Package org.biojava.spark.mappers

Class PairwiseSequenceComparison

  • All Implemented Interfaces:
    java.io.Serializable, org.apache.spark.api.java.function.Function<scala.Tuple2<scala.Tuple2<java.lang.String,​java.lang.String>,​scala.Tuple2<java.lang.String,​java.lang.String>>,​scala.Tuple5<java.lang.String,​java.lang.String,​java.lang.Float,​java.lang.Float,​java.lang.Float>>
    public class PairwiseSequenceComparison
extends java.lang.Object
implements org.apache.spark.api.java.function.Function<scala.Tuple2<scala.Tuple2<java.lang.String,​java.lang.String>,​scala.Tuple2<java.lang.String,​java.lang.String>>,​scala.Tuple5<java.lang.String,​java.lang.String,​java.lang.Float,​java.lang.Float,​java.lang.Float>>
    Performs a pairwise alignment and returns a Tuple5. These are the returned elements: - name1 - name2 - overlap1 - overlap2 - percentage identical residues in the alignment
    See Also:
    Serialized Form

    • Constructor Summary

      Constructors 
      Constructor Description
      PairwiseSequenceComparison​(java.util.List<scala.Tuple2<java.lang.String,​java.lang.String>> sequences, float minOverlap, float minPercid)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      scala.Tuple5<java.lang.String,​java.lang.String,​java.lang.Float,​java.lang.Float,​java.lang.Float> call​(scala.Tuple2<scala.Tuple2<java.lang.String,​java.lang.String>,​scala.Tuple2<java.lang.String,​java.lang.String>> tuple)  

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • PairwiseSequenceComparison

        public PairwiseSequenceComparison​(java.util.List<scala.Tuple2<java.lang.String,​java.lang.String>> sequences,
                                  float minOverlap,
                                  float minPercid)

    • Method Detail

      • call

        public scala.Tuple5<java.lang.String,​java.lang.String,​java.lang.Float,​java.lang.Float,​java.lang.Float> call​(scala.Tuple2<scala.Tuple2<java.lang.String,​java.lang.String>,​scala.Tuple2<java.lang.String,​java.lang.String>> tuple)
                                                                                                                             throws java.lang.Exception
        Specified by:
        call in interface org.apache.spark.api.java.function.Function<scala.Tuple2<scala.Tuple2<java.lang.String,​java.lang.String>,​scala.Tuple2<java.lang.String,​java.lang.String>>,​scala.Tuple5<java.lang.String,​java.lang.String,​java.lang.Float,​java.lang.Float,​java.lang.Float>>
        Throws:
        java.lang.Exception