org.biojava.nbio.core.sequence.location

Class InsdcParser<S extends AbstractSequence<C>,C extends Compound>

java.lang.Object

org.biojava.nbio.core.sequence.location.InsdcParser<S,C>

public class InsdcParser<S extends AbstractSequence<C>,C extends Compound>
extends Object

Parser for working with INSDC style locations. This class supports the full range of location types generated by Genbank, INSDC and ENA.

Author:

ayates, jgrzebyta, Paolo Pavan

Field Summary

Fields

Modifier and Type	Field and Description
protected Integer	featureGlobalEnd these variables are used to compute the global start and end of complex features
protected Integer	featureGlobalStart these variables are used to compute the global start and end of complex features
protected static Pattern	genbankSplitPattern Decodes a split pattern.
protected static String	locationSplitPattern designed to recursively split a location string in tokens.
protected static Pattern	singleLocationPattern parse a location. if group(1) is null than the feature is on the positive strand, group(2) start position, group(3) end position.

Constructor Summary

Constructors

Constructor and Description
InsdcParser()
InsdcParser(DataSource dataSource)

Method Summary

Modifier and Type	Method and Description
DataSource	getDataSource()
static void	main(String[] args)
List<AbstractLocation>	parse(Reader reader) Reader based version of the parse methods.
Location	parse(String locationString) Main method for parsing a location from a String instance
void	setComplexFeaturesAppendMode(org.biojava.nbio.core.sequence.location.InsdcParser.complexFeaturesAppendEnum complexFeaturesAppendMode)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

singleLocationPattern

protected static final Pattern singleLocationPattern

parse a location. if group(1) is null than the feature is on the positive strand, group(2) start position, group(3) end position.

genbankSplitPattern

protected static final Pattern genbankSplitPattern

Decodes a split pattern. Split patterns are a composition of multiple locationsString qualified by actions: join(location,location, ... location): The indicated elements should be joined (placed end-to-end) to form one contiguous sequence. order(location,location, ... location): The elements can be found in the specified order (5' to 3' direction), nothing is implied about their reasonableness bond(location,location...location): Found in protein files. These generally are used to describe disulfide bonds. complement(location,location...location): consider locations in their complement versus takes in input a comma splitted location string. The split must be done for outer level commas group(1) is the qualifier group(2) is the location string to getFeatures. In case of complex splits it will contain the nested expression Not really sure that they are not declared obsolete but they are still in several files.

locationSplitPattern

protected static final String locationSplitPattern

designed to recursively split a location string in tokens. Valid tokens are those divided by coma that are not inside a bracket. I. e. split on the comma only if that comma has zero, or an even number of quotes ahead of it.

See Also:

Constant Field Values

featureGlobalStart

protected Integer featureGlobalStart

these variables are used to compute the global start and end of complex features

featureGlobalEnd

protected Integer featureGlobalEnd

these variables are used to compute the global start and end of complex features

Constructor Detail

InsdcParser

public InsdcParser()

InsdcParser

public InsdcParser(DataSource dataSource)

Method Detail

setComplexFeaturesAppendMode

public void setComplexFeaturesAppendMode(org.biojava.nbio.core.sequence.location.InsdcParser.complexFeaturesAppendEnum complexFeaturesAppendMode)

getDataSource

public DataSource getDataSource()

parse

public Location parse(String locationString)
               throws ParserException

Main method for parsing a location from a String instance

Parameters:

locationString - Represents a logical location

Returns:

The parsed location

Throws:

ParserException - thrown in the event of any error during parsing

parse

public List<AbstractLocation> parse(Reader reader)
                             throws IOException,
                                    ParserException

Reader based version of the parse methods.

Parameters:

reader - The source of the data; assumes that end of the reader stream is the end of the location string to parse

Returns:

The parsed location

Throws:

IOException - Thrown with any reader error

ParserException - Thrown with any error with parsing locations

main

public static void main(String[] args)