cisd.base.unix.Unix.Stat
 
getUidForUserName(String) - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the uid of the userName, or -1, if no user with this name exists.
getUserFullName() - Method in class ch.systemsx.cisd.base.unix.Unix.Password
 
getUserName() - Method in class ch.systemsx.cisd.base.unix.Unix.Password
 
getUsername() - Static method in class ch.systemsx.cisd.base.utilities.OSUtilities
 
getValue() - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray.ArrayEntry
The value of this entry.
getVersion() - Method in class ch.systemsx.cisd.base.utilities.AbstractBuildAndEnvironmentInfo
 

H

hashCode() - Method in class ch.systemsx.cisd.base.io.AdapterIInputStreamToInputStream
 
hashCode() - Method in class ch.systemsx.cisd.base.io.AdapterInputStreamToIInputStream
 
hashCode() - Method in class ch.systemsx.cisd.base.io.AdapterIOutputStreamToOutputStream
 
hashCode() - Method in class ch.systemsx.cisd.base.io.AdapterOutputStreamToIOutputStream
 
hashCode() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
hashCode() - Method in class ch.systemsx.cisd.base.mdarray.MDArray
 
hashCode() - Method in class ch.systemsx.cisd.base.mdarray.MDByteArray
 
hashCode() - Method in class ch.systemsx.cisd.base.mdarray.MDDoubleArray
 
hashCode() - Method in class ch.systemsx.cisd.base.mdarray.MDFloatArray
 
hashCode() - Method in class ch.systemsx.cisd.base.mdarray.MDIntArray
 
hashCode() - Method in class ch.systemsx.cisd.base.mdarray.MDLongArray
 
hashCode() - Method in class ch.systemsx.cisd.base.mdarray.MDShortArray
 
hyperRowLength - Variable in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
 

I

ICallableNameProvider - Interface in ch.systemsx.cisd.base.namedthread
A name provider for a Callable.
IErrorStrategy - Interface in ch.systemsx.cisd.base.exceptions
A strategy role for dealing with errors.
IImageTransformer - Interface in ch.systemsx.cisd.base.image
Interface for classes which can transform images.
IImageTransformerFactory - Interface in ch.systemsx.cisd.base.image
Factory creating an IImageTransformer.
IInputStream - Interface in ch.systemsx.cisd.base.io
An interface for InputStream.
incNumberOfHyperRows(int) - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Increase the number of hyper-rows by count.
INSTANCE - Static variable in class ch.systemsx.cisd.base.BuildAndEnvironmentInfo
 
INT_SIZE - Static variable in class ch.systemsx.cisd.base.convert.NativeData
Size of an int value in bytes.
InterruptedExceptionUnchecked - Exception in ch.systemsx.cisd.base.exceptions
Exception that signals that whoever gets it should stop its current work.
InterruptedExceptionUnchecked() - Constructor for exception ch.systemsx.cisd.base.exceptions.InterruptedExceptionUnchecked
 
InterruptedExceptionUnchecked(InterruptedException) - Constructor for exception ch.systemsx.cisd.base.exceptions.InterruptedExceptionUnchecked
 
intToByte(int[], NativeData.ByteOrder, int, int) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a int[] array to a byte[] array.
intToByte(int[], NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a int[] array to a byte[] array.
IOExceptionUnchecked - Exception in ch.systemsx.cisd.base.exceptions
A CheckedExceptionTunnel for an IOException.
IOExceptionUnchecked(IOException) - Constructor for exception ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked
Returns an IOExceptionUnchecked from a IOException.
IOExceptionUnchecked(String) - Constructor for exception ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked
Returns an IOExceptionUnchecked from a newly created IOException with given msg.
IOExceptionUnchecked(Throwable) - Constructor for exception ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked
Returns an IOExceptionUnchecked from newly created IOException with given throwable as its cause.
IOutputStream - Interface in ch.systemsx.cisd.base.io
An interface for OutputStream.
IRandomAccessFile - Interface in ch.systemsx.cisd.base.io
The interface of RandomAccessFile.
IRunnableNameProvider - Interface in ch.systemsx.cisd.base.namedthread
A name provider for a Runnable.
isAddPoolName() - Method in class ch.systemsx.cisd.base.namedthread.NamingThreadFactory
 
isCleanSources() - Method in class ch.systemsx.cisd.base.utilities.AbstractBuildAndEnvironmentInfo
 
isCreateDaemonThreads() - Method in class ch.systemsx.cisd.base.namedthread.NamingThreadFactory
 
isFloatingPoint() - Method in enum ch.systemsx.cisd.base.convert.NativeArrayEncoding
Returns true, if the encoded array is a float array.
isInteger() - Method in enum ch.systemsx.cisd.base.convert.NativeArrayEncoding
Returns true, if the encoded array is an int array.
isMacOS() - Static method in class ch.systemsx.cisd.base.utilities.OSUtilities
 
isOperational() - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns true, if the native library has been loaded successfully and the link utilities are operational, false otherwise.
isProcessRunning(int) - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns true, if the process with pid is currently running and false, if it is not running or if process detection is not available ( Unix.canDetectProcesses() == false).
isRoot() - Static method in class ch.systemsx.cisd.base.utilities.OSUtilities
 
isSymbolicLink(String) - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns true if fileName is a symbolic link and false otherwise.
isSymbolicLink() - Method in class ch.systemsx.cisd.base.unix.Unix.Stat
Returns true, if this link is a symbolic link.
IStreamingImageTransformer - Interface in ch.systemsx.cisd.base.image
Interface for classes which can transform images in a streaming mode.
IStreamingImageTransformerFactory - Interface in ch.systemsx.cisd.base.image
Factory creating an IStreamingImageTransformer.
isUnix() - Static method in class ch.systemsx.cisd.base.utilities.OSUtilities
 
isUseNativeLib() - Static method in class ch.systemsx.cisd.base.convert.NativeData
Returns true, if this class uses the native library and false otherwise.
isWindows() - Static method in class ch.systemsx.cisd.base.utilities.OSUtilities
 
ISynchronizable - Interface in ch.systemsx.cisd.base.io
A roles that allows to synchronize a resource with an underlying resource.
iterator() - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
 

J

JsonObject - Annotation Type in ch.systemsx.cisd.base.annotation
Annotation all JSON transfered classes should be marked with.

