A B C D E G H I L M N P Q R S T U V X Z

A

add(Resource, Object) - Method in class uk.ac.cam.spectra.DateProperty
 
add(Resource, Object) - Method in class uk.ac.cam.spectra.IntegerProperty
 
add(Resource, Object) - Method in class uk.ac.cam.spectra.LiteralProperty
 
add(Resource, Object) - Method in interface uk.ac.cam.spectra.MetadataProperty
 
asProperty(Model) - Method in class uk.ac.cam.spectra.LiteralProperty
 
asProperty(Model) - Method in interface uk.ac.cam.spectra.MetadataProperty
 
asXML(Model, String) - Method in class uk.ac.cam.spectra.EmbargoMetadataEncoder
Convert any embargo metadata in the model (in the form of "automatic"/"manual" release and embargo period in months) and use the configured open and closed license details to create a full XML description of the embargo.

B

buildPath(String...) - Static method in class uk.ac.cam.spectra.Util
Builds a platform specific file path from the path name parts passed in.

C

chemical_compound_class - Static variable in class uk.ac.cam.spectra.SpectraMetadata
 
chemical_formula - Static variable in class uk.ac.cam.spectra.SpectraMetadata
 
chemical_systematic_name - Static variable in class uk.ac.cam.spectra.SpectraMetadata
 
chemist - Static variable in class uk.ac.cam.spectra.SpectraMetadata
 
CIF_MIME_TYPE - Static variable in class uk.ac.cam.spectra.Constants
CIF's mimetype.
CML_NS - Static variable in class uk.ac.cam.spectra.Constants
The CML namespace.
CML_XPATH - Static variable in class uk.ac.cam.spectra.Constants
A XOM XPath context for extracting information from CML.
CMLType - Class in uk.ac.cam.spectra
CML file support, mainly implemented in Jumbo.
CMLType() - Constructor for class uk.ac.cam.spectra.CMLType
 
Combine - Enum in uk.ac.cam.spectra
Simple enumeration of ways of combining metadata
Constants - Class in uk.ac.cam.spectra
Global constants needed throughout the code.
Constants() - Constructor for class uk.ac.cam.spectra.Constants
 
convertName(String) - Method in class uk.ac.cam.spectra.CMLType
Returns the same filename
convertName(String) - Method in interface uk.ac.cam.spectra.DataFileType
Converts the source file name into a conventional CML name - this will usually consist of replacing the standard file extension for the source format with ".cml.xml"
copy(File, File) - Static method in class uk.ac.cam.spectra.Util
DEWISOTT.

D

DataFileException - Exception in uk.ac.cam.spectra
An exception representing some problem in handling the data in a file (rather than e.g.
DataFileException() - Constructor for exception uk.ac.cam.spectra.DataFileException
 
DataFileException(String, Throwable) - Constructor for exception uk.ac.cam.spectra.DataFileException
 
DataFileException(String) - Constructor for exception uk.ac.cam.spectra.DataFileException
 
DataFileException(Throwable) - Constructor for exception uk.ac.cam.spectra.DataFileException
 
DataFileType - Interface in uk.ac.cam.spectra
This interface and the DataProcess class define the functionality required of file handling components, performing file validation, conversion to CML and metadata extraction.
DataProcess - Class in uk.ac.cam.spectra
Data object that holds input data, processing instructions and output data for file processing.
DataProcess() - Constructor for class uk.ac.cam.spectra.DataProcess
 
DateProperty - Class in uk.ac.cam.spectra
Metadata property with a Date literal value.
DateProperty(String, String) - Constructor for class uk.ac.cam.spectra.DateProperty
 
