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A
- ALPHABET - Static variable in class org.embl.ebi.escience.baclava.Base64
- The 64 valid Base64 values.
B
- BAD_ENCODING - Static variable in class org.embl.ebi.escience.baclava.Base64
- Baclava - class org.embl.ebi.escience.baclava.Baclava.
- Provides general functionality, mostly in the form of static methods, for bundling and unbundling the myGrid data document format.
- Baclava() - Constructor for class org.embl.ebi.escience.baclava.Baclava
- BaclavaIterator - class org.embl.ebi.escience.baclava.BaclavaIterator.
- This provides an Iterator interface with a single additional method to allow reset of the iterator to its starting state.
- BaclavaIterator(Collection) - Constructor for class org.embl.ebi.escience.baclava.BaclavaIterator
- BaclavaNS - Static variable in class org.embl.ebi.escience.baclava.Baclava
- The namespace prefix for tags in the myGrid data document format
- Base64 - class org.embl.ebi.escience.baclava.Base64.
- Encodes and decodes to and from Base64 notation.
- Base64() - Constructor for class org.embl.ebi.escience.baclava.Base64
- Defeats instantiation.
- Base64.InputStream - class org.embl.ebi.escience.baclava.Base64.InputStream.
- A
Base64#InputStreamwill read data from another java.io.InputStream, given in the constructor, and encode/decode to/from Base64 notation on the fly. - Base64.InputStream(InputStream) - Constructor for class org.embl.ebi.escience.baclava.Base64.InputStream
- Constructs a
Base64#InputStreamin DECODE mode. - Base64.InputStream(InputStream, int) - Constructor for class org.embl.ebi.escience.baclava.Base64.InputStream
- Constructs a
Base64#InputStreamin either ENCODE or DECODE mode. - Base64.OutputStream - class org.embl.ebi.escience.baclava.Base64.OutputStream.
- A
Base64#OutputStreamwill write data to another java.io.OutputStream, given in the constructor, and encode/decode to/from Base64 notation on the fly. - Base64.OutputStream(OutputStream) - Constructor for class org.embl.ebi.escience.baclava.Base64.OutputStream
- Constructs a
Base64#OutputStreamin ENCODE mode. - Base64.OutputStream(OutputStream, int) - Constructor for class org.embl.ebi.escience.baclava.Base64.OutputStream
- Constructs a
Base64#OutputStreamin either ENCODE or DECODE mode. - b4 - Variable in class org.embl.ebi.escience.baclava.Base64.OutputStream
- breakLines - Variable in class org.embl.ebi.escience.baclava.Base64.InputStream
- breakLines - Variable in class org.embl.ebi.escience.baclava.Base64.OutputStream
- buffer - Variable in class org.embl.ebi.escience.baclava.Base64.InputStream
- buffer - Variable in class org.embl.ebi.escience.baclava.Base64.OutputStream
- bufferLength - Variable in class org.embl.ebi.escience.baclava.Base64.InputStream
- bufferLength - Variable in class org.embl.ebi.escience.baclava.Base64.OutputStream
C
- close() - Method in class org.embl.ebi.escience.baclava.Base64.OutputStream
- Flushes and closes (I think, in the superclass) the stream.
- currentState - Variable in class org.embl.ebi.escience.baclava.JoinIterator
D
- DECODABET - Static variable in class org.embl.ebi.escience.baclava.Base64
- Translates a Base64 value to either its 6-bit reconstruction value or a negative number indicating some other meaning.
- DECODE - Static variable in class org.embl.ebi.escience.baclava.Base64
- Specify decoding.
- DONT_BREAK_LINES - Static variable in class org.embl.ebi.escience.baclava.Base64
- Don't break lines when encoding (violates strict Base64 specification)
- DataThing - class org.embl.ebi.escience.baclava.DataThing.
- A simple wrapper around an arbitrary Collection object which allows lookup and storage of any metadata within the collection or its children.
- DataThing(Element) - Constructor for class org.embl.ebi.escience.baclava.DataThing
- Construct a new DataThing from the supplied XML Jdom Element.
- DataThing(Object) - Constructor for class org.embl.ebi.escience.baclava.DataThing
- Create and bind a new SemanticMarkup object to the DataThing itself, it's not totally clear there's a need for this but it does no harm so why not?
- decode(byte[], int, int) - Static method in class org.embl.ebi.escience.baclava.Base64
- Very low-level access to decoding ASCII characters in the form of a byte array.
- decode(String) - Static method in class org.embl.ebi.escience.baclava.Base64
- Decodes data from Base64 notation, automatically detecting gzip-compressed data and decompressing it.
- decode4to3(byte[]) - Static method in class org.embl.ebi.escience.baclava.Base64
- Decodes the first four bytes of array fourBytes and returns an array up to three bytes long with the decoded values.
- decode4to3(byte[], int, byte[], int) - Static method in class org.embl.ebi.escience.baclava.Base64
- Decodes four bytes from array source and writes the resulting bytes (up to three of them) to destination.
