public class Feature
extends org.apache.avro.specific.SpecificRecordBase
implements org.apache.avro.specific.SpecificRecord
Modifier and Type | Class and Description |
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static class |
Feature.Builder
RecordBuilder for Feature instances.
|
Modifier and Type | Field and Description |
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List<String> |
aliases
Deprecated.
|
Map<String,String> |
attributes
Deprecated.
|
Boolean |
circular
Deprecated.
|
List<Dbxref> |
dbxrefs
Deprecated.
|
String |
derivesFrom
Deprecated.
|
Long |
end
Deprecated.
|
String |
exonId
Deprecated.
|
String |
featureId
Deprecated.
|
String |
featureType
Deprecated.
|
Integer |
frame
Deprecated.
|
String |
gap
Deprecated.
|
String |
geneId
Deprecated.
|
String |
name
Deprecated.
|
List<String> |
notes
Deprecated.
|
List<OntologyTerm> |
ontologyTerms
Deprecated.
|
List<String> |
parentIds
Deprecated.
|
Integer |
phase
Deprecated.
|
String |
referenceName
Deprecated.
|
String |
sampleId
Deprecated.
|
static org.apache.avro.Schema |
SCHEMA$ |
Double |
score
Deprecated.
|
String |
source
Deprecated.
|
Long |
start
Deprecated.
|
Strand |
strand
Deprecated.
|
String |
target
Deprecated.
|
String |
transcriptId
Deprecated.
|
Constructor and Description |
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Feature()
Default constructor.
|
Feature(String featureId,
String sampleId,
String name,
String source,
String featureType,
String referenceName,
Long start,
Long end,
Strand strand,
Integer phase,
Integer frame,
Double score,
String geneId,
String transcriptId,
String exonId,
List<String> aliases,
List<String> parentIds,
String target,
String gap,
String derivesFrom,
List<String> notes,
List<Dbxref> dbxrefs,
List<OntologyTerm> ontologyTerms,
Boolean circular,
Map<String,String> attributes)
All-args constructor.
|
Modifier and Type | Method and Description |
---|---|
static org.apache.avro.message.BinaryMessageDecoder<Feature> |
createDecoder(org.apache.avro.message.SchemaStore resolver)
Create a new BinaryMessageDecoder instance for this class that uses the specified
SchemaStore . |
static Feature |
fromByteBuffer(ByteBuffer b)
Deserializes a Feature from a ByteBuffer.
|
Object |
get(int field$) |
List<String> |
getAliases()
Gets the value of the 'aliases' field.
|
Map<String,String> |
getAttributes()
Gets the value of the 'attributes' field.
|
Boolean |
getCircular()
Gets the value of the 'circular' field.
|
static org.apache.avro.Schema |
getClassSchema() |
List<Dbxref> |
getDbxrefs()
Gets the value of the 'dbxrefs' field.
|
static org.apache.avro.message.BinaryMessageDecoder<Feature> |
getDecoder()
Return the BinaryMessageDecoder instance used by this class.
|
String |
getDerivesFrom()
Gets the value of the 'derivesFrom' field.
|
Long |
getEnd()
Gets the value of the 'end' field.
|
String |
getExonId()
Gets the value of the 'exonId' field.
|
String |
getFeatureId()
Gets the value of the 'featureId' field.
|
String |
getFeatureType()
Gets the value of the 'featureType' field.
|
Integer |
getFrame()
Gets the value of the 'frame' field.
|
String |
getGap()
Gets the value of the 'gap' field.
|
String |
getGeneId()
Gets the value of the 'geneId' field.
|
String |
getName()
Gets the value of the 'name' field.
|
List<String> |
getNotes()
Gets the value of the 'notes' field.
|
List<OntologyTerm> |
getOntologyTerms()
Gets the value of the 'ontologyTerms' field.
|
List<String> |
getParentIds()
Gets the value of the 'parentIds' field.
|
Integer |
getPhase()
Gets the value of the 'phase' field.
|
String |
getReferenceName()
Gets the value of the 'referenceName' field.
|
String |
getSampleId()
Gets the value of the 'sampleId' field.
|
org.apache.avro.Schema |
getSchema() |
Double |
getScore()
Gets the value of the 'score' field.
|
String |
getSource()
Gets the value of the 'source' field.
|
Long |
getStart()
Gets the value of the 'start' field.
|
Strand |
getStrand()
Gets the value of the 'strand' field.
|
String |
getTarget()
Gets the value of the 'target' field.
|
String |
getTranscriptId()
Gets the value of the 'transcriptId' field.
|
static Feature.Builder |
newBuilder()
Creates a new Feature RecordBuilder.
|
static Feature.Builder |
newBuilder(Feature.Builder other)
Creates a new Feature RecordBuilder by copying an existing Builder.
|
static Feature.Builder |
newBuilder(Feature other)
Creates a new Feature RecordBuilder by copying an existing Feature instance.
|
void |
put(int field$,
Object value$) |
void |
readExternal(ObjectInput in) |
void |
setAliases(List<String> value)
Sets the value of the 'aliases' field.
|
void |
setAttributes(Map<String,String> value)
Sets the value of the 'attributes' field.
