Class GenbankSequenceParser<S extends AbstractSequence<C>,C extends Compound>
- java.lang.Object
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- org.biojava.nbio.core.sequence.io.GenbankSequenceParser<S,C>
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- All Implemented Interfaces:
SequenceParserInterface
public class GenbankSequenceParser<S extends AbstractSequence<C>,C extends Compound> extends java.lang.Object implements SequenceParserInterface
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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.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 formatprotected 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
java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<DBReferenceInfo>>
mapDB
protected static java.lang.String
MEDLINE_TAG
protected static java.lang.String
ORGANISM_TAG
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
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
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Constructor Summary
Constructors Constructor Description GenbankSequenceParser()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description CompoundSet<?>
getCompoundType()
java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<DBReferenceInfo>>
getDatabaseReferences()
java.util.HashMap<java.lang.String,java.util.ArrayList<AbstractFeature>>
getFeatures()
java.util.ArrayList<AbstractFeature>
getFeatures(java.lang.String keyword)
java.lang.String
getHeader()
java.util.ArrayList<java.lang.String>
getKeyWords()
java.lang.String
getSequence(java.io.BufferedReader bufferedReader, int sequenceLength)
GenericGenbankHeaderParser<S,C>
getSequenceHeaderParser()
void
parseFeatures(AbstractSequence<C> sequence)
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Field Detail
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mapDB
public java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<DBReferenceInfo>> mapDB
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GENBANK_FORMAT
public static final java.lang.String GENBANK_FORMAT
The name of this format- See Also:
- Constant Field Values
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LOCUS_TAG
protected static final java.lang.String LOCUS_TAG
- See Also:
- Constant Field Values
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DEFINITION_TAG
protected static final java.lang.String DEFINITION_TAG
- See Also:
- Constant Field Values
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ACCESSION_TAG
protected static final java.lang.String ACCESSION_TAG
- See Also:
- Constant Field Values
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VERSION_TAG
protected static final java.lang.String VERSION_TAG
- See Also:
- Constant Field Values
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KEYWORDS_TAG
protected static final java.lang.String KEYWORDS_TAG
- See Also:
- Constant Field Values
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SOURCE_TAG
protected static final java.lang.String SOURCE_TAG
- See Also:
- Constant Field Values
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ORGANISM_TAG
protected static final java.lang.String ORGANISM_TAG
- See Also:
- Constant Field Values
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REFERENCE_TAG
protected static final java.lang.String REFERENCE_TAG
- See Also:
- Constant Field Values
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AUTHORS_TAG
protected static final java.lang.String AUTHORS_TAG
- See Also:
- Constant Field Values
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CONSORTIUM_TAG
protected static final java.lang.String CONSORTIUM_TAG
- See Also:
- Constant Field Values
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TITLE_TAG
protected static final java.lang.String TITLE_TAG
- See Also:
- Constant Field Values
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JOURNAL_TAG
protected static final java.lang.String JOURNAL_TAG
- See Also:
- Constant Field Values
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PUBMED_TAG
protected static final java.lang.String PUBMED_TAG
- See Also:
- Constant Field Values
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MEDLINE_TAG
protected static final java.lang.String MEDLINE_TAG
- See Also:
- Constant Field Values
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REMARK_TAG
protected static final java.lang.String REMARK_TAG
- See Also:
- Constant Field Values
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COMMENT_TAG
protected static final java.lang.String COMMENT_TAG
- See Also:
- Constant Field Values
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FEATURE_TAG
protected static final java.lang.String FEATURE_TAG
- See Also:
- Constant Field Values
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BASE_COUNT_TAG_FULL
protected static final java.lang.String BASE_COUNT_TAG_FULL
- See Also:
- Constant Field Values
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BASE_COUNT_TAG
protected static final java.lang.String BASE_COUNT_TAG
- See Also:
- Constant Field Values
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START_SEQUENCE_TAG
protected static final java.lang.String START_SEQUENCE_TAG
- See Also:
- Constant Field Values
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END_SEQUENCE_TAG
protected static final java.lang.String END_SEQUENCE_TAG
- See Also:
- Constant Field Values
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lp
protected static final java.util.regex.Pattern lp
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vp
protected static final java.util.regex.Pattern vp
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refRange
protected static final java.util.regex.Pattern refRange
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refp
protected static final java.util.regex.Pattern refp
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dbxp
protected static final java.util.regex.Pattern dbxp
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locationParser
protected static final InsdcParser locationParser
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sectp
protected static final java.util.regex.Pattern sectp
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readableFiles
protected static final java.util.regex.Pattern readableFiles
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headerLine
protected static final java.util.regex.Pattern headerLine
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Method Detail
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getSequence
public java.lang.String getSequence(java.io.BufferedReader bufferedReader, int sequenceLength) throws java.io.IOException
- Specified by:
getSequence
in interfaceSequenceParserInterface
- Returns:
- Throws:
java.io.IOException
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getHeader
public java.lang.String getHeader()
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getSequenceHeaderParser
public GenericGenbankHeaderParser<S,C> getSequenceHeaderParser()
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getDatabaseReferences
public java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<DBReferenceInfo>> getDatabaseReferences()
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getKeyWords
public java.util.ArrayList<java.lang.String> getKeyWords()
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getFeatures
public java.util.ArrayList<AbstractFeature> getFeatures(java.lang.String keyword)
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getFeatures
public java.util.HashMap<java.lang.String,java.util.ArrayList<AbstractFeature>> getFeatures()
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parseFeatures
public void parseFeatures(AbstractSequence<C> sequence)
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getCompoundType
public CompoundSet<?> getCompoundType()
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