Serialized Form

  • Package gorsat.commands

  • Package gorsat.process

    • Class gorsat.process.GorSpark extends java.lang.Object implements Serializable

      • Serialized Fields

        • gorcmd
          java.lang.String gorcmd
        • gorroot
          java.lang.String gorroot
        • header
          java.lang.String header
        • jobId
          java.lang.String jobId
        • nor
          boolean nor
        • schema
          org.apache.spark.sql.types.StructType schema
        • uri
          java.lang.String uri

    • Class gorsat.process.GorSparkExternalFunction extends java.lang.Object implements Serializable

      • Serialized Fields

        • cmd
          java.lang.String cmd
        • fetchHeader
          boolean fetchHeader
        • goroot
          java.lang.String goroot
        • header
          java.lang.String header

    • Class gorsat.process.GorSparkMaterialize extends GorSpark implements Serializable

      • Serialized Fields

        • max
          int max

    • Class gorsat.process.ProcessIteratorAdaptor extends org.gorpipe.model.gor.iterators.RowSource implements Serializable

      • Serialized Fields

        • allowerror
          boolean allowerror
        • breader
          java.io.BufferedReader breader
        • errorStr
          java.lang.StringBuilder errorStr
        • is
          java.io.InputStream is
        • line
          java.lang.String line
        • mustReCheck
          boolean mustReCheck
        • myHasNext
          boolean myHasNext
        • nor
          boolean nor
        • outThread
          gorsat.process.ProcessIteratorAdaptor.OutThread outThread
        • proc
          java.lang.Process proc
        • processName
          java.lang.String processName
        • rowSource
          java.util.Iterator<org.gorpipe.gor.model.Row> rowSource
        • skipheader
          boolean skipheader

  • Package gorsat.spark

    • Class gorsat.spark.GordFunction extends java.lang.Object implements Serializable

      • Serialized Fields

        • encoder
          org.apache.spark.sql.catalyst.encoders.ExpressionEncoder<org.apache.spark.sql.Row> encoder
        • header
          java.lang.String header
        • serializer
          org.apache.spark.sql.catalyst.encoders.ExpressionEncoder.Serializer<org.apache.spark.sql.Row> serializer

    • Class gorsat.spark.GorFileFormat extends org.apache.spark.sql.execution.datasources.csv.CSVFileFormat implements Serializable

    • Class gorsat.spark.GorReaderFactory extends java.lang.Object implements Serializable

      • Serialized Fields

        • cacheDir
          java.lang.String cacheDir
        • cacheFile
          java.lang.String cacheFile
        • jobId
          java.lang.String jobId
        • projectRoot
          java.lang.String projectRoot
        • redisUri
          java.lang.String redisUri
        • schema
          org.apache.spark.sql.types.StructType schema
        • useCpp
          java.lang.String useCpp

    • Class gorsat.spark.GorSpecificInputPartition extends java.lang.Object implements Serializable

      • Serialized Fields

        • i
          int[] i
        • j
          int[] j

    • Class gorsat.spark.GorSpecificReaderFactory extends java.lang.Object implements Serializable

  • Package org.gorpipe.spark

    • Class org.gorpipe.spark.GorFilterFunction extends org.gorpipe.gor.function.GorRowFilterFunction<org.gorpipe.gor.model.Row> implements Serializable

    • Class org.gorpipe.spark.GorHeaderInferFunction extends java.lang.Object implements Serializable

      • Serialized Fields

        • convMap
          java.util.Map<java.lang.String,​java.lang.Character> convMap

    • Class org.gorpipe.spark.GorPartition extends java.lang.Object implements Serializable

      • Serialized Fields

        • p
          int p

    • Class org.gorpipe.spark.GorPipeFunction extends java.lang.Object implements Serializable

      • Serialized Fields

        • cmd
          java.lang.String cmd
        • header
          java.lang.String header

