de.unibi.techfak.InSilicoDicer.OperatingPackage
Class Operator

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

All Implemented Interfaces:

java.io.Serializable

public class Operator
extends java.lang.Object
implements java.io.Serializable

Author:

Sylvia Tippmann Jan Kr�ger The Operator Object is the central object which holds the complete configuration and every variable and provides getter and setter for them.

See Also:

Serialized Form

Field Summary

static long

serialVersionUID set serial Version of current opbject

Constructor Summary

Operator()
DefaultConstructor, load the program properties from local directory.

Operator(java.net.URL url)
Constructor, load the program properties from URL

Method Summary

double[]	calcAverageValues(java.util.Vector dataVec) Calculate array of average values(scores) from more than one precursor
void	createDatabaseFromFile(java.lang.String path, java.lang.String dbName) Deprecated.
int[]	findStartInSinglePC(int startINalign, java.util.Vector align)
ICalcConservationAction	getCalcconservationaction()
int	getCutoff()
PrecursorContainer	getDatabase() Get the actual Database to work with
java.io.File	getFile()
IFoldingAction	getFoldingaction()
java.util.Hashtable	getGenuineHash()
int	getIndelScore()
static Operator	getInstance() Singleton
int	getMatureSize()
java.lang.String	getMethod()
int	getMirnaPOSinALIGN()
int[]	getMirnaPOSinPC()
int	getMScore()
IMultipleAlignAction	getMultiplealignaction()
java.lang.String	getPath()
java.util.Properties	getProperties()
int	getRpScore()
IScoreAction	getScoreaction()
int	getSmoothWinSizeEx()
int	getSmoothWinSizeIn()
Status	getStatus()
int	predictMatureMiRNAex(java.util.Vector dataVec) Predicts Position of mature miRNA on extrinsic data by... 1) finding start position of the window with MAXIMAL sum (relative to alignment) !
int	predictMatureMiRNAin(java.util.Vector dataVec) Predicts Position of mature miRNA on instrinsic data 1) calculating the avarage value of all precursors 2) finding the minimal value (relative to alignment) !
java.lang.String	readFile(java.lang.String filename) Reads a File
java.util.Vector	run_extrinsicAction() Actions & Predction with EXTRINSIC method
java.util.Vector	run_intrinsicAction() Action & Prediction with INTRINSIC method
java.util.Vector	run_intrinsicPlusAction() Action & Prediction with INTRINSIC extended method
void	setActionPCs(PrecursorContainer actionPCs)
void	setCalcconservationaction(ICalcConservationAction calcconservationaction)
void	setCutoff(int cutoff)
void	setDatabase(java.lang.String dbName) Set the choosen Database as Database to search in
void	setEprofileAlignVec(java.util.Vector eprofileAlignVec)
void	setEprofileConsVec(java.util.Vector eprofileConsVec)
void	setFile(java.io.File file)
void	setFoldingaction(IFoldingAction foldingaction)
void	setGenuineHash(java.util.Hashtable genuineHash)
void	setIplotScoreVec(java.util.Vector iplotScoreVec)
void	setIprofileAlignScoreVec(java.util.Vector iprofileAlignScoreVec)
void	setIprofileAlignVec(java.util.Vector iprofileAlignVec)
void	setMatureSize(int matureSize)
void	setMethod(java.lang.String method)
void	setMirnaPOSinALIGN(int mirnaPOSinALIGN)
void	setMirnaPOSinPC(int[] mirnaPOSinPC)
void	setMultiplealignaction(IMultipleAlignAction multiplealignaction)
void	setPath(java.lang.String path)
void	setPropertieserties(java.util.Properties properties)
void	setScoreaction(IScoreAction scoreaction)
void	setSmoothWinSizeEx(int smoothWinSizeEx)
void	setSmoothWinSizeIn(int smoothWinSizeIn)
void	setStatus(Status status)
java.lang.String	show_extrinsicResults() Create output for EXTRINSIC method
java.lang.String	show_intrinsicPlusResults() Create output of INTRINSIC extended method
java.lang.String	show_intrinsicResults() Create output of INTRINSIC method

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

Operator

public Operator()

DefaultConstructor, load the program properties from local directory.

