A B C D E F G I J K L M N O P R S T U V W

A

accept(File) - Method in class org.biolegato.tables.CSVFile

Determines whether a file is a CSV file (based on extension).

ACCEPTSQ - Static variable in interface org.biolegato.tables.CSVFileConstants

Lexical state.

ACCEPTSQ - Static variable in interface org.biolegato.tables.TSVFileConstants

Lexical state.

addColumns(String[]) - Method in class org.biolegato.tables.TableCanvas

Adds a list of column headers to the current table model.

addEscapes(String) - Static method in error org.biolegato.tables.TokenMgrError

Replaces unprintable characters by their escaped (or unicode escaped) equivalents in the given string

adjustBeginLineColumn(int, int) - Method in class org.biolegato.tables.SimpleCharStream

Method to adjust line and column numbers for the start of a token.

B

backup(int) - Method in class org.biolegato.tables.SimpleCharStream

Backup a number of characters.

beginColumn - Variable in class org.biolegato.tables.Token

The column number of the first character of this Token.

beginLine - Variable in class org.biolegato.tables.Token

The line number of the first character of this Token.

BeginToken() - Method in class org.biolegato.tables.SimpleCharStream

Start.

bufcolumn - Variable in class org.biolegato.tables.SimpleCharStream

buffer - Variable in class org.biolegato.tables.SimpleCharStream

bufline - Variable in class org.biolegato.tables.SimpleCharStream

bufpos - Variable in class org.biolegato.tables.SimpleCharStream

Position in buffer.

C

CDELIM - Static variable in interface org.biolegato.tables.CSVFileConstants

RegularExpression Id.

CDELIM - Static variable in interface org.biolegato.tables.TSVFileConstants

RegularExpression Id.

CHAR - Static variable in interface org.biolegato.tables.CSVFileConstants

RegularExpression Id.

CHAR - Static variable in interface org.biolegato.tables.TSVFileConstants

RegularExpression Id.

CHARS - Static variable in interface org.biolegato.tables.CSVFileConstants

RegularExpression Id.

CHARS - Static variable in interface org.biolegato.tables.TSVFileConstants

RegularExpression Id.

column - Variable in class org.biolegato.tables.SimpleCharStream

columnLetter(int) - Static method in class org.biolegato.tables.TableCanvas

Converts a number into a column letter(s).

CSVFile - Class in org.biolegato.tables

CSV (Comma Separated Values) file format parser.

CSVFile() - Constructor for class org.biolegato.tables.CSVFile

Creates a new instance of CSVFile

CSVFile(InputStream) - Constructor for class org.biolegato.tables.CSVFile

Constructor with InputStream.

CSVFile(InputStream, String) - Constructor for class org.biolegato.tables.CSVFile

Constructor with InputStream and supplied encoding

CSVFile(Reader) - Constructor for class org.biolegato.tables.CSVFile

Constructor.

CSVFile(CSVFileTokenManager) - Constructor for class org.biolegato.tables.CSVFile

Constructor with generated Token Manager.

CSVFileConstants - Interface in org.biolegato.tables

Token literal values and constants.

CSVFileTokenManager - Class in org.biolegato.tables

Token Manager.

CSVFileTokenManager(SimpleCharStream) - Constructor for class org.biolegato.tables.CSVFileTokenManager

Constructor.

CSVFileTokenManager(SimpleCharStream, int) - Constructor for class org.biolegato.tables.CSVFileTokenManager

Constructor.

curChar - Variable in class org.biolegato.tables.CSVFileTokenManager

curChar - Variable in class org.biolegato.tables.TSVFileTokenManager

currentToken - Variable in exception org.biolegato.tables.ParseException

This is the last token that has been consumed successfully.

D

DBL_EST - Static variable in class org.biolegato.tables.CSVFile

An empty 2D string array for calling the List.toArray method.

DBL_EST - Static variable in class org.biolegato.tables.TSVFile

An empty 2D string array for calling the List.toArray method.

DCHAR - Static variable in interface org.biolegato.tables.CSVFileConstants

RegularExpression Id.

