Uses of Class
org.biojava.nbio.core.exceptions.ParserException
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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 -
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Uses of ParserException in org.biojava.nbio.alignment.io
Methods in org.biojava.nbio.alignment.io that throw ParserException Modifier and Type Method Description StockholmStructure
StockholmFileParser. parse(InputStream inStream)
parsesInputStream
and returns a the first contained alignment in aStockholmStructure
object.StockholmStructure
StockholmFileParser. parse(String filename)
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.List<StockholmStructure>
StockholmFileParser. parse(String filename, int max)
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 ParserException Modifier and Type Method 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)
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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 Description static List<String>
IOUtils. getList(BufferedReader br)
Returns the contents of a buffered reader as a list of stringsstatic List<String>
IOUtils. 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 Modifier and Type Method 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
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