Operator

public Operator(java.net.URL url)

Constructor, load the program properties from URL

Parameters:

url - - URL where to load the program properties

Method Detail

getInstance

public static Operator getInstance()

Singleton

Returns:

Operator

readFile

public java.lang.String readFile(java.lang.String filename)

Reads a File

Parameters:

filename -

Returns:

Content of file.

createDatabaseFromFile

public void createDatabaseFromFile(java.lang.String path,
                                   java.lang.String dbName)
                            throws java.io.IOException

Deprecated.

Creates a database from a fasta file

Parameters:

path -

dbName -

Throws:

java.io.IOException

setDatabase

public void setDatabase(java.lang.String dbName)

Set the choosen Database as Database to search in

Parameters:

dbName -

getDatabase

public PrecursorContainer getDatabase()

Get the actual Database to work with

Returns:

actual Precursor Database

getCalcconservationaction

public ICalcConservationAction getCalcconservationaction()

Returns:

Returns the calcconservationaction.

setCalcconservationaction

public void setCalcconservationaction(ICalcConservationAction calcconservationaction)

Parameters:

calcconservationaction - The calcconservationaction to set.

getFoldingaction

public IFoldingAction getFoldingaction()

Returns:

Returns the foldingaction.

setFoldingaction

public void setFoldingaction(IFoldingAction foldingaction)

Parameters:

foldingaction - The foldingaction to set.

getMultiplealignaction

public IMultipleAlignAction getMultiplealignaction()

Returns:

Returns the multiplealignaction.

setMultiplealignaction

public void setMultiplealignaction(IMultipleAlignAction multiplealignaction)

Parameters:

multiplealignaction - The multiplealignaction to set.

getScoreaction

public IScoreAction getScoreaction()

Returns:

Returns the scoreaction.

setScoreaction

public void setScoreaction(IScoreAction scoreaction)

Parameters:

scoreaction - The scoreaction to set.

calcAverageValues

public double[] calcAverageValues(java.util.Vector dataVec)

Calculate array of average values(scores) from more than one precursor

Parameters:

dataVec -

Returns:

array of average values

predictMatureMiRNAin

public int predictMatureMiRNAin(java.util.Vector dataVec)

Predicts Position of mature miRNA on instrinsic data 1) calculating the avarage value of all precursors 2) finding the minimal value (relative to alignment) ! apply 'findStartInSinglePC' method to get the position of mature miRNA relative to the precursor

Parameters:

dataVec - Vector of aligned-scores for every Precursor

Returns:

start position of mature miRNA based on alignment

predictMatureMiRNAex

public int predictMatureMiRNAex(java.util.Vector dataVec)

Predicts Position of mature miRNA on extrinsic data by... 1) finding start position of the window with MAXIMAL sum (relative to alignment) ! apply 'findStartInSinglePC' method to get the position of mature miRNA relative to the precursor

Parameters:

dataVec - Vector which consists one array of conservation values

Returns:

start position of mature miRNA based on alignment

findStartInSinglePC

public int[] findStartInSinglePC(int startINalign,
                                 java.util.Vector align)

Parameters:

startINalign -

align -

Returns:

Start- and end-position of predicted miRNA based on single Precursor

run_intrinsicAction

public java.util.Vector run_intrinsicAction()

Action & Prediction with INTRINSIC method

Returns:

Vector of scored precursors

show_intrinsicResults

public java.lang.String show_intrinsicResults()

Create output of INTRINSIC method

Returns:

String of intrinsic results

run_intrinsicPlusAction

public java.util.Vector run_intrinsicPlusAction()

Action & Prediction with INTRINSIC extended method

Returns:

Vector of profile

show_intrinsicPlusResults

public java.lang.String show_intrinsicPlusResults()

Create output of INTRINSIC extended method

Returns:

String of intrinsic results

run_extrinsicAction

public java.util.Vector run_extrinsicAction()

Actions & Predction with EXTRINSIC method

Returns:

Vector of conservation

show_extrinsicResults

public java.lang.String show_extrinsicResults()