DAV_NS - Static variable in class uk.ac.cam.spectra.Constants
 
DC_NS - Static variable in class uk.ac.cam.spectra.Constants
The Dublin Core element namespace.
decode(RDFNode) - Method in class uk.ac.cam.spectra.LiteralProperty
 
decode(RDFNode) - Method in interface uk.ac.cam.spectra.MetadataProperty
 
decodeDate(Literal) - Method in class uk.ac.cam.spectra.DateProperty
 
decodeInteger(RDFNode) - Method in class uk.ac.cam.spectra.IntegerProperty
 
DSPACE_NS - Static variable in class uk.ac.cam.spectra.Constants
 

E

EBANK_NS - Static variable in class uk.ac.cam.spectra.Constants
The eBank namespace.
EBANKTERMS_NS - Static variable in class uk.ac.cam.spectra.Constants
The eBank terms namespace.
element - Variable in class uk.ac.cam.spectra.LiteralProperty
 
embargo_date - Static variable in class uk.ac.cam.spectra.SpectraMetadata
 
embargo_period - Static variable in class uk.ac.cam.spectra.SpectraMetadata
 
embargo_release - Static variable in class uk.ac.cam.spectra.SpectraMetadata
 
EmbargoMetadataEncoder - Class in uk.ac.cam.spectra
Configuration of embargo and method to combine a set of licensing preferences with an embargo release mechanism and period (usually supplied by the user, and in RDF) configuratio encode Spectra embargo metadata as XML.
EmbargoMetadataEncoder() - Constructor for class uk.ac.cam.spectra.EmbargoMetadataEncoder
 
equals(Object) - Method in class uk.ac.cam.spectra.LiteralProperty
 
experiment_date - Static variable in class uk.ac.cam.spectra.SpectraMetadata
 
experiment_ref - Static variable in class uk.ac.cam.spectra.SpectraMetadata
 

G

getClosedLicenseDescription() - Method in class uk.ac.cam.spectra.EmbargoMetadataEncoder
 
getClosedLicenseMachineReadable() - Method in class uk.ac.cam.spectra.EmbargoMetadataEncoder
 
getClosedLicenseURL() - Method in class uk.ac.cam.spectra.EmbargoMetadataEncoder
 
getConvertedCml() - Method in class uk.ac.cam.spectra.DataProcess
 
getElement() - Method in class uk.ac.cam.spectra.LiteralProperty
 
getElement() - Method in interface uk.ac.cam.spectra.MetadataProperty
Predicate element name.
getErrors() - Method in class uk.ac.cam.spectra.Validation
 
getExtractedMetadata() - Method in class uk.ac.cam.spectra.DataProcess
 
getInChI(CMLMolecule) - Method in class uk.ac.cam.spectra.CMLType
Jockeys JNI InChI to find the InChI for a single molecule.
getInChIs(Document) - Method in class uk.ac.cam.spectra.CMLType
Gets InChIs for the top level molecules in the CML file.
getMetadataPackageUri() - Method in class uk.ac.cam.spectra.DataProcess
Accessor for the metadataPackageUri.
getMimeType() - Method in class uk.ac.cam.spectra.CMLType
Returns the CML MIME Type
getMimeType() - Method in interface uk.ac.cam.spectra.DataFileType
Returns the MIME type of the source file format.
getNamespace() - Method in class uk.ac.cam.spectra.LiteralProperty
 
getNamespace() - Method in interface uk.ac.cam.spectra.MetadataProperty
Predicate namespace.
getOpenLicenseDescription() - Method in class uk.ac.cam.spectra.EmbargoMetadataEncoder
 
getOpenLicenseMachineReadable() - Method in class uk.ac.cam.spectra.EmbargoMetadataEncoder
 
getOpenLicenseURL() - Method in class uk.ac.cam.spectra.EmbargoMetadataEncoder
 
getPerformConversion() - Method in class uk.ac.cam.spectra.DataProcess
Accessor for the conversion processing instruction flag.
getPerformExtraction() - Method in class uk.ac.cam.spectra.DataProcess
Accessor for the metadata extraction processing instruction flag.
getPerformValidation() - Method in class uk.ac.cam.spectra.DataProcess
Accessor for the metadata extraction processing instruction flag.
getSourceFile() - Method in class uk.ac.cam.spectra.DataProcess
Accessor for the sourceFile field.
getValidation() - Method in class uk.ac.cam.spectra.DataProcess
Returns the results of any validation performed.
getWarnings() - Method in class uk.ac.cam.spectra.Validation
 
