DB canvas v1.0.0 API
A B C D E F G I J K L M N O P Q R S T U V W 

A

actionPerformed(ActionEvent) - Method in class org.biolegato.database.fields.DBCommandThread
Runs the command.
addEscapes(String) - Static method in error org.biolegato.database.TokenMgrError
Replaces unprintable characters by their escaped (or unicode escaped) equivalents in the given string
addListDataListener(ListDataListener) - Method in class org.biolegato.database.EntriesListModel
Adds a listener to the list model's collection of listener objects
addListDataListener(ListDataListener) - Method in class org.biolegato.database.SchemaListModel
 
adjustBeginLineColumn(int, int) - Method in class org.biolegato.database.SimpleCharStream
Method to adjust line and column numbers for the start of a token.
assertIndent(int) - Method in class org.biolegato.database.DBPCD
Asserts indentation level (calls token_source.testIndent)

B

backup(int) - Method in class org.biolegato.database.SimpleCharStream
Backup a number of characters.
beginColumn - Variable in class org.biolegato.database.Token
The column number of the first character of this Token.
beginLine - Variable in class org.biolegato.database.Token
The line number of the first character of this Token.
BeginToken() - Method in class org.biolegato.database.SimpleCharStream
Start.
Bool() - Method in class org.biolegato.database.DBPCD
Parses a boolean token into a java boolean
BooleanField - Class in org.biolegato.database.fields
 
BooleanField(String) - Constructor for class org.biolegato.database.fields.BooleanField
Creates a new instance of a boolean field.
BooleanField(String, String) - Constructor for class org.biolegato.database.fields.BooleanField
Creates a new instance of a boolean field.
booleanValues - Static variable in class org.biolegato.database.fields.BooleanField
 
booleanValues - Static variable in class org.biolegato.database.fields.DBCommand
 
browseTable(String) - Method in class org.biolegato.database.DBCanvas
Displays the brows table canvas for the BLDB
bufcolumn - Variable in class org.biolegato.database.SimpleCharStream
 
buffer - Variable in class org.biolegato.database.SimpleCharStream
 
bufline - Variable in class org.biolegato.database.SimpleCharStream
 
bufpos - Variable in class org.biolegato.database.SimpleCharStream
Position in buffer.

C

CDELIM - Static variable in interface org.biolegato.database.ValuesFileConstants
RegularExpression Id.
CHAR - Static variable in interface org.biolegato.database.ValuesFileConstants
RegularExpression Id.
checkupdate() - Method in class org.biolegato.database.EntriesListModel
Checks for updates to the entries within a database schema and updates the list model when changes are detected.
checkupdate() - Method in class org.biolegato.database.SchemaListModel
 
choice_list - Variable in class org.biolegato.database.fields.ReferenceField
The list containing the data.
close() - Method in class org.biolegato.database.DBCanvas
Action for command buttons to close the window.
close() - Method in class org.biolegato.database.JDBCDBConnection
 
COEL - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
column - Variable in class org.biolegato.database.SimpleCharStream
 
COMMENT - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
conn - Variable in class org.biolegato.database.EntriesListModel
The SQL connection object to use for retrieving the entries
connect() - Method in class org.biolegato.database.JDBCDBConnection
 
createTable(Statement) - Method in class org.biolegato.database.DBSchema
Writes the CREATE TABLE representation of the database schema to a writer object
createTable(Appendable) - Method in class org.biolegato.database.fields.BooleanField
Writes the CREATE TABLE representation of the current database field to a writer object
createTable(Appendable) - Method in class org.biolegato.database.fields.DBCommand
Writes the CREATE TABLE representation of the current database field to a writer object
createTable(Appendable) - Method in interface org.biolegato.database.fields.DBField
Writes the CREATE TABLE representation of the current database field to a writer object
createTable(Appendable) - Method in class org.biolegato.database.fields.DBTextField
Writes the CREATE TABLE representation of the current database field to a writer object
createTable(Appendable) - Method in class org.biolegato.database.fields.DecimalField
Writes the CREATE TABLE representation of the current database field to a writer object
createTable(Appendable) - Method in class org.biolegato.database.fields.NumberField
Writes the CREATE TABLE representation of the current database field to a writer object
createTable(Appendable) - Method in class org.biolegato.database.fields.ReferenceField
Writes the CREATE TABLE representation of the current database field to a writer object
createTransferable(JComponent) - Method in class org.biolegato.database.schemaeditor.FieldTransferHandler
This creates the Transferable object.
curChar - Variable in class org.biolegato.database.DBPCDTokenManager
 
curChar - Variable in class org.biolegato.database.ValuesFileTokenManager
 
currentToken - Variable in exception org.biolegato.database.ParseException
This is the last token that has been consumed successfully.

