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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.
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