getXsiType() - Method in class uk.ac.cam.spectra.DateProperty
 
getXsiType() - Method in class uk.ac.cam.spectra.IntegerProperty
 
getXsiType() - Method in class uk.ac.cam.spectra.LiteralProperty
Base literals don't have an xsi type.
getXsiType() - Method in interface uk.ac.cam.spectra.MetadataProperty
 

H

handle - Static variable in class uk.ac.cam.spectra.SpectraMetadata
 
hasErrors() - Method in class uk.ac.cam.spectra.Validation
 
hashCode() - Method in class uk.ac.cam.spectra.LiteralProperty
 
hasWarnings() - Method in class uk.ac.cam.spectra.Validation
 

I

inchi - Static variable in class uk.ac.cam.spectra.SpectraMetadata
 
institution - Static variable in class uk.ac.cam.spectra.SpectraMetadata
 
IntegerProperty - Class in uk.ac.cam.spectra
A metadata literal with an integer value.
IntegerProperty(String, String) - Constructor for class uk.ac.cam.spectra.IntegerProperty
 
isLiteral() - Method in class uk.ac.cam.spectra.LiteralProperty
 
isLiteral() - Method in interface uk.ac.cam.spectra.MetadataProperty
 

L

LiteralProperty - Class in uk.ac.cam.spectra
Basic literal property, supporting string value literals.
LiteralProperty(String, String) - Constructor for class uk.ac.cam.spectra.LiteralProperty
 

M

MetadataProperty - Interface in uk.ac.cam.spectra
A munging of a predicate URI and object type, to remove some of the complexities of RDF and XSI types from API clients.
METS_NS - Static variable in class uk.ac.cam.spectra.Constants
The METS namespace.
move(File, File) - Static method in class uk.ac.cam.spectra.Util
Yet another method that java.io.File should possess, performs an atomic move if possible, otherwise a non-atomic one.

N

namespace - Variable in class uk.ac.cam.spectra.LiteralProperty
 

P

parseDate(String) - Static method in class uk.ac.cam.spectra.Util
Parse a date according to a number of standard formats.
PREMIS_NS - Static variable in class uk.ac.cam.spectra.Constants
The Premis namespace.
print(Document, OutputStream, boolean) - Static method in class uk.ac.cam.spectra.Util
Prints a XOM document to an outputstream without having to remember the serializer voodoo.
process(DataProcess) - Method in class uk.ac.cam.spectra.CMLType
Effectively validates on any operation where cml is not supplied.
process(DataProcess) - Method in interface uk.ac.cam.spectra.DataFileType
Handle a set of data processing; the process object holds both input information and what processing should be done.

Q

queryUniqueAttribute(Document, String, XPathContext) - Static method in class uk.ac.cam.spectra.Util
Utility method to return the result of an xpath query you know is going to return a single text node.

R

rmr(File) - Static method in class uk.ac.cam.spectra.Util
 

S

setClosedLicenseDescription(String) - Method in class uk.ac.cam.spectra.EmbargoMetadataEncoder
 
setClosedLicenseMachineReadable(String) - Method in class uk.ac.cam.spectra.EmbargoMetadataEncoder
 
setClosedLicenseURL(String) - Method in class uk.ac.cam.spectra.EmbargoMetadataEncoder
 
setConvertedCml(Document) - Method in class uk.ac.cam.spectra.DataProcess
Accessor for the converted CML.
setExtractedMetadata(Model) - Method in class uk.ac.cam.spectra.DataProcess
Accessor for the extracted metadata.
setMetadataPackageUri(String) - Method in class uk.ac.cam.spectra.DataProcess
Accessor for the metadata package URI.
setOpenLicenseDescription(String) - Method in class uk.ac.cam.spectra.EmbargoMetadataEncoder
 