D

DATA - Static variable in interface org.biolegato.database.DBPCDConstants
Lexical state.
dbBack() - Method in class org.biolegato.database.DBCanvas
The code for displaying the database home screen/page
DBCanvas - Class in org.biolegato.database
The run window is used within the menu system to display options for running programs
DBCanvas() - Constructor for class org.biolegato.database.DBCanvas
Creates a new instance of BioLegato's database canvas
DBCanvas(Map<? extends Object, ? extends Object>) - Constructor for class org.biolegato.database.DBCanvas
Creates a new instance of BioLegato's database canvas
dbcanvas - Variable in class org.biolegato.database.schemaeditor.FieldGenerator
 
dbcanvasSelf - Variable in class org.biolegato.database.DBCanvas
A self reference to the current object (this is used for customized subclass code defined within the class's methods).
DBCommand - Class in org.biolegato.database.fields
 
DBCommand(String) - Constructor for class org.biolegato.database.fields.DBCommand
Creates a new instance of a boolean field.
DBCommand(String, String) - Constructor for class org.biolegato.database.fields.DBCommand
Creates a new instance of a boolean field.
DBCommandThread - Class in org.biolegato.database.fields
Class used for making abstract actions which launch threads.
DBCommandThread(String, boolean) - Constructor for class org.biolegato.database.fields.DBCommandThread
Creates a new instance of CommandThread.
DBCommandThread(String, Map<String, String>, boolean) - Constructor for class org.biolegato.database.fields.DBCommandThread
Creates a new instance of CommandThread.
DBField - Interface in org.biolegato.database.fields
 
DBPCD - Class in org.biolegato.database
A class used to parse PCD schema files into BioLegato.
DBPCD(InputStream) - Constructor for class org.biolegato.database.DBPCD
Constructor with InputStream.
DBPCD(InputStream, String) - Constructor for class org.biolegato.database.DBPCD
Constructor with InputStream and supplied encoding
DBPCD(Reader) - Constructor for class org.biolegato.database.DBPCD
Constructor.
DBPCD(DBPCDTokenManager) - Constructor for class org.biolegato.database.DBPCD
Constructor with generated Token Manager.
DBPCDConstants - Interface in org.biolegato.database
Token literal values and constants.
dbpcdout(int, Appendable, boolean) - Method in class org.biolegato.database.fields.BooleanField
Writes the DBPCD representation of the database field to a writer object
dbpcdout(int, Appendable, boolean) - Method in class org.biolegato.database.fields.DBCommand
Writes the DBPCD representation of the database field to a writer object
dbpcdout(int, Appendable, boolean) - Method in interface org.biolegato.database.fields.DBField
Writes the DBPCD representation of the database field to a writer object
dbpcdout(int, Appendable, boolean) - Method in class org.biolegato.database.fields.DBTextField
Writes the DBPCD representation of the database field to a writer object
dbpcdout(int, Appendable, boolean) - Method in class org.biolegato.database.fields.DecimalField
Writes the DBPCD representation of the database field to a writer object
dbpcdout(int, Appendable, boolean) - Method in class org.biolegato.database.fields.NumberField
Writes the DBPCD representation of the database field to a writer object
dbpcdout(int, Appendable, boolean) - Method in class org.biolegato.database.fields.ReferenceField
Writes the DBPCD representation of the database field to a writer object
DBPCDTokenManager - Class in org.biolegato.database
Token Manager.
DBPCDTokenManager(SimpleCharStream) - Constructor for class org.biolegato.database.DBPCDTokenManager
Constructor.
DBPCDTokenManager(SimpleCharStream, int) - Constructor for class org.biolegato.database.DBPCDTokenManager
Constructor.
DBSchema - Class in org.biolegato.database
 
DBSchema(String) - Constructor for class org.biolegato.database.DBSchema
 
DBSchema(String, KeyableField) - Constructor for class org.biolegato.database.DBSchema
 
DBSchema(String, KeyableField, DBField) - Constructor for class org.biolegato.database.DBSchema
 
DBSchema(String, KeyableField, DBField, Collection<DBField>) - Constructor for class org.biolegato.database.DBSchema
 
DBTextField - Class in org.biolegato.database.fields
 
DBTextField(String) - Constructor for class org.biolegato.database.fields.DBTextField
Creates a new instance of a text field.
DBTextField(String, String) - Constructor for class org.biolegato.database.fields.DBTextField
Creates a new instance of a text field.
DCHAR - Static variable in interface org.biolegato.database.ValuesFileConstants
RegularExpression Id.
debug - Static variable in class org.biolegato.database.DBPCD
Whether to operate in debug mode
debugStream - Variable in class org.biolegato.database.DBPCDTokenManager
Debug output.
debugStream - Variable in class org.biolegato.database.ValuesFileTokenManager
Debug output.
Decimal() - Method in class org.biolegato.database.DBPCD
Parses a decimal number from a PCD file into a Java double
DECIMAL - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
DecimalField - Class in org.biolegato.database.fields
 
DecimalField(String) - Constructor for class org.biolegato.database.fields.DecimalField
Creates a new instance of a decimal field.
DecimalField(String, String) - Constructor for class org.biolegato.database.fields.DecimalField
Creates a new instance of a decimal field.
DEFAULT - Static variable in interface org.biolegato.database.DBPCDConstants
Lexical state.
DEFAULT - Static variable in interface org.biolegato.database.ValuesFileConstants
Lexical state.
DIGITS - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
disable_tracing() - Method in class org.biolegato.database.DBPCD
Disable tracing.
disable_tracing() - Method in class org.biolegato.database.ValuesFile
Disable tracing.
display() - Method in class org.biolegato.database.DBCanvas
Displays the command parameter window.
Done() - Method in class org.biolegato.database.SimpleCharStream
Reset buffer when finished.
DOUBLEQ - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
DQEND - Static variable in interface org.biolegato.database.ValuesFileConstants
RegularExpression Id.
DQSTART - Static variable in interface org.biolegato.database.ValuesFileConstants
RegularExpression Id.
DQUOTE - Static variable in interface org.biolegato.database.ValuesFileConstants
Lexical state.
dragMouseMoved(DragSourceDragEvent) - Method in class org.biolegato.database.schemaeditor.FieldTransferHandler
 
