de.unibi.techfak.InSilicoDicer.Actions.CalcConservation
Interface ICalcConservationAction

All Superinterfaces:

Action

All Known Implementing Classes:

CalcCons_Entropy, CalcCons_Entropy_seed

public interface ICalcConservationAction
extends Action

Author:

Sylvia 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 CALCULATON OF CONSERVATION, the class MUST implement this Interface to fit in the program flow. Especially this Action step, Calculation if Conservation among several precursors awaits futher improvement. One could think of a sequence-/position-specific calculation. 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

calcCons(java.util.Vector align) Calculates Cobservation profile by column by column

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

getStatus, setStatus

Method Detail

calcCons

java.util.Vector calcCons(java.util.Vector align)

Calculates Cobservation profile by column by column

Parameters:

align -

Returns:

Vector of conservation values per column