setOpenLicenseMachineReadable(String) - Method in class uk.ac.cam.spectra.EmbargoMetadataEncoder
 
setOpenLicenseURL(String) - Method in class uk.ac.cam.spectra.EmbargoMetadataEncoder
 
setPerformConversion(boolean) - Method in class uk.ac.cam.spectra.DataProcess
Accessor for conversion processing instruction flag.
setPerformExtraction(boolean) - Method in class uk.ac.cam.spectra.DataProcess
Accessor for conversion processing instruction flag.
setPerformValidation(boolean) - Method in class uk.ac.cam.spectra.DataProcess
 
setSourceFile(File) - Method in class uk.ac.cam.spectra.DataProcess
 
setValidation(Validation) - Method in class uk.ac.cam.spectra.DataProcess
 
SIMPLE_ISO_DATE_FORMAT - Static variable in class uk.ac.cam.spectra.Constants
Simple ISO day date format.
SPECTRA_NMR_NS - Static variable in class uk.ac.cam.spectra.Constants
 
SPECTRA_NS - Static variable in class uk.ac.cam.spectra.Constants
SPECTRa's namespace.
SpectraMetadata - Class in uk.ac.cam.spectra
Enumeration of metadata fields, giving namespace, element and xsi type uri for each field, plus library functions for encoding Spectra embargo metadata as XML.
supervisor - Static variable in class uk.ac.cam.spectra.SpectraMetadata
 

T

toString() - Method in class uk.ac.cam.spectra.Validation
 
toURI() - Method in class uk.ac.cam.spectra.LiteralProperty
 
toURI() - Method in interface uk.ac.cam.spectra.MetadataProperty
Get predicate URI.
toURIString() - Method in class uk.ac.cam.spectra.LiteralProperty
 
toURIString() - Method in interface uk.ac.cam.spectra.MetadataProperty
Convenience method when dealing with frameworks that model uris as strings.

U

uk.ac.cam.spectra - package uk.ac.cam.spectra
 
Util - Class in uk.ac.cam.spectra
Usual grab bag of utility functions that don't fit anywhere else conveniently.

V

valid(RDFNode, Model) - Method in class uk.ac.cam.spectra.DateProperty
 
valid(RDFNode, Model) - Method in class uk.ac.cam.spectra.IntegerProperty
 
valid(RDFNode, Model) - Method in class uk.ac.cam.spectra.LiteralProperty
 
valid(RDFNode, Model) - Method in interface uk.ac.cam.spectra.MetadataProperty
 
Validation - Class in uk.ac.cam.spectra
Bean to hold the results of a data file validation.
Validation() - Constructor for class uk.ac.cam.spectra.Validation
 
valueOf(String) - Static method in enum uk.ac.cam.spectra.Combine
Returns the enum constant of this type with the specified name.
values() - Static method in enum uk.ac.cam.spectra.Combine
Returns an array containing the constants of this enum type, in the order they're declared.

X

XLINK_NS - Static variable in class uk.ac.cam.spectra.Constants
The XLink namespace.
XPATH_CTX - Static variable in class uk.ac.cam.spectra.Constants
A XOM XPath context that can be used wherever the standard namespace prefices have been employed.
XSI_BOOLEAN - Static variable in class uk.ac.cam.spectra.Constants
 
XSI_DATE - Static variable in class uk.ac.cam.spectra.Constants
 
XSI_INTEGER - Static variable in class uk.ac.cam.spectra.Constants
 
XSI_NS - Static variable in class uk.ac.cam.spectra.Constants
The XMLSchema-instance namespace.

Z

zip(File, File) - Method in class uk.ac.cam.spectra.Zipper
Zip a directory.
Zipper - Class in uk.ac.cam.spectra
Utility object for creating zip files of directories.
Zipper() - Constructor for class uk.ac.cam.spectra.Zipper
 

A B C D E G H I L M N P Q R S T U V X Z

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