SequenceParserInterface
public class GenbankSequenceParser<S extends AbstractSequence<C>,C extends Compound> extends java.lang.Object implements SequenceParserInterface
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 |
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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 |
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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 |
|
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 |
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protected static java.util.regex.Pattern |
readableFiles |
|
protected static java.lang.String |
REFERENCE_TAG |
|
protected static java.util.regex.Pattern |
refp |
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protected static java.util.regex.Pattern |
refRange |
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protected static java.lang.String |
REMARK_TAG |
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protected static java.util.regex.Pattern |
sectp |
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protected static java.lang.String |
SOURCE_TAG |
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protected static java.lang.String |
START_SEQUENCE_TAG |
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protected static java.lang.String |
TITLE_TAG |
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protected static java.lang.String |
VERSION_TAG |
|
protected static java.util.regex.Pattern |
vp |
Constructor | Description |
---|---|
GenbankSequenceParser() |
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) |
public java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<DBReferenceInfo>> mapDB
public static final java.lang.String GENBANK_FORMAT
protected static final java.lang.String LOCUS_TAG
protected static final java.lang.String DEFINITION_TAG
protected static final java.lang.String ACCESSION_TAG
protected static final java.lang.String VERSION_TAG
protected static final java.lang.String KEYWORDS_TAG
protected static final java.lang.String SOURCE_TAG
protected static final java.lang.String ORGANISM_TAG
protected static final java.lang.String REFERENCE_TAG
protected static final java.lang.String AUTHORS_TAG
protected static final java.lang.String CONSORTIUM_TAG
protected static final java.lang.String TITLE_TAG
protected static final java.lang.String JOURNAL_TAG
protected static final java.lang.String PUBMED_TAG
protected static final java.lang.String MEDLINE_TAG
protected static final java.lang.String REMARK_TAG
protected static final java.lang.String COMMENT_TAG
protected static final java.lang.String FEATURE_TAG
protected static final java.lang.String BASE_COUNT_TAG_FULL
protected static final java.lang.String BASE_COUNT_TAG
protected static final java.lang.String START_SEQUENCE_TAG
protected static final java.lang.String END_SEQUENCE_TAG
protected static final java.util.regex.Pattern lp
protected static final java.util.regex.Pattern vp
protected static final java.util.regex.Pattern refRange
protected static final java.util.regex.Pattern refp
protected static final java.util.regex.Pattern dbxp
protected static final InsdcParser locationParser
protected static final java.util.regex.Pattern sectp
protected static final java.util.regex.Pattern readableFiles
protected static final java.util.regex.Pattern headerLine
public java.lang.String getSequence(java.io.BufferedReader bufferedReader, int sequenceLength) throws java.io.IOException
getSequence
in interface SequenceParserInterface
java.io.IOException
public java.lang.String getHeader()
public GenericGenbankHeaderParser<S,C> getSequenceHeaderParser()
public java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<DBReferenceInfo>> getDatabaseReferences()
public java.util.ArrayList<java.lang.String> getKeyWords()
public java.util.ArrayList<AbstractFeature> getFeatures(java.lang.String keyword)
public java.util.HashMap<java.lang.String,java.util.ArrayList<AbstractFeature>> getFeatures()
public void parseFeatures(AbstractSequence<C> sequence)
public CompoundSet<?> getCompoundType()