public class TranscriptEffect
extends org.apache.avro.specific.SpecificRecordBase
implements org.apache.avro.specific.SpecificRecord
Modifier and Type | Class and Description |
---|---|
static class |
TranscriptEffect.Builder
RecordBuilder for TranscriptEffect instances.
|
Modifier and Type | Field and Description |
---|---|
String |
alternateAllele
Deprecated.
|
String |
biotype
Deprecated.
|
Integer |
cdnaLength
Deprecated.
|
Integer |
cdnaPosition
Deprecated.
|
Integer |
cdsLength
Deprecated.
|
Integer |
cdsPosition
Deprecated.
|
Integer |
distance
Deprecated.
|
List<String> |
effects
Deprecated.
|
String |
featureId
Deprecated.
|
String |
featureType
Deprecated.
|
String |
geneId
Deprecated.
|
String |
geneName
Deprecated.
|
String |
genomicHgvs
Deprecated.
|
List<VariantAnnotationMessage> |
messages
Deprecated.
|
String |
proteinHgvs
Deprecated.
|
Integer |
proteinLength
Deprecated.
|
Integer |
proteinPosition
Deprecated.
|
Integer |
rank
Deprecated.
|
static org.apache.avro.Schema |
SCHEMA$ |
Integer |
total
Deprecated.
|
String |
transcriptHgvs
Deprecated.
|
Constructor and Description |
---|
TranscriptEffect()
Default constructor.
|
TranscriptEffect(String alternateAllele,
List<String> effects,
String geneName,
String geneId,
String featureType,
String featureId,
String biotype,
Integer rank,
Integer total,
String genomicHgvs,
String transcriptHgvs,
String proteinHgvs,
Integer cdnaPosition,
Integer cdnaLength,
Integer cdsPosition,
Integer cdsLength,
Integer proteinPosition,
Integer proteinLength,
Integer distance,
List<VariantAnnotationMessage> messages)
All-args constructor.
|
Modifier and Type | Method and Description |
---|---|
static org.apache.avro.message.BinaryMessageDecoder<TranscriptEffect> |
createDecoder(org.apache.avro.message.SchemaStore resolver)
Create a new BinaryMessageDecoder instance for this class that uses the specified
SchemaStore . |
static TranscriptEffect |
fromByteBuffer(ByteBuffer b)
Deserializes a TranscriptEffect from a ByteBuffer.
|
Object |
get(int field$) |
String |
getAlternateAllele()
Gets the value of the 'alternateAllele' field.
|
String |
getBiotype()
Gets the value of the 'biotype' field.
|
Integer |
getCdnaLength()
Gets the value of the 'cdnaLength' field.
|
Integer |
getCdnaPosition()
Gets the value of the 'cdnaPosition' field.
|
Integer |
getCdsLength()
Gets the value of the 'cdsLength' field.
|
Integer |
getCdsPosition()
Gets the value of the 'cdsPosition' field.
|
static org.apache.avro.Schema |
getClassSchema() |
static org.apache.avro.message.BinaryMessageDecoder<TranscriptEffect> |
getDecoder()
Return the BinaryMessageDecoder instance used by this class.
|
Integer |
getDistance()
Gets the value of the 'distance' field.
|
List<String> |
getEffects()
Gets the value of the 'effects' field.
|
String |
getFeatureId()
Gets the value of the 'featureId' field.
|
String |
getFeatureType()
Gets the value of the 'featureType' field.
|
String |
getGeneId()
Gets the value of the 'geneId' field.
|
String |
getGeneName()
Gets the value of the 'geneName' field.
|
String |
getGenomicHgvs()
Gets the value of the 'genomicHgvs' field.
|
List<VariantAnnotationMessage> |
getMessages()
Gets the value of the 'messages' field.
|
String |
getProteinHgvs()
Gets the value of the 'proteinHgvs' field.
|
Integer |
getProteinLength()
Gets the value of the 'proteinLength' field.
|
Integer |
getProteinPosition()
Gets the value of the 'proteinPosition' field.
|
Integer |
getRank()
Gets the value of the 'rank' field.
|
org.apache.avro.Schema |
getSchema() |
Integer |
getTotal()
Gets the value of the 'total' field.
