de.unibi.techfak.InSilicoDicer.Actions.ScorePrecursor
Class Score_Gaasterland

java.lang.Object
  de.unibi.techfak.InSilicoDicer.Actions.ScorePrecursor.Score_Gaasterland

All Implemented Interfaces:

Action, IScoreAction

public class Score_Gaasterland
extends java.lang.Object
implements IScoreAction

Author:

Sylvia Tippmann

Field Summary

int

win

Constructor Summary

Score_Gaasterland()

Method Summary

double	countIntMm2IntBulges(java.lang.String viennaWin) Computes the ratio of internal mismatches to internal bulges.
int	countMismatches(java.lang.String viennaWin) Counts the number of all mismatches in the subsequence.
int	countTerminalMM(java.lang.String viennaWin) Counts the number of terminal mismatches in the subsequence.
java.util.Vector	formula(PrecursorContainer pc) Scores the window (mature miRNA) by a defined Formula
Status	getStatus() Returns the status of current Action
int	isU(java.lang.String precursor, int count) Checks whether the substring starts with an 'U'.
void	setStatus(Status status) Set the status of current Action

Methods inherited from class java.lang.Object

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

Field Detail

win

public int win

Constructor Detail

Score_Gaasterland

public Score_Gaasterland()

Method Detail

countMismatches

public int countMismatches(java.lang.String viennaWin)

Counts the number of all mismatches in the subsequence.

Parameters:

viennaWin -

Returns:

number of mismatches

countTerminalMM

public int countTerminalMM(java.lang.String viennaWin)

Counts the number of terminal mismatches in the subsequence.

Parameters:

viennaWin -

Returns:

Number of terminal mismatches

countIntMm2IntBulges

public double countIntMm2IntBulges(java.lang.String viennaWin)

Computes the ratio of internal mismatches to internal bulges.

Parameters:

viennaWin -

Returns:

Ratio internal mismatches to internal bulges

isU

public int isU(java.lang.String precursor,
               int count)

Checks whether the substring starts with an 'U'.

Parameters:

precursor -

count -

Returns:

1 if char is not U, 0 otherwise

formula

public java.util.Vector formula(PrecursorContainer pc)

Description copied from interface: IScoreAction

Scores the window (mature miRNA) by a defined Formula

Specified by:

formula in interface IScoreAction

Returns:

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

getStatus

public Status getStatus()

Description copied from interface: Action

Returns the status of current Action

Specified by:

getStatus in interface Action

Returns:

Status of this Action

setStatus

public void setStatus(Status status)

Description copied from interface: Action

Set the status of current Action

Specified by:

setStatus in interface Action

Parameters:

status - - Status to be set