Index (OME Common Java 6.0.18 API)

A B C D E F G H I L M N O P R S T U V W X Y Z
All Classes|All Packages

A

AbstractNIOHandle - Class in loci.common: A wrapper for buffered NIO logic that implements the IRandomAccess interface.
AbstractNIOHandle() - Constructor for class loci.common.AbstractNIOHandle
AbstractService - Class in loci.common.services
AbstractService() - Constructor for class loci.common.services.AbstractService
addStatusListener(StatusListener) - Method in interface loci.common.StatusReporter
allocate(int...) - Static method in class loci.common.DataTools: Allocates a 1-dimensional byte array matching the product of the given sizes.
allocate(long, int) - Method in class loci.common.NIOByteBufferProvider: Allocates or maps the desired file data into memory.
allocateDirect(long, int) - Method in class loci.common.NIOByteBufferProvider: Allocates memory and copies the desired file data into it.
allocateMappedByteBuffer(long, int) - Method in class loci.common.NIOByteBufferProvider: Memory maps the desired file data into memory.
ALT_ZVI - Static variable in class loci.common.DateTools
ALT_ZVI_EPOCH - Static variable in class loci.common.DateTools
available() - Method in class loci.common.NIOInputStream
available() - Method in class loci.common.RandomAccessInputStream
avoidUndeclaredNamespaces(String) - Static method in class loci.common.xml.XMLTools: Replaces NS:tag with NS_tag for undeclared namespaces

B

BaseHandler - Class in loci.common.xml: Top-level SAX handler.
BaseHandler() - Constructor for class loci.common.xml.BaseHandler
bucketExists(String) - Method in interface loci.common.services.S3ClientService: Check whether a bucket exists
bucketExists(String) - Method in class loci.common.services.S3ClientServiceImpl
buffer - Variable in class loci.common.ByteArrayHandle: Backing ByteBuffer.
buffer - Variable in class loci.common.NIOFileHandle: The buffer itself.
bufferSize - Variable in class loci.common.NIOFileHandle: The buffer size.
bufferStartPosition - Variable in class loci.common.NIOFileHandle: The absolute position of the start of the buffer.
ByteArrayHandle - Class in loci.common: A wrapper for a byte array that implements the IRandomAccess interface.
ByteArrayHandle() - Constructor for class loci.common.ByteArrayHandle: Creates a random access byte stream to write to a byte array.
ByteArrayHandle(byte[]) - Constructor for class loci.common.ByteArrayHandle: Creates a random access byte stream to read from, and write to, the bytes specified by the byte[] argument.
ByteArrayHandle(int) - Constructor for class loci.common.ByteArrayHandle: Creates a random access byte stream to read from, and write to.
ByteArrayHandle(ByteBuffer) - Constructor for class loci.common.ByteArrayHandle: Creates a random access byte stream to read from, and write to, the supplied ByteBuffer.
byteBufferProvider - Variable in class loci.common.NIOFileHandle: Provider class for NIO byte buffers, allocated or memory mapped.
bytesToDouble(byte[], boolean) - Static method in class loci.common.DataTools: Translates up to the first 8 bytes of a byte array to a double.
bytesToDouble(byte[], int, boolean) - Static method in class loci.common.DataTools: Translates up to the first 8 bytes of a byte array beyond the given offset to a double.
bytesToDouble(byte[], int, int, boolean) - Static method in class loci.common.DataTools: Translates up to the first len bytes of a byte array beyond the given offset to a double.
bytesToDouble(short[], boolean) - Static method in class loci.common.DataTools: Translates up to the first 8 bytes of a byte array to a double.
bytesToDouble(short[], int, boolean) - Static method in class loci.common.DataTools: Translates up to the first 8 bytes of a byte array beyond the given offset to a double.
bytesToDouble(short[], int, int, boolean) - Static method in class loci.common.DataTools: Translates up to the first len bytes of a byte array beyond the given offset to a double.
bytesToFloat(byte[], boolean) - Static method in class loci.common.DataTools: Translates up to the first 4 bytes of a byte array to a float.
bytesToFloat(byte[], int, boolean) - Static method in class loci.common.DataTools: Translates up to the first 4 bytes of a byte array beyond a given offset to a float.
bytesToFloat(byte[], int, int, boolean) - Static method in class loci.common.DataTools: Translates up to the first len bytes of a byte array beyond the given offset to a float.
bytesToFloat(short[], boolean) - Static method in class loci.common.DataTools: Translates up to the first 4 bytes of a byte array to a float.
bytesToFloat(short[], int, boolean) - Static method in class loci.common.DataTools: Translates up to the first 4 bytes of a byte array beyond a given offset to a float.
bytesToFloat(short[], int, int, boolean) - Static method in class loci.common.DataTools: Translates up to the first len bytes of a byte array beyond a given offset to a float.
bytesToHex(byte[]) - Static method in class loci.common.DataTools: Translates the given byte array into a String of hexadecimal digits.
bytesToInt(byte[], boolean) - Static method in class loci.common.DataTools: Translates up to the first 4 bytes of a byte array to an int.
bytesToInt(byte[], int, boolean) - Static method in class loci.common.DataTools: Translates up to the first 4 bytes of a byte array beyond the given offset to an int.
bytesToInt(byte[], int, int, boolean) - Static method in class loci.common.DataTools: Translates up to the first len bytes of a byte array beyond the given offset to an int.
bytesToInt(short[], boolean) - Static method in class loci.common.DataTools: Translates up to the first 4 bytes of a byte array to an int.
bytesToInt(short[], int, boolean) - Static method in class loci.common.DataTools: Translates up to the first 4 bytes of a byte array beyond the given offset to an int.
bytesToInt(short[], int, int, boolean) - Static method in class loci.common.DataTools: Translates up to the first len bytes of a byte array beyond the given offset to an int.
bytesToLong(byte[], boolean) - Static method in class loci.common.DataTools: Translates up to the first 8 bytes of a byte array to a long.
bytesToLong(byte[], int, boolean) - Static method in class loci.common.DataTools: Translates up to the first 8 bytes of a byte array beyond the given offset to a long.
bytesToLong(byte[], int, int, boolean) - Static method in class loci.common.DataTools: Translates up to the first len bytes of a byte array beyond the given offset to a long.
bytesToLong(short[], boolean) - Static method in class loci.common.DataTools: Translates up to the first 8 bytes of a byte array to a long.
bytesToLong(short[], int, boolean) - Static method in class loci.common.DataTools: Translates up to the first 8 bytes of a byte array beyond the given offset to a long.
bytesToLong(short[], int, int, boolean) - Static method in class loci.common.DataTools: Translates up to the first len bytes of a byte array beyond the given offset to a long.
bytesToShort(byte[], boolean) - Static method in class loci.common.DataTools: Translates up to the first 2 bytes of a byte array to a short.
bytesToShort(byte[], int, boolean) - Static method in class loci.common.DataTools: Translates up to the first 2 bytes of a byte array beyond the given offset to a short.
bytesToShort(byte[], int, int, boolean) - Static method in class loci.common.DataTools: Translates up to the first len bytes of a byte array beyond the given offset to a short.
bytesToShort(short[], boolean) - Static method in class loci.common.DataTools: Translates up to the first 2 bytes of a byte array to a short.
bytesToShort(short[], int, boolean) - Static method in class loci.common.DataTools: Translates up to the first 2 bytes of a byte array byond the given offset to a short.
bytesToShort(short[], int, int, boolean) - Static method in class loci.common.DataTools: Translates up to the first len bytes of a byte array byond the given offset to a short.
BZip2Handle - Class in loci.common: StreamHandle implementation for reading from BZip2-compressed files or byte arrays.
BZip2Handle(String) - Constructor for class loci.common.BZip2Handle: Construct a new BZip2Handle corresponding to the given file.

