de.unibi.techfak.InSilicoDicer.OperatingPackage
Class Evaluation

java.lang.Object
  de.unibi.techfak.InSilicoDicer.OperatingPackage.Evaluation

public class Evaluation
extends java.lang.Object

Author:

Sylvia Tippman This class performs prediction of mature miRNA on all precursors of the input fasta file with all 3 prediction methods: - Intrinsic Prediction - Intrinsic Prediction with multiple alignment - Extrinsic Prediction The positions yielded with each prediction method is compared to the position of mature miRNA derived from miRNA registry. The results are shown in a table. Note: Evaluation only makes sense if the precursors you input are already contained in the miRNA registry. With this class you can check whethter your implemented action classes give reliable results / how close you are to the experimantal verified position of mature miRNA.

Constructor Summary

Evaluation()

Method Summary

void	evaluate() Starts the evaluation: Calculation of mature miRNA position with intrinsic, intrinsicPlus and extrinsic method.
void	fillArrays(PrecursorContainer lonelyPCs, int i) Calculates Postion of mature miRNA by aligning similar Precursors Intrinsic & Extrinsic
void	fillSingleArrays(PrecursorContainer lonelyPCs, int i) Calculates Position of mature miRNA just by scoring the Precursor no alignment with others!
void	printResults() Prints the results in a table.

Methods inherited from class java.lang.Object

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

Constructor Detail

Evaluation

public Evaluation()

Method Detail

evaluate

public void evaluate()

Starts the evaluation: Calculation of mature miRNA position with intrinsic, intrinsicPlus and extrinsic method. Prints out a table (calling printResults() ) conataining mature miRNA position for all precursors.

fillSingleArrays

public void fillSingleArrays(PrecursorContainer lonelyPCs,
                             int i)

Calculates Position of mature miRNA just by scoring the Precursor no alignment with others!

Parameters:

lonelyPCs -

i -

fillArrays

public void fillArrays(PrecursorContainer lonelyPCs,
                       int i)

Calculates Postion of mature miRNA by aligning similar Precursors Intrinsic & Extrinsic

Parameters:

lonelyPCs -

i -

printResults

public void printResults()

Prints the results in a table.