de.unibi.techfak.InSilicoDicer.Actions.ScorePrecursor
Interface IScoreAction

All Superinterfaces:

Action

All Known Implementing Classes:

Score_Gaasterland

public interface IScoreAction
extends Action

Author:

Sylvia Tippmann This Tool is created to provide a flexible usage. The algorithms to predict mature miRNA are based on 4 basic Actions: - Multiple alignment of precursor sequences - calculation of conservation among precursor sequences - Folding/secondary structure prediction of precursors - Scoring of precursor's sequence and secondary structure If you want to create a new class for SCORING precursors, the class MUST implement this Interface to fit in the program flow. Especially this Action step, the scoring of precursors accoriding to its possible mature miRNA properties awaits futher improvement. One could think of completely other scoring shemes. NOTE: After implementing a new Class for any Action step, compile it and add the absolute path of this .class file to the apropriate list in 'var/conf.properties' to include it in the tool. Otherwise the tool and the user will notice the class exists.

Method Summary

java.util.Vector

formula(PrecursorContainer pc) Scores the window (mature miRNA) by a defined Formula

Methods inherited from interface de.unibi.techfak.InSilicoDicer.Actions.Action

getStatus, setStatus

Method Detail

formula

java.util.Vector formula(PrecursorContainer pc)

Scores the window (mature miRNA) by a defined Formula

Parameters:

pc -

Returns:

Vector of scores (containing arrays with scores for each precursor)