C

cacheDirectoryListings(boolean) - Static method in class loci.common.Location: Turn cacheing of directory listings on or off.
cacheObject(String, StreamHandle.Settings) - Static method in class loci.common.S3Handle: Download an S3 object to a file system cache if it doesn't already exist
canHandleScheme(String) - Static method in class loci.common.S3Handle: Return true if this is a URL with an s3 scheme
canRead() - Method in class loci.common.Location: If the underlying location is a URL, this method will return true if the URL exists.
canWrite() - Method in class loci.common.Location: If the underlying location is a URL, this method will always return false.
CaseInsensitiveLocation - Class in loci.common: Deprecated.
use Location instead
CaseInsensitiveLocation(File) - Constructor for class loci.common.CaseInsensitiveLocation: Deprecated.
CaseInsensitiveLocation(String) - Constructor for class loci.common.CaseInsensitiveLocation: Deprecated.
CaseInsensitiveLocation(String, String) - Constructor for class loci.common.CaseInsensitiveLocation: Deprecated.
CaseInsensitiveLocation(CaseInsensitiveLocation, String) - Constructor for class loci.common.CaseInsensitiveLocation: Deprecated.
CaseInsensitiveLocation(Location) - Constructor for class loci.common.CaseInsensitiveLocation: Deprecated.
CBZip2InputStream - Class in loci.common: An input stream that decompresses from the BZip2 format (without the file header chars) to be read as any other stream.
CBZip2InputStream(InputStream) - Constructor for class loci.common.CBZip2InputStream: Constructs a new CBZip2InputStream which decompresses bytes read from the specified stream.
channel - Variable in class loci.common.NIOFileHandle: The file channel backed by the random access file.
channel - Variable in class loci.common.NIOInputStream: The file channel backed by the random access file.
checkClassDependency(Class<? extends Object>) - Method in class loci.common.services.AbstractService: Checks a given class dependency at runtime to ensure that a given class will be available.
checkValidId(String) - Static method in class loci.common.Location: Checks that the given id points at a valid data stream.
cleanStaleCacheEntries() - Static method in class loci.common.Location: Remove any cached directory listings that have expired.
clearDirectoryListingsCache() - Static method in class loci.common.Location: Clear the directory listings cache.
close() - Method in class loci.common.ByteArrayHandle
close() - Method in class loci.common.CBZip2InputStream
close() - Method in class loci.common.FileHandle
close() - Method in interface loci.common.IRandomAccess: Closes this random access stream and releases any system resources associated with the stream.
close() - Method in class loci.common.NIOFileHandle
close() - Method in class loci.common.NIOInputStream: Closes the streams.
close() - Method in class loci.common.RandomAccessInputStream: Closes the streams.
close() - Method in class loci.common.RandomAccessOutputStream
close() - Method in class loci.common.StreamHandle
close() - Method in class loci.common.ZipHandle
COBOL - Static variable in class loci.common.DateTools
COBOL_EPOCH - Static variable in class loci.common.DateTools
CodedEnum - Interface in loci.common.enumeration: Enumeration which is coded.
connect() - Method in class loci.common.S3Handle: Connect to the server
Constants - Class in loci.common: Constants that are used within many classes in loci.common.
Constants() - Constructor for class loci.common.Constants
containsPoint(int, int) - Method in class loci.common.Region: Returns true if the point specified by the given X and Y coordinates is contained within this region.
containsValue(int[], int) - Static method in class loci.common.DataTools: Returns true if the given value is contained in the given array.
convertDate(long, int) - Static method in class loci.common.DateTools: Converts the given timestamp into an ISO8601 date.
convertDate(long, int, String) - Static method in class loci.common.DateTools: Converts the given timestamp into a date string with the given format.
convertDate(long, int, String, boolean) - Static method in class loci.common.DateTools: Converts the given timestamp into a date string with the given format.
CRC - Class in loci.common: A simple class to hold and calculate the CRC for sanity checking the data.
CRC() - Constructor for class loci.common.CRC
CRC_32_TABLE - Static variable in class loci.common.CRC
createBuilder() - Static method in class loci.common.xml.XMLTools: Creates a new DocumentBuilder via DocumentBuilderFactory or logs and throws a RuntimeException.
createDocument() - Static method in class loci.common.xml.XMLTools: Calls DocumentBuilder.newDocument() on a new builder.
createNewFile() - Method in class loci.common.Location: Creates a new empty file named by this Location's path name iff a file with this name does not already exist.

D

DataTools - Class in loci.common: A utility class with convenience methods for reading, writing and decoding words.
DateTools - Class in loci.common: A utility class with convenience methods for working with dates.
DebugTools - Class in loci.common: A utility class with convenience methods for debugging.
DEFAULT_BLOCK_SIZE - Static variable in class loci.common.NIOInputStream: Block size to use when searching through the stream.
DEFAULT_BLOCK_SIZE - Static variable in class loci.common.RandomAccessInputStream: Block size to use when searching through the stream.
DEFAULT_HEADER - Static variable in class loci.common.IniTable: Default header name when no header is available.
DEFAULT_S3_PROTOCOL - Static variable in class loci.common.S3Handle: Default protocol for fetching s3://
defaultBufferSize - Static variable in class loci.common.NIOFileHandle: Default NIO buffer size to facilitate buffered I/O.
defaultRWBufferSize - Static variable in class loci.common.NIOFileHandle: Default NIO buffer size to facilitate buffered I/O for read/write streams.
delete() - Method in class loci.common.Location: Deletes this file.
deleteOnExit() - Method in class loci.common.Location: Request that this file be deleted when the JVM terminates.
DependencyException - Exception in loci.common.services: Exception thrown when there is an object instantiation error or error processing dependencies.
DependencyException(String) - Constructor for exception loci.common.services.DependencyException: Default constructor.
DependencyException(String, Class<? extends Service>) - Constructor for exception loci.common.services.DependencyException: Default constructor.
DependencyException(String, Class<? extends Service>, Throwable) - Constructor for exception loci.common.services.DependencyException: Default constructor.
DependencyException(Throwable) - Constructor for exception loci.common.services.DependencyException: Default constructor.
doublesToBytes(double[], boolean) - Static method in class loci.common.DataTools: Translates an array of double values into an array of byte values.
doubleToBytes(double, boolean) - Static method in class loci.common.DataTools: Translates the double value into an array of eight bytes.
downloadObject(Path) - Method in class loci.common.S3Handle
downsample(byte[], int, int, double, int, boolean, boolean, int, boolean) - Method in interface loci.common.image.IImageScaler: Downsamples the given image.
downsample(byte[], int, int, double, int, boolean, boolean, int, boolean) - Method in class loci.common.image.SimpleImageScaler
dumpXML(String, Document, Element) - Static method in class loci.common.xml.XMLTools: Dumps the given OME-XML DOM tree to a string.
dumpXML(String, Document, Element, boolean) - Static method in class loci.common.xml.XMLTools: Dumps the given OME-XML DOM tree to a string.

E

enableIJLogging(boolean) - Static method in class loci.common.DebugTools: Enable SLF4J logging using logback, in the context of ImageJ.
enableIJLogging(boolean, Appender<ILoggingEvent>) - Static method in class loci.common.LogbackTools
enableLogging() - Static method in class loci.common.DebugTools: Attempts to enable SLF4J logging via logback or log4j.
enableLogging() - Static method in class loci.common.Log4jTools: Attempts to enable SLF4J logging via log4j without an external configuration file.
enableLogging() - Static method in class loci.common.LogbackTools: Initializes logback without an external configuration file.
enableLogging(String) - Static method in class loci.common.DebugTools: Attempts to enable SLF4J logging and set the root logger level.
encoding - Variable in class loci.common.RandomAccessInputStream
ENCODING - Static variable in class loci.common.Constants
EnumException - Exception in loci.common.enumeration
EnumException() - Constructor for exception loci.common.enumeration.EnumException
EnumException(String) - Constructor for exception loci.common.enumeration.EnumException
EnumException(String, Throwable) - Constructor for exception loci.common.enumeration.EnumException
EnumException(Throwable) - Constructor for exception loci.common.enumeration.EnumException
EOF_ERROR_MSG - Static variable in class loci.common.AbstractNIOHandle: Error message to be used when instantiating an EOFException.
EPSILON - Static variable in class loci.common.Constants
equals(Object) - Method in class loci.common.Location
equals(Object) - Method in class loci.common.Region
error(SAXParseException) - Method in class loci.common.xml.ParserErrorHandler
error(SAXParseException) - Method in class loci.common.xml.ValidationErrorHandler
escapeXML(String) - Static method in class loci.common.xml.XMLTools: Escape special characters.
exec(String) - Method in class loci.common.ReflectedUniverse: Deprecated.

Executes a command in the universe.
exists() - Method in class loci.common.AbstractNIOHandle
exists() - Method in class loci.common.FileHandle
exists() - Method in interface loci.common.IRandomAccess: Returns whether this refers to a valid object
exists() - Method in class loci.common.Location: Returns whether or not the pathname exists.
exists() - Method in class loci.common.S3Handle: Does this represent an accessible location?
exists() - Method in class loci.common.StreamHandle

F

fatalError(SAXParseException) - Method in class loci.common.xml.ParserErrorHandler
fatalError(SAXParseException) - Method in class loci.common.xml.ValidationErrorHandler
file - Variable in class loci.common.NIOInputStream: The file.
file - Variable in class loci.common.RandomAccessInputStream: The file name.
file - Variable in class loci.common.StreamHandle: Name of the open stream.
FileHandle - Class in loci.common: A wrapper for RandomAccessFile that implements the IRandomAccess interface.
FileHandle(File, String) - Constructor for class loci.common.FileHandle: Creates a random access file stream to read from, and optionally to write to, the file specified by the File argument.
FileHandle(String, String) - Constructor for class loci.common.FileHandle: Creates a random access file stream to read from, and optionally to write to, a file with the specified name.
filename - Variable in class loci.common.NIOInputStream: The file name.
FILENAME_FORMAT - Static variable in class loci.common.DateTools: Human readable timestamp filename string
findString(boolean, int, String...) - Method in class loci.common.NIOInputStream: Reads or skips a string ending with one of the given terminating substrings, using the specified block size for buffering.
findString(boolean, int, String...) - Method in class loci.common.RandomAccessInputStream: Reads or skips a string ending with one of the given terminating substrings, using the specified block size for buffering.
findString(boolean, String...) - Method in class loci.common.NIOInputStream: Reads or skips a string ending with one of the given terminating substrings.
findString(boolean, String...) - Method in class loci.common.RandomAccessInputStream: Reads or skips a string ending with one of the given terminating substrings.
findString(int, String...) - Method in class loci.common.NIOInputStream: Reads a string ending with one of the given terminating substrings, using the specified block size for buffering.
findString(int, String...) - Method in class loci.common.RandomAccessInputStream: Reads a string ending with one of the given terminating substrings, using the specified block size for buffering.
findString(String...) - Method in class loci.common.NIOInputStream: Reads a string ending with one of the given terminating substrings.
findString(String...) - Method in class loci.common.RandomAccessInputStream: Reads a string ending with one of the given terminating substrings.
flattenIntoHashMap() - Method in class loci.common.IniList: Flattens all of the INI tables into a single HashMap whose keys are of the format "[table name] table key".
floatsToBytes(float[], boolean) - Static method in class loci.common.DataTools: Translates an array of float values into an array of byte values.
floatToBytes(float, boolean) - Static method in class loci.common.DataTools: Translates the float value into an array of four bytes.
flush() - Method in class loci.common.RandomAccessOutputStream
force - Variable in class loci.common.ReflectedUniverse: Deprecated.