K

keepAliveTime(long) - Method in class ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor
Same as ThreadPoolExecutor.setKeepAliveTime(long, TimeUnit), but uses always TimeUnit.MILLISECONDS and returns the object itself for chaining.

L

length() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
length() - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
Returns the length of this file.
length() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
LINE_SEPARATOR - Static variable in class ch.systemsx.cisd.base.utilities.OSUtilities
Platform specific line separator.
loadNativeLibrary(String) - Static method in class ch.systemsx.cisd.base.utilities.NativeLibraryUtilities
Loads the native library libraryName.
LONG_SIZE - Static variable in class ch.systemsx.cisd.base.convert.NativeData
Size of a long value in bytes.
longDimensions() - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Returns a copy of the dimensions of the multi-dimensional array as long[].
longToByte(long[], NativeData.ByteOrder, int, int) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a long[] array to a byte[] array.
longToByte(long[], NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a long[] array to a byte[] array.

M

main(String[]) - Static method in class ch.systemsx.cisd.base.BuildAndEnvironmentInfo
Shows build and environment information on the console.
mark(int) - Method in class ch.systemsx.cisd.base.io.AdapterIInputStreamToInputStream
 
mark(int) - Method in class ch.systemsx.cisd.base.io.AdapterInputStreamToIInputStream
 
mark(int) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
mark(int) - Method in interface ch.systemsx.cisd.base.io.IInputStream
 
mark(int) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
markSupported() - Method in class ch.systemsx.cisd.base.io.AdapterIInputStreamToInputStream
 
markSupported() - Method in class ch.systemsx.cisd.base.io.AdapterInputStreamToIInputStream
 
markSupported() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
markSupported() - Method in interface ch.systemsx.cisd.base.io.IInputStream
 
markSupported() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
maximumPoolSize(int) - Method in class ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor
Same as ThreadPoolExecutor.setMaximumPoolSize(int), but returns the object itself for chaining.
MDAbstractArray<T> - Class in ch.systemsx.cisd.base.mdarray
Base class of a multi-dimensional array.
MDAbstractArray(int[], int, int) - Constructor for class ch.systemsx.cisd.base.mdarray.MDAbstractArray
 