|
String |
getTranscriptHgvs()
Gets the value of the 'transcriptHgvs' field.
|
static TranscriptEffect.Builder |
newBuilder()
Creates a new TranscriptEffect RecordBuilder.
|
static TranscriptEffect.Builder |
newBuilder(TranscriptEffect.Builder other)
Creates a new TranscriptEffect RecordBuilder by copying an existing Builder.
|
static TranscriptEffect.Builder |
newBuilder(TranscriptEffect other)
Creates a new TranscriptEffect RecordBuilder by copying an existing TranscriptEffect instance.
|
void |
put(int field$,
Object value$) |
void |
readExternal(ObjectInput in) |
void |
setAlternateAllele(String value)
Sets the value of the 'alternateAllele' field.
|
void |
setBiotype(String value)
Sets the value of the 'biotype' field.
|
void |
setCdnaLength(Integer value)
Sets the value of the 'cdnaLength' field.
|
void |
setCdnaPosition(Integer value)
Sets the value of the 'cdnaPosition' field.
|
void |
setCdsLength(Integer value)
Sets the value of the 'cdsLength' field.
|
void |
setCdsPosition(Integer value)
Sets the value of the 'cdsPosition' field.
|
void |
setDistance(Integer value)
Sets the value of the 'distance' field.
|
void |
setEffects(List<String> value)
Sets the value of the 'effects' field.
|
void |
setFeatureId(String value)
Sets the value of the 'featureId' field.
|
void |
setFeatureType(String value)
Sets the value of the 'featureType' field.
|
void |
setGeneId(String value)
Sets the value of the 'geneId' field.
|
void |
setGeneName(String value)
Sets the value of the 'geneName' field.
|
void |
setGenomicHgvs(String value)
Sets the value of the 'genomicHgvs' field.
|
void |
setMessages(List<VariantAnnotationMessage> value)
Sets the value of the 'messages' field.
|
void |
setProteinHgvs(String value)
Sets the value of the 'proteinHgvs' field.
|
void |
setProteinLength(Integer value)
Sets the value of the 'proteinLength' field.
|
void |
setProteinPosition(Integer value)
Sets the value of the 'proteinPosition' field.
|
void |
setRank(Integer value)
Sets the value of the 'rank' field.
|
void |
setTotal(Integer value)
Sets the value of the 'total' field.
|
void |
setTranscriptHgvs(String value)
Sets the value of the 'transcriptHgvs' field.
|
ByteBuffer |
toByteBuffer()
Serializes this TranscriptEffect to a ByteBuffer.
|
void |
writeExternal(ObjectOutput out) |
public static final org.apache.avro.Schema SCHEMA$
@Deprecated public String alternateAllele
@Deprecated public List<String> effects
@Deprecated public String geneName
@Deprecated public String geneId
@Deprecated public String featureType
@Deprecated public String featureId
@Deprecated public String biotype
@Deprecated public Integer rank
@Deprecated public Integer total
@Deprecated public String genomicHgvs
@Deprecated public String transcriptHgvs
@Deprecated public String proteinHgvs
@Deprecated public Integer cdnaPosition
@Deprecated public Integer cdnaLength
@Deprecated public Integer cdsPosition
@Deprecated public Integer cdsLength
@Deprecated public Integer proteinPosition
@Deprecated public Integer proteinLength
@Deprecated public Integer distance
@Deprecated public List<VariantAnnotationMessage> messages
public TranscriptEffect()
newBuilder()
.public TranscriptEffect(String alternateAllele, List<String> effects, String geneName, String geneId, String featureType, String featureId, String biotype, Integer rank, Integer total, String genomicHgvs, String transcriptHgvs, String proteinHgvs, Integer cdnaPosition, Integer cdnaLength, Integer cdsPosition, Integer cdsLength, Integer proteinPosition, Integer proteinLength, Integer distance, List<VariantAnnotationMessage> messages)
alternateAllele
- Alternate allele for this variant annotation.effects
- One or more annotations (also referred to as effects or consequences) of the
variant in the context of the feature identified by featureId. Must be
Sequence Ontology (SO, see http://www.sequenceontology.org) term names, e.g.