DCHAR - Static variable in interface org.biolegato.tables.TSVFileConstants

RegularExpression Id.

debugStream - Variable in class org.biolegato.tables.CSVFileTokenManager

Debug output.

debugStream - Variable in class org.biolegato.tables.TSVFileTokenManager

Debug output.

DEFAULT - Static variable in interface org.biolegato.tables.CSVFileConstants

Lexical state.

DEFAULT - Static variable in interface org.biolegato.tables.TSVFileConstants

Lexical state.

disable_tracing() - Method in class org.biolegato.tables.CSVFile

Disable tracing.

disable_tracing() - Method in class org.biolegato.tables.TSVFile

Disable tracing.

display() - Method in class org.biolegato.tables.TableCanvas

Displays the table canvas within a BioLegato window.

Done() - Method in class org.biolegato.tables.SimpleCharStream

Reset buffer when finished.

DQEND - Static variable in interface org.biolegato.tables.CSVFileConstants

RegularExpression Id.

DQEND - Static variable in interface org.biolegato.tables.TSVFileConstants

RegularExpression Id.

DQSTART - Static variable in interface org.biolegato.tables.CSVFileConstants

RegularExpression Id.

DQSTART - Static variable in interface org.biolegato.tables.TSVFileConstants

RegularExpression Id.

DQUOTE - Static variable in interface org.biolegato.tables.CSVFileConstants

Lexical state.

DQUOTE - Static variable in interface org.biolegato.tables.TSVFileConstants

Lexical state.

E

enable_tracing() - Method in class org.biolegato.tables.CSVFile

Enable tracing.

enable_tracing() - Method in class org.biolegato.tables.TSVFile

Enable tracing.

endColumn - Variable in class org.biolegato.tables.Token

The column number of the last character of this Token.

endLine - Variable in class org.biolegato.tables.Token

The line number of the last character of this Token.

EOF - Static variable in interface org.biolegato.tables.CSVFileConstants

End of File.

EOF - Static variable in interface org.biolegato.tables.TSVFileConstants

End of File.

eol - Variable in exception org.biolegato.tables.ParseException

The end of line string for this machine.

EST - Static variable in class org.biolegato.tables.CSVFile

An empty 1D string array for calling the List.toArray method.

EST - Static variable in class org.biolegato.tables.TSVFile

An empty 1D string array for calling the List.toArray method.

ExpandBuff(boolean) - Method in class org.biolegato.tables.SimpleCharStream

expectedTokenSequences - Variable in exception org.biolegato.tables.ParseException

Each entry in this array is an array of integers.

F

FillBuff() - Method in class org.biolegato.tables.SimpleCharStream

G

generateParseException() - Method in class org.biolegato.tables.CSVFile

Generate ParseException.

generateParseException() - Method in class org.biolegato.tables.TSVFile

Generate ParseException.

getBeginColumn() - Method in class org.biolegato.tables.SimpleCharStream

Get token beginning column number.

getBeginLine() - Method in class org.biolegato.tables.SimpleCharStream

Get token beginning line number.

getColumn() - Method in class org.biolegato.tables.SimpleCharStream

Deprecated.

getData() - Method in class org.biolegato.tables.TableCanvas

Returns the current/selected data in the canvas as a 2D string array.

getData(boolean) - Method in class org.biolegato.tables.TableCanvas

Returns the current/selected data in the canvas as a 2D string array.

getDescription() - Method in class org.biolegato.tables.CSVFile

Returns a description of the file format that can be displayed to the user.

getEndColumn() - Method in class org.biolegato.tables.SimpleCharStream

Get token end column number.

getEndLine() - Method in class org.biolegato.tables.SimpleCharStream

Get token end line number.

GetImage() - Method in class org.biolegato.tables.SimpleCharStream

Get token literal value.

getLine() - Method in class org.biolegato.tables.SimpleCharStream

Deprecated.

getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class org.biolegato.tables.RowHeaderRenderer

Handles rendering the row numbers for the table object.

getMessage() - Method in error org.biolegato.tables.TokenMgrError

You can also modify the body of this method to customize your error messages.

getNextToken() - Method in class org.biolegato.tables.CSVFile

Get the next Token.

getNextToken() - Method in class org.biolegato.tables.CSVFileTokenManager

Get the next Token.

getNextToken() - Method in class org.biolegato.tables.TSVFile

Get the next Token.

getNextToken() - Method in class org.biolegato.tables.TSVFileTokenManager

Get the next Token.

getPluginName() - Method in class org.biolegato.tables.TableCanvas

Deprecated.

vestigial code from a previous BioLegato framework structure.