MDAbstractArray.ArrayEntry - Class in ch.systemsx.cisd.base.mdarray
A class to represent an entry (index and value) of a MDArray, used for iteration.
MDArray<T> - Class in ch.systemsx.cisd.base.mdarray
A multi-dimensional array of generic type T.
MDArray(Class<T>, long[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDArray
Creates an empty MDArray with the dimensions.
MDArray(Class<T>, long[], long) - Constructor for class ch.systemsx.cisd.base.mdarray.MDArray
Creates an empty MDArray with the dimensions.
MDArray(T[], long[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDArray
Creates a MDArray from the given flattenedArray and dimensions.
MDArray(T[], long[], boolean) - Constructor for class ch.systemsx.cisd.base.mdarray.MDArray
Creates a MDArray from the given flattenedArray and dimensions.
MDArray(Class<T>, int[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDArray
Creates an empty MDArray with the dimensions.
MDArray(Class<T>, int[], int) - Constructor for class ch.systemsx.cisd.base.mdarray.MDArray
Creates an empty MDArray with the dimensions.
MDArray(T[], int[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDArray
Creates a MDArray from the given flattenedArray and dimensions.
MDArray(T[], int[], boolean) - Constructor for class ch.systemsx.cisd.base.mdarray.MDArray
Creates a MDArray from the given flattenedArray and dimensions.
MDByteArray - Class in ch.systemsx.cisd.base.mdarray
A multi-dimensional byte array.
MDByteArray(long[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDByteArray
Creates an empty MDIntArray with the dimensions.
MDByteArray(long[], long) - Constructor for class ch.systemsx.cisd.base.mdarray.MDByteArray
Creates an empty MDByteArray with the dimensions.
MDByteArray(byte[], long[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDByteArray
Creates a MDByteArray from the given flattenedArray and dimensions.
MDByteArray(byte[], long[], boolean) - Constructor for class ch.systemsx.cisd.base.mdarray.MDByteArray
Creates a MDByteArray from the given flattenedArray and dimensions.
MDByteArray(int[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDByteArray
Creates an empty MDByteArray with the dimensions.
MDByteArray(int[], int) - Constructor for class ch.systemsx.cisd.base.mdarray.MDByteArray
Creates an empty MDByteArray with the dimensions.
MDByteArray(byte[], int[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDByteArray
Creates a MDByteArray from the given flattenedArray and dimensions.
MDByteArray(byte[], int[], boolean) - Constructor for class ch.systemsx.cisd.base.mdarray.MDByteArray
Creates a MDByteArray from the given flattenedArray and dimensions.
MDByteArray(byte[][]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDByteArray
Creates a MDByteArray from the given matrix of rank 2.
MDByteArray(byte[][], int[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDByteArray
Creates a MDByteArray from the given matrix of rank 2 and the dimension which need to be less or equal the dimensions of matrix.
MDDoubleArray - Class in ch.systemsx.cisd.base.mdarray
A multi-dimensional double array.
MDDoubleArray(long[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDDoubleArray
Creates an empty MDIntArray with the dimensions.
MDDoubleArray(long[], long) - Constructor for class ch.systemsx.cisd.base.mdarray.MDDoubleArray
Creates an empty MDDoubleArray with the dimensions.
MDDoubleArray(double[], long[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDDoubleArray
Creates a MDDoubleArray from the given flattenedArray and dimensions.
MDDoubleArray(double[], long[], boolean) - Constructor for class ch.systemsx.cisd.base.mdarray.MDDoubleArray
Creates a MDDoubleArray from the given flattenedArray and dimensions.
MDDoubleArray(int[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDDoubleArray
Creates an empty MDDoubleArray with the dimensions.
MDDoubleArray(int[], int) - Constructor for class ch.systemsx.cisd.base.mdarray.MDDoubleArray
Creates an empty MDDoubleArray with the dimensions.
MDDoubleArray(double[], int[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDDoubleArray
Creates a MDDoubleArray from the given flattenedArray and dimensions.
MDDoubleArray(double[], int[], boolean) - Constructor for class ch.systemsx.cisd.base.mdarray.MDDoubleArray
Creates a MDDoubleArray from the given flattenedArray and dimensions.
MDDoubleArray(double[][]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDDoubleArray
Creates a MDDoubleArray from the given matrix of rank 2.
MDDoubleArray(double[][], int[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDDoubleArray
Creates a MDDoubleArray from the given matrix of rank 2 and the dimension which need to be less or equal the dimensions of matrix.
MDFloatArray - Class in ch.systemsx.cisd.base.mdarray
A multi-dimensional float array.
MDFloatArray(long[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDFloatArray
Creates an empty MDIntArray with the dimensions.
MDFloatArray(long[], long) - Constructor for class ch.systemsx.cisd.base.mdarray.MDFloatArray
Creates an empty MDFloatArray with the dimensions.
MDFloatArray(float[], long[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDFloatArray
Creates a MDFloatArray from the given flattenedArray and dimensions.
MDFloatArray(float[], long[], boolean) - Constructor for class ch.systemsx.cisd.base.mdarray.MDFloatArray
Creates a MDFloatArray from the given flattenedArray and dimensions.
MDFloatArray(int[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDFloatArray
Creates an empty MDFloatArray with the dimensions.
MDFloatArray(int[], int) - Constructor for class ch.systemsx.cisd.base.mdarray.MDFloatArray
Creates an empty MDFloatArray with the dimensions.
MDFloatArray(float[], int[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDFloatArray
Creates a MDFloatArray from the given flattenedArray and dimensions.
MDFloatArray(float[], int[], boolean) - Constructor for class ch.systemsx.cisd.base.mdarray.MDFloatArray
Creates a MDFloatArray from the given flattenedArray and dimensions.
MDFloatArray(float[][]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDFloatArray
Creates a MDFloatArray from the given matrix of rank 2.
MDFloatArray(float[][], int[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDFloatArray
Creates a MDFloatArray from the given matrix of rank 2 and the dimension which need to be less or equal the dimensions of matrix.
MDIntArray - Class in ch.systemsx.cisd.base.mdarray
A multi-dimensional int array.
MDIntArray(long[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDIntArray
Creates an empty MDIntArray with the dimensions.
MDIntArray(long[], long) - Constructor for class ch.systemsx.cisd.base.mdarray.MDIntArray
Creates an empty MDIntArray with the dimensions.
MDIntArray(int[], long[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDIntArray
Creates a MDIntArray from the given flattenedArray and dimensions.
MDIntArray(int[], long[], boolean) - Constructor for class ch.systemsx.cisd.base.mdarray.MDIntArray
Creates a MDIntArray from the given flattenedArray and dimensions.
MDIntArray(int[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDIntArray
Creates an empty MDIntArray with the dimensions.
MDIntArray(int[], int) - Constructor for class ch.systemsx.cisd.base.mdarray.MDIntArray
Creates an empty MDIntArray with the dimensions.
MDIntArray(int[], int[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDIntArray
Creates a MDIntArray from the given flattenedArray and dimensions.
MDIntArray(int[], int[], boolean) - Constructor for class ch.systemsx.cisd.base.mdarray.MDIntArray
Creates a MDIntArray from the given flattenedArray and dimensions.
MDIntArray(int[][]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDIntArray
Creates a MDIntArray from the given matrix of rank 2.
MDIntArray(int[][], int[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDIntArray
Creates a MDIntArray from the given matrix of rank 2 and the dimension which need to be less or equal the dimensions of matrix.
MDLongArray - Class in ch.systemsx.cisd.base.mdarray
A multi-dimensional long array.
MDLongArray(long[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDLongArray
Creates an empty MDIntArray with the dimensions.
MDLongArray(long[], long) - Constructor for class ch.systemsx.cisd.base.mdarray.MDLongArray
Creates an empty MDLongArray with the dimensions.
MDLongArray(long[], long[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDLongArray
Creates a MDLongArray from the given flattenedArray and dimensions.
MDLongArray(long[], long[], boolean) - Constructor for class ch.systemsx.cisd.base.mdarray.MDLongArray
Creates a MDLongArray from the given flattenedArray and dimensions.
MDLongArray(int[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDLongArray
Creates an empty MDLongArray with the dimensions.
MDLongArray(int[], int) - Constructor for class ch.systemsx.cisd.base.mdarray.MDLongArray
Creates an empty MDLongArray with the dimensions.
MDLongArray(long[], int[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDLongArray
Creates a MDLongArray from the given flattenedArray and dimensions.
MDLongArray(long[], int[], boolean) - Constructor for class ch.systemsx.cisd.base.mdarray.MDLongArray
Creates a MDLongArray from the given flattenedArray and dimensions.
MDLongArray(long[][]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDLongArray
Creates a MDLongArray from the given matrix of rank 2.
MDLongArray(long[][], int[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDLongArray
Creates a MDLongArray from the given matrix of rank 2 and the dimension which need to be less or equal the dimensions of matrix.
MDShortArray - Class in ch.systemsx.cisd.base.mdarray
A multi-dimensional short array.
MDShortArray(long[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDShortArray
Creates an empty MDIntArray with the dimensions.
MDShortArray(long[], long) - Constructor for class ch.systemsx.cisd.base.mdarray.MDShortArray
Creates an empty MDShortArray with the dimensions.
MDShortArray(short[], long[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDShortArray
Creates a MDShortArray from the given flattenedArray and dimensions.
MDShortArray(short[], long[], boolean) - Constructor for class ch.systemsx.cisd.base.mdarray.MDShortArray
Creates a MDShortArray from the given flattenedArray and dimensions.
MDShortArray(int[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDShortArray
Creates an empty MDShortArray with the dimensions.
MDShortArray(int[], int) - Constructor for class ch.systemsx.cisd.base.mdarray.MDShortArray
Creates an empty MDShortArray with the dimensions.
MDShortArray(short[], int[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDShortArray
Creates a MDShortArray from the given flattenedArray and dimensions.
MDShortArray(short[], int[], boolean) - Constructor for class ch.systemsx.cisd.base.mdarray.MDShortArray
Creates a MDShortArray from the given flattenedArray and dimensions.
MDShortArray(short[][]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDShortArray
Creates a MDShortArray from the given matrix of rank 2.
MDShortArray(short[][], int[]) - Constructor for class ch.systemsx.cisd.base.mdarray.MDShortArray
Creates a MDShortArray from the given matrix of rank 2 and the dimension which need to be less or equal the dimensions of matrix.

