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 Object implements SequenceParserInterface

Field Summary

Fields

Modifier and Type

Field

Description

protected static final String

ACCESSION_TAG

protected static final String

AUTHORS_TAG

protected static final String

BASE_COUNT_TAG

protected static final String

BASE_COUNT_TAG_FULL

protected static final String

COMMENT_TAG

protected static final String

CONSORTIUM_TAG

protected static final Pattern

dbxp

protected static final String

DEFINITION_TAG

protected static final String

END_SEQUENCE_TAG

protected static final String

FEATURE_TAG

static final String

GENBANK_FORMAT

The name of this format

protected static final Pattern

headerLine

protected static final String

JOURNAL_TAG

protected static final String

KEYWORDS_TAG

protected static final InsdcParser

locationParser

protected static final String

LOCUS_TAG

protected static final Pattern

lp

LinkedHashMap<String,ArrayList<DBReferenceInfo>>

mapDB

protected static final String

MEDLINE_TAG

protected static final String

ORGANISM_TAG

protected static final String

PUBMED_TAG

protected static final Pattern

readableFiles

protected static final String

REFERENCE_TAG

protected static final Pattern

refp

protected static final Pattern

refRange

protected static final String

REMARK_TAG

protected static final Pattern

sectp

protected static final String

SOURCE_TAG

protected static final String

START_SEQUENCE_TAG

protected static final String

TITLE_TAG

protected static final String

VERSION_TAG

protected static final Pattern

vp
Constructor Summary

Constructors

Constructor

Description

GenbankSequenceParser()
Method Summary

Modifier and Type

Method

Description

CompoundSet<?>

getCompoundType()

LinkedHashMap<String,ArrayList<DBReferenceInfo>>

getDatabaseReferences()

HashMap<String,ArrayList<AbstractFeature>>

getFeatures()

ArrayList<AbstractFeature>

getFeatures(String keyword)

String

getHeader()

ArrayList<String>

getKeyWords()

String

getSequence(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 Details
- mapDB
  
  public LinkedHashMap<String,ArrayList<DBReferenceInfo>> mapDB
- GENBANK_FORMAT
  
  public static final String GENBANK_FORMAT
  
  The name of this format
  See Also:
  
  Constant Field Values
- LOCUS_TAG
  
  protected static final String LOCUS_TAG
  See Also:
  
  Constant Field Values
- DEFINITION_TAG
  
  protected static final String DEFINITION_TAG
  See Also:
  
  Constant Field Values
- ACCESSION_TAG
  
  protected static final String ACCESSION_TAG
  See Also:
  
  Constant Field Values
- VERSION_TAG
  
  protected static final String VERSION_TAG
  See Also:
  
  Constant Field Values
- KEYWORDS_TAG
  
  protected static final String KEYWORDS_TAG
  See Also:
  
  Constant Field Values
- SOURCE_TAG
  
  protected static final String SOURCE_TAG
  See Also:
  
  Constant Field Values
- ORGANISM_TAG
  
  protected static final String ORGANISM_TAG
  See Also:
  
  Constant Field Values
- REFERENCE_TAG
  
  protected static final String REFERENCE_TAG
  See Also:
  
  Constant Field Values
- AUTHORS_TAG
  
  protected static final String AUTHORS_TAG
  See Also:
  
  Constant Field Values
- CONSORTIUM_TAG
  
  protected static final String CONSORTIUM_TAG
  See Also:
  
  Constant Field Values
- TITLE_TAG
  
  protected static final String TITLE_TAG
  See Also:
  
  Constant Field Values
- JOURNAL_TAG
  
  protected static final String JOURNAL_TAG
  See Also:
  
  Constant Field Values
- PUBMED_TAG
  
  protected static final String PUBMED_TAG
  See Also:
  
  Constant Field Values
- MEDLINE_TAG
  
  protected static final String MEDLINE_TAG
  See Also:
  
  Constant Field Values
- REMARK_TAG
  
  protected static final String REMARK_TAG
  See Also:
  
  Constant Field Values
- COMMENT_TAG
  
  protected static final String COMMENT_TAG
  See Also:
  
  Constant Field Values
- FEATURE_TAG
  
  protected static final String FEATURE_TAG
  See Also:
  
  Constant Field Values
- BASE_COUNT_TAG_FULL
  
  protected static final String BASE_COUNT_TAG_FULL
  See Also:
  
  Constant Field Values
- BASE_COUNT_TAG
  
  protected static final String BASE_COUNT_TAG
  See Also:
  
  Constant Field Values
- START_SEQUENCE_TAG
  
  protected static final String START_SEQUENCE_TAG
  See Also:
  
  Constant Field Values
- END_SEQUENCE_TAG
  
  protected static final String END_SEQUENCE_TAG
  See Also:
  
  Constant Field Values
- lp
  
  protected static final Pattern lp
- vp
  
  protected static final Pattern vp
- refRange
  
  protected static final Pattern refRange
- refp
  
  protected static final Pattern refp
- dbxp
  
  protected static final Pattern dbxp
- locationParser
  
  protected static final InsdcParser locationParser
- sectp
  
  protected static final Pattern sectp
- readableFiles
  
  protected static final Pattern readableFiles
- headerLine
  
  protected static final Pattern headerLine
Constructor Details
- GenbankSequenceParser
  
  public GenbankSequenceParser()
Method Details
- getSequence
  
  public String getSequence(BufferedReader bufferedReader, int sequenceLength) throws IOException
  
  Specified by:
  
  getSequence in interface SequenceParserInterface
  
  Returns:
  
  Throws:
  
  IOException
- getHeader
  
  public String getHeader()
- getSequenceHeaderParser
  
  public GenericGenbankHeaderParser<S,C> getSequenceHeaderParser()
- getDatabaseReferences
  
  public LinkedHashMap<String,ArrayList<DBReferenceInfo>> getDatabaseReferences()
- getKeyWords
  
  public ArrayList<String> getKeyWords()
- getFeatures
  
  public ArrayList<AbstractFeature> getFeatures(String keyword)
- getFeatures
  
  public HashMap<String,ArrayList<AbstractFeature>> getFeatures()
- parseFeatures
  
  public void parseFeatures(AbstractSequence<C> sequence)
- getCompoundType
  
  public CompoundSet<?> getCompoundType()

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

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

mapDB

GENBANK_FORMAT

LOCUS_TAG

DEFINITION_TAG

ACCESSION_TAG

VERSION_TAG

KEYWORDS_TAG

SOURCE_TAG

ORGANISM_TAG

REFERENCE_TAG

AUTHORS_TAG

CONSORTIUM_TAG

TITLE_TAG

JOURNAL_TAG

PUBMED_TAG

MEDLINE_TAG

REMARK_TAG

COMMENT_TAG

FEATURE_TAG

BASE_COUNT_TAG_FULL

BASE_COUNT_TAG

START_SEQUENCE_TAG

END_SEQUENCE_TAG

lp

vp

refRange

refp

dbxp

locationParser

sectp

readableFiles

headerLine

Constructor Details

GenbankSequenceParser

Method Details

getSequence

getHeader

getSequenceHeaderParser

getDatabaseReferences

getKeyWords

getFeatures

getFeatures

parseFeatures

getCompoundType