Whether to force our way past restrictive access modifiers.
formatDate(String, String) - Static method in class loci.common.DateTools: Formats the given date as an ISO 8601 date.
formatDate(String, String[]) - Static method in class loci.common.DateTools: Formats the given date as an ISO 8601 date.
formatDate(String, String[], boolean) - Static method in class loci.common.DateTools: Formats the given date as an ISO 8601 date.
formatDate(String, String[], boolean, String) - Static method in class loci.common.DateTools: Formats the given date as an ISO 8601 date.
formatDate(String, String[], String) - Static method in class loci.common.DateTools: Formats the given date as an ISO 8601 date.
formatDate(String, String, boolean) - Static method in class loci.common.DateTools: Formats the given date as an ISO 8601 date.
formatDate(String, String, boolean, String) - Static method in class loci.common.DateTools: Formats the given date as an ISO 8601 date.
formatDate(String, String, String) - Static method in class loci.common.DateTools: Formats the given date as an ISO 8601 date.
fp - Variable in class loci.common.StreamHandle: Current position within the stream.

G

GENERIC - loci.common.Location.UrlType
get(String) - Method in class loci.common.StreamHandle.Settings
getAbsoluteFile() - Method in class loci.common.Location: Return the absolute form of this abstract location.
getAbsolutePath() - Method in class loci.common.Location: Return the absolute form of this abstract location.
getBaseURI() - Method in class loci.common.xml.LSInputI
getBucket() - Method in class loci.common.S3Handle
getBufferSize() - Method in class loci.common.NIOFileHandle
getByteBuffer() - Method in class loci.common.ByteArrayHandle: Gets the byte buffer backing this handle.
getBytes() - Method in class loci.common.ByteArrayHandle: Gets a byte array representing the current state of this ByteArrayHandle.
getByteStream() - Method in class loci.common.xml.LSInputI
getCacheKey() - Method in class loci.common.S3Handle
getCanonicalFile() - Method in class loci.common.Location: Returns the canonical path to this file.
getCanonicalPath() - Method in class loci.common.Location: Returns the canonical path to this file.
getCertifiedText() - Method in class loci.common.xml.LSInputI
getCharacterStream() - Method in class loci.common.xml.LSInputI
getCode() - Method in interface loci.common.enumeration.CodedEnum: Retrieves the integer "code" for this enumeration.
getEncoding() - Method in class loci.common.xml.LSInputI
getEntryCount() - Method in class loci.common.ZipHandle
getEntryName() - Method in class loci.common.ZipHandle
getErrorCount() - Method in class loci.common.xml.ValidationErrorHandler
getFailureClass() - Method in exception loci.common.services.DependencyException: Returns the class that was used during a failed instantiation.
getFieldName(Class<?>, int) - Static method in class loci.common.DebugTools: This method uses reflection to scan the values of the given class's static fields, returning the first matching field's name.
getFileChannel() - Method in class loci.common.NIOFileHandle
getFilePointer() - Method in class loci.common.ByteArrayHandle
getFilePointer() - Method in class loci.common.FileHandle
getFilePointer() - Method in interface loci.common.IRandomAccess: Returns the current offset in this stream.
getFilePointer() - Method in class loci.common.NIOFileHandle
getFilePointer() - Method in class loci.common.NIOInputStream
getFilePointer() - Method in class loci.common.RandomAccessInputStream
getFilePointer() - Method in class loci.common.RandomAccessOutputStream
getFilePointer() - Method in class loci.common.StreamHandle
getFileTimestamp() - Static method in class loci.common.DateTools
getFinalCRC() - Method in class loci.common.CRC
getGlobalCRC() - Method in class loci.common.CRC
getHandle(String) - Static method in class loci.common.Location: Gets an IRandomAccess object that can read from the given file.
getHandle(String, boolean) - Static method in class loci.common.Location: Gets an IRandomAccess object that can read from or write to the given file.
getHandle(String, boolean, boolean) - Static method in class loci.common.Location: Gets an IRandomAccess object that can read from or write to the given file.
getHandle(String, boolean, boolean, int) - Static method in class loci.common.Location: Gets an IRandomAccess object that can read from or write to the given file.
getHeaders() - Method in class loci.common.IniList: Gets the table names (headers) in the list.
getIdMap() - Static method in class loci.common.Location: Return the id mapping.
getInputStream() - Method in class loci.common.NIOInputStream
getInputStream() - Method in class loci.common.ZipHandle
getInstance(Class<T>) - Method in class loci.common.services.ServiceFactory: Retrieves an instance of a given service.
getMappedFile(String) - Static method in class loci.common.Location: Gets the random access handle for the given id.
getMappedId(String) - Static method in class loci.common.Location: Gets the actual filename on disk for the given id.
getMillisFromTicks(long, long) - Static method in class loci.common.DateTools: Converts from two-word tick representation to milliseconds.
getName() - Method in class loci.common.Location: Returns the name of this file, i.e.
getObject(String, String, long) - Method in interface loci.common.services.S3ClientService: Read an object
getObject(String, String, long) - Method in class loci.common.services.S3ClientServiceImpl
getObject(String, String, String) - Method in interface loci.common.services.S3ClientService: Download an object
getObject(String, String, String) - Method in class loci.common.services.S3ClientServiceImpl
getOrder() - Method in class loci.common.ByteArrayHandle
getOrder() - Method in class loci.common.FileHandle
getOrder() - Method in interface loci.common.IRandomAccess: Returns the current order (endianness) of the stream.
getOrder() - Method in class loci.common.NIOFileHandle
getOrder() - Method in class loci.common.StreamHandle
getParent() - Method in class loci.common.Location: Returns the pathname string of this abstract pathname's parent, or null if this pathname does not have a parent directory.
getParentFile() - Method in class loci.common.Location: Returns the abstract pathname of this abstract pathname's parent, or null if this pathname does not name a parent directory.
getPath() - Method in class loci.common.Location: Returns the file's path.
getPath() - Method in class loci.common.S3Handle
getPort() - Method in class loci.common.S3Handle
getProgressMaximum() - Method in class loci.common.StatusEvent
getProgressValue() - Method in class loci.common.StatusEvent
getPublicId() - Method in class loci.common.xml.LSInputI
getRandomAccessFile() - Method in class loci.common.FileHandle
getRandomAccessFile() - Method in class loci.common.NIOFileHandle
getRemoteCacheRootDir() - Method in class loci.common.StreamHandle.Settings
getSchemaAsStream(String) - Method in interface loci.common.xml.XMLTools.SchemaReader: Get the given XML schema definition as an InputStream.
getServer() - Method in class loci.common.S3Handle
getStackTrace(Throwable) - Static method in class loci.common.DebugTools: Extracts the given exception's corresponding stack trace to a string.
getStatusMessage() - Method in class loci.common.StatusEvent
getStringData() - Method in class loci.common.xml.LSInputI
getStylesheet(String, Class<?>) - Static method in class loci.common.xml.XMLTools: Gets an XSLT template from the given resource location.
getSystemId() - Method in class loci.common.xml.LSInputI
getTable(String) - Method in class loci.common.IniList: Gets the table with the given name (header).
getTime(String, String) - Static method in class loci.common.DateTools: Converts a string date in the given format to a long timestamp (in Unix format: milliseconds since January 1, 1970).
getTime(String, String, String) - Static method in class loci.common.DateTools: Converts a string date in the given format to a long timestamp (in Unix format: milliseconds since January 1, 1970) with special milliseconds handling.
getTimestamp() - Static method in class loci.common.DateTools
getVar(String) - Method in class loci.common.ReflectedUniverse: Deprecated.

Returns the value of a variable or field in the universe.
getXML(Document) - Static method in class loci.common.xml.XMLTools: Converts the given DOM back to a string.
GZipHandle - Class in loci.common: StreamHandle implementation for reading from gzip-compressed files or byte arrays.
GZipHandle(String) - Constructor for class loci.common.GZipHandle: Construct a new GZipHandle for the given file.

H

HandleException - Exception in loci.common: HandleException is the exception thrown when something goes wrong in one of the custom I/O classes.
HandleException() - Constructor for exception loci.common.HandleException
HandleException(String) - Constructor for exception loci.common.HandleException
HandleException(String, Throwable) - Constructor for exception loci.common.HandleException
HandleException(Throwable) - Constructor for exception loci.common.HandleException
hashCode() - Method in class loci.common.Location
hashCode() - Method in class loci.common.Region
HEADER_KEY - Static variable in class loci.common.IniTable: Key to use for storing header value (in brackets).
height - Variable in class loci.common.Region

I

IImageScaler - Interface in loci.common.image: Interface defining image scaling operations.
indentXML(String) - Static method in class loci.common.xml.XMLTools: Indents XML to be more readable.
indentXML(String, boolean) - Static method in class loci.common.xml.XMLTools: Indents XML to be more readable, avoiding any whitespace injection into CDATA if the preserveCData flag is set.
indentXML(String, int) - Static method in class loci.common.xml.XMLTools: Indents XML by the given spacing to be more readable.
indentXML(String, int, boolean) - Static method in class loci.common.xml.XMLTools: Indents XML by the given spacing to be more readable, avoiding any whitespace injection into CDATA if the preserveCData flag is set.
indexOf(int[], int) - Static method in class loci.common.DataTools: Returns the index of the first occurrence of the given value in the given array.
indexOf(Object[], Object) - Static method in class loci.common.DataTools: Returns the index of the first occurrence of the given value in the given Object array.
IniList - Class in loci.common: A data structure containing a parsed list of INI key/value tables.
IniList() - Constructor for class loci.common.IniList
IniParser - Class in loci.common: A simple parser for INI configuration files.
IniParser() - Constructor for class loci.common.IniParser
IniTable - Class in loci.common: A data structure containing a parsed list of INI key/value tables.
IniTable() - Constructor for class loci.common.IniTable
INITIAL_LENGTH - Static variable in class loci.common.ByteArrayHandle: Initial length of a new file.
initialiseCRC() - Method in class loci.common.CRC
initialize() - Method in class loci.common.S3Handle: Check bucket or object exists
initialize(String, int, String, String, String, String) - Method in interface loci.common.services.S3ClientService: Initialise the S3 client
initialize(String, int, String, String, String, String) - Method in class loci.common.services.S3ClientServiceImpl
IniWriter - Class in loci.common: A simple writer for INI configuration files.
IniWriter() - Constructor for class loci.common.IniWriter
intersection(Region) - Method in class loci.common.Region: Returns a Region representing the intersection of this Region with the given Region.
intersects(Region) - Method in class loci.common.Region
intsToBytes(int[], boolean) - Static method in class loci.common.DataTools: Translates an array of int values into an array of byte values.
intToBytes(int, boolean) - Static method in class loci.common.DataTools: Translates the int value into an array of four bytes.
invalidateCache() - Static method in class loci.common.CaseInsensitiveLocation: Deprecated.