drop() - Method in class org.biolegato.database.schemaeditor.FieldGenerator
 

E

edit(Connection, Container, String) - Method in class org.biolegato.database.DBSchema
 
edit(Connection, Container, Map<String, String>) - Method in class org.biolegato.database.fields.BooleanField
Displays the content of a field within a dataset entry.
edit(Connection, Container, Map<String, String>) - Method in class org.biolegato.database.fields.DBCommand
 
edit(Connection, Container, Map<String, String>) - Method in interface org.biolegato.database.fields.DBField
Displays the content of a field within a dataset entry.
edit(Connection, Container, Map<String, String>) - Method in class org.biolegato.database.fields.DBTextField
Displays the content of a field within a dataset entry.
edit(Connection, Container, Map<String, String>) - Method in class org.biolegato.database.fields.DecimalField
Displays the content of a field within a dataset entry.
edit(Connection, Container, Map<String, String>) - Method in class org.biolegato.database.fields.NumberField
Displays the content of a field within a dataset entry.
edit(Connection, Container, Map<String, String>) - Method in class org.biolegato.database.fields.ReferenceField
Displays the content of a field within a dataset entry.
editWindow(Container) - Method in class org.biolegato.database.fields.ReferenceField
Populates a container with the component objects necessary for editing the current widget
enable_tracing() - Method in class org.biolegato.database.DBPCD
Enable tracing.
enable_tracing() - Method in class org.biolegato.database.ValuesFile
Enable tracing.
endColumn - Variable in class org.biolegato.database.Token
The column number of the last character of this Token.
endLine - Variable in class org.biolegato.database.Token
The line number of the last character of this Token.
entries - Variable in class org.biolegato.database.EntriesListModel
The current 'cached' list of database entries for the given schema This is used as a reference and modified by the function checkupdate.
EntriesListModel - Class in org.biolegato.database
A list model object for displaying the entries of a given table/schema within a database.
EntriesListModel(Connection, DBSchema) - Constructor for class org.biolegato.database.EntriesListModel
Creates a new instance of the entries list model object - a list model for displaying all of the entries of a schema.
EntriesListModel.Entry - Class in org.biolegato.database
A class used to store the relationship between a database key and the database name-column value for a given database entry.
EntriesListModel.Entry(String, String) - Constructor for class org.biolegato.database.EntriesListModel.Entry
Constructs a new schema entry object for use within the list model
EOF - Static variable in interface org.biolegato.database.DBPCDConstants
End of File.
EOF - Static variable in interface org.biolegato.database.ValuesFileConstants
End of File.
EOL - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
eol - Variable in exception org.biolegato.database.ParseException
The end of line string for this machine.
equals(Object) - Method in class org.biolegato.database.EntriesListModel.Entry
Tests an arbitrary object 'o' for equality with the current entry object.
ExpandBuff(boolean) - Method in class org.biolegato.database.SimpleCharStream
 
expectedTokenSequences - Variable in exception org.biolegato.database.ParseException
Each entry in this array is an array of integers.

F

FieldGenerator - Class in org.biolegato.database.schemaeditor
Abstract interface to generate database fields Acknowledgement - Bryan E.
FieldGenerator(DBCanvas, Icon, String, Class) - Constructor for class org.biolegato.database.schemaeditor.FieldGenerator
 
FieldTransferHandler - Class in org.biolegato.database.schemaeditor
Database field transfer handler - for dragging and dropping database fields Acknowledgement - Bryan E.
FieldTransferHandler() - Constructor for class org.biolegato.database.schemaeditor.FieldTransferHandler
 
FillBuff() - Method in class org.biolegato.database.SimpleCharStream
 
finalize() - Method in class org.biolegato.database.EntriesListModel
An overridden finalize method - if the updateThread variable is used to ensure continuous dynamic updating, then we must stop the thread when the object is deleted to avoid memory leak and Exception throwing.
finalize() - Method in class org.biolegato.database.SchemaListModel
 
findIndex(String) - Method in class org.biolegato.database.EntriesListModel
Determine the index value for a given database key within the list model
FLAVOUR - Static variable in class org.biolegato.database.schemaeditor.FieldGenerator
 

