BiojavaAdamContext

Instance Constructors

new BiojavaAdamContext(ac: ADAMContext, readConverter: Converter[Fastq, Read], dnaSequenceConverter: Converter[DNASequence, Sequence], dnaSequenceFeaturesConverter: Converter[DNASequence, List[Feature]], proteinSequenceConverter: Converter[ProteinSequence, Sequence], proteinSequenceFeaturesConverter: Converter[ProteinSequence, List[Feature]], rnaSequenceConverter: Converter[RNASequence, Sequence], rnaSequenceFeaturesConverter: Converter[RNASequence, List[Feature]])

ac
ADAMContext to extend.
readConverter
Convert Biojava Fastq to bdg-formats Read.
dnaSequenceConverter
Convert Biojava DNASequence to bdg-formats Sequence.
dnaSequenceFeaturesConverter
Convert Biojava DNASequence to a list of bdg-formats Features.
proteinSequenceConverter
Convert Biojava ProteinSequence to bdg-formats Sequence
proteinSequenceFeaturesConverter
Convert Biojava ProteinSequence to a list of bdg-formats Features
rnaSequenceConverter
Convert Biojava RNASequence to bdg-formats Sequence
rnaSequenceFeaturesConverter
Convert Biojava RNASequence to a list of bdg-formats Features

Value Members

final def !=(arg0: Any): Boolean

Definition Classes
AnyRef → Any
final def ##(): Int

Definition Classes
AnyRef → Any
final def ==(arg0: Any): Boolean

Definition Classes
AnyRef → Any
val ac: ADAMContext

ADAMContext to extend.
final def asInstanceOf[T0]: T0

Definition Classes
Any
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
val dnaSequenceConverter: Converter[DNASequence, Sequence]

Convert Biojava DNASequence to bdg-formats Sequence.
val dnaSequenceFeaturesConverter: Converter[DNASequence, List[Feature]]

Convert Biojava DNASequence to a list of bdg-formats Features.
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def equals(arg0: Any): Boolean

Definition Classes
AnyRef → Any
def finalize(): Unit

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( classOf[java.lang.Throwable] )
final def getClass(): Class[_]

Definition Classes
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def hashCode(): Int

Definition Classes
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final def isInstanceOf[T0]: Boolean

Definition Classes
Any
def isTraceEnabled(): Boolean

Attributes
protected
Definition Classes
Logging
def loadBiojavaFastaDna(path: String): SequenceDataset

Load the specified path in FASTA format as DNA sequences with Biojava.
Load the specified path in FASTA format as DNA sequences with Biojava.
path
path in FASTA format, must not be null
returns
RDD of DNA sequences

Exceptions thrown
IOException if an I/O error occurs
def loadBiojavaFastaProtein(path: String): SequenceDataset

Load the specified path in FASTA format as protein sequences with Biojava.
Load the specified path in FASTA format as protein sequences with Biojava.
path
path in FASTA format, must not be null
returns
RDD of protein sequences

Exceptions thrown
IOException if an I/O error occurs
def loadBiojavaFastaRna(path: String): SequenceDataset

Load the specified path in FASTA format as RNA sequences with Biojava.
Load the specified path in FASTA format as RNA sequences with Biojava.
path
path in FASTA format, must not be null
returns
RDD of RNA sequences

Exceptions thrown
IOException if an I/O error occurs
def loadBiojavaFastqReads(path: String): ReadDataset

Load the specified path in FASTQ format as reads with Biojava.
Load the specified path in FASTQ format as reads with Biojava.
path
path in FASTQ format, must not be null
returns
RDD of reads

Exceptions thrown
IOException if an I/O error occurs
def loadBiojavaGenbankDna(path: String): SequenceDataset

Load the specified path in Genbank format as DNA sequences with Biojava.
Load the specified path in Genbank format as DNA sequences with Biojava.
path
path in Genbank format, must not be null
returns
RDD of DNA sequences

Exceptions thrown
IOException if an I/O error occurs
def loadBiojavaGenbankDnaFeatures(path: String): FeatureDataset

Load the specified path in Genbank format as DNA sequence features with Biojava.
Load the specified path in Genbank format as DNA sequence features with Biojava.
path
path in Genbank format, must not be null
returns
RDD of DNA sequence features

Exceptions thrown
Exception if an I/O error occurs
def loadBiojavaGenbankProtein(path: String): SequenceDataset

