public class CodemlTP
extends java.lang.Object
GUICodemlOptions,
GUIAlignmentEditor,
GUIResultsView,
FileFormat| 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.
|
| 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.
|
public static final java.lang.String MSAFileKey
public static final java.lang.String TreeFileKey
public static final java.lang.String OutputFileKey
public static final java.lang.String ControlFileKey
public CodemlTP(Utilities utilities)
public double[] getChiSquare2DF()
getChiSquare2DFtoStr(int)public double[] getChiSquare4DF()
getChiSquare4DFtoStr(int)public java.lang.String[] getChiSquare2DFtoStr(int precision)
precision - integer determining the precision.getChiSquare2DF()public java.lang.String[] getChiSquare4DFtoStr(int precision)
precision - integer determining the precision.getChiSquare4DF()public java.lang.String getCDLocation(java.lang.String key)
key - key for a specific codeml location.public void setCDLocation(java.lang.String key,
java.lang.String value)
key - the key specifying the location.value - the location for the corresponding key.public boolean extractBEBResults(int selectedIndex,
java.lang.String[] searchmodel)
selectedIndex - the index from where to match rows to be extracted (0 or 1).searchmodel - indication of the model to be found and searched.public java.lang.String[] getExtractedBEB()
public java.lang.String[] getLikelihoodValues()
public java.lang.String[] getNumberParam()
public java.lang.String extractedBEBtoFile(java.lang.String filepath)
filepath - the path pointing to file were to save BEB.public java.util.HashMap<java.lang.String,java.lang.String> getExtractedBEBAsTable()
public void collectResultsInfo(java.lang.String models)
models - the models for which to collect information.public java.lang.String getLnlTable(java.lang.String file)
file - the file where to save table.collectResultsInfo(java.lang.String)public java.lang.String getRatioTable(java.lang.String file)
file - the file where to save table.collectResultsInfo(java.lang.String)