G

generateParseException() - Method in class org.biolegato.database.DBPCD
Generate ParseException.
generateParseException() - Method in class org.biolegato.database.ValuesFile
Generate ParseException.
getBeginColumn() - Method in class org.biolegato.database.SimpleCharStream
Get token beginning column number.
getBeginLine() - Method in class org.biolegato.database.SimpleCharStream
Get token beginning line number.
getColumn() - Method in class org.biolegato.database.SimpleCharStream
Deprecated.
getCurrentSchema() - Method in class org.biolegato.database.DBCanvas
Returns the current schema
getElementAt(int) - Method in class org.biolegato.database.EntriesListModel
Returns a specific Entry object for the given index
getElementAt(int) - Method in class org.biolegato.database.SchemaListModel
 
getEndColumn() - Method in class org.biolegato.database.SimpleCharStream
Get token end column number.
getEndLine() - Method in class org.biolegato.database.SimpleCharStream
Get token end line number.
getEntries() - Method in class org.biolegato.database.DBCanvas
Get all of the entries for the current database schema
getEntries(Connection, DBSchema) - Static method in class org.biolegato.database.EntriesListModel
Get all of the entries for the current database schema
GetImage() - Method in class org.biolegato.database.SimpleCharStream
Get token literal value.
getIndent() - Method in class org.biolegato.database.DBPCDTokenManager
Returns the current indentation level
getInstance() - Method in class org.biolegato.database.fields.ReferenceField
Returns the value of the variable.
getKey() - Method in class org.biolegato.database.DBSchema
 
getKey() - Method in class org.biolegato.database.EntriesListModel.Entry
Returns the schema key value for the database entry
getLine() - Method in class org.biolegato.database.SimpleCharStream
Deprecated.
getMessage() - Method in error org.biolegato.database.TokenMgrError
You can also modify the body of this method to customize your error messages.
getName() - Method in class org.biolegato.database.fields.BooleanField
Returns the database SQL name of the current field
getName() - Method in class org.biolegato.database.fields.DBCommand
Returns the database SQL name of the current field
getName() - Method in interface org.biolegato.database.fields.DBField
Returns the database SQL name of the current field
getName() - Method in class org.biolegato.database.fields.DBTextField
Returns the database SQL name of the current field
getName() - Method in class org.biolegato.database.fields.DecimalField
Returns the database SQL name of the current field
getName() - Method in class org.biolegato.database.fields.NumberField
Returns the database SQL name of the current field
getName() - Method in class org.biolegato.database.fields.ReferenceField
Returns the database SQL name of the current field
getNameCol() - Method in class org.biolegato.database.DBSchema
 
getNextToken() - Method in class org.biolegato.database.DBPCD
Get the next Token.
getNextToken() - Method in class org.biolegato.database.DBPCDTokenManager
Get the next Token.
getNextToken() - Method in class org.biolegato.database.ValuesFile
Get the next Token.
getNextToken() - Method in class org.biolegato.database.ValuesFileTokenManager
Get the next Token.
getPluginName() - Method in class org.biolegato.database.DBCanvas
Returns the name of this canvas (i.e.
getSchemas() - Method in class org.biolegato.database.DBCanvas
 
getSchemas(String) - Static method in class org.biolegato.database.SchemaListModel
Get all of the schemas available for the database canvas
getSize() - Method in class org.biolegato.database.EntriesListModel
Returns the current size of the list model (the # of database entries for the current schema)
getSize() - Method in class org.biolegato.database.SchemaListModel
 
getSourceActions(JComponent) - Method in class org.biolegato.database.schemaeditor.FieldTransferHandler
This is queried to see whether the component can be copied, moved, both or neither.
GetSuffix(int) - Method in class org.biolegato.database.SimpleCharStream
Get the suffix.
getTable() - Method in class org.biolegato.database.DBSchema
 
getTabSize(int) - Method in class org.biolegato.database.SimpleCharStream
 
getToken(int) - Method in class org.biolegato.database.DBPCD
Get the specific Token.
getToken(int) - Method in class org.biolegato.database.ValuesFile
Get the specific Token.
getTransferData(DataFlavor) - Method in class org.biolegato.database.schemaeditor.FieldGenerator
One of three methods defined by the Transferable interface.
getTransferDataFlavors() - Method in class org.biolegato.database.schemaeditor.FieldGenerator
One of three methods defined by the Transferable interface.
getType() - Method in class org.biolegato.database.fields.BooleanField
Returns the database SQL type of the current field
getType() - Method in class org.biolegato.database.fields.DBTextField
Returns the database SQL type of the current field
getType() - Method in class org.biolegato.database.fields.DecimalField
Returns the database SQL type of the current field
getType() - Method in class org.biolegato.database.fields.NumberField
Returns the database SQL type of the current field
getValue() - Method in class org.biolegato.database.fields.BooleanField
Returns the database SQL value of the current field
getValue() - Method in class org.biolegato.database.fields.DBTextField
Returns the database SQL value of the current field
getValue() - Method in class org.biolegato.database.fields.DecimalField
Returns the database SQL value of the current field
getValue() - Method in interface org.biolegato.database.fields.KeyableField
Returns the value of the current field
getValue() - Method in class org.biolegato.database.fields.NumberField
Returns the database SQL value of the current field
getValue() - Method in class org.biolegato.database.Token
An optional attribute value of the Token.

I

ID - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
Ident() - Method in class org.biolegato.database.DBPCD
Parses an identifier token from a PCD file into a Java String
image - Variable in class org.biolegato.database.Token
The string image of the token.
inBuf - Variable in class org.biolegato.database.SimpleCharStream
 
INDENT_SIZE - Static variable in class org.biolegato.database.DBPCDTokenManager
Used to store the size of an indent in spaces This is necessary for calculations within the Java program
indices - Variable in class org.biolegato.database.fields.ReferenceField
The list of indices selected
input_stream - Variable in class org.biolegato.database.DBPCDTokenManager
 
input_stream - Variable in class org.biolegato.database.ValuesFileTokenManager
 
inputStream - Variable in class org.biolegato.database.SimpleCharStream
 
isDataFlavorSupported(DataFlavor) - Method in class org.biolegato.database.schemaeditor.FieldGenerator
One of three methods defined by the Transferable interface.

