A C D E F G H I J L M O P R S T U V X

A

AbstractEncoding - Class in uk.ac.ebi.xchars.domain.encoding

This class ...

AbstractEncoding() - Constructor for class uk.ac.ebi.xchars.domain.encoding.AbstractEncoding

AbstractEncoding(String) - Constructor for class uk.ac.ebi.xchars.domain.encoding.AbstractEncoding

add(String, Object) - Method in class uk.ac.ebi.xchars.domain.XCharsClass

addEncoding(EncodingType, Encoding) - Method in class uk.ac.ebi.xchars.domain.encoding.EncodingSet

C

Character - Class in uk.ac.ebi.xchars.domain

Character(String, EncodingSet) - Constructor for class uk.ac.ebi.xchars.domain.Character

Character(String, EncodingSet, Definition) - Constructor for class uk.ac.ebi.xchars.domain.Character

character - Variable in class uk.ac.ebi.xchars.domain.Formatting

CHARACTER_TAG - Variable in class uk.ac.ebi.xchars.utilities.XCharsParser

XML tag of the character as defined in the DTD

characterAndEncodings - Variable in class uk.ac.ebi.xchars.domain.XCharsClass

characterClasses - Variable in class uk.ac.ebi.xchars.helper.SpecialCharactersHelper

characterClasses - Variable in class uk.ac.ebi.xchars.SpecialCharacters

Map of character classes (see specialCharacters.xml).

characterClasses - Variable in class uk.ac.ebi.xchars.utilities.XCharsParser

Map of character classes (see specialCharacters.xml).

CHEBI_CODE - Static variable in class uk.ac.ebi.xchars.domain.EncodingType

CHEBI ASCII code encoding type.

ChebiAsciiEncoding - Class in uk.ac.ebi.xchars.domain.encoding

ChebiAsciiEncoding

ChebiAsciiEncoding(String) - Constructor for class uk.ac.ebi.xchars.domain.encoding.ChebiAsciiEncoding

CLASS_TAG - Variable in class uk.ac.ebi.xchars.utilities.XCharsParser

XML tag of the class as defined in the DTD

code - Variable in class uk.ac.ebi.xchars.XMLErrorReport

The error code.

compareTo(Object) - Method in class uk.ac.ebi.xchars.SpecialCharacters.Octet

COMPOSED - Static variable in class uk.ac.ebi.xchars.domain.EncodingType

COMPOSED code encoding type.

ComposedEncoding - Class in uk.ac.ebi.xchars.domain.encoding

This class ...

ComposedEncoding(List) - Constructor for class uk.ac.ebi.xchars.domain.encoding.ComposedEncoding

content - Variable in class uk.ac.ebi.xchars.domain.Character

content - Variable in class uk.ac.ebi.xchars.domain.Definition

CONTENT_TAG - Variable in class uk.ac.ebi.xchars.utilities.XCharsParser

XML tag attribute of the content as defined in the DTD -> parent is definition

copy(ImageUsageConstant) - Static method in class uk.ac.ebi.xchars.domain.ImageUsageConstant

copy(SpecialCharacters) - Static method in class uk.ac.ebi.xchars.SpecialCharacters

countNumberOfOccurences(String, String) - Static method in class uk.ac.ebi.xchars.utilities.XCharsValidator

Counts the number of occurences a string is found.

createValidator() - Static method in class uk.ac.ebi.xchars.SpecialCharacters

Creates the XcharsValidator - will throw an exception if the INSTANCE of Xchars is null.

D

data - Variable in exception uk.ac.ebi.xchars.exceptions.UnsupportedElementException

decimalValue - Variable in class uk.ac.ebi.xchars.SpecialCharacters.Octet

decodeOctetSequence(List) - Static method in class uk.ac.ebi.xchars.SpecialCharacters

decodeTags(String) - Method in class uk.ac.ebi.xchars.XMLErrorReport

decodeUTF8(String) - Static method in class uk.ac.ebi.xchars.SpecialCharacters

DEFAULT_XML_FILE_NAME - Static variable in class uk.ac.ebi.xchars.SpecialCharacters

DefaultEncoding - Class in uk.ac.ebi.xchars.domain.encoding

This class ...