N

NamedCallable<T> - Interface in ch.systemsx.cisd.base.namedthread
A Callable with a name.
NamedRunnable - Interface in ch.systemsx.cisd.base.namedthread
A Runnable with a name.
NamingThreadFactory - Class in ch.systemsx.cisd.base.namedthread
A ThreadFactory that gives (non-standard) names to new threads.
NamingThreadFactory(String) - Constructor for class ch.systemsx.cisd.base.namedthread.NamingThreadFactory
 
NamingThreadPoolExecutor - Class in ch.systemsx.cisd.base.namedthread
A ThreadPoolExecutor that allows to attach names to the threads it manages.
NamingThreadPoolExecutor(String) - Constructor for class ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor
Creates a new (caching) NamingThreadPoolExecutor with the given initial parameters.
NamingThreadPoolExecutor(String, int) - Constructor for class ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor
Creates a new (caching) NamingThreadPoolExecutor with the given initial parameters.
NamingThreadPoolExecutor(String, int, int, long, TimeUnit, BlockingQueue<Runnable>, RejectedExecutionHandler) - Constructor for class ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor
Creates a new NamingThreadPoolExecutor with the given initial parameters.
NamingThreadPoolExecutor(String, int, int, long, TimeUnit, BlockingQueue<Runnable>) - Constructor for class ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor
Creates a new NamingThreadPoolExecutor with the given initial parameters.
NamingThreadPoolExecutor(int, int, long, TimeUnit, BlockingQueue<Runnable>, NamingThreadFactory, RejectedExecutionHandler) - Constructor for class ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor
Creates a new NamingThreadPoolExecutor with the given initial parameters.
NamingThreadPoolExecutor(int, int, long, TimeUnit, BlockingQueue<Runnable>, NamingThreadFactory) - Constructor for class ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor
Creates a new NamingThreadPoolExecutor with the given initial parameters.
NativeArrayEncoding - Enum in ch.systemsx.cisd.base.convert
An enum for encoding array of numbers (integer or float) in native (host) format.
NativeData - Class in ch.systemsx.cisd.base.convert
This class encapsulates native methods to deal with arrays of numbers, converting from numbers to bytes and bytes to numbers.
NativeData() - Constructor for class ch.systemsx.cisd.base.convert.NativeData
 
NativeData.ByteOrder - Enum in ch.systemsx.cisd.base.convert
Byte Order enumeration.
NativeLibraryUtilities - Class in ch.systemsx.cisd.base.utilities
A utility class for loading native shared libraries (following the JNI specification).
NativeLibraryUtilities() - Constructor for class ch.systemsx.cisd.base.utilities.NativeLibraryUtilities
 
NativeTaggedArray - Class in ch.systemsx.cisd.base.convert
A utility class that supports encoding and decoding of arrays of primitive number types to byte arrays such that the characteristics of the number type (float or integer, byte order, element size) and the dimensions are known and can be checked for correctness when converted back to the number type.
NativeTaggedArray() - Constructor for class ch.systemsx.cisd.base.convert.NativeTaggedArray
 
NativeTaggedArray.NativeArrayTag - Class in ch.systemsx.cisd.base.convert
A class to return the array encoding and dimensions of a native tagged array.
newThread(Runnable) - Method in class ch.systemsx.cisd.base.namedthread.NamingThreadFactory
 
numberOfHyperRows() - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Returns the current number of hyper rows of of this array.

O

OSUtilities - Class in ch.systemsx.cisd.base.utilities
Some useful methods related to the operating system.
OSUtilities() - Constructor for class ch.systemsx.cisd.base.utilities.OSUtilities
 

P

PoolNameThread - Class in ch.systemsx.cisd.base.namedthread
A Thread that knows its pool name.
PoolNameThread(Runnable, String, boolean) - Constructor for class ch.systemsx.cisd.base.namedthread.PoolNameThread
 
printFullStackTrace() - Method in exception ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel
Like Throwable.printStackTrace(), but includes the tunnel's stacktrace as well.
printFullStackTrace(PrintStream) - Method in exception ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel
Like CheckedExceptionTunnel.printStackTrace(PrintStream), but includes the tunnel's stacktrace as well.
printFullStackTrace(PrintWriter) - Method in exception ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel
Like CheckedExceptionTunnel.printStackTrace(PrintWriter), but includes the tunnel's stacktrace as well.
printStackTrace(PrintStream) - Method in exception ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel
 
printStackTrace(PrintWriter) - Method in exception ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel
 

R

RandomAccessFileImpl - Class in ch.systemsx.cisd.base.io
The file implementation of IRandomAccessFile.
RandomAccessFileImpl(RandomAccessFile) - Constructor for class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
RandomAccessFileImpl(String, String) - Constructor for class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
RandomAccessFileImpl(File, String) - Constructor for class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
rank() - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Returns the rank of the array.
read() - Method in class ch.systemsx.cisd.base.io.AdapterIInputStreamToInputStream
 
read(byte[], int, int) - Method in class ch.systemsx.cisd.base.io.AdapterIInputStreamToInputStream
 
read(byte[]) - Method in class ch.systemsx.cisd.base.io.AdapterIInputStreamToInputStream
 
read() - Method in class ch.systemsx.cisd.base.io.AdapterInputStreamToIInputStream
 
read(byte[], int, int) - Method in class ch.systemsx.cisd.base.io.AdapterInputStreamToIInputStream
 
read(byte[]) - Method in class ch.systemsx.cisd.base.io.AdapterInputStreamToIInputStream
 
read() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
read(byte[]) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
read(byte[], int, int) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
read() - Method in interface ch.systemsx.cisd.base.io.IInputStream
 
read(byte[]) - Method in interface ch.systemsx.cisd.base.io.IInputStream
 
read(byte[], int, int) - Method in interface ch.systemsx.cisd.base.io.IInputStream
 
read() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
read(byte[], int, int) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
read(byte[]) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
readBoolean() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
readBoolean() - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
readBoolean() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
readByte() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
readByte() - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
readByte() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
readChar() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
readChar() - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
readChar() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
readDouble() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
readDouble() - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
readDouble() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
readFloat() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
readFloat() - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
readFloat() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
readFully(byte[]) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
readFully(byte[], int, int) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
readFully(byte[]) - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
readFully(byte[], int, int) - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
readFully(byte[]) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
readFully(byte[], int, int) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
readInt() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
readInt() - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
readInt() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
readLine() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
readLine() - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
readLine() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
readLong() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
readLong() - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
readLong() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
readShort() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
readShort() - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
readShort() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
readUnsignedByte() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
readUnsignedByte() - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
readUnsignedByte() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
readUnsignedShort() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
readUnsignedShort() - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
readUnsignedShort() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
readUTF() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
readUTF() - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
readUTF() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
reset() - Method in class ch.systemsx.cisd.base.io.AdapterIInputStreamToInputStream
 
reset() - Method in class ch.systemsx.cisd.base.io.AdapterInputStreamToIInputStream
 
reset() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
reset() - Method in interface ch.systemsx.cisd.base.io.IInputStream
 
reset() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
ResourceUtilities - Class in ch.systemsx.cisd.base.utilities
Utilities for handling Java resources.
ResourceUtilities() - Constructor for class ch.systemsx.cisd.base.utilities.ResourceUtilities
 
Retry10 - Class in ch.systemsx.cisd.base.tests
An RetryAnalyzerCount extension which sets the count to 10.
Retry10() - Constructor for class ch.systemsx.cisd.base.tests.Retry10
 
Retry50 - Class in ch.systemsx.cisd.base.tests
An RetryAnalyzerCount extension which sets the count to 50.
Retry50() - Constructor for class ch.systemsx.cisd.base.tests.Retry50
 
retryMethod(ITestResult) - Method in class ch.systemsx.cisd.base.tests.Retry10
 
retryMethod(ITestResult) - Method in class ch.systemsx.cisd.base.tests.Retry50
 

S

S_IRGRP - Static variable in class ch.systemsx.cisd.base.unix.Unix
read by group
S_IROTH - Static variable in class ch.systemsx.cisd.base.unix.Unix
read by others
S_IRUSR - Static variable in class ch.systemsx.cisd.base.unix.Unix
read by owner
S_ISGID - Static variable in class ch.systemsx.cisd.base.unix.Unix
set group ID on execution
S_ISUID - Static variable in class ch.systemsx.cisd.base.unix.Unix
set user ID on execution
S_ISVTX - Static variable in class ch.systemsx.cisd.base.unix.Unix
sticky bit
S_IWGRP - Static variable in class ch.systemsx.cisd.base.unix.Unix
write by group
S_IWOTH - Static variable in class ch.systemsx.cisd.base.unix.Unix
write by others
S_IWUSR - Static variable in class ch.systemsx.cisd.base.unix.Unix
write by owner
S_IXGRP - Static variable in class ch.systemsx.cisd.base.unix.Unix
execute/search by group
S_IXOTH - Static variable in class ch.systemsx.cisd.base.unix.Unix
execute/search by others
S_IXUSR - Static variable in class ch.systemsx.cisd.base.unix.Unix
execute/search by owner
seek(long) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
seek(long) - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
Sets the file-pointer offset, measured from the beginning of this file, at which the next read or write occurs.
seek(long) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
set(T, int...) - Method in class ch.systemsx.cisd.base.mdarray.MDArray
Sets the value of array at the position defined by indices.
set(T, int) - Method in class ch.systemsx.cisd.base.mdarray.MDArray
Sets the value of a one-dimension array at the position defined by index.
set(T, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDArray
Sets the value of a two-dimensional array at the position defined by indexX and indexY.
set(T, int, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDArray
Sets the value of a three-dimensional array at the position defined by indexX, indexY and indexZ.
set(byte, int...) - Method in class ch.systemsx.cisd.base.mdarray.MDByteArray
Sets the value of array at the position defined by indices.
set(byte, int) - Method in class ch.systemsx.cisd.base.mdarray.MDByteArray
Sets the value of a one-dimension array at the position defined by index.
set(byte, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDByteArray
Sets the value of a two-dimensional array at the position defined by indexX and indexY.
set(byte, int, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDByteArray
Sets the value of a three-dimensional array at the position defined by indexX, indexY and indexZ.
set(double, int...) - Method in class ch.systemsx.cisd.base.mdarray.MDDoubleArray
Sets the value of array at the position defined by indices.
set(double, int) - Method in class ch.systemsx.cisd.base.mdarray.MDDoubleArray
Sets the value of a one-dimension array at the position defined by index.
set(double, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDDoubleArray
Sets the value of a two-dimensional array at the position defined by indexX and indexY.
set(double, int, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDDoubleArray
Sets the value of a three-dimensional array at the position defined by indexX, indexY and indexZ.
set(float, int...) - Method in class ch.systemsx.cisd.base.mdarray.MDFloatArray
Sets the value of array at the position defined by indices.
set(float, int) - Method in class ch.systemsx.cisd.base.mdarray.MDFloatArray
Sets the value of a one-dimension array at the position defined by index.
set(float, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDFloatArray
Sets the value of a two-dimensional array at the position defined by indexX and indexY.
set(float, int, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDFloatArray
Sets the value of a three-dimensional array at the position defined by indexX, indexY and indexZ.
set(int, int...) - Method in class ch.systemsx.cisd.base.mdarray.MDIntArray
Sets the value of array at the position defined by indices.
set(int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDIntArray
Sets the value of a one-dimension array at the position defined by index.
set(int, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDIntArray
Sets the value of a two-dimensional array at the position defined by indexX and indexY.
set(int, int, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDIntArray
Sets the value of a three-dimensional array at the position defined by indexX, indexY and indexZ.
set(long, int...) - Method in class ch.systemsx.cisd.base.mdarray.MDLongArray
Sets the value of array at the position defined by indices.
set(long, int) - Method in class ch.systemsx.cisd.base.mdarray.MDLongArray
Sets the value of a one-dimension array at the position defined by index.
set(long, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDLongArray
Sets the value of a two-dimensional array at the position defined by indexX and indexY.
set(long, int, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDLongArray
Sets the value of a three-dimensional array at the position defined by indexX, indexY and indexZ.
set(short, int...) - Method in class ch.systemsx.cisd.base.mdarray.MDShortArray
Sets the value of array at the position defined by indices.
set(short, int) - Method in class ch.systemsx.cisd.base.mdarray.MDShortArray
Sets the value of a one-dimension array at the position defined by index.
set(short, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDShortArray
Sets the value of a two-dimensional array at the position defined by indexX and indexY.
set(short, int, int, int) - Method in class ch.systemsx.cisd.base.mdarray.MDShortArray
Sets the value of a three-dimensional array at the position defined by indexX, indexY and indexZ.
setAccessMode(String, short) - Static method in class ch.systemsx.cisd.base.unix.Unix
Sets the access mode of filename to the specified mode value.
setAddPoolName(boolean) - Method in class ch.systemsx.cisd.base.namedthread.NamingThreadFactory
 
