Uses of Class
org.biojava.nbio.core.exceptions.ParserException
Packages that use ParserException
Package
Description
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Uses of ParserException in org.biojava.nbio.alignment.io
Methods in org.biojava.nbio.alignment.io that throw ParserExceptionModifier and TypeMethodDescriptionStockholmFileParser.parse
(InputStream inStream) parsesInputStream
and returns a the first contained alignment in aStockholmStructure
object.Parses a Stockholm file and returns aStockholmStructure
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.Parses a Stockholm file and returns aStockholmStructure
object with its content.
This function doesn't close the file after doing its assigned job; to allow for further calls ofStockholmFileParser.parseNext(int)
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Uses of ParserException in org.biojava.nbio.core.sequence.io
Methods in org.biojava.nbio.core.sequence.io that throw ParserExceptionModifier and TypeMethodDescriptionvoid
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
void
GenericGenbankHeaderParser.setVersion
(int version) The last accession passed to this routine will always be the one used. -
Uses of ParserException in org.biojava.nbio.core.sequence.io.util
Methods in org.biojava.nbio.core.sequence.io.util that throw ParserExceptionModifier and TypeMethodDescriptionIOUtils.getList
(BufferedReader br) Returns the contents of a buffered reader as a list of stringsIOUtils.getList
(InputStream is) Delegates toIOUtils.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