- decodeToObject(String) - Static method in class org.embl.ebi.escience.baclava.Base64
- Attempts to decode Base64 data and deserialize a Java Object within.
- drill(int, List, Collection) - Method in class org.embl.ebi.escience.baclava.DataThing
- Drill into a collection, adding items to the list if we're at the desired depth, this makes the underlying assumption that the collection contains either collections or objects, but never a mix of both.
E
- ENCODE - Static variable in class org.embl.ebi.escience.baclava.Base64
- Specify encoding.
- EQUALS_SIGN - Static variable in class org.embl.ebi.escience.baclava.Base64
- The equals sign (=) as a byte.
- EQUALS_SIGN_ENC - Static variable in class org.embl.ebi.escience.baclava.Base64
- emptyIterator - Variable in class org.embl.ebi.escience.baclava.JoinIterator
- encode - Variable in class org.embl.ebi.escience.baclava.Base64.InputStream
- encode - Variable in class org.embl.ebi.escience.baclava.Base64.OutputStream
- encode3to4(byte[]) - Static method in class org.embl.ebi.escience.baclava.Base64
- Encodes the first three bytes of array threeBytes and returns a four-byte array in Base64 notation.
- encode3to4(byte[], int) - Static method in class org.embl.ebi.escience.baclava.Base64
- Encodes up to the first three bytes of array threeBytes and returns a four-byte array in Base64 notation.
- encode3to4(byte[], byte[], int) - Static method in class org.embl.ebi.escience.baclava.Base64
- Encodes up to the first three bytes of array threeBytes and returns a four-byte array in Base64 notation.
- encode3to4(byte[], int, int, byte[], int) - Static method in class org.embl.ebi.escience.baclava.Base64
- Encodes up to three bytes of the array source and writes the resulting four Base64 bytes to destination.
- encodeBytes(byte[]) - Static method in class org.embl.ebi.escience.baclava.Base64
- Encodes a byte array into Base64 notation.
- encodeBytes(byte[], int) - Static method in class org.embl.ebi.escience.baclava.Base64
- Encodes a byte array into Base64 notation.
- encodeBytes(byte[], int, int) - Static method in class org.embl.ebi.escience.baclava.Base64
- Encodes a byte array into Base64 notation.
- encodeBytes(byte[], int, int, int) - Static method in class org.embl.ebi.escience.baclava.Base64
- Encodes a byte array into Base64 notation.
- encodeObject(Serializable) - Static method in class org.embl.ebi.escience.baclava.Base64
- Serializes an object and returns the Base64-encoded version of that serialized object.
- encodeObject(Serializable, int) - Static method in class org.embl.ebi.escience.baclava.Base64
- Serializes an object and returns the Base64-encoded version of that serialized object.
F
- flushBase64() - Method in class org.embl.ebi.escience.baclava.Base64.OutputStream
- Method added by PHIL.
G
- GZIP - Static variable in class org.embl.ebi.escience.baclava.Base64
- Specify that data should be gzip-compressed.
- getDataObject() - Method in class org.embl.ebi.escience.baclava.DataThing
- Get the underlying data object, this is the first level of the data document.
- getElement() - Method in class org.embl.ebi.escience.baclava.DataThing
- Return the JDom Element corresponding to this DataThing represented as XML
- getIcon() - Method in class org.embl.ebi.escience.baclava.DataThing
- Get a display icon for this DataThing, currently this is based on the MIME type from the syntactic type string.
- getMetadata() - Method in class org.embl.ebi.escience.baclava.DataThing
- Return the SemanticMarkup object associated with the DataThing itself
- getMetadataForObject(Object, boolean) - Method in class org.embl.ebi.escience.baclava.DataThing
- Get the SemanticMarkup associated with an object in this DataThing.
- getSyntacticType() - Method in class org.embl.ebi.escience.baclava.DataThing
- Get the syntax type of this DataThing.
- getSyntacticTypeForObject(Object) - Method in class org.embl.ebi.escience.baclava.DataThing
H
- handlerClassForClass - Static variable in class org.embl.ebi.escience.baclava.Baclava
- hasNext() - Method in class org.embl.ebi.escience.baclava.BaclavaIterator
- hasNext() - Method in class org.embl.ebi.escience.baclava.JoinIterator
- The join has next if any iterator within it has a next value of true
I
- IteratorTest - class org.embl.ebi.escience.baclava.IteratorTest.
- Tests the functionality of the various Baclava iterator widgets
- IteratorTest() - Constructor for class org.embl.ebi.escience.baclava.IteratorTest
- initialized - Variable in class org.embl.ebi.escience.baclava.JoinIterator
- internalIterator - Variable in class org.embl.ebi.escience.baclava.BaclavaIterator
- iterator(String) - Method in class org.embl.ebi.escience.baclava.DataThing
- Given a desired type, return the BaclavaIterator that provides DataThing objects of this type.
