Package org.biojava.nbio.core.sequence.io

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

java.lang.Object

org.biojava.nbio.core.sequence.io.GenbankSequenceParser<S,C>

All Implemented Interfaces:

SequenceParserInterface

public class GenbankSequenceParser<S extends AbstractSequence<C>,C extends Compound>
extends java.lang.Object
implements SequenceParserInterface

Field Summary

Fields

Modifier and Type	Field	Description
protected static java.lang.String	ACCESSION_TAG
protected static java.lang.String	AUTHORS_TAG
protected static java.lang.String	BASE_COUNT_TAG
protected static java.lang.String	BASE_COUNT_TAG_FULL
protected static java.lang.String	COMMENT_TAG
protected static java.lang.String	CONSORTIUM_TAG
protected static java.lang.String	DBLINK
protected static java.lang.String	DBSOURCE
protected static java.util.regex.Pattern	dbxp
protected static java.lang.String	DEFINITION_TAG
protected static java.lang.String	END_SEQUENCE_TAG
protected static java.lang.String	FEATURE_TAG
static java.lang.String	GENBANK_FORMAT	The name of this format
protected static java.util.regex.Pattern	headerLine
protected static java.lang.String	JOURNAL_TAG
protected static java.lang.String	KEYWORDS_TAG
protected static InsdcParser	locationParser
protected static java.lang.String	LOCUS_TAG
protected static java.util.regex.Pattern	lp
protected static java.lang.String	MEDLINE_TAG
protected static java.lang.String	ORGANISM_TAG
protected static java.lang.String	PRIMARY
protected static java.lang.String	PUBMED_TAG
protected static java.util.regex.Pattern	readableFiles
protected static java.lang.String	REFERENCE_TAG
protected static java.util.regex.Pattern	refp
protected static java.util.regex.Pattern	refRange
protected static java.lang.String	REMARK_TAG
protected static java.util.regex.Pattern	sectp	sections start at a line and continue till the first line afterwards with a non-whitespace first character we want to match any of the following as a new section within a section \s{0,8} word \s{0,7} value \s{21} /word = value \s{21} /word
protected static java.lang.String	SOURCE_TAG
protected static java.lang.String	START_SEQUENCE_TAG
protected static java.lang.String	TITLE_TAG
protected static java.lang.String	VERSION_TAG
protected static java.util.regex.Pattern	vp

Constructor Summary

Constructors

Constructor	Description
GenbankSequenceParser()

Method Summary

Modifier and Type	Method	Description
CompoundSet<?>	getCompoundType()
java.util.Map<java.lang.String,java.util.List<DBReferenceInfo>>	getDatabaseReferences()
java.util.Map<java.lang.String,java.util.List<AbstractFeature<AbstractSequence<C>,C>>>	getFeatures()
java.util.List<AbstractFeature<AbstractSequence<C>,C>>	getFeatures(java.lang.String keyword)
java.lang.String	getHeader()
java.util.List<java.lang.String>	getKeyWords()
java.lang.String	getSequence(java.io.BufferedReader bufferedReader, int sequenceLength)
GenericGenbankHeaderParser<S,C>	getSequenceHeaderParser()
void	parseFeatures(AbstractSequence<C> sequence)

Methods inherited from class java.lang.Object

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

Field Detail

GENBANK_FORMAT

public static final java.lang.String GENBANK_FORMAT

The name of this format

See Also:

Constant Field Values

LOCUS_TAG

protected static final java.lang.String LOCUS_TAG

See Also:

Constant Field Values

DEFINITION_TAG

protected static final java.lang.String DEFINITION_TAG

See Also:

Constant Field Values

ACCESSION_TAG

protected static final java.lang.String ACCESSION_TAG

See Also:

Constant Field Values

VERSION_TAG

protected static final java.lang.String VERSION_TAG

See Also:

Constant Field Values

KEYWORDS_TAG

protected static final java.lang.String KEYWORDS_TAG

See Also:

