org.jbei.ice.lib.parsers.genbank

Class GenBankParser

java.lang.Object

org.jbei.ice.lib.entry.HasEntry

org.jbei.ice.lib.parsers.AbstractParser

org.jbei.ice.lib.parsers.genbank.GenBankParser

public class GenBankParser
extends AbstractParser

Genbank parser and generator. The Genbank file format is defined in gbrel.txt located at ftp://ftp.ncbi.nlm.nih.gov/genbank/gbrel.txt

This parser also handles some incorrectly formatted and obsolete genbank files.

Author:

Timothy Ham

Field Summary

Fields

Modifier and Type	Field and Description
static String	ACCESSION_TAG
static String	BASE_COUNT_TAG
static String	BASE_TAG
static String	COMMENT_TAG
static String	CONTIG_TAG
static String	DBLINK_TAG
static String	DEFINITION_TAG
static String	END_TAG
static String	FEATURES_TAG
static String	KEYWORDS_TAG
static String	LOCUS_TAG
static String	NID_TAG
static String	ORGANISM_TAG
static String	ORIGIN_TAG
static String	PROJECT_TAG
static String	REFERENCE_TAG
static String	SEGMENT_TAG
static String	SOURCE_TAG
static String	VERSION_TAG

Fields inherited from class org.jbei.ice.lib.parsers.AbstractParser

entry, fileName, partData, userId

Fields inherited from class org.jbei.ice.lib.entry.HasEntry

accountDAO, entryDAO

Constructor Summary

Constructors

Constructor and Description
GenBankParser()

Method Summary

Modifier and Type	Method and Description
List<String>	getErrors()
DNASequence	parse(String textSequence)
protected FeaturesTag	parseFeaturesTag(Tag tag)

Methods inherited from class org.jbei.ice.lib.parsers.AbstractParser

cleanSequence, save

Methods inherited from class org.jbei.ice.lib.entry.HasEntry

getEntry

Methods inherited from class java.lang.Object

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

Field Detail

LOCUS_TAG

public static final String LOCUS_TAG

See Also:

Constant Field Values

DEFINITION_TAG

public static final String DEFINITION_TAG

See Also:

Constant Field Values

ACCESSION_TAG

public static final String ACCESSION_TAG

See Also:

Constant Field Values

VERSION_TAG

public static final String VERSION_TAG

See Also:

Constant Field Values

NID_TAG

public static final String NID_TAG

See Also:

Constant Field Values

PROJECT_TAG

public static final String PROJECT_TAG

See Also:

Constant Field Values

DBLINK_TAG

public static final String DBLINK_TAG

See Also:

Constant Field Values

KEYWORDS_TAG

public static final String KEYWORDS_TAG

See Also:

Constant Field Values

SEGMENT_TAG

public static final String SEGMENT_TAG

See Also:

Constant Field Values

SOURCE_TAG

public static final String SOURCE_TAG

See Also:

Constant Field Values

ORGANISM_TAG

public static final String ORGANISM_TAG

See Also:

Constant Field Values

REFERENCE_TAG

public static final String REFERENCE_TAG

See Also:

Constant Field Values

COMMENT_TAG

public static final String COMMENT_TAG

See Also:

Constant Field Values

FEATURES_TAG

public static final String FEATURES_TAG

See Also:

Constant Field Values

BASE_COUNT_TAG

public static final String BASE_COUNT_TAG

See Also:

Constant Field Values

CONTIG_TAG

public static final String CONTIG_TAG

See Also:

Constant Field Values

ORIGIN_TAG

public static final String ORIGIN_TAG

See Also:

Constant Field Values

END_TAG

public static final String END_TAG

See Also:

Constant Field Values

BASE_TAG

public static final String BASE_TAG

See Also:

Constant Field Values

Constructor Detail

GenBankParser

public GenBankParser()

Method Detail

getErrors

public List<String> getErrors()

parse

public DNASequence parse(String textSequence)
                  throws InvalidFormatParserException

Overrides:

parse in class AbstractParser

Throws:

InvalidFormatParserException

parseFeaturesTag

protected FeaturesTag parseFeaturesTag(Tag tag)
                                throws InvalidFormatParserException

Throws:

InvalidFormatParserException