setByteOrder(ByteOrder) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
setByteOrder(ByteOrder) - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
Sets the byte-order (endiness) of the random access file.
setByteOrder(ByteOrder) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
setCreateDaemonThreads(boolean) - Method in class ch.systemsx.cisd.base.namedthread.NamingThreadFactory
 
setLength(long) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
setLength(long) - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
Sets the length of this file.
setLength(long) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
setOwner(String, int, int) - Static method in class ch.systemsx.cisd.base.unix.Unix
Sets the owner of filename to the specified uid and gid values.
setRunnableName(String) - Method in class ch.systemsx.cisd.base.namedthread.PoolNameThread
Sets the thread's name to the runnableName, possibly adding the pool name if addPoolName has been set to true in the constructor.
setThreadFactory(NamingThreadFactory) - Method in class ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor
Sets the thread factory of this pool executor.
setThreadFactory(ThreadFactory) - Method in class ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor
setToObject(T, int...) - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Sets the element of the array specified by indices to the particular value.
setToObject(T, int) - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Sets the element of the array specified by linearIndex to the particular value.
setToObject(T, int...) - Method in class ch.systemsx.cisd.base.mdarray.MDArray
 
setToObject(T, int) - Method in class ch.systemsx.cisd.base.mdarray.MDArray
 
setToObject(Byte, int...) - Method in class ch.systemsx.cisd.base.mdarray.MDByteArray
 
setToObject(Byte, int) - Method in class ch.systemsx.cisd.base.mdarray.MDByteArray
 
setToObject(Double, int...) - Method in class ch.systemsx.cisd.base.mdarray.MDDoubleArray
 
setToObject(Double, int) - Method in class ch.systemsx.cisd.base.mdarray.MDDoubleArray
 
setToObject(Float, int...) - Method in class ch.systemsx.cisd.base.mdarray.MDFloatArray
 
setToObject(Float, int) - Method in class ch.systemsx.cisd.base.mdarray.MDFloatArray
 
setToObject(Integer, int...) - Method in class ch.systemsx.cisd.base.mdarray.MDIntArray
 
setToObject(Integer, int) - Method in class ch.systemsx.cisd.base.mdarray.MDIntArray
 
setToObject(Long, int...) - Method in class ch.systemsx.cisd.base.mdarray.MDLongArray
 
setToObject(Long, int) - Method in class ch.systemsx.cisd.base.mdarray.MDLongArray
 
setToObject(Short, int...) - Method in class ch.systemsx.cisd.base.mdarray.MDShortArray
 
setToObject(Short, int) - Method in class ch.systemsx.cisd.base.mdarray.MDShortArray
 
setUp() - Method in class ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase
 
SHORT_SIZE - Static variable in class ch.systemsx.cisd.base.convert.NativeData
Size of a short value in bytes.
shortToByte(short[], NativeData.ByteOrder, int, int) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a short[] array to a byte[] array.
shortToByte(short[], NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeData
Converts a short[] array to a byte[] array.
size - Variable in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
 
size(int) - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Returns the extent of the array along its dim-th axis.
size() - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Returns the number of elements in the array.
skip(long) - Method in class ch.systemsx.cisd.base.io.AdapterIInputStreamToInputStream
 
skip(long) - Method in class ch.systemsx.cisd.base.io.AdapterInputStreamToIInputStream
 
skip(long) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
skip(long) - Method in interface ch.systemsx.cisd.base.io.IInputStream
 
skip(long) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
skipBytes(int) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
skipBytes(int) - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
skipBytes(int) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
StopException - Exception in ch.systemsx.cisd.base.exceptions
An exception that signals that Thread.stop() has been called on the current thread.
StopException() - Constructor for exception ch.systemsx.cisd.base.exceptions.StopException
 
submit(Runnable) - Method in class ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor
 
submit(Runnable, T) - Method in class ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor
 
submit(Callable<T>) - Method in class ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor
 
synchronize() - Method in class ch.systemsx.cisd.base.io.AdapterOutputStreamToIOutputStream
 
synchronize() - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
synchronize() - Method in interface ch.systemsx.cisd.base.io.IOutputStream
 
synchronize() - Method in interface ch.systemsx.cisd.base.io.ISynchronizable
Performs a synchronization of the resource.
synchronize() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 

T

TARGETS_DIRECTORY - Static variable in class ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase
 
TimeoutExceptionUnchecked - Exception in ch.systemsx.cisd.base.exceptions
Exception thrown when a blocking operation times out.
TimeoutExceptionUnchecked() - Constructor for exception ch.systemsx.cisd.base.exceptions.TimeoutExceptionUnchecked
 