Remove (invalidate) cached content for all directories.
invalidateCache(File) - Static method in class loci.common.CaseInsensitiveLocation: Deprecated.

Remove (invalidate) cached content for the specified directory.
IRandomAccess - Interface in loci.common: Interface for random access into structures (e.g., files or arrays).
isAbsolute() - Method in class loci.common.Location: Returns whether or not this file's path is absolute.
isAccessibilityIgnored() - Method in class loci.common.ReflectedUniverse: Deprecated.

Gets whether access modifiers (protected, private, etc.) are ignored.
isBitOnByteBoundary() - Method in class loci.common.RandomAccessInputStream: Checks if the current position is on a byte boundary, that is the next bit in the byte array is the first bit in a byte.
isBucket() - Method in class loci.common.S3Handle: Is this an accessible bucket? TODO: If this bucket doesn't exist do we return false or thrown an exception?
isBZip2File(String) - Static method in class loci.common.BZip2Handle: Returns true if the given filename is a BZip2 file.
isDirectory() - Method in class loci.common.Location: Returns whether or not this file is a directory.
isEnabled() - Static method in class loci.common.DebugTools: Checks whether SLF4J logging has been enabled via logback or log4j.
isEnabled() - Static method in class loci.common.Log4jTools: Checks whether the log4j framework was successfully enabled
isEnabled() - Static method in class loci.common.LogbackTools: Checks whether logback has been enabled.
isFile() - Method in class loci.common.Location: Returns whether or not this file is a regular file (i.e.
isGZipFile(String) - Static method in class loci.common.GZipHandle
isHidden() - Method in class loci.common.Location: Returns whether or not this file is marked hidden by the filesystem.
isInstance(Class<?>, Object) - Static method in class loci.common.ReflectedUniverse: Deprecated.

Returns whether the given object is compatible with the specified class for the purposes of reflection.
isLittleEndian - Variable in class loci.common.NIOInputStream: Endianness of the stream.
isLittleEndian() - Method in class loci.common.NIOInputStream
isLittleEndian() - Method in class loci.common.RandomAccessInputStream: Gets the endianness of the stream.
isLittleEndian() - Method in class loci.common.RandomAccessOutputStream: Gets the endianness of the stream.
ISO8601_FORMAT - Static variable in class loci.common.DateTools: ISO 8601 date output formatter without milliseconds.
ISO8601_FORMAT_MS - Static variable in class loci.common.DateTools: ISO 8601 date output formatter with milliseconds.
isReadWrite - Variable in class loci.common.NIOFileHandle: Whether or not the file is opened read/write.
isWarning() - Method in class loci.common.StatusEvent
isZipFile(String) - Static method in class loci.common.ZipHandle

L

lastModified() - Method in class loci.common.Location: Return the last modification time of the file.
length - Variable in class loci.common.RandomAccessInputStream
length - Variable in class loci.common.StreamHandle: Length of the stream.
length() - Method in class loci.common.ByteArrayHandle
length() - Method in class loci.common.FileHandle
length() - Method in interface loci.common.IRandomAccess: Returns the length of this stream.
length() - Method in class loci.common.Location: Return the file length in bytes.
length() - Method in class loci.common.NIOFileHandle
length() - Method in class loci.common.NIOInputStream: Gets the number of bytes in the file.
length() - Method in class loci.common.RandomAccessInputStream
length() - Method in class loci.common.RandomAccessOutputStream
length() - Method in class loci.common.S3Handle
length() - Method in class loci.common.services.S3ClientStat: Get length (size) of object
length() - Method in class loci.common.StreamHandle
list() - Method in class loci.common.Location: Return a list of relative file names in this directory, or null if this file is not a directory.
list(boolean) - Method in class loci.common.Location: Return a list of all of the files in this directory.
listFiles() - Method in class loci.common.Location: Return a list of files in this directory, or null if this file is not a directory.
listing - Variable in class loci.common.Location.ListingsResult
loader - Variable in class loci.common.ReflectedUniverse: Deprecated.

Class loader for imported classes.
Location - Class in loci.common: Pseudo-extension of File that supports reading over HTTP (among other things).
Location(File) - Constructor for class loci.common.Location: Construct a Location using the given file on disk.
Location(String) - Constructor for class loci.common.Location: Construct a Location using the given path.
Location(String, String) - Constructor for class loci.common.Location: Construct a Location using the given directory and relative path.
Location(Location, String) - Constructor for class loci.common.Location: Construct a Location using the given directory and relative path.
Location.ListingsResult - Class in loci.common
Location.UrlType - Enum in loci.common
loci.common - package loci.common
loci.common.enumeration - package loci.common.enumeration
loci.common.image - package loci.common.image
loci.common.services - package loci.common.services
loci.common.xml - package loci.common.xml
Log4jTools - Class in loci.common: A utility class with convenience methods for log4j.
LogbackTools - Class in loci.common: A utility class with convenience methods for logback.
longsToBytes(long[], boolean) - Static method in class loci.common.DataTools: Translates an array of long values into an array of byte values.
longToBytes(long, boolean) - Static method in class loci.common.DataTools: Translates the long value into an array of eight bytes.
LSInputI - Class in loci.common.xml: A simple bean implementation of the LSInput interface.
LSInputI() - Constructor for class loci.common.xml.LSInputI

M

main(String[]) - Static method in class loci.common.ReflectedUniverse: Deprecated.

Allows exploration of a reflected universe in an interactive environment.
makeDataArray(byte[], int, boolean, boolean) - Static method in class loci.common.DataTools: Convert a byte array to the appropriate 1D primitive type array.
makeDataArray2D(byte[], int, boolean, boolean, int) - Static method in class loci.common.DataTools: Convert a byte array to the appropriate 2D primitive type array.
makeSigned(byte[]) - Static method in class loci.common.DataTools
makeSigned(int[]) - Static method in class loci.common.DataTools
makeSigned(short[]) - Static method in class loci.common.DataTools
mapFile(String, IRandomAccess) - Static method in class loci.common.Location: Maps the given id to the given IRandomAccess object.
mapId(String, String) - Static method in class loci.common.Location: Maps the given id to an actual filename on disk.
mapMode - Variable in class loci.common.NIOFileHandle: The default map mode for the file.
mark - Variable in class loci.common.StreamHandle: Marked position within the stream.
mark(int) - Method in class loci.common.NIOInputStream
mark(int) - Method in class loci.common.RandomAccessInputStream
markedPos - Variable in class loci.common.RandomAccessInputStream
markSupported() - Method in class loci.common.NIOInputStream
markSupported() - Method in class loci.common.RandomAccessInputStream
MAX_OVERHEAD - Static variable in class loci.common.RandomAccessInputStream: Maximum size of the buffer used by the DataInputStream.
MAX_SEARCH_SIZE - Static variable in class loci.common.NIOInputStream: Maximum number of bytes to search when searching through the stream.
MAX_SEARCH_SIZE - Static variable in class loci.common.RandomAccessInputStream: Maximum number of bytes to search when searching through the stream.
maximum - Variable in class loci.common.StatusEvent: Current progress maximum.
MICROSOFT - Static variable in class loci.common.DateTools
MICROSOFT_EPOCH - Static variable in class loci.common.DateTools
MINIMUM_JAVA_VERSION - Static variable in class loci.common.NIOByteBufferProvider: The minimum Java version we know is safe for memory mapped I/O.
mkdirs() - Method in class loci.common.Location: Creates a directory structures described by this Location's internal File instance.