- iterators - Variable in class org.embl.ebi.escience.baclava.JoinIterator
J
- JoinIterator - class org.embl.ebi.escience.baclava.JoinIterator.
- Provides an Iterator that iterates over the orthogonal join of a set of BaclavaIterator instances.
- JoinIterator(BaclavaIterator[]) - Constructor for class org.embl.ebi.escience.baclava.JoinIterator
- The iterator is constructed with an array of BaclavaIterator instances and creates an iterator that iterates over the orthogonal join of this set, where the iterator at position 0 in the array is regarded as the outermost one
L
- lineLength - Variable in class org.embl.ebi.escience.baclava.Base64.InputStream
- lineLength - Variable in class org.embl.ebi.escience.baclava.Base64.OutputStream
M
- MAX_LINE_LENGTH - Static variable in class org.embl.ebi.escience.baclava.Base64
- Maximum line length (76) of Base64 output.
- main(String[]) - Static method in class org.embl.ebi.escience.baclava.IteratorTest
- metadataMap - Variable in class org.embl.ebi.escience.baclava.DataThing
- myMarkup - Variable in class org.embl.ebi.escience.baclava.DataThing
N
- NEW_LINE - Static variable in class org.embl.ebi.escience.baclava.Base64
- The new line character (\n) as a byte.
- NO_OPTIONS - Static variable in class org.embl.ebi.escience.baclava.Base64
- No options specified.
- NoMetadataFoundException - exception org.embl.ebi.escience.baclava.NoMetadataFoundException.
- Thrown when metadata is requested for an object, no empty metadata element is defined and there is no data stored.
- NoMetadataFoundException() - Constructor for class org.embl.ebi.escience.baclava.NoMetadataFoundException
- NoMetadataFoundException(String) - Constructor for class org.embl.ebi.escience.baclava.NoMetadataFoundException
- NoMetadataFoundException(String, Exception) - Constructor for class org.embl.ebi.escience.baclava.NoMetadataFoundException
- NoMetadataFoundException(Exception) - Constructor for class org.embl.ebi.escience.baclava.NoMetadataFoundException
- next() - Method in class org.embl.ebi.escience.baclava.BaclavaIterator
- next() - Method in class org.embl.ebi.escience.baclava.JoinIterator
- Get an array of objects corresponding to the current next state of the join of the member iterators
- nextState - Variable in class org.embl.ebi.escience.baclava.JoinIterator
- numSigBytes - Variable in class org.embl.ebi.escience.baclava.Base64.InputStream
O
- options - Variable in class org.embl.ebi.escience.baclava.Base64.InputStream
- options - Variable in class org.embl.ebi.escience.baclava.Base64.OutputStream
- org.embl.ebi.escience.baclava - package org.embl.ebi.escience.baclava
P
- position - Variable in class org.embl.ebi.escience.baclava.Base64.InputStream
- position - Variable in class org.embl.ebi.escience.baclava.Base64.OutputStream
R
- read() - Method in class org.embl.ebi.escience.baclava.Base64.InputStream
- Reads enough of the input stream to convert to/from Base64 and returns the next byte.
- read(byte[], int, int) - Method in class org.embl.ebi.escience.baclava.Base64.InputStream
- Calls
Base64.InputStream.read()55 repeatedly until the end of stream is reached or len bytes are read. - remove() - Method in class org.embl.ebi.escience.baclava.BaclavaIterator
- remove() - Method in class org.embl.ebi.escience.baclava.JoinIterator
- Calls to the remove operation are not allowed from this iterator
- reset() - Method in class org.embl.ebi.escience.baclava.BaclavaIterator
- resumeEncoding() - Method in class org.embl.ebi.escience.baclava.Base64.OutputStream
- Resumes encoding of the stream.
S
- suspendEncoding - Variable in class org.embl.ebi.escience.baclava.Base64.OutputStream
- suspendEncoding() - Method in class org.embl.ebi.escience.baclava.Base64.OutputStream
- Suspends encoding of the stream.
T
- theDataObject - Variable in class org.embl.ebi.escience.baclava.DataThing
U
- underlyingCollection - Variable in class org.embl.ebi.escience.baclava.BaclavaIterator
W
- WHITE_SPACE_ENC - Static variable in class org.embl.ebi.escience.baclava.Base64
- write(int) - Method in class org.embl.ebi.escience.baclava.Base64.OutputStream
- Writes the byte to the output stream after converting to/from Base64 notation.
- write(byte[], int, int) - Method in class org.embl.ebi.escience.baclava.Base64.OutputStream
- Calls
Base64.OutputStream.write(int)55 repeatedly until len bytes are written.
X
- XMLHandler - interface org.embl.ebi.escience.baclava.XMLHandler.
- Specifies the methods required for a plugin handler class to serialize and deserialize objects to and from the myGrid data document format.
A B C D E F G H I J L M N O P R S T U W X
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