    • Class org.gorpipe.spark.GorpipeRDD extends org.apache.spark.rdd.RDD<T extends java.lang.Object> implements Serializable

      • Serialized Fields

        • evidence$5
          scala.reflect.ClassTag<T extends java.lang.Object> evidence$5
        • gor
          boolean gor
        • header
          java.lang.String header
        • org$gorpipe$spark$GorpipeRDD$$encoder
          org.apache.spark.sql.catalyst.encoders.ExpressionEncoder<T extends java.lang.Object> org$gorpipe$spark$GorpipeRDD$$encoder
        • pipeStep
          gorsat.Commands.Analysis pipeStep

    • Class org.gorpipe.spark.GorpWriter extends java.lang.Object implements Serializable

      • Serialized Fields

        • path
          java.lang.String path

    • Class org.gorpipe.spark.GorQueryRDD extends org.apache.spark.rdd.RDD<java.lang.String> implements Serializable

      • Serialized Fields

        • cacheDirectory
          java.lang.String cacheDirectory
        • cacheFiles
          java.lang.String[] cacheFiles
        • commandSignatures
          java.lang.String[] commandSignatures
        • commandsToExecute
          java.lang.String[] commandsToExecute
        • jobIds
          java.lang.String[] jobIds
        • projectDirectory
          java.lang.String projectDirectory
        • redisUri
          java.lang.String redisUri

    • Class org.gorpipe.spark.GorRDD extends org.apache.spark.rdd.RDD<org.gorpipe.gor.model.Row> implements Serializable

      • Serialized Fields

        • evidence$6
          scala.reflect.ClassTag<T extends java.lang.Object> evidence$6
        • gor
          boolean gor
        • gorcmd
          java.lang.String gorcmd
        • header
          java.lang.String header

    • Class org.gorpipe.spark.GorSparkArrayInferFunction extends java.lang.Object implements Serializable

    • Class org.gorpipe.spark.GorSparkRow extends SparkRow implements Serializable

    • Class org.gorpipe.spark.GorSparkRowBase extends org.gorpipe.gor.model.Row implements Serializable

    • Class org.gorpipe.spark.GorSparkRowFilterFunction extends org.gorpipe.gor.function.GorRowFilterFunction<org.gorpipe.gor.model.Row> implements Serializable

    • Class org.gorpipe.spark.GorSparkRowInferFunction extends org.gorpipe.gor.function.GorRowInferFunction implements Serializable

    • Class org.gorpipe.spark.GorSparkRowMapFunction extends org.gorpipe.gor.function.GorRowMapFunction implements Serializable

      • Serialized Fields

        • schema
          org.apache.spark.sql.types.StructType schema

    • Class org.gorpipe.spark.GorSparkRowQueryFunction extends org.gorpipe.gor.function.GorRowQueryFunction implements Serializable

    • Class org.gorpipe.spark.Gorz extends java.lang.Object implements Serializable

      • Serialized Fields

        • block
          java.lang.String block
        • CHROM
          java.lang.String CHROM
        • POS
          int POS

    • Class org.gorpipe.spark.Gorz$ extends scala.runtime.AbstractFunction3<java.lang.String,​java.lang.Object,​java.lang.String,​org.gorpipe.spark.Gorz> implements Serializable

      • Serialization Methods

        • readResolve
          private java.lang.Object readResolve()

    • Class org.gorpipe.spark.GorzFlatMap extends java.lang.Object implements Serializable

      • Serialized Fields

        • buffer
          byte[] buffer

    • Class org.gorpipe.spark.GorzIterator extends java.lang.Object implements Serializable

      • Serialized Fields

        • header
          java.lang.String header

    • Class org.gorpipe.spark.GorzStr extends java.lang.Object implements Serializable

      • Serialized Fields

        • block
          java.lang.String block
        • CHROM
          java.lang.String CHROM
        • POS
          java.lang.String POS