DefaultEncoding() - Constructor for class uk.ac.ebi.xchars.domain.encoding.DefaultEncoding

defaultEncoding - Variable in class uk.ac.ebi.xchars.domain.encoding.EncodingSet

definition - Variable in class uk.ac.ebi.xchars.domain.Character

This contains the definition of the instace and additional examples.

Definition - Class in uk.ac.ebi.xchars.domain

Definition

Definition() - Constructor for class uk.ac.ebi.xchars.domain.Definition

definition - Variable in class uk.ac.ebi.xchars.domain.XCharsClass

This contains the definition of the class and additional examples.

DEFINITION_TAG - Variable in class uk.ac.ebi.xchars.utilities.XCharsParser

XML tag of the definition as defined in the DTD

E

elements - Variable in class uk.ac.ebi.xchars.domain.encoding.ComposedEncoding

EMBEDDED_ELEMENT_ERROR - Static variable in class uk.ac.ebi.xchars.XMLErrorReport

Error code for an embedded tag.

encodeCharacters(String, EncodingType) - Method in class uk.ac.ebi.xchars.SpecialCharacters

encodeFormattings(String, EncodingType) - Method in class uk.ac.ebi.xchars.SpecialCharacters

encoding - Variable in class uk.ac.ebi.xchars.domain.Character

Encoding - Interface in uk.ac.ebi.xchars.domain.encoding

ENCODING_TAG - Variable in class uk.ac.ebi.xchars.utilities.XCharsParser

XML tag attribute of the encoding as defined in the DTD -> parent formatting/character

EncodingFactory - Class in uk.ac.ebi.xchars.domain.encoding

This class ...

EncodingFactory() - Constructor for class uk.ac.ebi.xchars.domain.encoding.EncodingFactory

EncodingSet - Class in uk.ac.ebi.xchars.domain.encoding

This class ...

EncodingSet() - Constructor for class uk.ac.ebi.xchars.domain.encoding.EncodingSet

EncodingSet(Map, Encoding) - Constructor for class uk.ac.ebi.xchars.domain.encoding.EncodingSet

EncodingSet(EncodingSet) - Constructor for class uk.ac.ebi.xchars.domain.encoding.EncodingSet

encodingSet - Variable in class uk.ac.ebi.xchars.domain.encoding.EncodingSet

EncodingType - Class in uk.ac.ebi.xchars.domain

This class stores all currently supported encoding types.

EncodingType(String) - Constructor for class uk.ac.ebi.xchars.domain.EncodingType

Sets the value of the EncodingType.

END_TAG_ERROR - Static variable in class uk.ac.ebi.xchars.XMLErrorReport

Error code for a missing end tag.

endIndex - Variable in exception uk.ac.ebi.xchars.exceptions.UnsupportedElementException

equals(Object) - Method in class uk.ac.ebi.xchars.domain.EncodingType

equals(Object) - Method in class uk.ac.ebi.xchars.SpecialCharacters.Octet

EXAMPLE_TAG - Variable in class uk.ac.ebi.xchars.utilities.XCharsParser

XML tag attribute of the example as defined in the DTD -> parent is definition

examples - Variable in class uk.ac.ebi.xchars.domain.Definition

EXTENDED_HTML - Static variable in class uk.ac.ebi.xchars.domain.EncodingType

Encoded HTML encoding type.

ExtendedHTMLEncoding - Class in uk.ac.ebi.xchars.domain.encoding

This class ...

ExtendedHTMLEncoding(String) - Constructor for class uk.ac.ebi.xchars.domain.encoding.ExtendedHTMLEncoding

F

FILE - Static variable in class uk.ac.ebi.xchars.domain.ImageUsageConstant

fileLocation - Variable in class uk.ac.ebi.xchars.utilities.XCharsParser

The input stream if the xml file is in the class path.

findEndTagStart(String, String, int, int, String) - Static method in class uk.ac.ebi.xchars.utilities.XCharsValidator

This method finds the index of the correct end tag.