|
void |
setCircular(Boolean value)
Sets the value of the 'circular' field.
|
void |
setDbxrefs(List<Dbxref> value)
Sets the value of the 'dbxrefs' field.
|
void |
setDerivesFrom(String value)
Sets the value of the 'derivesFrom' field.
|
void |
setEnd(Long value)
Sets the value of the 'end' field.
|
void |
setExonId(String value)
Sets the value of the 'exonId' field.
|
void |
setFeatureId(String value)
Sets the value of the 'featureId' field.
|
void |
setFeatureType(String value)
Sets the value of the 'featureType' field.
|
void |
setFrame(Integer value)
Sets the value of the 'frame' field.
|
void |
setGap(String value)
Sets the value of the 'gap' field.
|
void |
setGeneId(String value)
Sets the value of the 'geneId' field.
|
void |
setName(String value)
Sets the value of the 'name' field.
|
void |
setNotes(List<String> value)
Sets the value of the 'notes' field.
|
void |
setOntologyTerms(List<OntologyTerm> value)
Sets the value of the 'ontologyTerms' field.
|
void |
setParentIds(List<String> value)
Sets the value of the 'parentIds' field.
|
void |
setPhase(Integer value)
Sets the value of the 'phase' field.
|
void |
setReferenceName(String value)
Sets the value of the 'referenceName' field.
|
void |
setSampleId(String value)
Sets the value of the 'sampleId' field.
|
void |
setScore(Double value)
Sets the value of the 'score' field.
|
void |
setSource(String value)
Sets the value of the 'source' field.
|
void |
setStart(Long value)
Sets the value of the 'start' field.
|
void |
setStrand(Strand value)
Sets the value of the 'strand' field.
|
void |
setTarget(String value)
Sets the value of the 'target' field.
|
void |
setTranscriptId(String value)
Sets the value of the 'transcriptId' field.
|
ByteBuffer |
toByteBuffer()
Serializes this Feature to a ByteBuffer.
|
void |
writeExternal(ObjectOutput out) |
public static final org.apache.avro.Schema SCHEMA$
@Deprecated public String featureId
@Deprecated public String sampleId
@Deprecated public String name
@Deprecated public String source
@Deprecated public String featureType
@Deprecated public String referenceName
@Deprecated public Long start
@Deprecated public Long end
@Deprecated public Strand strand
@Deprecated public Integer phase
@Deprecated public Integer frame
@Deprecated public Double score
@Deprecated public String geneId
@Deprecated public String transcriptId
@Deprecated public String exonId
@Deprecated public List<String> aliases
@Deprecated public List<String> parentIds
@Deprecated public String target
@Deprecated public String gap
@Deprecated public String derivesFrom
@Deprecated public List<String> notes
@Deprecated public List<Dbxref> dbxrefs
@Deprecated public List<OntologyTerm> ontologyTerms
@Deprecated public Boolean circular
@Deprecated public Map<String,String> attributes
public Feature()
newBuilder()
.public Feature(String featureId, String sampleId, String name, String source, String featureType, String referenceName, Long start, Long end, Strand strand, Integer phase, Integer frame, Double score, String geneId, String transcriptId, String exonId, List<String> aliases, List<String> parentIds, String target, String gap, String derivesFrom, List<String> notes, List<Dbxref> dbxrefs, List<OntologyTerm> ontologyTerms, Boolean circular, Map<String,String> attributes)
featureId
- Identifier for this feature. ID tag in GFF3.sampleId
- Sample identifier for this feature. Join with Sample.id for sample metadata.
sampleId tag in GFF3.name
- Display name for this feature, e.g. DVL1. Name tag in GFF3, optional column 4 "name"
in BED format.source
- Source of this feature, typically the algorithm or operating procedure that generated
this feature, e.g. GeneWise. Column 2 "source" in GFF3.featureType
- Feature type, constrained by some formats to a term from the Sequence Ontology (SO),
e.g. gene, mRNA, exon, or a SO accession number (SO:0000704, SO:0000234, SO:0000147,
respectively). Column 3 "type" in GFF3.referenceName
- Reference this feature is located on. Column 1 "seqid" in GFF3, column 1 "chrom"
in BED format.start
- Start position for this feature, in zero-based coordinate system with closed-open
intervals. This may require conversion from the coordinate system of the native
file format. Column 4 "start" in GFF3, column 2 "chromStart" in BED format.end
- End position for this feature, in zero-based coordinate system with closed-open
intervals. This may require conversion from the coordinate system of the native
file format. Column 5 "end" in GFF3, column 3 "chromEnd" in BED format.strand
- Strand for this feature. Column 7 "strand" in GFF3, optional column 6 "strand"
in BED format.phase
- For features of type "CDS", the phase indicates where the feature begins with reference
to the reading frame. The phase is one of the integers 0, 1, or 2, indicating the number
of bases that should be removed from the beginning of this feature to reach the first base
of the next codon. Column 8 "phase" in GFF3.frame
- For features of type "CDS", the frame indicates whether the first base of the CDS segment is
the first (frame 0), second (frame 1) or third (frame 2) in the codon of the ORF. Column 8
"frame" in GFF2/GTF format.score
- Score for this feature. Column 6 "score" in GFF3, optional column 5
"score" in BED format.geneId