N

NIOByteBufferProvider - Class in loci.common: Provides a facade to byte buffer allocation that enables FileChannel.map() usage on platforms where it's unlikely to give us problems and heap allocation where it is.
NIOByteBufferProvider(FileChannel, FileChannel.MapMode) - Constructor for class loci.common.NIOByteBufferProvider: Default constructor.
NIOFileHandle - Class in loci.common: A wrapper for buffered NIO logic that implements the IRandomAccess interface.
NIOFileHandle(File, String) - Constructor for class loci.common.NIOFileHandle: Creates a random access file stream to read from, and optionally to write to, the file specified by the File argument.
NIOFileHandle(File, String, int) - Constructor for class loci.common.NIOFileHandle: Creates a random access file stream to read from, and optionally to write to, the file specified by the File argument.
NIOFileHandle(String, String) - Constructor for class loci.common.NIOFileHandle: Creates a random access file stream to read from, and optionally to write to, a file with the specified name.
NIOInputStream - Class in loci.common: NIOInputStream provides methods for "intelligent" reading of files and byte arrays.
NIOInputStream(byte[]) - Constructor for class loci.common.NIOInputStream: Constructs a random access stream around the given byte array.
NIOInputStream(String) - Constructor for class loci.common.NIOInputStream: Constructs an NIOInputStream around the given file.
NIOInputStream(IRandomAccess) - Constructor for class loci.common.NIOInputStream: Constructs a random access stream around the given handle.
normalizeDoubles(double[]) - Static method in class loci.common.DataTools: Normalize the given double array so that the minimum value maps to 0.0 and the maximum value maps to 1.0.
normalizeFloats(float[]) - Static method in class loci.common.DataTools: Normalize the given float array so that the minimum value maps to 0.0 and the maximum value maps to 1.0.
notifyListeners(StatusEvent) - Method in interface loci.common.StatusReporter

O

ok() - Method in class loci.common.xml.ValidationErrorHandler
openTextResource(String) - Static method in class loci.common.IniParser: Opens a buffered reader for the given resource.
openTextResource(String, Class<?>) - Static method in class loci.common.IniParser: Opens a buffered reader for the given resource.
order - Variable in class loci.common.NIOFileHandle: The buffer's byte ordering.
order - Variable in class loci.common.StreamHandle: Byte ordering of this stream.
order(boolean) - Method in class loci.common.NIOInputStream: Sets the endianness of the stream.
order(boolean) - Method in class loci.common.RandomAccessInputStream: Sets the endianness of the stream.
order(boolean) - Method in class loci.common.RandomAccessOutputStream: Sets the endianness of the stream.
outStream - Variable in class loci.common.StreamHandle: OutputStream to be used for writing.

P

parseByte(String) - Static method in class loci.common.DataTools: Parses the input string into a byte
parseDate(String, String, String) - Static method in class loci.common.DateTools: Parse the given date as a Joda instant
parseDOM(File) - Static method in class loci.common.xml.XMLTools: Parses a DOM from the given XML file on disk.
parseDOM(InputStream) - Static method in class loci.common.xml.XMLTools: Parses a DOM from the given XML input stream.
parseDOM(String) - Static method in class loci.common.xml.XMLTools: Parses a DOM from the given XML string.
parseDouble(String) - Static method in class loci.common.DataTools: Parses the input string into a double accounting for the locale decimal separator
parseFloat(String) - Static method in class loci.common.DataTools: Parses the input string into a float accounting for the locale decimal separator
parseINI(BufferedReader) - Method in class loci.common.IniParser: Parses the INI-style configuration data from the given input stream.
parseINI(File) - Method in class loci.common.IniParser: Parses the INI-style wrapping the given file in a BufferedReader
parseINI(String) - Method in class loci.common.IniParser: Parses the INI-style configuration data from the given resource.
parseINI(String, Class<?>) - Method in class loci.common.IniParser: Parses the INI-style configuration data from the given resource, using the given class to find the resource.
parseInteger(String) - Static method in class loci.common.DataTools: Parses the input string into an integer
parseLong(String) - Static method in class loci.common.DataTools: Parses the input string into a long
ParserErrorHandler - Class in loci.common.xml: Used by various XMLTools methods to handle XML parsing errors.
ParserErrorHandler() - Constructor for class loci.common.xml.ParserErrorHandler
parseShort(String) - Static method in class loci.common.DataTools: Parses the input string into a short
parseXML(byte[], DefaultHandler) - Static method in class loci.common.xml.XMLTools: Parses the XML contained in the given byte array into using the specified XML handler.
parseXML(InputStream, DefaultHandler) - Static method in class loci.common.xml.XMLTools: Parses the XML contained in the given InputStream using the specified XML handler.
parseXML(String) - Static method in class loci.common.xml.XMLTools: Parses the given XML string into a list of key/value pairs.
parseXML(String, DefaultHandler) - Static method in class loci.common.xml.XMLTools: Parses the given XML string using the specified XML handler.
parseXML(RandomAccessInputStream, DefaultHandler) - Static method in class loci.common.xml.XMLTools: Parses the XML contained in the given input stream into using the specified XML handler.
position - Variable in class loci.common.NIOFileHandle: The absolute position within the file.
progress - Variable in class loci.common.StatusEvent: Current progress value.

