IMPACT_S

Class DatamonkeyTP

java.lang.Object

IMPACT_S.DatamonkeyTP

public class DatamonkeyTP
extends java.lang.Object

Class to handle Datamonkey results and generate data from models SLAC, FEL, REL, MEME and FUBAR.

Author:

Emanuel Maldonado

Field Summary

Fields

Modifier and Type	Field and Description
static int	CommonModels Common Models (All selected models common sites) code = 9.
static java.lang.String	FELFileLocKey FEL input file key.
static int	FELmodel FEL model code = 1.
static java.lang.String	FUBARFileLocKey FUBAR input file key.
static int	FUBARmodel FUBAR model code = 4.
static java.lang.String	MEMEFileLocKey MEME input file key.
static int	MEMEmodel MEME model code = 3.
static java.lang.String	RELFileLocKey REL input file key.
static int	RELmodel REL model code = 2.
static java.lang.String	SLACFileLocKey SLAC input file key.
static int	SLACmodel SLAC model code = 0.

Constructor Summary

Constructors

Constructor and Description
DatamonkeyTP(Utilities utilities) Initialize Datamonkey tab.

Method Summary

Modifier and Type	Method and Description
java.lang.String	getCommonSites(java.lang.String models, boolean posneg, java.lang.String filepath) Get all common sites among all selected models.
java.lang.String	getDLocation(java.lang.String key) Get Datamonkey location.
java.util.HashMap<java.lang.String,java.lang.String>	getModelTable(char table, boolean posneg) Select which positive or negative selection to use, given also the table code.
void	retrieveFEL(double signiflevel) Retrieve FEL method Positive and Negative selection.
void	retrieveFUBAR(double signiflevel) Retrieve FUBAR method Positive and Negative selection.
void	retrieveMEME(double signiflevel) Retrieve MEME method Positive selection.
void	retrieveREL(double signiflevel) Retrieve REL method Positive and Negative selection.
void	retrieveSLAC(double signiflevel) Retrieve SLAC method Positive and Negative selection.
void	setDLocation(java.lang.String key, java.lang.String location) Set Datamonkey location.
java.lang.String	writeSelectionToFile(int dmmodel, boolean posneg, java.lang.String filepath) Write selected datamonkey summary of sites to file, given model code and if positive or negative selection.

Methods inherited from class java.lang.Object

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

Field Detail

SLACFileLocKey

public static final java.lang.String SLACFileLocKey

SLAC input file key.

See Also:

Constant Field Values

FELFileLocKey

public static final java.lang.String FELFileLocKey

FEL input file key.

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Constant Field Values

RELFileLocKey

public static final java.lang.String RELFileLocKey

REL input file key.

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Constant Field Values

MEMEFileLocKey

public static final java.lang.String MEMEFileLocKey

MEME input file key.

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Constant Field Values

FUBARFileLocKey

public static final java.lang.String FUBARFileLocKey

FUBAR input file key.

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Constant Field Values

SLACmodel

public static final int SLACmodel

SLAC model code = 0.

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Constant Field Values

FELmodel

public static final int FELmodel

FEL model code = 1.

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Constant Field Values

RELmodel

public static final int RELmodel

REL model code = 2.

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Constant Field Values

MEMEmodel

public static final int MEMEmodel

MEME model code = 3.

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Constant Field Values

FUBARmodel

public static final int FUBARmodel

FUBAR model code = 4.

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Constant Field Values

CommonModels

public static final int CommonModels

Common Models (All selected models common sites) code = 9.

See Also:

Constant Field Values

Constructor Detail

DatamonkeyTP

public DatamonkeyTP(Utilities utilities)

Initialize Datamonkey tab.

Parameters:

utilities - object from the class Utilities.

Method Detail

setDLocation

public void setDLocation(java.lang.String key,
                         java.lang.String location)

Set Datamonkey location.

Parameters:

key - access key for location

location - datamonkey files location.

getDLocation

public java.lang.String getDLocation(java.lang.String key)

Get Datamonkey location.

Parameters:

key - Access key to location.

Returns:

datamonkey location.

retrieveSLAC

public void retrieveSLAC(double signiflevel)

Retrieve SLAC method Positive and Negative selection. This is based on the p-value and dN >/< dS conditions.

Parameters:

signiflevel - user selected significance level.

retrieveFEL

public void retrieveFEL(double signiflevel)

Retrieve FEL method Positive and Negative selection. This is based on the p-value and dN >/< dS conditions.

Parameters:

signiflevel - user selected significance level.

retrieveREL

public void retrieveREL(double signiflevel)

Retrieve REL method Positive and Negative selection. This is based on the Empirical Bayes Factor.

Parameters:

signiflevel - user selected significance level.

retrieveMEME

public void retrieveMEME(double signiflevel)

Retrieve MEME method Positive selection. This is based on the p-value.

Parameters:

signiflevel - user selected significance level.

retrieveFUBAR

public void retrieveFUBAR(double signiflevel)

Retrieve FUBAR method Positive and Negative selection. This is based on the posterior probabilities.

Parameters:

signiflevel - user selected significance level.

getCommonSites

public java.lang.String getCommonSites(java.lang.String models,
                                       boolean posneg,
                                       java.lang.String filepath)

Get all common sites among all selected models.

Parameters:

models - integer string of selected models codes.

posneg - if true get positive selection; otherwise, get negative.

filepath - file path were to save the results.

Returns:

file path of saved result; or null if no data available from at least two models.

getModelTable

public java.util.HashMap<java.lang.String,java.lang.String> getModelTable(char table,
                                                                          boolean posneg)

Select which positive or negative selection to use, given also the table code.

Parameters:

table - table model code. (see below)

posneg - if true get positive selection; otherwise, get negative.

Returns:

selected table for either positive or negative selection.

See Also:

SLACmodel, FELmodel, RELmodel, MEMEmodel, FUBARmodel, CommonModels

writeSelectionToFile

public java.lang.String writeSelectionToFile(int dmmodel,
                                             boolean posneg,
                                             java.lang.String filepath)

Write selected datamonkey summary of sites to file, given model code and if positive or negative selection.

Parameters:

dmmodel - datamonkey model code. (see below)

posneg - if true write positive selection; otherwise, negative selection results.

filepath - file path were to save results.

Returns:

file path of the model positive or negative selection results; or null if MEME model was selected for negative selection.

See Also:

SLACmodel, FELmodel, RELmodel, MEMEmodel, FUBARmodel