Formatting - Class in uk.ac.ebi.xchars.domain

Formatting(Character, EncodingSet, EncodingSet) - Constructor for class uk.ac.ebi.xchars.domain.Formatting

FORMATTING_TAG - Variable in class uk.ac.ebi.xchars.utilities.XCharsParser

XML tag of the formatting as defined in the DTD

formattingClasses - Variable in class uk.ac.ebi.xchars.SpecialCharacters

Map of formatting classes (see specialCharacters.xml).

formattingClasses - Variable in class uk.ac.ebi.xchars.utilities.XCharsParser

Map of formatting classes (see specialCharacters.xml).

G

getBody(List, int, int[], EncodingType[]) - Method in class uk.ac.ebi.xchars.helper.SpecialCharactersHelper

Creates the body of the output.

getCharacter() - Method in class uk.ac.ebi.xchars.domain.Formatting

getCharacterAndEncodings() - Method in class uk.ac.ebi.xchars.domain.XCharsClass

getCharacterClasses() - Method in class uk.ac.ebi.xchars.SpecialCharacters

getCode() - Method in class uk.ac.ebi.xchars.XMLErrorReport

getComposedEncoding(Node) - Method in class uk.ac.ebi.xchars.utilities.XCharsParser

getContent() - Method in class uk.ac.ebi.xchars.domain.Character

getContent() - Method in class uk.ac.ebi.xchars.domain.Definition

getDecimalValue() - Method in class uk.ac.ebi.xchars.SpecialCharacters.Octet

getDefaultEncoding() - Method in class uk.ac.ebi.xchars.domain.encoding.EncodingSet

getDefinition() - Method in class uk.ac.ebi.xchars.domain.Character

getDefinition() - Method in class uk.ac.ebi.xchars.domain.XCharsClass

getDefinition(Node) - Method in class uk.ac.ebi.xchars.utilities.XCharsParser

getEncoding(String, EncodingType) - Method in class uk.ac.ebi.xchars.domain.Character

Retrieves the encoding of the given character of the defined encoding type.

getEncoding(EncodingType) - Method in class uk.ac.ebi.xchars.domain.encoding.EncodingSet

getEncodingSet() - Method in class uk.ac.ebi.xchars.domain.encoding.EncodingSet

getEncodingSet(Node) - Method in class uk.ac.ebi.xchars.utilities.XCharsParser

Stores the actual encoding information of a character.

getErrorMessage() - Method in class uk.ac.ebi.xchars.XMLErrorReport

getExamples() - Method in class uk.ac.ebi.xchars.domain.Definition

getFormattingClasses() - Method in class uk.ac.ebi.xchars.SpecialCharacters

getHeader(int, int[], EncodingType[]) - Method in class uk.ac.ebi.xchars.helper.SpecialCharactersHelper

Creates the header of the output.

getHexValue() - Method in class uk.ac.ebi.xchars.SpecialCharacters.Octet

getHorizontalLine(int, int[], EncodingType[]) - Method in class uk.ac.ebi.xchars.helper.SpecialCharactersHelper

Creates a horizontal line with the same length as the header.

getHtmlElement() - Method in class uk.ac.ebi.xchars.domain.encoding.HTMLEncoding

getImagePath() - Method in class uk.ac.ebi.xchars.SpecialCharacters

getImageUsageConstant() - Method in class uk.ac.ebi.xchars.domain.encoding.GIFEncoding

getImageUsageConstant() - Method in class uk.ac.ebi.xchars.domain.encoding.JPGEncoding

getInstance(String, String) - Static method in class uk.ac.ebi.xchars.SpecialCharacters

getInstance(String) - Static method in class uk.ac.ebi.xchars.SpecialCharacters

This getInstance method assumes that the xml file is the in classpath and that the classLoader will pick it out based on the XML file name or the default xml file name.

getLhs() - Method in class uk.ac.ebi.xchars.domain.Formatting

getMaxElementLength() - Method in class uk.ac.ebi.xchars.helper.SpecialCharactersHelper

Returns the length of the longest XML element.

getMaxEncodingLength(EncodingType, List) - Method in class uk.ac.ebi.xchars.helper.SpecialCharactersHelper