R

raf - Variable in class loci.common.FileHandle: The random access file object backing this FileHandle.
raf - Variable in class loci.common.NIOFileHandle: The random access file object backing this FileHandle.
raf - Variable in class loci.common.NIOInputStream
raf - Variable in class loci.common.RandomAccessInputStream
RandomAccessInputStream - Class in loci.common: Top-level class for reading from various data sources.
RandomAccessInputStream(byte[]) - Constructor for class loci.common.RandomAccessInputStream: Constructs a random access stream around the given byte array.
RandomAccessInputStream(String) - Constructor for class loci.common.RandomAccessInputStream: Constructs a hybrid RandomAccessFile/DataInputStream around the given file.
RandomAccessInputStream(String, int) - Constructor for class loci.common.RandomAccessInputStream: Constructs a hybrid RandomAccessFile/DataInputStream around the given file.
RandomAccessInputStream(IRandomAccess) - Constructor for class loci.common.RandomAccessInputStream: Constructs a random access stream around the given handle.
RandomAccessInputStream(IRandomAccess, String) - Constructor for class loci.common.RandomAccessInputStream: Constructs a random access stream around the given handle, and with the associated file path.
RandomAccessOutputStream - Class in loci.common: RandomAccessOutputStream provides methods for writing to files and byte arrays.
RandomAccessOutputStream(byte[]) - Constructor for class loci.common.RandomAccessOutputStream: Constructs a random access stream around the given byte array.
RandomAccessOutputStream(String) - Constructor for class loci.common.RandomAccessOutputStream: Constructs a random access stream around the given file.
RandomAccessOutputStream(IRandomAccess) - Constructor for class loci.common.RandomAccessOutputStream: Constructs a random access stream around the given handle.
read() - Method in class loci.common.CBZip2InputStream
read() - Method in class loci.common.NIOInputStream: Alias for readByte().
read() - Method in class loci.common.RandomAccessInputStream
read(byte[]) - Method in class loci.common.ByteArrayHandle
read(byte[]) - Method in class loci.common.FileHandle
read(byte[]) - Method in interface loci.common.IRandomAccess: Reads up to b.length bytes of data from this stream into an array of bytes.
read(byte[]) - Method in class loci.common.NIOFileHandle
read(byte[]) - Method in class loci.common.NIOInputStream: Read bytes from the stream into the given array.
read(byte[]) - Method in class loci.common.RandomAccessInputStream: Read bytes from the stream into the given array.
read(byte[]) - Method in class loci.common.StreamHandle
read(byte[], int, int) - Method in class loci.common.ByteArrayHandle
read(byte[], int, int) - Method in class loci.common.CBZip2InputStream
read(byte[], int, int) - Method in class loci.common.FileHandle
read(byte[], int, int) - Method in interface loci.common.IRandomAccess: Reads up to len bytes of data from this stream into an array of bytes.
read(byte[], int, int) - Method in class loci.common.NIOFileHandle
read(byte[], int, int) - Method in class loci.common.NIOInputStream: Read n bytes from the stream into the given array at the specified offset.
read(byte[], int, int) - Method in class loci.common.RandomAccessInputStream: Read n bytes from the stream into the given array at the specified offset.
read(byte[], int, int) - Method in class loci.common.StreamHandle
read(Kryo, Input) - Method in class loci.common.RandomAccessInputStream
read(ByteBuffer) - Method in class loci.common.ByteArrayHandle
read(ByteBuffer) - Method in class loci.common.FileHandle
read(ByteBuffer) - Method in interface loci.common.IRandomAccess: Reads up to buffer.capacity() bytes of data from this stream into a ByteBuffer.
read(ByteBuffer) - Method in class loci.common.NIOFileHandle
read(ByteBuffer) - Method in class loci.common.RandomAccessInputStream: Read bytes from the stream into the given buffer.
read(ByteBuffer) - Method in class loci.common.StreamHandle
read(ByteBuffer, int, int) - Method in class loci.common.ByteArrayHandle
read(ByteBuffer, int, int) - Method in class loci.common.FileHandle
read(ByteBuffer, int, int) - Method in interface loci.common.IRandomAccess: Reads up to len bytes of data from this stream into a ByteBuffer.
read(ByteBuffer, int, int) - Method in class loci.common.NIOFileHandle
read(ByteBuffer, int, int) - Method in class loci.common.RandomAccessInputStream: Read n bytes from the stream into the given buffer at the specified offset.
read(ByteBuffer, int, int) - Method in class loci.common.StreamHandle
readBits(int) - Method in class loci.common.RandomAccessInputStream: Returns an int value representing the value of the bits read from the byte array, from the current position.
readBoolean() - Method in class loci.common.ByteArrayHandle
readBoolean() - Method in class loci.common.FileHandle
readBoolean() - Method in class loci.common.NIOFileHandle
readBoolean() - Method in class loci.common.NIOInputStream: Read an input byte and return true if the byte is nonzero.
readBoolean() - Method in class loci.common.RandomAccessInputStream: Read an input byte and return true if the byte is nonzero.
readBoolean() - Method in class loci.common.StreamHandle
readByte() - Method in class loci.common.ByteArrayHandle
readByte() - Method in class loci.common.FileHandle
readByte() - Method in class loci.common.NIOFileHandle
readByte() - Method in class loci.common.NIOInputStream: Read one byte and return it.
readByte() - Method in class loci.common.RandomAccessInputStream: Read one byte and return it.
readByte() - Method in class loci.common.StreamHandle
readByteToString(int) - Method in class loci.common.RandomAccessInputStream: Reads a byte array of the given length byte by byte.
readChar() - Method in class loci.common.ByteArrayHandle
readChar() - Method in class loci.common.FileHandle
readChar() - Method in class loci.common.NIOFileHandle
readChar() - Method in class loci.common.NIOInputStream: Read an input char.
readChar() - Method in class loci.common.RandomAccessInputStream: Read an input char.
readChar() - Method in class loci.common.StreamHandle
readCString() - Method in class loci.common.NIOInputStream: Read a string of arbitrary length, terminated by a null char.
readCString() - Method in class loci.common.RandomAccessInputStream: Read a string of arbitrary length, terminated by a null char.
readDouble() - Method in class loci.common.ByteArrayHandle
readDouble() - Method in class loci.common.FileHandle
readDouble() - Method in class loci.common.NIOFileHandle
readDouble() - Method in class loci.common.NIOInputStream: Read eight bytes and return a double value.
readDouble() - Method in class loci.common.RandomAccessInputStream: Read eight bytes and return a double value.
readDouble() - Method in class loci.common.StreamHandle
readFile(String) - Static method in class loci.common.DataTools: Reads the contents of the given file into a string.
readFloat() - Method in class loci.common.ByteArrayHandle
readFloat() - Method in class loci.common.FileHandle
readFloat() - Method in class loci.common.NIOFileHandle
readFloat() - Method in class loci.common.NIOInputStream: Read four bytes and return a float value.
readFloat() - Method in class loci.common.RandomAccessInputStream: Read four bytes and return a float value.
readFloat() - Method in class loci.common.StreamHandle
readFully(byte[]) - Method in class loci.common.ByteArrayHandle
readFully(byte[]) - Method in class loci.common.FileHandle
readFully(byte[]) - Method in class loci.common.NIOFileHandle
readFully(byte[]) - Method in class loci.common.NIOInputStream: Read bytes from the stream into the given array.
readFully(byte[]) - Method in class loci.common.RandomAccessInputStream: Read bytes from the stream into the given array.
readFully(byte[]) - Method in class loci.common.StreamHandle
readFully(byte[], int, int) - Method in class loci.common.ByteArrayHandle
readFully(byte[], int, int) - Method in class loci.common.FileHandle
readFully(byte[], int, int) - Method in class loci.common.NIOFileHandle
readFully(byte[], int, int) - Method in class loci.common.NIOInputStream: Read n bytes from the stream into the given array at the specified offset.
readFully(byte[], int, int) - Method in class loci.common.RandomAccessInputStream: Read n bytes from the stream into the given array at the specified offset.
readFully(byte[], int, int) - Method in class loci.common.StreamHandle
readInt() - Method in class loci.common.ByteArrayHandle
readInt() - Method in class loci.common.FileHandle
readInt() - Method in class loci.common.NIOFileHandle
readInt() - Method in class loci.common.NIOInputStream: Read four input bytes and return an int value.
readInt() - Method in class loci.common.RandomAccessInputStream: Read four input bytes and return an int value.
readInt() - Method in class loci.common.StreamHandle
readLine() - Method in class loci.common.ByteArrayHandle
readLine() - Method in class loci.common.FileHandle
readLine() - Method in class loci.common.NIOFileHandle
readLine() - Method in class loci.common.NIOInputStream: Read the next line of text from the input stream.
readLine() - Method in class loci.common.RandomAccessInputStream: Read the next line of text from the input stream.
readLine() - Method in class loci.common.StreamHandle
readLong() - Method in class loci.common.ByteArrayHandle
readLong() - Method in class loci.common.FileHandle
readLong() - Method in class loci.common.NIOFileHandle
readLong() - Method in class loci.common.NIOInputStream: Read eight input bytes and return a long value.
readLong() - Method in class loci.common.RandomAccessInputStream: Read eight input bytes and return a long value.
readLong() - Method in class loci.common.StreamHandle
readShort() - Method in class loci.common.ByteArrayHandle
readShort() - Method in class loci.common.FileHandle
readShort() - Method in class loci.common.NIOFileHandle
readShort() - Method in class loci.common.NIOInputStream: Read two input bytes and return a short value.
readShort() - Method in class loci.common.RandomAccessInputStream: Read two input bytes and return a short value.
readShort() - Method in class loci.common.StreamHandle
readString(int) - Method in class loci.common.NIOInputStream: Read a string of length n.
readString(int) - Method in class loci.common.RandomAccessInputStream: Read a string of up to length n.
readString(String) - Method in class loci.common.NIOInputStream: Reads a string ending with one of the characters in the given string.
readString(String) - Method in class loci.common.RandomAccessInputStream: Reads a string ending with one of the characters in the given string.
readUnsignedByte() - Method in class loci.common.ByteArrayHandle
readUnsignedByte() - Method in class loci.common.FileHandle
readUnsignedByte() - Method in class loci.common.NIOFileHandle
readUnsignedByte() - Method in class loci.common.NIOInputStream: Read an input byte and zero extend it appropriately.
readUnsignedByte() - Method in class loci.common.RandomAccessInputStream: Read an input byte and zero extend it appropriately.
readUnsignedByte() - Method in class loci.common.StreamHandle
readUnsignedInt() - Method in class loci.common.RandomAccessInputStream: Read four input bytes and return an unsigned value.
readUnsignedShort() - Method in class loci.common.ByteArrayHandle
readUnsignedShort() - Method in class loci.common.FileHandle
readUnsignedShort() - Method in class loci.common.NIOFileHandle
readUnsignedShort() - Method in class loci.common.NIOInputStream: Read two bytes and return an int in the range 0 through 65535.
readUnsignedShort() - Method in class loci.common.RandomAccessInputStream: Read two bytes and return an int in the range 0 through 65535.
readUnsignedShort() - Method in class loci.common.StreamHandle
readUTF() - Method in class loci.common.ByteArrayHandle
readUTF() - Method in class loci.common.FileHandle
readUTF() - Method in class loci.common.NIOFileHandle
readUTF() - Method in class loci.common.NIOInputStream: Read a string that has been encoded using a modified UTF-8 format.
readUTF() - Method in class loci.common.RandomAccessInputStream: Read a string that has been encoded using a modified UTF-8 format.
readUTF() - Method in class loci.common.StreamHandle
ReflectedUniverse - Class in loci.common: Deprecated.
ReflectedUniverse() - Constructor for class loci.common.ReflectedUniverse: Deprecated.

Constructs a new reflected universe.
ReflectedUniverse(ClassLoader) - Constructor for class loci.common.ReflectedUniverse: Deprecated.

Constructs a new reflected universe that uses the given class loader.
ReflectedUniverse(URL[]) - Constructor for class loci.common.ReflectedUniverse: Deprecated.

Constructs a new reflected universe, with the given URLs representing additional search paths for imported classes (in addition to the CLASSPATH).
ReflectException - Exception in loci.common: ReflectException is the exception thrown when something goes wrong performing a reflected operation with ReflectedUniverse.
ReflectException() - Constructor for exception loci.common.ReflectException
ReflectException(String) - Constructor for exception loci.common.ReflectException
ReflectException(String, Throwable) - Constructor for exception loci.common.ReflectException
ReflectException(Throwable) - Constructor for exception loci.common.ReflectException
Region - Class in loci.common: A class for representing a rectangular region.
Region() - Constructor for class loci.common.Region
Region(int, int, int, int) - Constructor for class loci.common.Region
removeStatusListener(StatusListener) - Method in interface loci.common.StatusReporter
reset() - Static method in class loci.common.Location: Clear all caches and reset cache-related bookkeeping variables to their original values.
reset() - Method in class loci.common.NIOInputStream
reset() - Method in class loci.common.RandomAccessInputStream
resetStream() - Method in class loci.common.BZip2Handle
resetStream() - Method in class loci.common.GZipHandle
resetStream() - Method in class loci.common.S3Handle
resetStream() - Method in class loci.common.StreamHandle: Close and reopen the stream; the stream pointer and mark should be reset to 0.
resetStream() - Method in class loci.common.URLHandle
resetStream() - Method in class loci.common.ZipHandle
resetStream(long) - Method in class loci.common.S3Handle: Reset the stream to an offset position
resolveEntity(String, String) - Method in class loci.common.xml.BaseHandler