J

JDBCDBConnection - Class in org.biolegato.database
 
JDBCDBConnection(String, String, boolean) - Constructor for class org.biolegato.database.JDBCDBConnection
Creates a new PCD SQL connection object.
JDBCDBConnection(String, String, String, String) - Constructor for class org.biolegato.database.JDBCDBConnection
Creates a new PCD SQL connection object.
jj_nt - Variable in class org.biolegato.database.DBPCD
Next token.
jj_nt - Variable in class org.biolegato.database.ValuesFile
Next token.
jjFillToken() - Method in class org.biolegato.database.DBPCDTokenManager
 
jjFillToken() - Method in class org.biolegato.database.ValuesFileTokenManager
 
jjnewLexState - Static variable in class org.biolegato.database.DBPCDTokenManager
Lex State array.
jjnewLexState - Static variable in class org.biolegato.database.ValuesFileTokenManager
Lex State array.
jjstrLiteralImages - Static variable in class org.biolegato.database.DBPCDTokenManager
Token literal values.
jjstrLiteralImages - Static variable in class org.biolegato.database.ValuesFileTokenManager
Token literal values.

K

KeyableField - Interface in org.biolegato.database.fields
A subclass of DBField This subclass is used to provide easy access to methods which are only applicable to fields which can be used as the primary key for a BLDB database
kind - Variable in class org.biolegato.database.Token
An integer that describes the kind of this token.

L

label - Variable in class org.biolegato.database.fields.ReferenceField
the label for the text field
LexicalError(boolean, int, int, int, String, char) - Static method in error org.biolegato.database.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.database.DBPCDTokenManager
Lexer state names.
lexStateNames - Static variable in class org.biolegato.database.ValuesFileTokenManager
Lexer state names.
line - Variable in class org.biolegato.database.SimpleCharStream
 
listeners - Variable in class org.biolegato.database.EntriesListModel
The list of ListDataListener objects associated with the list model
listSelf - Variable in class org.biolegato.database.EntriesListModel
A self-reference for any specialized subclass objects defined within the scope of a method within this class.
loadSchema(String) - Method in class org.biolegato.database.DBCanvas
 

M

main(String[]) - Static method in class org.biolegato.database.DBCanvas
Starts BioLegato PCD canvas
main(String[]) - Static method in class org.biolegato.database.DBPCD
 
mainPanel - Variable in class org.biolegato.database.DBCanvas
The main panel object for the canvas (this is used for refreshing while in applet mode, so everything can be displayed within one window.
maxNextCharInd - Variable in class org.biolegato.database.SimpleCharStream
 
mouseClicked(MouseEvent) - Method in class org.biolegato.database.schemaeditor.FieldGenerator
 
mouseEntered(MouseEvent) - Method in class org.biolegato.database.schemaeditor.FieldGenerator
 
mouseExited(MouseEvent) - Method in class org.biolegato.database.schemaeditor.FieldGenerator
 
mousePressed(MouseEvent) - Method in class org.biolegato.database.schemaeditor.FieldGenerator
 
mouseReleased(MouseEvent) - Method in class org.biolegato.database.schemaeditor.FieldGenerator
 

N

name - Variable in class org.biolegato.database.fields.ReferenceField
The name of the table for which the references are stored.
nameCount - Static variable in class org.biolegato.database.schemaeditor.FieldGenerator
 
newToken(int, String) - Static method in class org.biolegato.database.Token
Returns a new Token object, by default.
newToken(int) - Static method in class org.biolegato.database.Token
 
next - Variable in class org.biolegato.database.Token
A reference to the next regular (non-special) token from the input stream.
nl() - Method in class org.biolegato.database.DBPCD
Matches new line characters including preceding whitespace
NL - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
Number() - Method in class org.biolegato.database.DBPCD
Parses a non-decimal number from a PCD file into a Java integer
NUMBER - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
NumberField - Class in org.biolegato.database.fields
 
NumberField(String) - Constructor for class org.biolegato.database.fields.NumberField
Creates a new instance of a number field.
NumberField(String, String, int, int) - Constructor for class org.biolegato.database.fields.NumberField
Creates a new instance of a text widget.

O

org.biolegato.database - package org.biolegato.database
 
org.biolegato.database.fields - package org.biolegato.database.fields
 
org.biolegato.database.schemaeditor - package org.biolegato.database.schemaeditor
 