Gets the length of the longest encoding of this type.

getName() - Method in class uk.ac.ebi.xchars.domain.XCharsClass

getNumberOfOctetsInSequence(SpecialCharacters.Octet) - Static method in class uk.ac.ebi.xchars.SpecialCharacters

getPos() - Method in class uk.ac.ebi.xchars.XMLErrorReport

getRelativePath() - Method in class uk.ac.ebi.xchars.domain.encoding.GIFEncoding

getRelativePath() - Method in class uk.ac.ebi.xchars.domain.encoding.JPGEncoding

getRhs() - Method in class uk.ac.ebi.xchars.domain.Formatting

getSpaces(int, int, char) - Method in class uk.ac.ebi.xchars.helper.SpecialCharactersHelper

Gets the spaces (or any other character) to be appended to the current string to get the same size of cells in a column.

getStringVectorIndex() - Method in class uk.ac.ebi.xchars.XMLErrorReport

getText() - Method in class uk.ac.ebi.xchars.XMLErrorReport

getUsage() - Method in class uk.ac.ebi.xchars.SpecialCharacters

getValue() - Method in class uk.ac.ebi.xchars.domain.encoding.AbstractEncoding

getValue() - Method in class uk.ac.ebi.xchars.domain.encoding.ChebiAsciiEncoding

getValue() - Method in class uk.ac.ebi.xchars.domain.encoding.ComposedEncoding

getValue() - Method in class uk.ac.ebi.xchars.domain.encoding.DefaultEncoding

getValue() - Method in interface uk.ac.ebi.xchars.domain.encoding.Encoding

getValue() - Method in class uk.ac.ebi.xchars.domain.encoding.ExtendedHTMLEncoding

getValue() - Method in class uk.ac.ebi.xchars.domain.encoding.GIFEncoding

getValue() - Method in class uk.ac.ebi.xchars.domain.encoding.HTMLCodeEncoding

getValue() - Method in class uk.ac.ebi.xchars.domain.encoding.HTMLEncoding

getValue() - Method in class uk.ac.ebi.xchars.domain.encoding.JPGEncoding

getValue() - Method in class uk.ac.ebi.xchars.domain.encoding.SwissProtEncoding

getValue() - Method in class uk.ac.ebi.xchars.domain.encoding.UnicodeEncoding

getValuesAsString(NodeList) - Method in class uk.ac.ebi.xchars.utilities.XCharsParser

Iterates over all the nodes and gets the values of the childnodes appended.

getVariableValue() - Method in class uk.ac.ebi.xchars.domain.encoding.AbstractEncoding

getXmlElements() - Method in class uk.ac.ebi.xchars.helper.SpecialCharactersHelper

Returns a list of all XML elements.

getXmlFileName() - Method in class uk.ac.ebi.xchars.SpecialCharacters

GIF - Static variable in class uk.ac.ebi.xchars.domain.EncodingType

GIF type.

GIFEncoding - Class in uk.ac.ebi.xchars.domain.encoding

Stores information needed to provide a GIF encoding for a character.

GIFEncoding(String, ImageUsageConstant, String) - Constructor for class uk.ac.ebi.xchars.domain.encoding.GIFEncoding

H

hashCode() - Method in class uk.ac.ebi.xchars.domain.EncodingType

hashCode() - Method in class uk.ac.ebi.xchars.SpecialCharacters.Octet

hasTags(String) - Static method in class uk.ac.ebi.xchars.utilities.XCharsValidator

Returns true if the text contains any greater than and less than tags.

HEX_ALPHABET - Static variable in class uk.ac.ebi.xchars.SpecialCharacters.Octet

hexValue - Variable in class uk.ac.ebi.xchars.SpecialCharacters.Octet

HTML - Static variable in class uk.ac.ebi.xchars.domain.EncodingType

HTML encoding type.

HTML_CODE - Static variable in class uk.ac.ebi.xchars.domain.EncodingType

HTML code encoding type.

HTMLCodeEncoding - Class in uk.ac.ebi.xchars.domain.encoding

This class ...