GetSuffix(int) - Method in class org.biolegato.tables.SimpleCharStream

Get the suffix.

getTabSize(int) - Method in class org.biolegato.tables.SimpleCharStream

getToken(int) - Method in class org.biolegato.tables.CSVFile

Get the specific Token.

getToken(int) - Method in class org.biolegato.tables.TSVFile

Get the specific Token.

getValue() - Method in class org.biolegato.tables.Token

An optional attribute value of the Token.

I

image - Variable in class org.biolegato.tables.Token

The string image of the token.

inBuf - Variable in class org.biolegato.tables.SimpleCharStream

input_stream - Variable in class org.biolegato.tables.CSVFileTokenManager

input_stream - Variable in class org.biolegato.tables.TSVFileTokenManager

inputStream - Variable in class org.biolegato.tables.SimpleCharStream

isFormat(Reader) - Method in class org.biolegato.tables.CSVFile

Used to auto-detect BioLegato table canvas formats.

isFormat(Reader) - Method in class org.biolegato.tables.TSVFile

Used to auto-detect BioLegato table canvas formats.

J

jj_nt - Variable in class org.biolegato.tables.CSVFile

Next token.

jj_nt - Variable in class org.biolegato.tables.TSVFile

Next token.

jjFillToken() - Method in class org.biolegato.tables.CSVFileTokenManager

jjFillToken() - Method in class org.biolegato.tables.TSVFileTokenManager

jjnewLexState - Static variable in class org.biolegato.tables.CSVFileTokenManager

Lex State array.

jjnewLexState - Static variable in class org.biolegato.tables.TSVFileTokenManager

Lex State array.

jjstrLiteralImages - Static variable in class org.biolegato.tables.CSVFileTokenManager

Token literal values.

jjstrLiteralImages - Static variable in class org.biolegato.tables.TSVFileTokenManager

Token literal values.

K

kind - Variable in class org.biolegato.tables.Token

An integer that describes the kind of this token.

L

LexicalError(boolean, int, int, int, String, char) - Static method in error org.biolegato.tables.TokenMgrError

Returns a detailed message for the Error when it is thrown by the token manager to indicate a lexical error.

lexStateNames - Static variable in class org.biolegato.tables.CSVFileTokenManager

Lexer state names.

lexStateNames - Static variable in class org.biolegato.tables.TSVFileTokenManager

Lexer state names.

line - Variable in class org.biolegato.tables.SimpleCharStream

M

main(String[]) - Static method in class org.biolegato.tables.TableCanvas

Starts a new instance of BioLegato, using the table canvas.

maxNextCharInd - Variable in class org.biolegato.tables.SimpleCharStream

N

newToken(int, String) - Static method in class org.biolegato.tables.Token

Returns a new Token object, by default.

newToken(int) - Static method in class org.biolegato.tables.Token

next - Variable in class org.biolegato.tables.Token

A reference to the next regular (non-special) token from the input stream.

O

org.biolegato.tables - package org.biolegato.tables

P

parseColumn() - Method in class org.biolegato.tables.CSVFile

Parses a column of the CSV data.

parseColumn() - Method in class org.biolegato.tables.TSVFile

Parses a column of the TSV data.

parseCSV(TableCanvas) - Method in class org.biolegato.tables.CSVFile

Parse CSV data into a table canvas.

parseDoubleArray() - Method in class org.biolegato.tables.CSVFile

Parse CSV data into a table canvas.

parseDoubleArray() - Method in class org.biolegato.tables.TSVFile

Parse TSV data into a table canvas.

ParseException - Exception in org.biolegato.tables

This exception is thrown when parse errors are encountered.

ParseException(Token, int[][], String[]) - Constructor for exception org.biolegato.tables.ParseException

This constructor is used by the method "generateParseException" in the generated parser.