Load the specified path in Genbank format as protein sequences with Biojava.
Load the specified path in Genbank format as protein sequences with Biojava.
path
path in Genbank format, must not be null
returns
RDD of protein sequences

Exceptions thrown
IOException if an I/O error occurs
def loadBiojavaGenbankProteinFeatures(path: String): FeatureDataset

Load the specified path in Genbank format as protein sequence features with Biojava.
Load the specified path in Genbank format as protein sequence features with Biojava.
path
path in Genbank format, must not be null
returns
RDD of protein sequence features

Exceptions thrown
Exception if an I/O error occurs
def loadBiojavaGenbankRna(path: String): SequenceDataset

Load the specified path in Genbank format as RNA sequences with Biojava.
Load the specified path in Genbank format as RNA sequences with Biojava.
path
path in Genbank format, must not be null
returns
RDD of RNA sequences

Exceptions thrown
IOException if an I/O error occurs
def loadBiojavaGenbankRnaFeatures(path: String): FeatureDataset

Load the specified path in Genbank format as RNA sequence features with Biojava.
Load the specified path in Genbank format as RNA sequence features with Biojava.
path
path in Genbank format, must not be null
returns
RDD of RNA sequence features

Exceptions thrown
Exception if an I/O error occurs
def loadFastqReads(path: String): ReadDataset

Load the specified path in FASTQ format as reads with Biojava.
Load the specified path in FASTQ format as reads with Biojava. Alias for loadBiojavaFastqReads.
path
path in FASTQ format, must not be null
returns
RDD of reads

Exceptions thrown
IOException if an I/O error occurs
def loadGenbankDna(path: String): SequenceDataset

Load the specified path in Genbank format as DNA sequences with Biojava.
Load the specified path in Genbank format as DNA sequences with Biojava. Alias for loadBiojavaGenbankDna.
path
path in Genbank format, must not be null
returns
RDD of DNA sequences

Exceptions thrown
IOException if an I/O error occurs
def loadGenbankDnaFeatures(path: String): FeatureDataset

Load the specified path in Genbank format as DNA sequence features with Biojava.
Load the specified path in Genbank format as DNA sequence features with Biojava. Alias for loadBiojavaGenbankDnaFeatures.
path
path in Genbank format, must not be null
returns
RDD of DNA sequence features

Exceptions thrown
Exception if an I/O error occurs
def loadGenbankProtein(path: String): SequenceDataset

Load the specified path in Genbank format as protein sequences with Biojava.
Load the specified path in Genbank format as protein sequences with Biojava. Alias for loadBiojavaGenbankProtein.
path
path in Genbank format, must not be null
returns
RDD of protein sequences

Exceptions thrown
IOException if an I/O error occurs
def loadGenbankProteinFeatures(path: String): FeatureDataset

Load the specified path in Genbank format as protein sequence features with Biojava.
Load the specified path in Genbank format as protein sequence features with Biojava. Alias for loadBiojavaGenbankProteinFeatures.
path
path in Genbank format, must not be null
returns
RDD of protein sequence features

Exceptions thrown
Exception if an I/O error occurs
def loadGenbankRna(path: String): SequenceDataset

Load the specified path in Genbank format as RNA sequences with Biojava.
Load the specified path in Genbank format as RNA sequences with Biojava. Alias for loadBiojavaGenbankRna.
path
path in Genbank format, must not be null
returns
RDD of RNA sequences

Exceptions thrown
IOException if an I/O error occurs
def loadGenbankRnaFeatures(path: String): FeatureDataset

Load the specified path in Genbank format as RNA sequence features with Biojava.
Load the specified path in Genbank format as RNA sequence features with Biojava. Alias for loadBiojavaGenbankRnaFeatures.
path
path in Genbank format, must not be null
returns
RDD of RNA sequence features

Exceptions thrown
Exception if an I/O error occurs
def log: Logger

Attributes
protected
Definition Classes
Logging
def logDebug(msg: ⇒ String, throwable: Throwable): Unit

Attributes
protected
Definition Classes
Logging
def logDebug(msg: ⇒ String): Unit

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protected
Definition Classes
Logging
def logError(msg: ⇒ String, throwable: Throwable): Unit

Attributes
protected
Definition Classes
Logging
def logError(msg: ⇒ String): Unit

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protected
Definition Classes
Logging
def logInfo(msg: ⇒ String, throwable: Throwable): Unit