- Gene identifier, e.g. ENSG00000107404. gene_id tag in GFF2/GTF.transcriptId
- Transcript identifier, e.g. ENST00000378891. transcript_id tag in GFF2/GTF.exonId
- Exon identifier, e.g. ENSE00001479184. exon_id tag in GFF2/GTF.aliases
- Secondary names or identifiers for this feature. Alias tag in GFF3.parentIds
- Parent feature identifiers. Parent tag in GFF3.target
- Target of a nucleotide-to-nucleotide or protein-to-nucleotide alignment
feature. The format of the value is "target_id start end [strand]", where
strand is optional and may be "+" or "-". Target tag in GFF3.gap
- Alignment of the feature to the target in CIGAR format. Gap tag in GFF3.derivesFrom
- Used to disambiguate the relationship between one feature and another when
the relationship is a temporal one rather than a purely structural "part of"
one. Derives_from tag in GFF3.notes
- Notes or comments for this feature. Note tag in GFF3.dbxrefs
- Database cross references for this feature. Dbxref tag in GFF3.ontologyTerms
- Ontology term cross references for this feature. Ontology_term tag in GFF3.circular
- True if this feature is circular. Is_circular tag in GFF3.attributes
- Additional feature attributes. Column 9 "attributes" in GFF3, excepting those
reserved tags parsed into other fields, such as parentIds, dbxrefs, and ontologyTerms.public static org.apache.avro.Schema getClassSchema()
public static org.apache.avro.message.BinaryMessageDecoder<Feature> getDecoder()
public static org.apache.avro.message.BinaryMessageDecoder<Feature> createDecoder(org.apache.avro.message.SchemaStore resolver)
SchemaStore
.resolver
- a SchemaStore
used to find schemas by fingerprintpublic ByteBuffer toByteBuffer() throws IOException
IOException
public static Feature fromByteBuffer(ByteBuffer b) throws IOException
IOException
public org.apache.avro.Schema getSchema()
getSchema
in interface org.apache.avro.generic.GenericContainer
getSchema
in class org.apache.avro.specific.SpecificRecordBase
public Object get(int field$)
get
in interface org.apache.avro.generic.IndexedRecord
get
in class org.apache.avro.specific.SpecificRecordBase
public void put(int field$, Object value$)
put
in interface org.apache.avro.generic.IndexedRecord
put
in class org.apache.avro.specific.SpecificRecordBase
public String getFeatureId()
public void setFeatureId(String value)
value
- the value to set.public String getSampleId()
public void setSampleId(String value)
value
- the value to set.public String getName()
public void setName(String value)
value
- the value to set.public String getSource()
public void setSource(String value)
value
- the value to set.public String getFeatureType()
public void setFeatureType(String value)
value
- the value to set.public String getReferenceName()
public void setReferenceName(String value)
value
- the value to set.public Long getStart()
public void setStart(Long value)
value
- the value to set.public Long getEnd()
public void setEnd(Long value)
value
- the value to set.public Strand getStrand()
public void setStrand(Strand value)
value
- the value to set.public Integer getPhase()
public void setPhase(Integer value)
value
- the value to set.public Integer getFrame()
public void setFrame(Integer value)
value
- the value to set.public Double getScore()
public void setScore(Double value)
value
- the value to set.public String getGeneId()
public void setGeneId(String value)
value
- the value to set.public String getTranscriptId()
public void setTranscriptId(String value)
value
- the value to set.public String getExonId()
public void setExonId(String value)
value
- the value to set.public List<String> getAliases()
public void setAliases(List<String> value)
value
- the value to set.public List<String> getParentIds()
public void setParentIds(List<String> value)
value
- the value to set.public String getTarget()
public void setTarget(String value)
value
- the value to set.public String getGap()
public void setGap(String value)
value
- the value to set.public String getDerivesFrom()
public void setDerivesFrom(String value)
value
- the value to set.public List<String> getNotes()
public void setNotes(List<String> value)
value
- the value to set.public List<Dbxref> getDbxrefs()
public void setDbxrefs(List<Dbxref> value)
value
- the value to set.public List<OntologyTerm> getOntologyTerms()
public void setOntologyTerms(List<OntologyTerm> value)
value
- the value to set.public Boolean getCircular()
public void setCircular(Boolean value)
value
- the value to set.public Map<String,String> getAttributes()
public void setAttributes(Map<String,String> value)
value
- the value to set.public static Feature.Builder newBuilder()
public static Feature.Builder newBuilder(Feature.Builder other)
other
- The existing builder to copy.public static Feature.Builder newBuilder(Feature other)
other
- The existing instance to copy.public void writeExternal(ObjectOutput out) throws IOException
writeExternal
in interface Externalizable
writeExternal
in class org.apache.avro.specific.SpecificRecordBase
IOException
public void readExternal(ObjectInput in) throws IOException
readExternal
in interface Externalizable
readExternal
in class org.apache.avro.specific.SpecificRecordBase
IOException
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