Constant Field Values

SOURCE_TAG

protected static final java.lang.String SOURCE_TAG

See Also:

Constant Field Values

ORGANISM_TAG

protected static final java.lang.String ORGANISM_TAG

See Also:

Constant Field Values

REFERENCE_TAG

protected static final java.lang.String REFERENCE_TAG

See Also:

Constant Field Values

AUTHORS_TAG

protected static final java.lang.String AUTHORS_TAG

See Also:

Constant Field Values

CONSORTIUM_TAG

protected static final java.lang.String CONSORTIUM_TAG

See Also:

Constant Field Values

TITLE_TAG

protected static final java.lang.String TITLE_TAG

See Also:

Constant Field Values

JOURNAL_TAG

protected static final java.lang.String JOURNAL_TAG

See Also:

Constant Field Values

PUBMED_TAG

protected static final java.lang.String PUBMED_TAG

See Also:

Constant Field Values

MEDLINE_TAG

protected static final java.lang.String MEDLINE_TAG

See Also:

Constant Field Values

REMARK_TAG

protected static final java.lang.String REMARK_TAG

See Also:

Constant Field Values

COMMENT_TAG

protected static final java.lang.String COMMENT_TAG

See Also:

Constant Field Values

FEATURE_TAG

protected static final java.lang.String FEATURE_TAG

See Also:

Constant Field Values

BASE_COUNT_TAG_FULL

protected static final java.lang.String BASE_COUNT_TAG_FULL

See Also:

Constant Field Values

BASE_COUNT_TAG

protected static final java.lang.String BASE_COUNT_TAG

See Also:

Constant Field Values

START_SEQUENCE_TAG

protected static final java.lang.String START_SEQUENCE_TAG

See Also:

Constant Field Values

DBSOURCE

protected static final java.lang.String DBSOURCE

See Also:

Constant Field Values

PRIMARY

protected static final java.lang.String PRIMARY

See Also:

Constant Field Values

DBLINK

protected static final java.lang.String DBLINK

See Also:

Constant Field Values

END_SEQUENCE_TAG

protected static final java.lang.String END_SEQUENCE_TAG

See Also:

Constant Field Values

lp

protected static final java.util.regex.Pattern lp

vp

protected static final java.util.regex.Pattern vp

refRange

protected static final java.util.regex.Pattern refRange

refp

protected static final java.util.regex.Pattern refp

dbxp

protected static final java.util.regex.Pattern dbxp

locationParser

protected static final InsdcParser locationParser

sectp

protected static final java.util.regex.Pattern sectp

sections start at a line and continue till the first line afterwards with a non-whitespace first character we want to match any of the following as a new section within a section \s{0,8} word \s{0,7} value \s{21} /word = value \s{21} /word

readableFiles

protected static final java.util.regex.Pattern readableFiles

headerLine

protected static final java.util.regex.Pattern headerLine

Constructor Detail

GenbankSequenceParser

public GenbankSequenceParser()

Method Detail

getSequence

public java.lang.String getSequence(java.io.BufferedReader bufferedReader,
                                    int sequenceLength)

Specified by:

getSequence in interface SequenceParserInterface

Returns:

getHeader

public java.lang.String getHeader()

getSequenceHeaderParser

public GenericGenbankHeaderParser<S,C> getSequenceHeaderParser()

getDatabaseReferences

public java.util.Map<java.lang.String,java.util.List<DBReferenceInfo>> getDatabaseReferences()

getKeyWords

public java.util.List<java.lang.String> getKeyWords()

getFeatures

public java.util.List<AbstractFeature<AbstractSequence<C>,C>> getFeatures(java.lang.String keyword)

getFeatures

public java.util.Map<java.lang.String,java.util.List<AbstractFeature<AbstractSequence<C>,C>>> getFeatures()

parseFeatures

public void parseFeatures(AbstractSequence<C> sequence)

getCompoundType

public CompoundSet<?> getCompoundType()