Attributes
protected
Definition Classes
Logging
def logInfo(msg: ⇒ String): Unit

Attributes
protected
Definition Classes
Logging
def logName: String

Attributes
protected
Definition Classes
Logging
def logTrace(msg: ⇒ String, throwable: Throwable): Unit

Attributes
protected
Definition Classes
Logging
def logTrace(msg: ⇒ String): Unit

Attributes
protected
Definition Classes
Logging
def logWarning(msg: ⇒ String, throwable: Throwable): Unit

Attributes
protected
Definition Classes
Logging
def logWarning(msg: ⇒ String): Unit

Attributes
protected
Definition Classes
Logging
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
val proteinSequenceConverter: Converter[ProteinSequence, Sequence]

Convert Biojava ProteinSequence to bdg-formats Sequence
val proteinSequenceFeaturesConverter: Converter[ProteinSequence, List[Feature]]

Convert Biojava ProteinSequence to a list of bdg-formats Features
val readConverter: Converter[Fastq, Read]

Convert Biojava Fastq to bdg-formats Read.
val rnaSequenceConverter: Converter[RNASequence, Sequence]

Convert Biojava RNASequence to bdg-formats Sequence
val rnaSequenceFeaturesConverter: Converter[RNASequence, List[Feature]]

Convert Biojava RNASequence to a list of bdg-formats Features
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def toString(): String

Definition Classes
AnyRef → Any
final def wait(): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )
final def wait(arg0: Long, arg1: Int): Unit

Definition Classes
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Annotations
@throws( ... )
final def wait(arg0: Long): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )

Related Docs: object BiojavaAdamContext | package adam

class BiojavaAdamContext extends Serializable with Logging

Instance Constructors

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

val ac: ADAMContext

final def asInstanceOf[T0]: T0

def clone(): AnyRef

val dnaSequenceConverter: Converter[DNASequence, Sequence]

val dnaSequenceFeaturesConverter: Converter[DNASequence, List[Feature]]

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def finalize(): Unit

final def getClass(): Class[_]

def hashCode(): Int

final def isInstanceOf[T0]: Boolean

def isTraceEnabled(): Boolean

def loadBiojavaFastaDna(path: String): SequenceDataset

def loadBiojavaFastaProtein(path: String): SequenceDataset

def loadBiojavaFastaRna(path: String): SequenceDataset

def loadBiojavaFastqReads(path: String): ReadDataset

def loadBiojavaGenbankDna(path: String): SequenceDataset

def loadBiojavaGenbankDnaFeatures(path: String): FeatureDataset

def loadBiojavaGenbankProtein(path: String): SequenceDataset

def loadBiojavaGenbankProteinFeatures(path: String): FeatureDataset

def loadBiojavaGenbankRna(path: String): SequenceDataset

def loadBiojavaGenbankRnaFeatures(path: String): FeatureDataset

def loadFastqReads(path: String): ReadDataset

def loadGenbankDna(path: String): SequenceDataset

def loadGenbankDnaFeatures(path: String): FeatureDataset

def loadGenbankProtein(path: String): SequenceDataset

def loadGenbankProteinFeatures(path: String): FeatureDataset

def loadGenbankRna(path: String): SequenceDataset

def loadGenbankRnaFeatures(path: String): FeatureDataset

def log: Logger

def logDebug(msg: ⇒ String, throwable: Throwable): Unit

def logDebug(msg: ⇒ String): Unit

def logError(msg: ⇒ String, throwable: Throwable): Unit

def logError(msg: ⇒ String): Unit

def logInfo(msg: ⇒ String, throwable: Throwable): Unit

def logInfo(msg: ⇒ String): Unit

def logName: String

def logTrace(msg: ⇒ String, throwable: Throwable): Unit

def logTrace(msg: ⇒ String): Unit

def logWarning(msg: ⇒ String, throwable: Throwable): Unit

def logWarning(msg: ⇒ String): Unit

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

val proteinSequenceConverter: Converter[ProteinSequence, Sequence]

val proteinSequenceFeaturesConverter: Converter[ProteinSequence, List[Feature]]

val readConverter: Converter[Fastq, Read]

val rnaSequenceConverter: Converter[RNASequence, Sequence]

val rnaSequenceFeaturesConverter: Converter[RNASequence, List[Feature]]

final def synchronized[T0](arg0: ⇒ T0): T0

def toString(): String

final def wait(): Unit

final def wait(arg0: Long, arg1: Int): Unit

final def wait(arg0: Long): Unit

Inherited from Logging

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped