org.biojava.spark.mappers

Class PairwiseSequenceComparison

java.lang.Object

org.biojava.spark.mappers.PairwiseSequenceComparison

All Implemented Interfaces:

Serializable, org.apache.spark.api.java.function.Function<scala.Tuple2<scala.Tuple2<String,String>,scala.Tuple2<String,String>>,scala.Tuple5<String,String,Float,Float,Float>>

public class PairwiseSequenceComparison
extends Object
implements org.apache.spark.api.java.function.Function<scala.Tuple2<scala.Tuple2<String,String>,scala.Tuple2<String,String>>,scala.Tuple5<String,String,Float,Float,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 and Description
PairwiseSequenceComparison(List<scala.Tuple2<String,String>> sequences, float minOverlap, float minPercid)

Method Summary

Modifier and Type	Method and Description
scala.Tuple5<String,String,Float,Float,Float>	call(scala.Tuple2<scala.Tuple2<String,String>,scala.Tuple2<String,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(List<scala.Tuple2<String,String>> sequences,
                                  float minOverlap,
                                  float minPercid)

Method Detail

call

public scala.Tuple5<String,String,Float,Float,Float> call(scala.Tuple2<scala.Tuple2<String,String>,scala.Tuple2<String,String>> tuple)
                                                   throws Exception

Specified by:

call in interface org.apache.spark.api.java.function.Function<scala.Tuple2<scala.Tuple2<String,String>,scala.Tuple2<String,String>>,scala.Tuple5<String,String,Float,Float,Float>>

Throws:

Exception