HTMLCodeEncoding(String) - Constructor for class uk.ac.ebi.xchars.domain.encoding.HTMLCodeEncoding

htmlElement - Variable in class uk.ac.ebi.xchars.domain.encoding.HTMLEncoding

HTMLEncoding - Class in uk.ac.ebi.xchars.domain.encoding

This class ...

HTMLEncoding(String, String) - Constructor for class uk.ac.ebi.xchars.domain.encoding.HTMLEncoding

I

imagePath - Variable in class uk.ac.ebi.xchars.SpecialCharacters

imagePath - Variable in class uk.ac.ebi.xchars.utilities.XCharsParser

imageUsageConstant - Variable in class uk.ac.ebi.xchars.domain.encoding.GIFEncoding

imageUsageConstant - Variable in class uk.ac.ebi.xchars.domain.encoding.JPGEncoding

ImageUsageConstant - Class in uk.ac.ebi.xchars.domain

This class ...

ImageUsageConstant(String) - Constructor for class uk.ac.ebi.xchars.domain.ImageUsageConstant

ImageUsageConstant(ImageUsageConstant) - Constructor for class uk.ac.ebi.xchars.domain.ImageUsageConstant

IMG_TAG - Static variable in class uk.ac.ebi.xchars.domain.ImageUsageConstant

INSTANCE - Static variable in class uk.ac.ebi.xchars.domain.encoding.DefaultEncoding

INSTANCE - Static variable in class uk.ac.ebi.xchars.SpecialCharacters

The sole instance.

INSTANCE - Static variable in class uk.ac.ebi.xchars.utilities.XCharsValidator

InvalidUTF8OctetSequenceException - Exception in uk.ac.ebi.xchars.exceptions

This class ...

InvalidUTF8OctetSequenceException(String) - Constructor for exception uk.ac.ebi.xchars.exceptions.InvalidUTF8OctetSequenceException

isSingleton - Variable in class uk.ac.ebi.xchars.domain.XCharsClass

isSingleton() - Method in class uk.ac.ebi.xchars.domain.XCharsClass

J

JPG - Static variable in class uk.ac.ebi.xchars.domain.EncodingType

JPEG type.

JPGEncoding - Class in uk.ac.ebi.xchars.domain.encoding

This class ...

JPGEncoding(String, ImageUsageConstant, String) - Constructor for class uk.ac.ebi.xchars.domain.encoding.JPGEncoding

L

lhs - Variable in class uk.ac.ebi.xchars.domain.Formatting

logger - Static variable in class uk.ac.ebi.xchars.utilities.XCharsValidator

M

main(String[]) - Static method in class uk.ac.ebi.xchars.utilities.XCharsOutput

main(String...) - Static method in class uk.ac.ebi.xchars.utilities.XCharsTranslator

Command line application to translate XChars markup.

myName - Variable in class uk.ac.ebi.xchars.domain.EncodingType

The value of the type.

O

OCTETS - Static variable in class uk.ac.ebi.xchars.SpecialCharacters.Octet

P

PARSER - Static variable in class uk.ac.ebi.xchars.utilities.XCharsValidator

parseSpecialCharacters() - Method in class uk.ac.ebi.xchars.utilities.XCharsParser

Parses the file specialCharacters.xml and stores the information in memory.

pathExists(String) - Static method in class uk.ac.ebi.xchars.SpecialCharacters

Checks if the given path is valid.

pos - Variable in class uk.ac.ebi.xchars.XMLErrorReport

Position of the error in the text.

printEncodings(EncodingType[]) - Method in class uk.ac.ebi.xchars.helper.SpecialCharactersHelper

Prints the encodings (if defined) of all characters of the given encoding types to a file named characterEncodings.txt in the working directory.

printEncodings(EncodingType[], File) - Method in class uk.ac.ebi.xchars.helper.SpecialCharactersHelper

Prints the encodings (if defined) of all characters of the given encoding types to the file characterEncodings.txt in the specified directory.

put(Object, Object) - Method in class uk.ac.ebi.xchars.domain.XCharsClass.XCharsClassMap

Overriden in order to allow only Characters or Formattings in the same class.

