de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchBySequence
Class SWalign

java.lang.Object
  de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchBySequence.SWalign

All Implemented Interfaces:

ILocalAlign, java.io.Serializable

public class SWalign
extends java.lang.Object
implements ILocalAlign, java.io.Serializable

See Also:

Serialized Form

Field Summary

static long

serialVersionUID set serial Version of current opbject

Constructor Summary

SWalign()

Method Summary

int	align(int inDELscore, int rpSCORE, int matchSCORE, java.lang.String searchSeq, java.lang.String dbSeq) Executes a Local Alignment Action where searchSeq is the Nuleotide Sequence to align with all possible Precursor Sequences (dbSeq) in the miRNAdatabase
int	maximum(int x, int y, int z, int w)
void	swBuildMatrix(int inDELscore, int rpSCORE, int matchSCORE, java.lang.String searchSeq, java.lang.String dbSeq)
int	swFindMaxScore(int[][] matrix, java.lang.String searchSeq, java.lang.String dbSeq)

Methods inherited from class java.lang.Object

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

Field Detail

serialVersionUID

public static final long serialVersionUID

set serial Version of current opbject

See Also:

Constant Field Values

Constructor Detail

SWalign

public SWalign()

Method Detail

align

public int align(int inDELscore,
                 int rpSCORE,
                 int matchSCORE,
                 java.lang.String searchSeq,
                 java.lang.String dbSeq)

Description copied from interface: ILocalAlign

Executes a Local Alignment Action where searchSeq is the Nuleotide Sequence to align with all possible Precursor Sequences (dbSeq) in the miRNAdatabase

Specified by:

align in interface ILocalAlign

Returns:

The similarity of two precursor sequences.

maximum

public int maximum(int x,
                   int y,
                   int z,
                   int w)

swBuildMatrix

public void swBuildMatrix(int inDELscore,
                          int rpSCORE,
                          int matchSCORE,
                          java.lang.String searchSeq,
                          java.lang.String dbSeq)

swFindMaxScore

public int swFindMaxScore(int[][] matrix,
                          java.lang.String searchSeq,
                          java.lang.String dbSeq)