    • Class org.gorpipe.spark.GorzStr$ extends scala.runtime.AbstractFunction3<java.lang.String,​java.lang.String,​java.lang.String,​org.gorpipe.spark.GorzStr> implements Serializable

      • Serialization Methods

        • readResolve
          private java.lang.Object readResolve()

    • Class org.gorpipe.spark.HeaderFunction extends java.lang.Object implements Serializable

      • Serialized Fields

        • cmd
          java.lang.String cmd
        • header
          java.lang.String header

    • Class org.gorpipe.spark.HeaderInferFunction extends java.lang.Object implements Serializable

      • Serialized Fields

        • cmd
          java.lang.String cmd
        • header
          java.lang.String header

    • Class org.gorpipe.spark.LongGorSparkRow extends GorSparkRow implements Serializable

    • Class org.gorpipe.spark.NorFilterFunction extends org.gorpipe.gor.function.GorRowFilterFunction<org.gorpipe.gor.model.Row> implements Serializable

    • Class org.gorpipe.spark.NorSparkRowFilterFunction extends GorFilterFunction implements Serializable

    • Class org.gorpipe.spark.PgorRDD extends org.apache.spark.rdd.RDD<org.gorpipe.gor.model.Row> implements Serializable

      • Serialized Fields

        • filter
          java.lang.String filter
        • gorcmd
          java.lang.String gorcmd

    • Class org.gorpipe.spark.PipeFunction extends java.lang.Object implements Serializable

      • Serialized Fields

        • cmd
          java.lang.String cmd
        • header
          java.lang.String header

    • Class org.gorpipe.spark.QueryRDD extends org.apache.spark.rdd.RDD<java.lang.String> implements Serializable

      • Serialized Fields

        • cacheDir
          java.lang.String cacheDir
        • commandSignatures
          java.lang.String[] commandSignatures
        • commandsToExecute
          java.lang.String[] commandsToExecute
        • hash
          java.lang.String hash
        • header
          boolean header
        • projectDirectory
          java.lang.String projectDirectory
        • sparkSession
          org.apache.spark.sql.SparkSession sparkSession
        • sqlContext
          org.apache.spark.sql.SQLContext sqlContext

    • Class org.gorpipe.spark.Result extends java.lang.Object implements Serializable

      • Serialized Fields

        • ALT
          java.lang.String ALT
        • CHROM
          java.lang.String CHROM
        • ID
          java.lang.String ID
        • M
          java.lang.String M
        • POS
          int POS
        • REF
          java.lang.String REF

    • Class org.gorpipe.spark.Result$ extends scala.runtime.AbstractFunction6<java.lang.String,​java.lang.Object,​java.lang.String,​java.lang.String,​java.lang.String,​java.lang.String,​org.gorpipe.spark.Result> implements Serializable

      • Serialization Methods

        • readResolve
          private java.lang.Object readResolve()

    • Class org.gorpipe.spark.RowGorRDD extends org.gorpipe.spark.PgorRDD<org.gorpipe.gor.model.Row> implements Serializable

    • Class org.gorpipe.spark.SparkGOR.Dbsnp extends java.lang.Object implements Serializable

      • Serialized Fields

        • ALT
          java.lang.String ALT
        • CHROM
          java.lang.String CHROM
        • ID
          java.lang.String ID
        • POS
          int POS
        • REF
          java.lang.String REF

    • Class org.gorpipe.spark.SparkGOR.Dbsnp$ extends scala.runtime.AbstractFunction5<java.lang.String,​java.lang.Object,​java.lang.String,​java.lang.String,​java.lang.String,​org.gorpipe.spark.SparkGOR.Dbsnp> implements Serializable

      • Serialization Methods

        • readResolve
          private java.lang.Object readResolve()

    • Class org.gorpipe.spark.SparkGOR.Gene extends java.lang.Object implements Serializable