R

relativePath - Variable in class uk.ac.ebi.xchars.domain.encoding.GIFEncoding

relativePath - Variable in class uk.ac.ebi.xchars.domain.encoding.JPGEncoding

removeEncoding(Encoding) - Method in class uk.ac.ebi.xchars.domain.encoding.EncodingSet

removeFormatting(String) - Static method in class uk.ac.ebi.xchars.utilities.XCharsTranslator

rhs - Variable in class uk.ac.ebi.xchars.domain.Formatting

S

setCode(int) - Method in class uk.ac.ebi.xchars.XMLErrorReport

setContent(String) - Method in class uk.ac.ebi.xchars.domain.Definition

setDefaultEncoding(Encoding) - Method in class uk.ac.ebi.xchars.domain.encoding.EncodingSet

setDefinition(Definition) - Method in class uk.ac.ebi.xchars.domain.Character

setDefinition(Definition) - Method in class uk.ac.ebi.xchars.domain.XCharsClass

setEncodingSet(Map) - Method in class uk.ac.ebi.xchars.domain.encoding.EncodingSet

setExamples(List) - Method in class uk.ac.ebi.xchars.domain.Definition

setImagePath(String) - Method in class uk.ac.ebi.xchars.SpecialCharacters

setPos(int) - Method in class uk.ac.ebi.xchars.XMLErrorReport

setStringVectorIndex(int) - Method in class uk.ac.ebi.xchars.XMLErrorReport

setText(String) - Method in class uk.ac.ebi.xchars.XMLErrorReport

setUsage(ImageUsageConstant) - Method in class uk.ac.ebi.xchars.SpecialCharacters

specialCharacters - Variable in class uk.ac.ebi.xchars.helper.SpecialCharactersHelper

SpecialCharacters - Class in uk.ac.ebi.xchars

This class provides methods to retrieve display encodings for XML encoded special characters⁽¹⁾ defined in specialCharacters.xml and to validate text for correct usage of the XML encoded characters.

SpecialCharacters(String, String) - Constructor for class uk.ac.ebi.xchars.SpecialCharacters

Initialises the instance by parsing the XML files.

SpecialCharacters(String) - Constructor for class uk.ac.ebi.xchars.SpecialCharacters

This constructor creates an instance assuming the the xml file is in the classpath of the classloader.

SpecialCharacters(SpecialCharacters) - Constructor for class uk.ac.ebi.xchars.SpecialCharacters

SpecialCharacters.Octet - Class in uk.ac.ebi.xchars

Checks if the given String contains an invalid XML tag.

SpecialCharacters.Octet(String, int) - Constructor for class uk.ac.ebi.xchars.SpecialCharacters.Octet

SpecialCharactersHelper - Class in uk.ac.ebi.xchars.helper

This class provides methods to export/output the data processed by the SpecialCharacters class.

SpecialCharactersHelper(SpecialCharacters) - Constructor for class uk.ac.ebi.xchars.helper.SpecialCharactersHelper

Initialises the helper.

START_TAG_ERROR - Static variable in class uk.ac.ebi.xchars.XMLErrorReport

Error code for a missing start tag.

startIndex - Variable in exception uk.ac.ebi.xchars.exceptions.UnsupportedElementException

stringVectorIndex - Variable in class uk.ac.ebi.xchars.XMLErrorReport

Index of the Vector of Strings where the error occured.

SWISSPROT_CODE - Static variable in class uk.ac.ebi.xchars.domain.EncodingType

SWISSPROT code encoding type.

SwissProtEncoding - Class in uk.ac.ebi.xchars.domain.encoding

This class ...

SwissProtEncoding(String) - Constructor for class uk.ac.ebi.xchars.domain.encoding.SwissProtEncoding

T

TAG_FORMAT_ERROR - Static variable in class uk.ac.ebi.xchars.XMLErrorReport

Error code for a syntax error of the tag.

TAG_NAME_ERROR - Static variable in class uk.ac.ebi.xchars.XMLErrorReport

Error code for an invalid tag name.