S

S3 - loci.common.Location.UrlType
S3_MAX_FORWARD_SEEK - Static variable in class loci.common.S3Handle: If seeking more than this distance reset and reopen at offset
S3ClientService - Interface in loci.common.services: An S3 client
S3ClientServiceException - Exception in loci.common.services: Exception thrown when internal error specific to the S3 client is raised
S3ClientServiceException(String) - Constructor for exception loci.common.services.S3ClientServiceException: Constructor.
S3ClientServiceException(String, Throwable) - Constructor for exception loci.common.services.S3ClientServiceException: Constructor.
S3ClientServiceException(Throwable) - Constructor for exception loci.common.services.S3ClientServiceException: Constructor.
S3ClientServiceImpl - Class in loci.common.services: An S3 client
S3ClientServiceImpl() - Constructor for class loci.common.services.S3ClientServiceImpl: Default constructor.
S3ClientStat - Class in loci.common.services: Object stat (attributes) information
S3Handle - Class in loci.common: Provides random access to S3 buckets using the IRandomAccess interface.
S3Handle(String) - Constructor for class loci.common.S3Handle: Open an S3 file
S3Handle(String, boolean, StreamHandle.Settings) - Constructor for class loci.common.S3Handle: Open an S3 file
safeMultiply32(int...) - Static method in class loci.common.DataTools: Checks that the product of the given sizes does not exceed the 32-bit integer limit (i.e., Integer.MAX_VALUE).
safeMultiply64(long...) - Static method in class loci.common.DataTools: Checks that the product of the given sizes does not exceed the 64-bit integer limit (i.e., Long.MAX_VALUE).
samePrefix(String, String) - Static method in class loci.common.DataTools: Check if two filenames have the same prefix.
sanitize(String) - Static method in class loci.common.DataTools: Remove unprintable characters from the given string.
sanitizeDouble(String) - Static method in class loci.common.DataTools: Deprecated.
Use DataTools.parseDouble(String) instead
sanitizeXML(String) - Static method in class loci.common.xml.XMLTools: Remove invalid characters from an XML string.
saveINI(IniList, String) - Method in class loci.common.IniWriter: Saves the given IniList to the given file.
saveINI(IniList, String, boolean) - Method in class loci.common.IniWriter: Saves the given IniList to the given file.
saveINI(IniList, String, boolean, boolean) - Method in class loci.common.IniWriter: Saves the given IniList to the given file.
SCHEME_PARSER - Static variable in class loci.common.S3Handle
seek(long) - Method in class loci.common.ByteArrayHandle
seek(long) - Method in class loci.common.FileHandle
seek(long) - Method in interface loci.common.IRandomAccess: Sets the stream pointer offset, measured from the beginning of this stream, at which the next read or write occurs.
seek(long) - Method in class loci.common.NIOFileHandle
seek(long) - Method in class loci.common.NIOInputStream: Seeks to the given offset within the stream.
seek(long) - Method in class loci.common.RandomAccessInputStream: Seeks to the given offset within the stream.
seek(long) - Method in class loci.common.RandomAccessOutputStream: Seeks to the given offset within the stream.
seek(long) - Method in class loci.common.S3Handle
seek(long) - Method in class loci.common.StreamHandle
seek(long) - Method in class loci.common.URLHandle
Service - Interface in loci.common.services
ServiceException - Exception in loci.common.services: Exception thrown when there is an error within a given service.
ServiceException(String) - Constructor for exception loci.common.services.ServiceException: Default constructor.
ServiceException(String, Throwable) - Constructor for exception loci.common.services.ServiceException: Default constructor.
ServiceException(Throwable) - Constructor for exception loci.common.services.ServiceException: Default constructor.
ServiceFactory - Class in loci.common.services: Runtime instantiation of services.
ServiceFactory() - Constructor for class loci.common.services.ServiceFactory: Constructor loading service configuration from the default location.
ServiceFactory(String) - Constructor for class loci.common.services.ServiceFactory: Constructor loading service configuration from a given location.
setAccessibilityIgnored(boolean) - Method in class loci.common.ReflectedUniverse: Deprecated.

Sets whether access modifiers (protected, private, etc.) are ignored.
setBackslashContinuesLine(boolean) - Method in class loci.common.IniParser: Set whether or not a '\' at the end of a line signifies that the line continues on the following line.
setBaseURI(String) - Method in class loci.common.xml.LSInputI
setByteStream(InputStream) - Method in class loci.common.xml.LSInputI
setCacheDirectoryTimeout(double) - Static method in class loci.common.Location: Cache directory listings for this many seconds before relisting.
setCertifiedText(boolean) - Method in class loci.common.xml.LSInputI
setCharacterStream(Reader) - Method in class loci.common.xml.LSInputI
setCommentDelimiter(String) - Method in class loci.common.IniParser: Set the String that identifies a comment.
setDefaultBufferSize(int) - Static method in class loci.common.NIOFileHandle: Set the default buffer size for read-only files.
setDefaultReadWriteBufferSize(int) - Static method in class loci.common.NIOFileHandle: Set the default buffer size for read/write files.
setEncoding(String) - Method in class loci.common.RandomAccessInputStream: Sets the native encoding of the stream.
setEncoding(String) - Method in class loci.common.xml.LSInputI
setExtend(int) - Method in class loci.common.NIOInputStream: Sets the number of bytes by which to extend the stream.
setGlobalCRC(int) - Method in class loci.common.CRC
setIdMap(HashMap<String, Object>) - Static method in class loci.common.Location: Set the id mapping using the given HashMap.
setLength(long) - Method in class loci.common.AbstractNIOHandle: Sets the new length of the handle.
setLength(long) - Method in class loci.common.ByteArrayHandle
setLength(long) - Method in class loci.common.NIOFileHandle
setLength(long) - Method in class loci.common.RandomAccessInputStream: Sets the length of the stream.
setOrder(ByteOrder) - Method in class loci.common.ByteArrayHandle
setOrder(ByteOrder) - Method in class loci.common.FileHandle
setOrder(ByteOrder) - Method in interface loci.common.IRandomAccess: Sets the byte order (endianness) of the stream.
setOrder(ByteOrder) - Method in class loci.common.NIOFileHandle
setOrder(ByteOrder) - Method in class loci.common.StreamHandle
setPublicId(String) - Method in class loci.common.xml.LSInputI
setRootLevel(String) - Static method in class loci.common.DebugTools: Sets the root logger level.
setRootLevel(String) - Static method in class loci.common.Log4jTools: Sets the level of the root logger
setRootLevel(String) - Static method in class loci.common.LogbackTools: Sets the level of the root logger
setStringData(String) - Method in class loci.common.xml.LSInputI
setSystemId(String) - Method in class loci.common.xml.LSInputI
Settings() - Constructor for class loci.common.StreamHandle.Settings
setVar(String, boolean) - Method in class loci.common.ReflectedUniverse: Deprecated.

Registers a variable of primitive type boolean in the universe.
setVar(String, byte) - Method in class loci.common.ReflectedUniverse: Deprecated.

Registers a variable of primitive type byte in the universe.
setVar(String, char) - Method in class loci.common.ReflectedUniverse: Deprecated.

Registers a variable of primitive type char in the universe.
setVar(String, double) - Method in class loci.common.ReflectedUniverse: Deprecated.

Registers a variable of primitive type double in the universe.
setVar(String, float) - Method in class loci.common.ReflectedUniverse: Deprecated.

Registers a variable of primitive type float in the universe.
setVar(String, int) - Method in class loci.common.ReflectedUniverse: Deprecated.

Registers a variable of primitive type int in the universe.
setVar(String, long) - Method in class loci.common.ReflectedUniverse: Deprecated.

Registers a variable of primitive type long in the universe.
setVar(String, short) - Method in class loci.common.ReflectedUniverse: Deprecated.

Registers a variable of primitive type short in the universe.
setVar(String, Object) - Method in class loci.common.ReflectedUniverse: Deprecated.

Registers a variable in the universe.
shortsToBytes(short[], boolean) - Static method in class loci.common.DataTools: Translates an array of short values into an array of byte values.
shortToBytes(short, boolean) - Static method in class loci.common.DataTools: Translates the short value into an array of two bytes.
SimpleImageScaler - Class in loci.common.image: Basic implementation of IImageScaler.
SimpleImageScaler() - Constructor for class loci.common.image.SimpleImageScaler
skipBits(long) - Method in class loci.common.RandomAccessInputStream: Skips a number of bits in the BitBuffer.
skipBytes(int) - Method in class loci.common.ByteArrayHandle
skipBytes(int) - Method in class loci.common.FileHandle
skipBytes(int) - Method in class loci.common.NIOFileHandle
skipBytes(int) - Method in class loci.common.NIOInputStream: Skip n bytes within the stream.
skipBytes(int) - Method in class loci.common.RandomAccessInputStream: Skip n bytes within the stream.
skipBytes(int) - Method in class loci.common.RandomAccessOutputStream: Advances the current offset by the given number of bytes.
skipBytes(int) - Method in class loci.common.StreamHandle
skipBytes(long) - Method in class loci.common.ByteArrayHandle
skipBytes(long) - Method in class loci.common.FileHandle
skipBytes(long) - Method in interface loci.common.IRandomAccess: A long variant of DataInput.skipBytes(int).
skipBytes(long) - Method in class loci.common.NIOFileHandle
skipBytes(long) - Method in class loci.common.RandomAccessInputStream: Skip n bytes within the stream.
skipBytes(long) - Method in class loci.common.StreamHandle
statObject(String, String) - Method in interface loci.common.services.S3ClientService: Stat the object
statObject(String, String) - Method in class loci.common.services.S3ClientServiceImpl
status - Variable in class loci.common.StatusEvent: Current status message.
StatusEvent - Class in loci.common: An event indicating a status update.
StatusEvent(int, int, String) - Constructor for class loci.common.StatusEvent: Constructs a non-warning status event.
StatusEvent(int, int, String, boolean) - Constructor for class loci.common.StatusEvent: Constructs a status event.
StatusEvent(String) - Constructor for class loci.common.StatusEvent: Constructs a non-warning status event.
StatusEvent(String, boolean) - Constructor for class loci.common.StatusEvent: Constructs a status event.
StatusListener - Interface in loci.common: A listener for status updates.
StatusReporter - Interface in loci.common: A simple interface for objects wishing to report their status to listeners.
statusUpdated(StatusEvent) - Method in interface loci.common.StatusListener: Called when status is updated.
stream - Variable in class loci.common.StreamHandle: InputStream to be used for reading.
StreamHandle - Class in loci.common: Abstract IRandomAccess implementation for reading from InputStreams and writing to OutputStreams.
StreamHandle() - Constructor for class loci.common.StreamHandle: Construct a new StreamHandle.
StreamHandle.Settings - Class in loci.common
stripString(String) - Static method in class loci.common.DataTools: Remove null bytes from a string.
swap(char) - Static method in class loci.common.DataTools: Reverse the order of bytes in the given char.
swap(double) - Static method in class loci.common.DataTools: Reverse the order of bytes in the given double.
swap(float) - Static method in class loci.common.DataTools: Reverse the order of bytes in the given float.
swap(int) - Static method in class loci.common.DataTools: Reverse the order of bytes in the given int.
swap(long) - Static method in class loci.common.DataTools: Reverse the order of bytes in the given long.
swap(short) - Static method in class loci.common.DataTools: Reverse the order of bytes in the given short.