Create output for EXTRINSIC method

Returns:

String of extrinsic results

getSmoothWinSizeEx

public int getSmoothWinSizeEx()

Returns:

Returns the smoothWinSizeEx.

setSmoothWinSizeEx

public void setSmoothWinSizeEx(int smoothWinSizeEx)

Parameters:

smoothWinSizeEx - The smoothWinSizeEx to set.

getSmoothWinSizeIn

public int getSmoothWinSizeIn()

Returns:

Returns the smoothWinSizeIn.

setSmoothWinSizeIn

public void setSmoothWinSizeIn(int smoothWinSizeIn)

Parameters:

smoothWinSizeIn - The smoothWinSizeIn to set.

getIndelScore

public int getIndelScore()

Returns:

Returns the indelScore.

getMScore

public int getMScore()

Returns:

Returns the mScore.

getRpScore

public int getRpScore()

Returns:

Returns the rpScore.

getMirnaPOSinALIGN

public int getMirnaPOSinALIGN()

Returns:

Returns the mirnaPOSinALIGN.

setMirnaPOSinALIGN

public void setMirnaPOSinALIGN(int mirnaPOSinALIGN)

Parameters:

mirnaPOSinALIGN - The mirnaPOSinALIGN to set.

getMirnaPOSinPC

public int[] getMirnaPOSinPC()

Returns:

Returns the mirnaPOSinPC.

setMirnaPOSinPC

public void setMirnaPOSinPC(int[] mirnaPOSinPC)

Parameters:

mirnaPOSinPC - The mirnaPOAinPC to set.

getCutoff

public int getCutoff()

Returns:

Returns the cutoff.

setCutoff

public void setCutoff(int cutoff)

Parameters:

cutoff - The cutoff to set.

getMatureSize

public int getMatureSize()

Returns:

Returns the matureSize.

setMatureSize

public void setMatureSize(int matureSize)

Parameters:

matureSize - The matureSize to set.

getGenuineHash

public java.util.Hashtable getGenuineHash()

Returns:

Returns the genuineHash.

setGenuineHash

public void setGenuineHash(java.util.Hashtable genuineHash)

Parameters:

genuineHash - The genuineHash to set.

setActionPCs

public void setActionPCs(PrecursorContainer actionPCs)

Parameters:

actionPCs - The actionPCs to set.

setIplotScoreVec

public void setIplotScoreVec(java.util.Vector iplotScoreVec)

Parameters:

iplotScoreVec - The iplotScoreVec to set.

setIprofileAlignScoreVec

public void setIprofileAlignScoreVec(java.util.Vector iprofileAlignScoreVec)

Parameters:

iprofileAlignScoreVec - The iprofileAlignScoreVec to set.

setIprofileAlignVec

public void setIprofileAlignVec(java.util.Vector iprofileAlignVec)

Parameters:

iprofileAlignVec - The iprofileAlignVec to set.

setEprofileConsVec

public void setEprofileConsVec(java.util.Vector eprofileConsVec)

Parameters:

eprofileConsVec - The eprofileConsVec to set.

setEprofileAlignVec

public void setEprofileAlignVec(java.util.Vector eprofileAlignVec)

Parameters:

eprofileAlignVec - The eprofileAlignVec to set.

getMethod

public java.lang.String getMethod()

Returns:

Returns the method.

setMethod

public void setMethod(java.lang.String method)

Parameters:

method - The method to set.

getPath

public java.lang.String getPath()

Returns:

Returns the path.

setPath

public void setPath(java.lang.String path)

Parameters:

path - The path to set.

getProperties

public java.util.Properties getProperties()

Returns:

Returns the properties.

setPropertieserties

public void setPropertieserties(java.util.Properties properties)

Parameters:

propertieserties - The propertieserties to set.

getFile

public java.io.File getFile()

Returns:

Returns the filename.

setFile

public void setFile(java.io.File file)

Parameters:

filename - The filename to set.

getStatus

public Status getStatus()

Returns:

Returns the status.

setStatus

public void setStatus(Status status)

Parameters:

status - The status to set.