P

parse(Map<String, Widget>) - Method in class org.biolegato.database.ValuesFile
 
parseColumn() - Method in class org.biolegato.database.ValuesFile
 
ParseException - Exception in org.biolegato.database
This exception is thrown when parse errors are encountered.
ParseException(Token, int[][], String[]) - Constructor for exception org.biolegato.database.ParseException
This constructor is used by the method "generateParseException" in the generated parser.
ParseException() - Constructor for exception org.biolegato.database.ParseException
The following constructors are for use by you for whatever purpose you can think of.
ParseException(String) - Constructor for exception org.biolegato.database.ParseException
Constructor with message.
parseField(String, KeyableField, File, boolean) - Method in class org.biolegato.database.DBPCD
Parses a single PCD database field.
parseKeyableField() - Method in class org.biolegato.database.DBPCD
Parses a single Keyable (i.e.
parseRow(Map<String, Widget>) - Method in class org.biolegato.database.ValuesFile
 
parseSchema(File, boolean) - Method in class org.biolegato.database.DBPCD
Parses a PCD database schema.
pcdOut(int, Appendable) - Method in class org.biolegato.database.DBSchema
Writes the DBPCD representation of the database schema to a writer object
pcdOut(int, Appendable) - Method in class org.biolegato.database.JDBCDBConnection
Writes the BioPCD representation of the PCD SQL command
pcdOut(int, Appendable) - Method in class org.biolegato.database.PCDSQL
Writes the BioPCD representation of the PCD SQL command
PCDSQL - Class in org.biolegato.database
 
PCDSQL(JDBCDBConnection, String, boolean) - Constructor for class org.biolegato.database.PCDSQL
Creates a new PCD SQL query object.
prevCharIsCR - Variable in class org.biolegato.database.SimpleCharStream
 
prevCharIsLF - Variable in class org.biolegato.database.SimpleCharStream
 

Q

query() - Method in class org.biolegato.database.PCDSQL
 
quote(String) - Static method in class org.biolegato.database.fields.DBCommandThread
Quotes a string, so it will not be modified by replaceArguments

R

RDELIM - Static variable in interface org.biolegato.database.ValuesFileConstants
RegularExpression Id.
readChar() - Method in class org.biolegato.database.SimpleCharStream
Read a character.
readFile(String, Reader, boolean) - Method in class org.biolegato.database.DBCanvas
Reads data into the canvas
readSchema(String) - Method in class org.biolegato.database.DBCanvas
 
readValues(Reader, Map<String, Widget>) - Static method in class org.biolegato.database.ValuesFile
 
reference - Variable in class org.biolegato.database.fields.ReferenceField
The reference schema object - the schema which is being referenced This is really an arbitrary designation since both schemas 'root' and 'reference' can be read by the same table (i.e.
ReferenceField - Class in org.biolegato.database.fields
 
ReferenceField(String, DBSchema, DBSchema) - Constructor for class org.biolegato.database.fields.ReferenceField
Creates a new instance of a reference field.
ReferenceField(String, String, DBSchema, DBSchema) - Constructor for class org.biolegato.database.fields.ReferenceField
Creates a new instance of a reference field.
ReferenceField(String, String, String, KeyableField, String, KeyableField, DBField) - Constructor for class org.biolegato.database.fields.ReferenceField
Creates a new instance of a reference field.
refreshMainPanel(Component) - Method in class org.biolegato.database.DBCanvas
 
ReInit(InputStream) - Method in class org.biolegato.database.DBPCD
Reinitialise.
ReInit(InputStream, String) - Method in class org.biolegato.database.DBPCD
Reinitialise.
ReInit(Reader) - Method in class org.biolegato.database.DBPCD
Reinitialise.
ReInit(DBPCDTokenManager) - Method in class org.biolegato.database.DBPCD
Reinitialise.
ReInit(SimpleCharStream) - Method in class org.biolegato.database.DBPCDTokenManager
Reinitialise parser.
ReInit(SimpleCharStream, int) - Method in class org.biolegato.database.DBPCDTokenManager
Reinitialise parser.
ReInit(Reader, int, int, int) - Method in class org.biolegato.database.SimpleCharStream
Reinitialise.
ReInit(Reader, int, int) - Method in class org.biolegato.database.SimpleCharStream
Reinitialise.
ReInit(Reader) - Method in class org.biolegato.database.SimpleCharStream
Reinitialise.
ReInit(InputStream, String, int, int, int) - Method in class org.biolegato.database.SimpleCharStream
Reinitialise.
ReInit(InputStream, int, int, int) - Method in class org.biolegato.database.SimpleCharStream
Reinitialise.
ReInit(InputStream, String) - Method in class org.biolegato.database.SimpleCharStream
Reinitialise.
ReInit(InputStream) - Method in class org.biolegato.database.SimpleCharStream
Reinitialise.
ReInit(InputStream, String, int, int) - Method in class org.biolegato.database.SimpleCharStream
Reinitialise.
ReInit(InputStream, int, int) - Method in class org.biolegato.database.SimpleCharStream
Reinitialise.
ReInit(InputStream) - Method in class org.biolegato.database.ValuesFile
Reinitialise.
ReInit(InputStream, String) - Method in class org.biolegato.database.ValuesFile
Reinitialise.
ReInit(Reader) - Method in class org.biolegato.database.ValuesFile
Reinitialise.
ReInit(ValuesFileTokenManager) - Method in class org.biolegato.database.ValuesFile
Reinitialise.
ReInit(SimpleCharStream) - Method in class org.biolegato.database.ValuesFileTokenManager
Reinitialise parser.
ReInit(SimpleCharStream, int) - Method in class org.biolegato.database.ValuesFileTokenManager
Reinitialise parser.
removeListDataListener(ListDataListener) - Method in class org.biolegato.database.EntriesListModel
Removes a listener from the list model's collection of listener objects
removeListDataListener(ListDataListener) - Method in class org.biolegato.database.SchemaListModel
 
root - Variable in class org.biolegato.database.fields.ReferenceField
The root schema object - the schema which is being referenced from This is really an arbitrary designation since both schemas 'root' and 'reference' can be read by the same table (i.e.
run() - Method in class org.biolegato.database.fields.DBCommandThread
Used for running the command.

S

save(Connection, String) - Method in class org.biolegato.database.DBSchema
 
save(String) - Method in class org.biolegato.database.fields.BooleanField
Returns the SQL command(s) or fragment(s) necessary to save the current database field.
save(String) - Method in class org.biolegato.database.fields.DBCommand
Returns the SQL command(s) or fragment(s) necessary to save the current database field.
save(String) - Method in interface org.biolegato.database.fields.DBField
Returns the SQL command(s) or fragment(s) necessary to save the current database field.
save(String) - Method in class org.biolegato.database.fields.DBTextField
Returns the SQL command(s) or fragment(s) necessary to save the current database field.
save(String) - Method in class org.biolegato.database.fields.DecimalField
Returns the SQL command(s) or fragment(s) necessary to save the current database field.
save(String) - Method in class org.biolegato.database.fields.NumberField
Returns the SQL command(s) or fragment(s) necessary to save the current database field.
save(String) - Method in class org.biolegato.database.fields.ReferenceField
Returns the SQL command(s) or fragment(s) necessary to save the current database field.
SCHAR - Static variable in interface org.biolegato.database.ValuesFileConstants
RegularExpression Id.
schema - Variable in class org.biolegato.database.EntriesListModel
The database table/schema to display the entries for
schemaEditor(JFrame, Connection, String) - Method in class org.biolegato.database.DBSchema
 
schemaEditor(Connection, JFrame) - Method in class org.biolegato.database.fields.BooleanField
Displays the current field in an editor panel.
schemaEditor(Connection, JFrame) - Method in class org.biolegato.database.fields.DBCommand
Displays the current field in an editor panel.
schemaEditor(Connection, JFrame) - Method in interface org.biolegato.database.fields.DBField
Displays the current field in an editor panel.
schemaEditor(Connection, JFrame) - Method in class org.biolegato.database.fields.DBTextField
Displays the current field in an editor panel.
schemaEditor(Connection, JFrame) - Method in class org.biolegato.database.fields.DecimalField
Displays the current field in an editor panel.
schemaEditor(Connection, JFrame) - Method in class org.biolegato.database.fields.NumberField
Displays the current field in an editor panel.
schemaEditor(Connection, JFrame) - Method in class org.biolegato.database.fields.ReferenceField
Displays the current field in an editor panel.
SchemaFieldsPanel - Class in org.biolegato.database.schemaeditor
Field panel (for adding database fields to a BioLegato DB)
SchemaFieldsPanel(DBCanvas) - Constructor for class org.biolegato.database.schemaeditor.SchemaFieldsPanel
 
SchemaListModel - Class in org.biolegato.database
 
SchemaListModel(String) - Constructor for class org.biolegato.database.SchemaListModel
 
setDebugStream(PrintStream) - Method in class org.biolegato.database.DBPCDTokenManager
Set debug output.
setDebugStream(PrintStream) - Method in class org.biolegato.database.ValuesFileTokenManager
Set debug output.
setTabSize(int) - Method in class org.biolegato.database.SimpleCharStream
 
setValue(String) - Method in class org.biolegato.database.fields.ReferenceField
Changes the current default value for the widget.
shellCommand(String, String) - Static method in class org.biolegato.database.fields.DBCommandThread
Runs simple shell commands.
SIGN - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
SimpleCharStream - Class in org.biolegato.database
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.database.SimpleCharStream
Constructor.
SimpleCharStream(Reader, int, int) - Constructor for class org.biolegato.database.SimpleCharStream
Constructor.
SimpleCharStream(Reader) - Constructor for class org.biolegato.database.SimpleCharStream
Constructor.
SimpleCharStream(InputStream, String, int, int, int) - Constructor for class org.biolegato.database.SimpleCharStream
Constructor.
SimpleCharStream(InputStream, int, int, int) - Constructor for class org.biolegato.database.SimpleCharStream
Constructor.
SimpleCharStream(InputStream, String, int, int) - Constructor for class org.biolegato.database.SimpleCharStream
Constructor.
SimpleCharStream(InputStream, int, int) - Constructor for class org.biolegato.database.SimpleCharStream
Constructor.
SimpleCharStream(InputStream, String) - Constructor for class org.biolegato.database.SimpleCharStream
Constructor.
SimpleCharStream(InputStream) - Constructor for class org.biolegato.database.SimpleCharStream
Constructor.
SP - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
specialToken - Variable in class org.biolegato.database.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.database.ValuesFileConstants
RegularExpression Id.
SQSTART - Static variable in interface org.biolegato.database.ValuesFileConstants
RegularExpression Id.
SQUOTE - Static variable in interface org.biolegato.database.ValuesFileConstants
Lexical state.
staticFlag - Static variable in class org.biolegato.database.SimpleCharStream
Whether parser is static.
SwitchTo(int) - Method in class org.biolegato.database.DBPCDTokenManager
Switch to specified lex state.
SwitchTo(int) - Method in class org.biolegato.database.ValuesFileTokenManager
Switch to specified lex state.