TAG_TYPE_ERROR - Static variable in class uk.ac.ebi.xchars.XMLErrorReport

Error code for an invalid tag code.

text - Variable in class uk.ac.ebi.xchars.XMLErrorReport

The text where this error occured.

toString() - Method in class uk.ac.ebi.xchars.domain.EncodingType

Returns the type.

toString() - Method in class uk.ac.ebi.xchars.domain.ImageUsageConstant

toString() - Method in class uk.ac.ebi.xchars.XMLErrorReport

Provides a default way of printing the error message.

translate(Reader, Writer, boolean, boolean, EncodingType) - Static method in class uk.ac.ebi.xchars.utilities.XCharsTranslator

Translates XChars markup.

type - Variable in class uk.ac.ebi.xchars.domain.XCharsClass

TYPE_ATT - Variable in class uk.ac.ebi.xchars.utilities.XCharsParser

XML tag attribute of the class type as defined in the DTD

U

uk.ac.ebi.xchars - package uk.ac.ebi.xchars

This package contains classes for decoding and validation of encoded strings containing special characters.

uk.ac.ebi.xchars.domain - package uk.ac.ebi.xchars.domain

uk.ac.ebi.xchars.domain.encoding - package uk.ac.ebi.xchars.domain.encoding

uk.ac.ebi.xchars.exceptions - package uk.ac.ebi.xchars.exceptions

uk.ac.ebi.xchars.helper - package uk.ac.ebi.xchars.helper

uk.ac.ebi.xchars.utilities - package uk.ac.ebi.xchars.utilities

UNICODE - Static variable in class uk.ac.ebi.xchars.domain.EncodingType

Unicode encoding type.

UnicodeEncoding - Class in uk.ac.ebi.xchars.domain.encoding

This class ...

UnicodeEncoding(String) - Constructor for class uk.ac.ebi.xchars.domain.encoding.UnicodeEncoding

UnsupportedElementException - Exception in uk.ac.ebi.xchars.exceptions

This class ...

UnsupportedElementException(String, int, int, String) - Constructor for exception uk.ac.ebi.xchars.exceptions.UnsupportedElementException

usage - Variable in class uk.ac.ebi.xchars.domain.ImageUsageConstant

usage - Variable in class uk.ac.ebi.xchars.SpecialCharacters

usage - Variable in class uk.ac.ebi.xchars.utilities.XCharsParser

UTF8_CHARSET - Static variable in class uk.ac.ebi.xchars.SpecialCharacters

V

validate(String) - Method in class uk.ac.ebi.xchars.SpecialCharacters

Validates the XML tags of a given String.

validate(String) - Static method in class uk.ac.ebi.xchars.utilities.XCharsValidator

This validates a given text for the correct usage of XChars elements.

validateElementWithContent(String) - Static method in class uk.ac.ebi.xchars.utilities.XCharsValidator

validateElementWithoutContent(String, Matcher) - Static method in class uk.ac.ebi.xchars.utilities.XCharsValidator

validateNoIllegalArrows(String) - Static method in class uk.ac.ebi.xchars.utilities.XCharsValidator

validateWithReport(String) - Method in class uk.ac.ebi.xchars.SpecialCharacters

Validates the XML tags of a given String.

validateXMLElement(String, int, int, int, int, boolean) - Static method in class uk.ac.ebi.xchars.utilities.XCharsValidator

Validates just the core element i.e.

VALIDATOR - Static variable in class uk.ac.ebi.xchars.SpecialCharacters

The sole instance of the validator.

valueOf(String) - Static method in class uk.ac.ebi.xchars.domain.encoding.ChebiAsciiEncoding

valueOf(List) - Static method in class uk.ac.ebi.xchars.domain.encoding.ComposedEncoding

valueOf(EncodingType, String) - Static method in class uk.ac.ebi.xchars.domain.encoding.EncodingFactory

valueOf(String) - Static method in class uk.ac.ebi.xchars.domain.encoding.ExtendedHTMLEncoding

valueOf(String, ImageUsageConstant, String) - Static method in class uk.ac.ebi.xchars.domain.encoding.GIFEncoding

valueOf(String) - Static method in class uk.ac.ebi.xchars.domain.encoding.HTMLCodeEncoding