stop_gained, missense_variant, synonymous_variant, upstream_gene_variant.geneName
- Common gene name (HGNC), e.g. BRCA2. May be closest gene if annotation
is intergenic.geneId
- Gene identifier, e.g. Ensembl Gene identifier, ENSG00000139618. May be
closest gene if annotation is intergenic.featureType
- Feature type, may use Sequence Ontology term names. Typically transcript.featureId
- Feature identifier, e.g. Ensembl Transcript identifier and version, ENST00000380152.7.biotype
- Feature biotype, e.g. Protein coding or Non coding. See http://vega.sanger.ac.uk/info/about/gene_and_transcript_types.html.rank
- Intron or exon rank.total
- Total number of introns or exons.genomicHgvs
- HGVS.g description of the variant. See http://www.hgvs.org/mutnomen/recs-DNA.html.transcriptHgvs
- HGVS.c description of the variant. See http://www.hgvs.org/mutnomen/recs-DNA.html.proteinHgvs
- HGVS.p description of the variant, if coding. See http://www.hgvs.org/mutnomen/recs-prot.html.cdnaPosition
- cDNA sequence position (one based).cdnaLength
- cDNA sequence length in base pairs (one based).cdsPosition
- Coding sequence position (one based, includes START and STOP codons).cdsLength
- Coding sequence length in base pairs (one based, includes START and STOP codons).proteinPosition
- Protein sequence position (one based, includes START but not STOP).proteinLength
- Protein sequence length in amino acids (one based, includes START but not STOP).distance
- Distance in base pairs to the feature.messages
- Zero or more errors, warnings, or informative messages regarding variant annotation accuracy.public static org.apache.avro.Schema getClassSchema()
public static org.apache.avro.message.BinaryMessageDecoder<TranscriptEffect> getDecoder()
public static org.apache.avro.message.BinaryMessageDecoder<TranscriptEffect> createDecoder(org.apache.avro.message.SchemaStore resolver)
SchemaStore
.resolver
- a SchemaStore
used to find schemas by fingerprintpublic ByteBuffer toByteBuffer() throws IOException
IOException
public static TranscriptEffect 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 getAlternateAllele()
public void setAlternateAllele(String value)
value
- the value to set.public List<String> getEffects()
public void setEffects(List<String> value)
value
- the value to set.public String getGeneName()
public void setGeneName(String value)
value
- the value to set.public String getGeneId()
public void setGeneId(String value)
value
- the value to set.public String getFeatureType()
public void setFeatureType(String value)
value
- the value to set.public String getFeatureId()
public void setFeatureId(String value)
value
- the value to set.public String getBiotype()
public void setBiotype(String value)
value
- the value to set.public Integer getRank()
public void setRank(Integer value)
value
- the value to set.public Integer getTotal()
public void setTotal(Integer value)
value
- the value to set.public String getGenomicHgvs()
public void setGenomicHgvs(String value)
value
- the value to set.public String getTranscriptHgvs()
public void setTranscriptHgvs(String value)
value
- the value to set.public String getProteinHgvs()
public void setProteinHgvs(String value)
value
- the value to set.public Integer getCdnaPosition()
public void setCdnaPosition(Integer value)
value
- the value to set.public Integer getCdnaLength()
public void setCdnaLength(Integer value)
value
- the value to set.public Integer getCdsPosition()
public void setCdsPosition(Integer value)
value
- the value to set.public Integer getCdsLength()
public void setCdsLength(Integer value)
value
- the value to set.public Integer getProteinPosition()
public void setProteinPosition(Integer value)
value
- the value to set.public Integer getProteinLength()
public void setProteinLength(Integer value)
value
- the value to set.public Integer getDistance()
public void setDistance(Integer value)
value
- the value to set.public List<VariantAnnotationMessage> getMessages()
public void setMessages(List<VariantAnnotationMessage> value)
value
- the value to set.public static TranscriptEffect.Builder newBuilder()
public static TranscriptEffect.Builder newBuilder(TranscriptEffect.Builder other)
other
- The existing builder to copy.public static TranscriptEffect.Builder newBuilder(TranscriptEffect 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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