      • Serialized Fields

        • chr
          java.lang.String chr
        • end
          int end
        • Gene_Symbol
          java.lang.String Gene_Symbol
        • pos
          int pos

    • Class org.gorpipe.spark.SparkGOR.Gene$ extends scala.runtime.AbstractFunction4<java.lang.String,​java.lang.Object,​java.lang.Object,​java.lang.String,​org.gorpipe.spark.SparkGOR.Gene> implements Serializable

      • Serialization Methods

        • readResolve
          private java.lang.Object readResolve()

    • Class org.gorpipe.spark.SparkGOR.Skat extends java.lang.Object implements Serializable

      • Serialized Fields

        • chrom
          java.lang.String chrom
        • numMarkers
          int numMarkers
        • pvalue
          java.lang.String pvalue
        • start
          int start
        • stop
          int stop
        • tag
          java.lang.String tag

    • Class org.gorpipe.spark.SparkGOR.Skat$ extends scala.runtime.AbstractFunction6<java.lang.String,​java.lang.Object,​java.lang.Object,​java.lang.String,​java.lang.Object,​java.lang.String,​org.gorpipe.spark.SparkGOR.Skat> implements Serializable

      • Serialization Methods

        • readResolve
          private java.lang.Object readResolve()

    • Class org.gorpipe.spark.SparkGOR.Variants extends java.lang.Object implements Serializable

      • Serialized Fields

        • alt
          java.lang.String alt
        • cc
          int cc
        • chrom
          java.lang.String chrom
        • cr
          double cr
        • depth
          int depth
        • filter
          java.lang.String filter
        • formatZip
          java.lang.String formatZip
        • fs
          double fs
        • gl
          int gl
        • pn
          java.lang.String pn
        • pos
          int pos
        • ref
          java.lang.String ref

    • Class org.gorpipe.spark.SparkGOR.Variants$ extends scala.runtime.AbstractFunction12<java.lang.String,​java.lang.Object,​java.lang.String,​java.lang.String,​java.lang.Object,​java.lang.Object,​java.lang.Object,​java.lang.Object,​java.lang.String,​java.lang.Object,​java.lang.String,​java.lang.String,​org.gorpipe.spark.SparkGOR.Variants> implements Serializable

      • Serialization Methods

        • readResolve
          private java.lang.Object readResolve()

    • Class org.gorpipe.spark.SparkGorMonitor extends org.gorpipe.gor.monitor.GorMonitor implements Serializable

      • Serialized Fields

        • jedisPool
          redis.clients.jedis.JedisPool jedisPool
        • jobId
          java.lang.String jobId
        • uri
          java.lang.String uri
        • working
          boolean working

    • Class org.gorpipe.spark.SparkGorRow extends GorSparkRowBase implements Serializable

      • Serialized Fields

        • row
          org.gorpipe.gor.model.Row row
        • schema
          org.apache.spark.sql.types.StructType schema

    • Class org.gorpipe.spark.sparkGorTest.Person extends java.lang.Object implements Serializable

      • Serialized Fields

        • age
          long age
        • name
          java.lang.String name

    • Class org.gorpipe.spark.sparkGorTest.Person$ extends scala.runtime.AbstractFunction2<java.lang.String,​java.lang.Object,​org.gorpipe.spark.sparkGorTest.Person> implements Serializable

      • Serialization Methods

        • readResolve
          private java.lang.Object readResolve()

    • Class org.gorpipe.spark.SparkRow extends GorSparkRowBase implements Serializable

      • Serialized Fields

        • row
          org.apache.spark.sql.Row row

    • Class org.gorpipe.spark.TestGorRDD extends org.apache.spark.rdd.RDD<org.gorpipe.gor.model.Row> implements Serializable

      • Serialized Fields

        • gor
          boolean gor
        • gorcmd
          java.lang.String gorcmd
        • header
          java.lang.String header

  • Package org.gorpipe.spark.platform

  • Package org.gorpipe.spark.udfs