T

T_BOOL - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
T_BTN - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
T_DEC - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
T_EXEC - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
T_FALSE - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
T_INT - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
T_KEY - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
T_LABEL - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
T_MAX - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
T_MIN - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
T_NAME - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
T_NAMECOL - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
T_REF - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
T_SCHEMA - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
T_TABLE - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
T_TEXT - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
T_TRUE - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
TAB - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
tabSize - Variable in class org.biolegato.database.SimpleCharStream
 
testIndent(int) - Method in class org.biolegato.database.DBPCD
Tests indentation (NOTE: this calls the token manager)
Text() - Method in class org.biolegato.database.DBPCD
Parses a text token from a PCD file into a Java String
TEXT - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
token - Variable in class org.biolegato.database.DBPCD
Current token.
Token - Class in org.biolegato.database
Describes the input token stream.
Token() - Constructor for class org.biolegato.database.Token
No-argument constructor
Token(int) - Constructor for class org.biolegato.database.Token
Constructs a new token for the specified Image.
Token(int, String) - Constructor for class org.biolegato.database.Token
Constructs a new token for the specified Image and Kind.
token - Variable in class org.biolegato.database.ValuesFile
Current token.
token_source - Variable in class org.biolegato.database.DBPCD
Generated Token Manager.
token_source - Variable in class org.biolegato.database.ValuesFile
Generated Token Manager.
tokenImage - Static variable in interface org.biolegato.database.DBPCDConstants
Literal token values.
tokenImage - Variable in exception org.biolegato.database.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.database.ValuesFileConstants
Literal token values.
TokenMgrError - Error in org.biolegato.database
Token Manager Error.
TokenMgrError() - Constructor for error org.biolegato.database.TokenMgrError
No arg constructor.
TokenMgrError(String, int) - Constructor for error org.biolegato.database.TokenMgrError
Constructor with message and reason.
TokenMgrError(boolean, int, int, int, String, char, int) - Constructor for error org.biolegato.database.TokenMgrError
Full Constructor.
toString() - Method in class org.biolegato.database.EntriesListModel.Entry
Returns a string representation of the database entry object.
toString() - Method in class org.biolegato.database.Token
Returns the image.

U

unquote(String) - Static method in class org.biolegato.database.fields.DBCommandThread
Removes quotations added to a string by the 'quote' method
UpdateLineColumn(char) - Method in class org.biolegato.database.SimpleCharStream
 

V

ValuesFile - Class in org.biolegato.database
File format parser for a PCD values file
ValuesFile(InputStream) - Constructor for class org.biolegato.database.ValuesFile
Constructor with InputStream.
ValuesFile(InputStream, String) - Constructor for class org.biolegato.database.ValuesFile
Constructor with InputStream and supplied encoding
ValuesFile(Reader) - Constructor for class org.biolegato.database.ValuesFile
Constructor.
ValuesFile(ValuesFileTokenManager) - Constructor for class org.biolegato.database.ValuesFile
Constructor with generated Token Manager.
ValuesFileConstants - Interface in org.biolegato.database
Token literal values and constants.
ValuesFileTokenManager - Class in org.biolegato.database
Token Manager.
ValuesFileTokenManager(SimpleCharStream) - Constructor for class org.biolegato.database.ValuesFileTokenManager
Constructor.
ValuesFileTokenManager(SimpleCharStream, int) - Constructor for class org.biolegato.database.ValuesFileTokenManager
Constructor.
view(Connection, Container, String) - Method in class org.biolegato.database.DBSchema
 
view(Connection, Container, Map<String, String>) - Method in class org.biolegato.database.fields.BooleanField
Displays the content of a field within a dataset entry.
view(Connection, Container, Map<String, String>) - Method in class org.biolegato.database.fields.DBCommand
 
view(Connection, Container, Map<String, String>, boolean) - Method in class org.biolegato.database.fields.DBCommand
 
view(Connection, Container, Map<String, String>) - Method in interface org.biolegato.database.fields.DBField
Displays the content of a field within a dataset entry.
view(Connection, Container, Map<String, String>) - Method in class org.biolegato.database.fields.DBTextField
Displays the content of a field within a dataset entry.
view(Connection, Container, Map<String, String>) - Method in class org.biolegato.database.fields.DecimalField
Displays the content of a field within a dataset entry.
view(Connection, Container, Map<String, String>) - Method in class org.biolegato.database.fields.NumberField
Displays the content of a field within a dataset entry.
view(Connection, Container, Map<String, String>) - Method in class org.biolegato.database.fields.ReferenceField
Displays the content of a field within a dataset entry.

W

wclass - Variable in class org.biolegato.database.schemaeditor.FieldGenerator
 
widgets - Variable in class org.biolegato.database.DBCanvas
List of widgets for the window.
writeFile(String, Appendable, boolean) - Method in class org.biolegato.database.DBCanvas
Writes data out from the canvas
WSP - Static variable in interface org.biolegato.database.DBPCDConstants
RegularExpression Id.
WSP - Static variable in interface org.biolegato.database.ValuesFileConstants
RegularExpression Id.
A B C D E F G I J K L M N O P Q R S T U V W 
DB canvas v1.0.0 API

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