Uses of Class
org.biojava.nbio.core.exceptions.ParserException

Packages that use ParserException

Package	Description
org.biojava.nbio.alignment.io
org.biojava.nbio.core.sequence.io
org.biojava.nbio.core.sequence.io.util
org.biojava.nbio.core.sequence.location

Uses of ParserException in org.biojava.nbio.alignment.io

Methods in org.biojava.nbio.alignment.io that throw ParserException

Modifier and Type	Method and Description
StockholmStructure	StockholmFileParser.parse(InputStream inStream) parses InputStream and returns a the first contained alignment in a StockholmStructure object.
StockholmStructure	StockholmFileParser.parse(String filename) Parses a Stockholm file and returns a StockholmStructure object with its content. This function is meant to be used for single access to specific file and it closes the file after doing its assigned job.
List<StockholmStructure>	StockholmFileParser.parse(String filename, int max) Parses a Stockholm file and returns a StockholmStructure object with its content. This function doesn't close the file after doing its assigned job; to allow for further calls of StockholmFileParser.parseNext(int).

Uses of ParserException in org.biojava.nbio.core.sequence.io

Methods in org.biojava.nbio.core.sequence.io that throw ParserException

Modifier and Type	Method and Description
void	GenericGenbankHeaderParser.setAccession(String accession) The last accession passed to this routine will always be the one used.
void	GenericGenbankHeaderParser.setComment(String comment)
void	GenericGenbankHeaderParser.setDescription(String description)
void	GenericGenbankHeaderParser.setIdentifier(String identifier)
void	GenericGenbankHeaderParser.setName(String name)
void	GenericGenbankHeaderParser.setVersion(int version)

Uses of ParserException in org.biojava.nbio.core.sequence.io.util

Methods in org.biojava.nbio.core.sequence.io.util that throw ParserException

Modifier and Type	Method and Description
static List<String>	IOUtils.getList(BufferedReader br) Returns the contents of a buffered reader as a list of strings
static List<String>	IOUtils.getList(InputStream is) Delegates to IOUtils.getList(BufferedReader) by wrapping the InputStream in a valid reader.
static void	IOUtils.processReader(BufferedReader br, IOUtils.ReaderProcessor processor) Takes in a reader and a processor, reads every line from the given file and then invokes the processor.

Uses of ParserException in org.biojava.nbio.core.sequence.location

Methods in org.biojava.nbio.core.sequence.location that throw ParserException

Modifier and Type	Method and Description
List<AbstractLocation>	InsdcParser.parse(Reader reader) Reader based version of the parse methods.
Location	InsdcParser.parse(String locationString) Main method for parsing a location from a String instance