TimeoutExceptionUnchecked(String) - Constructor for exception ch.systemsx.cisd.base.exceptions.TimeoutExceptionUnchecked
 
TimeoutExceptionUnchecked(TimeoutException) - Constructor for exception ch.systemsx.cisd.base.exceptions.TimeoutExceptionUnchecked
 
toByteArray(float[]) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Converts data into a tagged array in native byte order.
toByteArray(float[], NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Converts data into a tagged array in given byte order.
toByteArray(MDFloatArray) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Converts data into a tagged array in native byte order.
toByteArray(MDFloatArray, NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Converts data into a tagged array in given byte order.
toByteArray(double[]) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Converts data into a tagged array in native byte order.
toByteArray(double[], NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Converts data into a tagged array in given byte order.
toByteArray(MDDoubleArray) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Converts data into a tagged array in native byte order.
toByteArray(MDDoubleArray, NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Converts data into a tagged array in given byte order.
toByteArray(short[]) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Converts data into a tagged array in native byte order.
toByteArray(short[], NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Converts data into a tagged array in given byte order.
toByteArray(MDShortArray) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Converts data into a tagged array in native byte order.
toByteArray(MDShortArray, NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Converts data into a tagged array in given byte order.
toByteArray(int[]) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Converts data into a tagged array in native byte order.
toByteArray(int[], NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Converts data into a tagged array in given byte order.
toByteArray(MDIntArray) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Converts data into a tagged array in native byte order.
toByteArray(MDIntArray, NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Converts data into a tagged array in given byte order.
toByteArray(long[]) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Converts data into a tagged array in native byte order.
toByteArray(long[], NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Converts data into a tagged array in given byte order.
toByteArray(MDLongArray) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Converts data into a tagged array in native byte order.
toByteArray(MDLongArray, NativeData.ByteOrder) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Converts data into a tagged array in given byte order.
toInt(long[]) - Static method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Converts the dimensions from long[] to int[].
toLong(int[]) - Static method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
Converts the dimensions from int[] to long[].
toMatrix() - Method in class ch.systemsx.cisd.base.mdarray.MDByteArray
Creates and returns a matrix from a two-dimensional array.
toMatrix() - Method in class ch.systemsx.cisd.base.mdarray.MDDoubleArray
Creates and returns a matrix from a two-dimensional array.
toMatrix() - Method in class ch.systemsx.cisd.base.mdarray.MDFloatArray
Creates and returns a matrix from a two-dimensional array.
toMatrix() - Method in class ch.systemsx.cisd.base.mdarray.MDIntArray
Creates and returns a matrix from a two-dimensional array.
toMatrix() - Method in class ch.systemsx.cisd.base.mdarray.MDLongArray
Creates and returns a matrix from a two-dimensional array.
toMatrix() - Method in class ch.systemsx.cisd.base.mdarray.MDShortArray
Creates and returns a matrix from a two-dimensional array.
toString() - Method in exception ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel
 
toString() - Method in class ch.systemsx.cisd.base.io.AdapterIInputStreamToInputStream
 
toString() - Method in class ch.systemsx.cisd.base.io.AdapterInputStreamToIInputStream
 
toString() - Method in class ch.systemsx.cisd.base.io.AdapterIOutputStreamToOutputStream
 
toString() - Method in class ch.systemsx.cisd.base.io.AdapterOutputStreamToIOutputStream
 
toString() - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
toString() - Method in class ch.systemsx.cisd.base.mdarray.MDAbstractArray
 
toString() - Method in class ch.systemsx.cisd.base.utilities.AbstractBuildAndEnvironmentInfo
Returns version, build number, Java VM, and OS in a four-liner as one String.
transform(BufferedImage) - Method in interface ch.systemsx.cisd.base.image.IImageTransformer
Transforms the specified image.
transform(InputStream) - Method in interface ch.systemsx.cisd.base.image.IStreamingImageTransformer
Transforms the image provided as the input stream.
transformToPNG(InputStream) - Method in interface ch.systemsx.cisd.base.image.IStreamingImageTransformer
Transforms the image provided as the input stream.
transformToPNGStream(InputStream, OutputStream) - Method in interface ch.systemsx.cisd.base.image.IStreamingImageTransformer
Transforms the image provided as the input stream.
tryCopyNativeLibraryToTempFile(String, boolean) - Static method in class ch.systemsx.cisd.base.utilities.NativeLibraryUtilities
Tries to copy a native library which is available as a resource to a temporary file.
tryCopyResourceToFile(String, Path, RandomAccessFile, boolean, String) - Static method in class ch.systemsx.cisd.base.utilities.ResourceUtilities
Tries to copy the resource with the given name to a file on the file system.
tryCopyResourceToTempFile(String, String, String) - Static method in class ch.systemsx.cisd.base.utilities.ResourceUtilities
Tries to copy the resource with the given name to a temporary file.
tryCopyResourceToTempFile(String, String, String, boolean) - Static method in class ch.systemsx.cisd.base.utilities.ResourceUtilities
Tries to copy the resource with the given name to a temporary file.
tryCopyResourceToTempFile(String, String, String, boolean, boolean, String) - Static method in class ch.systemsx.cisd.base.utilities.ResourceUtilities
Tries to copy the resource with the given name to a temporary file.
tryGetArrayTag(byte[]) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Returns the array tag of the native tagged array encoded in data, or null, if data does not encode a native tagged array.
tryGetEncoding(byte[]) - Static method in enum ch.systemsx.cisd.base.convert.NativeArrayEncoding
Returns the encoding for the given byteArr, or null, if byteArr is not an encoded array.
tryGetFileInfo(String) - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the information about fileName, or NullPointerException, if the information could not be obtained, e.g.
tryGetGroupByGid(int) - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the Unix.Group for the given gid, or null, if no group with that gid exists.
tryGetGroupByName(String) - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the Unix.Group for the given groupName, or null, if no group with that name exists.
tryGetGroupNameForGid(int) - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the name of the group identified by gid, or null, if no group with that gid exists.
tryGetLinkInfo(String) - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the information about linkName, or NullPointerException, if the information could not be obtained, e.g.
tryGetLinkInfo(String, boolean) - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the information about linkName, or null if the information can not be obtained, e.g.
tryGetSymbolicLink() - Method in class ch.systemsx.cisd.base.unix.Unix.Stat
 