ParseException() - Constructor for exception org.biolegato.tables.ParseException

The following constructors are for use by you for whatever purpose you can think of.

ParseException(String) - Constructor for exception org.biolegato.tables.ParseException

Constructor with message.

parseRow() - Method in class org.biolegato.tables.CSVFile

Parses a row of the CSV data.

parseRow() - Method in class org.biolegato.tables.TSVFile

Parses a row of the TSV data.

parseTSV(TableCanvas) - Method in class org.biolegato.tables.TSVFile

Parse TSV data into a table canvas.

prevCharIsCR - Variable in class org.biolegato.tables.SimpleCharStream

prevCharIsLF - Variable in class org.biolegato.tables.SimpleCharStream

R

RDELIM - Static variable in interface org.biolegato.tables.CSVFileConstants

RegularExpression Id.

RDELIM - Static variable in interface org.biolegato.tables.TSVFileConstants

RegularExpression Id.

readChar() - Method in class org.biolegato.tables.SimpleCharStream

Read a character.

readCSV(Reader) - Static method in class org.biolegato.tables.CSVFile

Reads CSV data from a Reader object into a 2D string array.

readFile(TableCanvas, Reader, boolean, boolean) - Static method in class org.biolegato.tables.CSVFile

Reads CSV data from a Reader object into a table canvas.

readFile(String, Reader, boolean, boolean) - Method in class org.biolegato.tables.TableCanvas

Reads a data into the canvas.

readFile(TableCanvas, Reader, boolean, boolean) - Static method in class org.biolegato.tables.TSVFile

Reads TSV data from a Reader object into a table canvas.

readTSV(Reader) - Static method in class org.biolegato.tables.TSVFile

Reads TSV data from a Reader object into a 2D string array.

ReInit(InputStream) - Method in class org.biolegato.tables.CSVFile

Reinitialise.

ReInit(InputStream, String) - Method in class org.biolegato.tables.CSVFile

Reinitialise.

ReInit(Reader) - Method in class org.biolegato.tables.CSVFile

Reinitialise.

ReInit(CSVFileTokenManager) - Method in class org.biolegato.tables.CSVFile

Reinitialise.

ReInit(SimpleCharStream) - Method in class org.biolegato.tables.CSVFileTokenManager

Reinitialise parser.

ReInit(SimpleCharStream, int) - Method in class org.biolegato.tables.CSVFileTokenManager

Reinitialise parser.

ReInit(Reader, int, int, int) - Method in class org.biolegato.tables.SimpleCharStream

Reinitialise.

ReInit(Reader, int, int) - Method in class org.biolegato.tables.SimpleCharStream

Reinitialise.

ReInit(Reader) - Method in class org.biolegato.tables.SimpleCharStream

Reinitialise.

ReInit(InputStream, String, int, int, int) - Method in class org.biolegato.tables.SimpleCharStream

Reinitialise.

ReInit(InputStream, int, int, int) - Method in class org.biolegato.tables.SimpleCharStream

Reinitialise.

ReInit(InputStream, String) - Method in class org.biolegato.tables.SimpleCharStream

Reinitialise.

ReInit(InputStream) - Method in class org.biolegato.tables.SimpleCharStream

Reinitialise.

ReInit(InputStream, String, int, int) - Method in class org.biolegato.tables.SimpleCharStream

Reinitialise.

ReInit(InputStream, int, int) - Method in class org.biolegato.tables.SimpleCharStream

Reinitialise.

ReInit(InputStream) - Method in class org.biolegato.tables.TSVFile

Reinitialise.

ReInit(InputStream, String) - Method in class org.biolegato.tables.TSVFile

Reinitialise.

ReInit(Reader) - Method in class org.biolegato.tables.TSVFile

Reinitialise.

ReInit(TSVFileTokenManager) - Method in class org.biolegato.tables.TSVFile

Reinitialise.

ReInit(SimpleCharStream) - Method in class org.biolegato.tables.TSVFileTokenManager

Reinitialise parser.

ReInit(SimpleCharStream, int) - Method in class org.biolegato.tables.TSVFileTokenManager

Reinitialise parser.

RowHeaderRenderer - Class in org.biolegato.tables

A class for rendering the row headers (line numbers) for a table.

RowHeaderRenderer(JTable) - Constructor for class org.biolegato.tables.RowHeaderRenderer

Creates a new instance of the row header renderer object.

S

SCHAR - Static variable in interface org.biolegato.tables.CSVFileConstants

RegularExpression Id.

SCHAR - Static variable in interface org.biolegato.tables.TSVFileConstants

RegularExpression Id.

selectAllA - Variable in class org.biolegato.tables.TableCanvas

The menu item "Select All"

setDebugStream(PrintStream) - Method in class org.biolegato.tables.CSVFileTokenManager

Set debug output.

setDebugStream(PrintStream) - Method in class org.biolegato.tables.TSVFileTokenManager

Set debug output.

setSelectionMode(TableCanvas.SelectionMode) - Method in class org.biolegato.tables.TableCanvas

Changes the SelectioMode of the TableCanvas

setTabSize(int) - Method in class org.biolegato.tables.SimpleCharStream

SimpleCharStream - Class in org.biolegato.tables

An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing).

SimpleCharStream(Reader, int, int, int) - Constructor for class org.biolegato.tables.SimpleCharStream

Constructor.

SimpleCharStream(Reader, int, int) - Constructor for class org.biolegato.tables.SimpleCharStream

Constructor.

SimpleCharStream(Reader) - Constructor for class org.biolegato.tables.SimpleCharStream

Constructor.

SimpleCharStream(InputStream, String, int, int, int) - Constructor for class org.biolegato.tables.SimpleCharStream

Constructor.

SimpleCharStream(InputStream, int, int, int) - Constructor for class org.biolegato.tables.SimpleCharStream

Constructor.

SimpleCharStream(InputStream, String, int, int) - Constructor for class org.biolegato.tables.SimpleCharStream

Constructor.

SimpleCharStream(InputStream, int, int) - Constructor for class org.biolegato.tables.SimpleCharStream

Constructor.

SimpleCharStream(InputStream, String) - Constructor for class org.biolegato.tables.SimpleCharStream

Constructor.

SimpleCharStream(InputStream) - Constructor for class org.biolegato.tables.SimpleCharStream

Constructor.

specialToken - Variable in class org.biolegato.tables.Token

This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.

SQEND - Static variable in interface org.biolegato.tables.CSVFileConstants

RegularExpression Id.

SQEND - Static variable in interface org.biolegato.tables.TSVFileConstants

RegularExpression Id.

SQSTART - Static variable in interface org.biolegato.tables.CSVFileConstants

RegularExpression Id.

SQSTART - Static variable in interface org.biolegato.tables.TSVFileConstants

RegularExpression Id.

SQUOTE - Static variable in interface org.biolegato.tables.CSVFileConstants

Lexical state.

SQUOTE - Static variable in interface org.biolegato.tables.TSVFileConstants

Lexical state.

stateChanged(ChangeEvent) - Method in class org.biolegato.tables.TableCanvasProperties

Update the font size when the font spinner's numerical value changes.

staticFlag - Static variable in class org.biolegato.tables.SimpleCharStream

Whether parser is static.

SwitchTo(int) - Method in class org.biolegato.tables.CSVFileTokenManager

Switch to specified lex state.

SwitchTo(int) - Method in class org.biolegato.tables.TSVFileTokenManager

Switch to specified lex state.

T

TableCanvas - Class in org.biolegato.tables

BioLegato's table canvas.

TableCanvas() - Constructor for class org.biolegato.tables.TableCanvas

Creates a new instance of a TableCanvas.

TableCanvas(Map<? extends Object, ? extends Object>) - Constructor for class org.biolegato.tables.TableCanvas

Creates a new instance of TableCanvas.

TableCanvas(ResultSet) - Constructor for class org.biolegato.tables.TableCanvas

Creates a new instance of TableCanvas, reading results from an SQL query into the table, by default.

TableCanvas(Map<? extends Object, ? extends Object>, ResultSet) - Constructor for class org.biolegato.tables.TableCanvas

Creates a new instance of TableCanvas, reading results from an SQL query into the table, by default.

