C D E F G H I S V Y

C

commentline(String) - Method in interface de.mpi_bremen.mgg.FastaValidator.FastaValidatorCallback
This method is invoked when a commentline occured.

D

de.mpi_bremen.mgg.FastaValidator - package de.mpi_bremen.mgg.FastaValidator
 

E

eof() - Method in interface de.mpi_bremen.mgg.FastaValidator.FastaValidatorCallback
This method is invoked at the end of file.

F

FastaFormatException - Exception in de.mpi_bremen.mgg.FastaValidator
Specialization of FastaValidatorException, which is thrown on semantic errors
FastaFormatException(String, int) - Constructor for exception de.mpi_bremen.mgg.FastaValidator.FastaFormatException
Constructs a FastaFormatException.
FastaHandlingException - Exception in de.mpi_bremen.mgg.FastaValidator
Thrown by implementations of the FastaValidatorCallback to indicate that their handling of the parsed data failed.
FastaHandlingException() - Constructor for exception de.mpi_bremen.mgg.FastaValidator.FastaHandlingException
Creates a new instance of this exception with null as its detail message and cause.
FastaHandlingException(String) - Constructor for exception de.mpi_bremen.mgg.FastaValidator.FastaHandlingException
Creates a new instance of this exception with the given detail message but no cause.
FastaHandlingException(Throwable) - Constructor for exception de.mpi_bremen.mgg.FastaValidator.FastaHandlingException
Creates a new instance of this exception with the given cause and a detail message containing the string representation of cause or code null if cause == null.
FastaHandlingException(String, Throwable) - Constructor for exception de.mpi_bremen.mgg.FastaValidator.FastaHandlingException
Creates a new instance of this exception with the given detail message and cause.
FastaValidator - Class in de.mpi_bremen.mgg.FastaValidator
The FastaValidator itself - main class of the package.
FastaValidator(FastaValidatorCallback) - Constructor for class de.mpi_bremen.mgg.FastaValidator.FastaValidator
Constructs a FastaValidator and binds event methods.
FastaValidator.Sequencetype - Enum in de.mpi_bremen.mgg.FastaValidator
Represents parsable sequencetypes.
FastaValidatorCallback - Interface in de.mpi_bremen.mgg.FastaValidator
Interface defining necessary FastaValidator-events.
FastaValidatorException - Exception in de.mpi_bremen.mgg.FastaValidator
General exception class, which is thrown when an error occurs during the parsing/validation process
FastaValidatorException() - Constructor for exception de.mpi_bremen.mgg.FastaValidator.FastaValidatorException
Constructs an empty FastaValidatorException.
FastaValidatorException(String) - Constructor for exception de.mpi_bremen.mgg.FastaValidator.FastaValidatorException
Constructs a FastaValidatorException with errormessage.
FastaValidatorLexer - Interface in de.mpi_bremen.mgg.FastaValidator
Interface defining neccessary methods of the lexer.

G

getCharacter() - Method in exception de.mpi_bremen.mgg.FastaValidator.InvalidCharacterException
Returns the invalid character which caused the error.
getLine() - Method in exception de.mpi_bremen.mgg.FastaValidator.FastaFormatException
Returns the line number of the error.
getLine() - Method in exception de.mpi_bremen.mgg.FastaValidator.InvalidCharacterException
Returns the line number of the error.
getSequencetype() - Method in class de.mpi_bremen.mgg.FastaValidator.FastaValidator
Returns current selected sequencetype.

H

header(String) - Method in interface de.mpi_bremen.mgg.FastaValidator.FastaValidatorCallback
This method is invoked when a headerline occured.

I

InvalidCharacterException - Exception in de.mpi_bremen.mgg.FastaValidator
Specialization of FastaValidatorException, which is thrown when an invalid character occurs
InvalidCharacterException(String, String, int) - Constructor for exception de.mpi_bremen.mgg.FastaValidator.InvalidCharacterException
Constructs an InvalidCharacterException.

S

seqline(String) - Method in interface de.mpi_bremen.mgg.FastaValidator.FastaValidatorCallback
This method is invoked when a sequenceline occured.
setSequencetype(FastaValidator.Sequencetype) - Method in class de.mpi_bremen.mgg.FastaValidator.FastaValidator
Sets the sequencetype to parse.

V

validate(String) - Method in class de.mpi_bremen.mgg.FastaValidator.FastaValidator
Validates/Parses a fasta-formatted file.
validate(Reader) - Method in class de.mpi_bremen.mgg.FastaValidator.FastaValidator
Validates/Parses a fasta-formatted source.
validate(FastaValidatorLexer) - Method in class de.mpi_bremen.mgg.FastaValidator.FastaValidator
 
valueOf(String) - Static method in enum de.mpi_bremen.mgg.FastaValidator.FastaValidator.Sequencetype
Returns the enum constant of this type with the specified name.
values() - Static method in enum de.mpi_bremen.mgg.FastaValidator.FastaValidator.Sequencetype
Returns an array containing the constants of this enum type, in the order they are declared.

Y

yylex() - Method in interface de.mpi_bremen.mgg.FastaValidator.FastaValidatorLexer
This method is used to start the lexer.

C D E F G H I S V Y