tryGetUserByName(String) - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the Unix.Password for the given userName, or null, if no user with that name exists.
tryGetUserByUid(int) - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the Unix.Password for the given userName, or null, if no user with that name exists.
tryGetUserNameForUid(int) - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the name of the user identified by uid.
tryReadSymbolicLink(String) - Static method in class ch.systemsx.cisd.base.unix.Unix
Returns the value of the symbolik link linkName, or null, if linkName is not a symbolic link.
tryToDoubleArray(byte[]) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Returns the tagged array data as a MDDoubleArray or null, if data is not a tagged (multi-dimensional) double array.
tryToDoubleArray1D(byte[]) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Returns the tagged array data as a double array or null, if data is not a tagged 1D double array.
tryToFloatArray(byte[]) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Returns the tagged array data as a MDFloatArray or null, if data is not a tagged (multi-dimensional) float array.
tryToFloatArray1D(byte[]) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Returns the tagged array data as a float array or null, if data is not a tagged 1D float array.
tryToIntArray(byte[]) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Returns the tagged array data as a MDIntArray or null, if data is not a tagged (multi-dimensional) int array.
tryToIntArray1D(byte[]) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Returns the tagged array data as an int array or null, if data is not a tagged 1D int array.
tryToLongArray(byte[]) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Returns the tagged array data as a MDLongArray or null, if data is not a tagged (multi-dimensional) long array.
tryToLongArray1D(byte[]) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Returns the tagged array data as a long array or null, if data is not a tagged 1D long array.
tryToShortArray(byte[]) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Returns the tagged array data as a MDShortArray or null, if data is not a tagged (multi-dimensional) short array.
tryToShortArray1D(byte[]) - Static method in class ch.systemsx.cisd.base.convert.NativeTaggedArray
Returns the tagged array data as a short array or null, if data is not a tagged 1D short array.

U

UNIT_TEST_ROOT_DIRECTORY - Static variable in class ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase
 
UNIT_TEST_WORKING_DIRECTORY - Static variable in class ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase
 
Unix - Class in ch.systemsx.cisd.base.unix
A utility class that provides access to common Unix system calls.
Unix() - Constructor for class ch.systemsx.cisd.base.unix.Unix
 
Unix.Group - Class in ch.systemsx.cisd.base.unix
A class representing the Unix group struct.
Unix.Password - Class in ch.systemsx.cisd.base.unix
A class representing the Unix passwd struct.
Unix.Stat - Class in ch.systemsx.cisd.base.unix
A class representing the Unix stat structure.
unwrapIfNecessary(Exception) - Static method in exception ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel
Returns the original exception before being wrapped, if the exception has been wrapped, or exception otherwise.
unwrapIfNecessary(Throwable) - Static method in exception ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel
Returns the original throwable before being wrapped, if the throwable has been wrapped, or exception otherwise.

V

valueOf(String) - Static method in enum ch.systemsx.cisd.base.convert.NativeArrayEncoding
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ch.systemsx.cisd.base.convert.NativeData.ByteOrder
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ch.systemsx.cisd.base.unix.FileLinkType
Returns the enum constant of this type with the specified name.
values() - Static method in enum ch.systemsx.cisd.base.convert.NativeArrayEncoding
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ch.systemsx.cisd.base.convert.NativeData.ByteOrder
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ch.systemsx.cisd.base.unix.FileLinkType
Returns an array containing the constants of this enum type, in the order they are declared.

W

warning(String) - Method in interface ch.systemsx.cisd.base.exceptions.IErrorStrategy
Called to issue a warning message.
workingDirectory - Variable in class ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase
 
wrapIfNecessary(Throwable) - Static method in exception ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel
wrapIfNecessary(Exception) - Static method in exception ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel
Returns a RuntimeException from an exception.
write(int) - Method in class ch.systemsx.cisd.base.io.AdapterIOutputStreamToOutputStream
 
write(byte[], int, int) - Method in class ch.systemsx.cisd.base.io.AdapterIOutputStreamToOutputStream
 
write(byte[]) - Method in class ch.systemsx.cisd.base.io.AdapterIOutputStreamToOutputStream
 
write(byte[], int, int) - Method in class ch.systemsx.cisd.base.io.AdapterOutputStreamToIOutputStream
 
write(byte[]) - Method in class ch.systemsx.cisd.base.io.AdapterOutputStreamToIOutputStream
 
write(int) - Method in class ch.systemsx.cisd.base.io.AdapterOutputStreamToIOutputStream
 
write(int) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
write(byte[]) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
write(byte[], int, int) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
write(int) - Method in interface ch.systemsx.cisd.base.io.IOutputStream
 
write(byte[]) - Method in interface ch.systemsx.cisd.base.io.IOutputStream
 
write(byte[], int, int) - Method in interface ch.systemsx.cisd.base.io.IOutputStream
 
write(int) - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
write(byte[]) - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
write(byte[], int, int) - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
write(int) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
write(byte[]) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
write(byte[], int, int) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
writeBoolean(boolean) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
writeBoolean(boolean) - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
writeBoolean(boolean) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
writeByte(int) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
writeByte(int) - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
writeByte(int) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
writeBytes(String) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
writeBytes(String) - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
writeBytes(String) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
writeChar(int) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
writeChar(int) - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
writeChar(int) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
writeChars(String) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
writeChars(String) - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
writeChars(String) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
writeDouble(double) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
writeDouble(double) - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
writeDouble(double) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
writeFloat(float) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
writeFloat(float) - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
writeFloat(float) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
writeInt(int) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
writeInt(int) - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
writeInt(int) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
writeLong(long) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
writeLong(long) - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
writeLong(long) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
writeShort(int) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
writeShort(int) - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
writeShort(int) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
writeUTF(String) - Method in class ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile
 
writeUTF(String) - Method in interface ch.systemsx.cisd.base.io.IRandomAccessFile
 
writeUTF(String) - Method in class ch.systemsx.cisd.base.io.RandomAccessFileImpl
 
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