TableCanvas(Map<? extends Object, ? extends Object>, String[][]) - Constructor for class org.biolegato.tables.TableCanvas

Creates a new instance of TableCanvas.

TableCanvas.SelectionMode - Enum in org.biolegato.tables

The selection modes available for the table canvas.

TableCanvasProperties - Class in org.biolegato.tables

A class for setting properties specific to the table canvas.

TableCanvasProperties(JFrame, JTable, JList) - Constructor for class org.biolegato.tables.TableCanvasProperties

Creates a new TableCanvasProperties object to change the properties of the table canvas.

tabSize - Variable in class org.biolegato.tables.SimpleCharStream

token - Variable in class org.biolegato.tables.CSVFile

Current token.

Token - Class in org.biolegato.tables

Describes the input token stream.

Token() - Constructor for class org.biolegato.tables.Token

No-argument constructor

Token(int) - Constructor for class org.biolegato.tables.Token

Constructs a new token for the specified Image.

Token(int, String) - Constructor for class org.biolegato.tables.Token

Constructs a new token for the specified Image and Kind.

token - Variable in class org.biolegato.tables.TSVFile

Current token.

token_source - Variable in class org.biolegato.tables.CSVFile

Generated Token Manager.

token_source - Variable in class org.biolegato.tables.TSVFile

Generated Token Manager.

tokenImage - Static variable in interface org.biolegato.tables.CSVFileConstants

Literal token values.

tokenImage - Variable in exception org.biolegato.tables.ParseException

This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred.

tokenImage - Static variable in interface org.biolegato.tables.TSVFileConstants

Literal token values.

TokenMgrError - Error in org.biolegato.tables

Token Manager Error.

TokenMgrError() - Constructor for error org.biolegato.tables.TokenMgrError

No arg constructor.

TokenMgrError(String, int) - Constructor for error org.biolegato.tables.TokenMgrError

Constructor with message and reason.

TokenMgrError(boolean, int, int, int, String, char, int) - Constructor for error org.biolegato.tables.TokenMgrError

Full Constructor.

toString() - Method in class org.biolegato.tables.Token

Returns the image.

TSV_FILTER - Static variable in class org.biolegato.tables.TSVFile

TSV file format filter (for file chooser objects).

TSVFile - Class in org.biolegato.tables

TSV (Tab Separated Values) file format parser.

TSVFile(InputStream) - Constructor for class org.biolegato.tables.TSVFile

Constructor with InputStream.

TSVFile(InputStream, String) - Constructor for class org.biolegato.tables.TSVFile

Constructor with InputStream and supplied encoding

TSVFile(Reader) - Constructor for class org.biolegato.tables.TSVFile

Constructor.

TSVFile(TSVFileTokenManager) - Constructor for class org.biolegato.tables.TSVFile

Constructor with generated Token Manager.

TSVFileConstants - Interface in org.biolegato.tables

Token literal values and constants.

TSVFileTokenManager - Class in org.biolegato.tables

Token Manager.

TSVFileTokenManager(SimpleCharStream) - Constructor for class org.biolegato.tables.TSVFileTokenManager

Constructor.

TSVFileTokenManager(SimpleCharStream, int) - Constructor for class org.biolegato.tables.TSVFileTokenManager

Constructor.

U

UpdateLineColumn(char) - Method in class org.biolegato.tables.SimpleCharStream

V

valueOf(String) - Static method in enum org.biolegato.tables.TableCanvas.SelectionMode

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.biolegato.tables.TableCanvas.SelectionMode

Returns an array containing the constants of this enum type, in the order they are declared.

W

writeFile(Appendable, String[][]) - Static method in class org.biolegato.tables.CSVFile

Writes a 2D string array as CSV data into an Appendable object.

writeFile(String, Appendable, boolean) - Method in class org.biolegato.tables.TableCanvas

Writes data out from the canvas to an Appendable object.

writeFile(Appendable, String[][]) - Static method in class org.biolegato.tables.TSVFile

Writes a 2D string array as TSV data into an Appendable object.

A B C D E F G I J K L M N O P R S T U V W