T

time - Variable in class loci.common.Location.ListingsResult
TIMESTAMP_FORMAT - Static variable in class loci.common.DateTools: Human readable timestamp string
toString() - Method in class loci.common.Location
toString() - Method in class loci.common.Region
toString() - Method in class loci.common.S3Handle
toString() - Method in exception loci.common.services.DependencyException
toString() - Method in class loci.common.StatusEvent
toURL() - Method in class loci.common.Location: Return a URL corresponding to this file.
transformXML(String, Templates) - Static method in class loci.common.xml.XMLTools: Transforms the given XML string using the specified XSLT stylesheet.
transformXML(Source, Templates) - Static method in class loci.common.xml.XMLTools: Transforms the given XML data using the specified XSLT stylesheet.

U

UNIX - Static variable in class loci.common.DateTools: Timestamp formats.
UNIX_EPOCH - Static variable in class loci.common.DateTools: Milliseconds until UNIX epoch.
unpackBytes(long, byte[], int, int, boolean) - Static method in class loci.common.DataTools: Translates nBytes of the given long and places the result in the given byte array.
updateCRC(int) - Method in class loci.common.CRC
URLHandle - Class in loci.common: Provides random access to URLs using the IRandomAccess interface.
URLHandle(String) - Constructor for class loci.common.URLHandle: Constructs a new URLHandle using the given URL.

V

validateLength(int) - Method in class loci.common.AbstractNIOHandle: Ensures that the handle has the correct length to be written to and extends it as required.
validateMode(String) - Method in class loci.common.AbstractNIOHandle: Ensures that the file mode is either "r" or "rw".
validateXML(String) - Static method in class loci.common.xml.XMLTools: Attempts to validate the given XML string using Java's XML validation facility.
validateXML(String, String) - Static method in class loci.common.xml.XMLTools: Attempts to validate the given XML string using Java's XML validation facility.
validateXML(String, String, XMLTools.SchemaReader) - Static method in class loci.common.xml.XMLTools: Attempts to validate the given XML string using Java's XML validation facility.
ValidationErrorHandler - Class in loci.common.xml: Used by validateXML to handle XML validation errors.
ValidationErrorHandler() - Constructor for class loci.common.xml.ValidationErrorHandler
valueOf(String) - Static method in enum loci.common.Location.UrlType: Returns the enum constant of this type with the specified name.
values() - Static method in enum loci.common.Location.UrlType: Returns an array containing the constants of this enum type, in the order they are declared.
variables - Variable in class loci.common.ReflectedUniverse: Deprecated.

Hashtable containing all variables present in the universe.

W

warning - Variable in class loci.common.StatusEvent: Whether or not this is a warning event.
warning(SAXParseException) - Method in class loci.common.xml.ParserErrorHandler
warning(SAXParseException) - Method in class loci.common.xml.ValidationErrorHandler
width - Variable in class loci.common.Region
write(byte[]) - Method in class loci.common.ByteArrayHandle
write(byte[]) - Method in class loci.common.FileHandle
write(byte[]) - Method in class loci.common.NIOFileHandle
write(byte[]) - Method in class loci.common.RandomAccessOutputStream
write(byte[]) - Method in class loci.common.StreamHandle
write(byte[], int, int) - Method in class loci.common.ByteArrayHandle
write(byte[], int, int) - Method in class loci.common.FileHandle
write(byte[], int, int) - Method in class loci.common.NIOFileHandle
write(byte[], int, int) - Method in class loci.common.RandomAccessOutputStream
write(byte[], int, int) - Method in class loci.common.StreamHandle
write(int) - Method in class loci.common.ByteArrayHandle
write(int) - Method in class loci.common.FileHandle
write(int) - Method in class loci.common.NIOFileHandle
write(int) - Method in class loci.common.RandomAccessOutputStream
write(int) - Method in class loci.common.StreamHandle
write(Kryo, Output) - Method in class loci.common.RandomAccessInputStream
write(ByteBuffer) - Method in class loci.common.ByteArrayHandle
write(ByteBuffer) - Method in class loci.common.FileHandle
write(ByteBuffer) - Method in interface loci.common.IRandomAccess: Writes up to buffer.capacity() bytes of data from the given ByteBuffer to this stream.
write(ByteBuffer) - Method in class loci.common.NIOFileHandle
write(ByteBuffer) - Method in class loci.common.RandomAccessOutputStream: Writes bytes to the stream from the given buffer.
write(ByteBuffer) - Method in class loci.common.StreamHandle
write(ByteBuffer, int, int) - Method in class loci.common.ByteArrayHandle
write(ByteBuffer, int, int) - Method in class loci.common.FileHandle
write(ByteBuffer, int, int) - Method in interface loci.common.IRandomAccess: Writes up to len bytes of data from the given ByteBuffer to this stream.
write(ByteBuffer, int, int) - Method in class loci.common.NIOFileHandle
write(ByteBuffer, int, int) - Method in class loci.common.RandomAccessOutputStream
write(ByteBuffer, int, int) - Method in class loci.common.StreamHandle
writeBits(int, int) - Method in class loci.common.RandomAccessOutputStream: Writes the given value using the given number of bits.
writeBits(String) - Method in class loci.common.RandomAccessOutputStream: Writes the bits represented by a bit string to the buffer.
writeBoolean(boolean) - Method in class loci.common.ByteArrayHandle
writeBoolean(boolean) - Method in class loci.common.FileHandle
writeBoolean(boolean) - Method in class loci.common.NIOFileHandle
writeBoolean(boolean) - Method in class loci.common.RandomAccessOutputStream
writeBoolean(boolean) - Method in class loci.common.StreamHandle
writeByte(int) - Method in class loci.common.ByteArrayHandle
writeByte(int) - Method in class loci.common.FileHandle
writeByte(int) - Method in class loci.common.NIOFileHandle
writeByte(int) - Method in class loci.common.RandomAccessOutputStream
writeByte(int) - Method in class loci.common.StreamHandle
writeBytes(String) - Method in class loci.common.ByteArrayHandle
writeBytes(String) - Method in class loci.common.FileHandle
writeBytes(String) - Method in class loci.common.NIOFileHandle
writeBytes(String) - Method in class loci.common.RandomAccessOutputStream
writeBytes(String) - Method in class loci.common.StreamHandle
writeChar(int) - Method in class loci.common.ByteArrayHandle
writeChar(int) - Method in class loci.common.FileHandle
writeChar(int) - Method in class loci.common.NIOFileHandle
writeChar(int) - Method in class loci.common.RandomAccessOutputStream
writeChar(int) - Method in class loci.common.StreamHandle
writeChars(String) - Method in class loci.common.ByteArrayHandle
writeChars(String) - Method in class loci.common.FileHandle
writeChars(String) - Method in class loci.common.NIOFileHandle
writeChars(String) - Method in class loci.common.RandomAccessOutputStream
writeChars(String) - Method in class loci.common.StreamHandle
writeDouble(double) - Method in class loci.common.ByteArrayHandle
writeDouble(double) - Method in class loci.common.FileHandle
writeDouble(double) - Method in class loci.common.NIOFileHandle
writeDouble(double) - Method in class loci.common.RandomAccessOutputStream
writeDouble(double) - Method in class loci.common.StreamHandle
writeFloat(float) - Method in class loci.common.ByteArrayHandle
writeFloat(float) - Method in class loci.common.FileHandle
writeFloat(float) - Method in class loci.common.NIOFileHandle
writeFloat(float) - Method in class loci.common.RandomAccessOutputStream
writeFloat(float) - Method in class loci.common.StreamHandle
writeInt(int) - Method in class loci.common.ByteArrayHandle
writeInt(int) - Method in class loci.common.FileHandle
writeInt(int) - Method in class loci.common.NIOFileHandle
writeInt(int) - Method in class loci.common.RandomAccessOutputStream
writeInt(int) - Method in class loci.common.StreamHandle
writeLine(String) - Method in class loci.common.RandomAccessOutputStream: Writes the given string followed by a newline character.
writeLong(long) - Method in class loci.common.ByteArrayHandle
writeLong(long) - Method in class loci.common.FileHandle
writeLong(long) - Method in class loci.common.NIOFileHandle
writeLong(long) - Method in class loci.common.RandomAccessOutputStream
writeLong(long) - Method in class loci.common.StreamHandle
writeShort(int) - Method in class loci.common.ByteArrayHandle
writeShort(int) - Method in class loci.common.FileHandle
writeShort(int) - Method in class loci.common.NIOFileHandle
writeShort(int) - Method in class loci.common.RandomAccessOutputStream
writeShort(int) - Method in class loci.common.StreamHandle
writeUTF(String) - Method in class loci.common.ByteArrayHandle
writeUTF(String) - Method in class loci.common.FileHandle
writeUTF(String) - Method in class loci.common.NIOFileHandle
writeUTF(String) - Method in class loci.common.RandomAccessOutputStream
writeUTF(String) - Method in class loci.common.StreamHandle
writeXML(OutputStream, Document) - Static method in class loci.common.xml.XMLTools: Writes the specified DOM to the given output stream.
writeXML(OutputStream, Document, boolean) - Static method in class loci.common.xml.XMLTools: Writes the specified DOM to the given output stream.
writeXML(Result, Document, boolean) - Static method in class loci.common.xml.XMLTools: Writes the specified DOM to the given stream.

X

x - Variable in class loci.common.Region
XMLTools - Class in loci.common.xml: A utility class for working with XML.
XMLTools.SchemaReader - Interface in loci.common.xml: A schema reader can provide InputStreams for certain XML schemas.

Y

y - Variable in class loci.common.Region

Z

ZipHandle - Class in loci.common: StreamHandle implementation for reading from Zip-compressed files or byte arrays.
ZipHandle(String) - Constructor for class loci.common.ZipHandle
ZipHandle(String, ZipEntry) - Constructor for class loci.common.ZipHandle: Constructs a new ZipHandle corresponding to the given entry of the specified Zip file.
ZVI - Static variable in class loci.common.DateTools
ZVI_EPOCH - Static variable in class loci.common.DateTools

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