IMPACT_S

Class CodemlTP

java.lang.Object

IMPACT_S.CodemlTP

public class CodemlTP
extends java.lang.Object

Class to handle PAML (Codeml) results and input data.

Author:

Emanuel Maldonado

See Also:

GUICodemlOptions, GUIAlignmentEditor, GUIResultsView, FileFormat

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	ControlFileKey Codeml control file key.
static java.lang.String	MSAFileKey Codeml input MSA file key.
static java.lang.String	OutputFileKey Codeml ouput file key.
static java.lang.String	TreeFileKey Codeml input Tree file key.

Constructor Summary

Constructors

Constructor and Description
CodemlTP(Utilities utilities)

Method Summary

Modifier and Type	Method and Description
void	collectResultsInfo(java.lang.String models) Collect codeml results file information.
boolean	extractBEBResults(int selectedIndex, java.lang.String[] searchmodel) Extract results from Bayes Empirical Bayes section.
java.lang.String	extractedBEBtoFile(java.lang.String filepath) Save extracted BEB section to file.
java.lang.String	getCDLocation(java.lang.String key) Get location for Codeml Panel, given key.
double[]	getChiSquare2DF() Get the Chi Square Critical Values for 2 Degrees of Freedom and significance of 0.05, 0.01 and 0.001 respectively.
java.lang.String[]	getChiSquare2DFtoStr(int precision) Get the Chi Square Critical Values as strings.
double[]	getChiSquare4DF() Get the Chi Square Critical Values for 4 Degrees of Freedom and significance of 0.05, 0.01 and 0.001 respectively.
java.lang.String[]	getChiSquare4DFtoStr(int precision) Get the Chi Square Critical Values as strings.
java.lang.String[]	getExtractedBEB() Get extracted BEB rows.
java.util.HashMap<java.lang.String,java.lang.String>	getExtractedBEBAsTable() Get BEB results as hashtable.
java.lang.String[]	getLikelihoodValues() Get the likelihood values found in codeml results, in specified or searched models.
java.lang.String	getLnlTable(java.lang.String file) Create CSV file from collected information.
java.lang.String[]	getNumberParam() Get the np values found in codeml results, in specified or searched models.
java.lang.String	getRatioTable(java.lang.String file) Create ratios (dN/dS) table from collected information.
void	setCDLocation(java.lang.String key, java.lang.String value) Set value for specified key.

Methods inherited from class java.lang.Object

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

Field Detail

MSAFileKey

public static final java.lang.String MSAFileKey

Codeml input MSA file key.

See Also:

Constant Field Values

TreeFileKey

public static final java.lang.String TreeFileKey

Codeml input Tree file key.

See Also:

Constant Field Values

OutputFileKey

public static final java.lang.String OutputFileKey

Codeml ouput file key.

See Also:

Constant Field Values

ControlFileKey

public static final java.lang.String ControlFileKey

Codeml control file key.

See Also:

Constant Field Values

Constructor Detail

CodemlTP

public CodemlTP(Utilities utilities)

Method Detail

getChiSquare2DF

public double[] getChiSquare2DF()

Get the Chi Square Critical Values for 2 Degrees of Freedom and significance of 0.05, 0.01 and 0.001 respectively. These values provide 4 decimal places.

Returns:

an array of double values by this order.

See Also:

getChiSquare2DFtoStr(int)

getChiSquare4DF

public double[] getChiSquare4DF()

Get the Chi Square Critical Values for 4 Degrees of Freedom and significance of 0.05, 0.01 and 0.001 respectively. These values provide 4 decimal places.

Returns:

an array of double values by this order.

See Also:

getChiSquare4DFtoStr(int)

getChiSquare2DFtoStr

public java.lang.String[] getChiSquare2DFtoStr(int precision)

Get the Chi Square Critical Values as strings. For 2 Degrees of Freedom and significance of 0.05, 0.01 and 0.001.

Parameters:

precision - integer determining the precision.

Returns:

an array of Strings; each position representing a value, by same original order.

See Also:

getChiSquare2DF()

getChiSquare4DFtoStr

public java.lang.String[] getChiSquare4DFtoStr(int precision)

Get the Chi Square Critical Values as strings. For 4 Degrees of Freedom and significance of 0.05, 0.01 and 0.001.

Parameters:

precision - integer determining the precision.

Returns:

an array of Strings; each position representing a value, by same original order.

See Also:

getChiSquare4DF()

getCDLocation

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

Get location for Codeml Panel, given key.

Parameters:

key - key for a specific codeml location.

Returns:

value the location for the specified key.

setCDLocation

public void setCDLocation(java.lang.String key,
                          java.lang.String value)

Set value for specified key.

Parameters:

key - the key specifying the location.

value - the location for the corresponding key.

extractBEBResults

public boolean extractBEBResults(int selectedIndex,
                                 java.lang.String[] searchmodel)

Extract results from Bayes Empirical Bayes section. This only is possible for Models (7,8) and (1,2). The Model (0,3) does not provide BEB results.

Parameters:

selectedIndex - the index from where to match rows to be extracted (0 or 1).

searchmodel - indication of the model to be found and searched.

Returns:

list of extracted rows.

getExtractedBEB

public java.lang.String[] getExtractedBEB()

Get extracted BEB rows.

Returns:

BEB rows; or empty if not successful.

getLikelihoodValues

public java.lang.String[] getLikelihoodValues()

Get the likelihood values found in codeml results, in specified or searched models.

Returns:

an array of two positions containing the values in same order as models were found. So, position 1 will match model 0,1 or 7 and position two will match model 3,2 or 8 respectively,
according to option chosen by the user. Returns null in case no valid values were found.

getNumberParam

public java.lang.String[] getNumberParam()

Get the np values found in codeml results, in specified or searched models.

Returns:

an array of two positions containing the values in same order as models were found. So, position 1 will match model 0,1 or 7 and position two will match model 3,2 or 8 respectively,
according to option chosen by the user. Returns null in case no valid values were found.

extractedBEBtoFile

public java.lang.String extractedBEBtoFile(java.lang.String filepath)

Save extracted BEB section to file.

Parameters:

filepath - the path pointing to file were to save BEB.

Returns:

path were saved.

getExtractedBEBAsTable

public java.util.HashMap<java.lang.String,java.lang.String> getExtractedBEBAsTable()

Get BEB results as hashtable. Sites as keys and BEB rows as values.

Returns:

BEB results; or null if nothing extracted.

collectResultsInfo

public void collectResultsInfo(java.lang.String models)

Collect codeml results file information.

Parameters:

models - the models for which to collect information.

getLnlTable

public java.lang.String getLnlTable(java.lang.String file)

Create CSV file from collected information.

Parameters:

file - the file where to save table.

Returns:

file path.

See Also:

collectResultsInfo(java.lang.String)

getRatioTable

public java.lang.String getRatioTable(java.lang.String file)

Create ratios (dN/dS) table from collected information.

Parameters:

file - the file where to save table.

Returns:

file path.

See Also:

collectResultsInfo(java.lang.String)