valueOf(String, String) - Static method in class uk.ac.ebi.xchars.domain.encoding.HTMLEncoding

valueOf(String, ImageUsageConstant, String) - Static method in class uk.ac.ebi.xchars.domain.encoding.JPGEncoding

valueOf(String) - Static method in class uk.ac.ebi.xchars.domain.encoding.SwissProtEncoding

valueOf(String) - Static method in class uk.ac.ebi.xchars.domain.encoding.UnicodeEncoding

valueOf(String) - Static method in class uk.ac.ebi.xchars.domain.EncodingType

valueOf(String) - Static method in class uk.ac.ebi.xchars.SpecialCharacters.Octet

valueOf(int) - Static method in class uk.ac.ebi.xchars.SpecialCharacters.Octet

valueOfComposedEncodingType(List) - Static method in class uk.ac.ebi.xchars.domain.encoding.EncodingFactory

valueOfGifEncodingType(String, ImageUsageConstant, String) - Static method in class uk.ac.ebi.xchars.domain.encoding.EncodingFactory

valueOfHtmlEncodingType(String, String) - Static method in class uk.ac.ebi.xchars.domain.encoding.EncodingFactory

valueOfJpegEncodingType(String, ImageUsageConstant, String) - Static method in class uk.ac.ebi.xchars.domain.encoding.EncodingFactory

variableValue - Variable in class uk.ac.ebi.xchars.domain.encoding.AbstractEncoding

X

XCharsClass - Class in uk.ac.ebi.xchars.domain

XCharsClass(String) - Constructor for class uk.ac.ebi.xchars.domain.XCharsClass

XCharsClass(String, Definition) - Constructor for class uk.ac.ebi.xchars.domain.XCharsClass

XCharsClass.XCharsClassMap - Class in uk.ac.ebi.xchars.domain

XCharsClass.XCharsClassMap() - Constructor for class uk.ac.ebi.xchars.domain.XCharsClass.XCharsClassMap

XCharsOutput - Class in uk.ac.ebi.xchars.utilities

This class ...

XCharsOutput() - Constructor for class uk.ac.ebi.xchars.utilities.XCharsOutput

XCharsParser - Class in uk.ac.ebi.xchars.utilities

XCharsParser parsers the SpecialCharcters XML file and places the characters in the characterClasses Map or the formattingClasses map.

XCharsParser(Map, Map, String, ImageUsageConstant, String, String) - Constructor for class uk.ac.ebi.xchars.utilities.XCharsParser

XCharsParser(Map, Map, String, ImageUsageConstant, String) - Constructor for class uk.ac.ebi.xchars.utilities.XCharsParser

XCharsTranslator - Class in uk.ac.ebi.xchars.utilities

Standalone application to translate XChars markup.
Usage:
java uk.ac.ebi.xchars.utilities.XCharsTranslator [-v] [-c] [-i <input>] [-o <output>] [-e <encoding>]

XCharsTranslator() - Constructor for class uk.ac.ebi.xchars.utilities.XCharsTranslator

XCharsValidator - Class in uk.ac.ebi.xchars.utilities

This class provides methods to validate strings for correct XChars usage.

XCharsValidator() - Constructor for class uk.ac.ebi.xchars.utilities.XCharsValidator

xml2Display(String) - Method in class uk.ac.ebi.xchars.SpecialCharacters

This method translates the XChars elements, contained in the given text, into the default display encoding.

xml2Display(String, EncodingType) - Method in class uk.ac.ebi.xchars.SpecialCharacters

This method returns the display encoding of the given string containing special character XML encoding.

XMLErrorReport - Class in uk.ac.ebi.xchars

This class stores XML Special Characters parsing error information.

XMLErrorReport() - Constructor for class uk.ac.ebi.xchars.XMLErrorReport

Initialises the object with default values.

XMLErrorReport(int, int, String) - Constructor for class uk.ac.ebi.xchars.XMLErrorReport

Initialises the object with the given values.

xmlFileName - Variable in class uk.ac.ebi.xchars.SpecialCharacters

The name of the XML file containing all special characters.

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