public class InsdcParser
extends java.lang.Object
Constructor and Description |
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InsdcParser() |
InsdcParser(DataSource dataSource) |
Modifier and Type | Method and Description |
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protected Point |
generatePoint(java.lang.String locationString,
java.lang.String uncertainString) |
protected AccessionID |
getAccession(java.lang.String accession) |
DataSource |
getDataSource() |
Location |
parse(java.io.Reader reader)
Reader based version of the parse methods.
|
protected java.util.List<Location> |
parse(java.io.Reader reader,
Strand strand) |
Location |
parse(java.lang.String locationString)
Main method for parsing a location from a String instance
|
protected Location |
parseLocation(java.lang.String location,
Strand strand) |
protected Location |
parseRange(java.util.regex.Matcher matcher,
Strand strand) |
protected Location |
parseSingle(java.util.regex.Matcher matcher,
Strand strand) |
public InsdcParser()
public InsdcParser(DataSource dataSource)
public DataSource getDataSource()
public Location parse(java.lang.String locationString) throws ParserException
locationString
- Represents a logical locationParserException
- thrown in the event of any error during parsingpublic Location parse(java.io.Reader reader) throws java.io.IOException, ParserException
reader
- The source of the data; assumes that end of the reader
stream is the end of the location string to parsejava.io.IOException
- Thrown with any reader errorParserException
- Thrown with any error with parsing locationsprotected java.util.List<Location> parse(java.io.Reader reader, Strand strand) throws java.io.IOException, ParserException
java.io.IOException
ParserException
protected Point generatePoint(java.lang.String locationString, java.lang.String uncertainString)
protected AccessionID getAccession(java.lang.String accession)