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MDACC Biostatistics |
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java.lang.Objectorg.mdanderson.biostat.geneclust.Settings
Settings - Load and store settings for user interface values.
Constructor Summary | |
Settings()
Class constructor |
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Settings(boolean isDemoEnabled)
Class constructor specifying if demo enabled |
Method Summary | |
String |
getAmplitude()
Returns the maximum value of signal used when generating matrix |
String |
getClassificationFileName()
Returns the classification file to use for supervised shaving. |
String |
getDegreesFreedom()
Returns the degrees of freedom needed by certain algorithms for noise generation |
String |
getGapTolerance()
Returns the gap tolerance. |
boolean |
getIsDisplayDataMatrix()
Returns the flag used to determine if samples graph should be displayed. |
boolean |
getIsDisplayGenesGraph()
Returns the flag used to determine if genes graph should be displayed. |
boolean |
getIsDisplaySamplesGraph()
Returns the flag used to determine if samples graph should be displayed. |
boolean |
getIsDisplayShaving()
Returns the flag used to determine if samples graph should be displayed. |
boolean |
getIsPerformSupervised()
Returns the flag used to determine if supervised shaving should be performed. |
String |
getModel()
Returns the model to use when generating matrix |
String |
getNoise()
Returns the type of noise to use when generating matrix |
String |
getNumColumns()
Returns the number of samples in the gene expression matrix (cell lines) |
String |
getNumExtClusters()
Returns the number of clusters to extract. |
String |
getNumPermutations()
Returns the number of permutations to find optimal cluster. |
String |
getNumRows()
Returns the number of rows in the gene expression matrix (genes) |
String |
getPercentSupervision()
Returns the supervision percentage. |
String |
getPercentToShave()
Returns the percent to shave. |
String |
getRawDataFileName()
Returns the raw data file to process. |
String |
getSelectedMode()
Returns the selected simulation mode. |
boolean |
isDemoMode()
Returns the selected simulation mode. |
void |
read(File file)
Reads the settings file and updates the associated GUI components with those values. |
void |
setAmplitude(String amplitude)
Sets the maximum value of signal used when generating matrix |
void |
setClassificationFileName(String classificationFileName)
Sets the classification file to use for supervised shaving. |
void |
setDegreesFreedom(String degreesFreedom)
Sets the degrees of freedom nneded by certain algorithms for noise generation |
void |
setGapTolerance(String gapTolerance)
Sets the gap tolerance. |
void |
setIsDisplayDataMatrix(boolean isDisplayDataMatrix)
Sets the flag used to determine if samples graph should be displayed. |
void |
setIsDisplayGenesGraph(boolean isDisplayGenesGraph)
Sets the flag used to determine if genes graph should be displayed. |
void |
setIsDisplaySamplesGraph(boolean isDisplaySamplesGraph)
Sets the flag used to determine if samples graph should be displayed. |
void |
setIsDisplayShaving(boolean isDisplayShaving)
Sets the flag used to determine if samples graph should be displayed. |
void |
setIsPerformSupervised(boolean isPerformSupervised)
Sets the flag used to determine if supervised shaving should be performed |
void |
setModel(String model)
Sets the model to use when generating matrix |
void |
setNoise(String noise)
Sets the type of noise to use when generating matrix |
void |
setNumColumns(String numColumns)
Sets the number of samples in the gene expression matrix (cell lines) |
void |
setNumExtClusters(String numExtClusters)
Sets the number of clusters to extract. |
void |
setNumPermutations(String numPermutations)
Sets the number of permutations to find optimal cluster. |
void |
setNumRows(String numRows)
Sets the number of rows in the gene expression matrix (genes) |
void |
setPercentSupervision(String percentSupervision)
Sets the supervision percentage. |
void |
setPercentToShave(String percentToShave)
Sets the percent to shave. |
void |
setRawDataFileName(String rawDataFileName)
Sets the raw data file to process. |
void |
setSelectedMode(boolean isDemoEnabled)
Sets the selected simulation mode. |
void |
setSelectedMode(String mode)
Sets the selected simulation mode. |
void |
write(File file)
Writes the current GUI component values to a settings file. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
public Settings()
public Settings(boolean isDemoEnabled)
isDemoEnabled
- if true, set demo enabled; otherwise, disable itMethod Detail |
public void read(File file) throws org.mdanderson.biostat.geneclust.FileVersionMismatchException, FileNotFoundException
file
- abstract pathname containing properties to read
FileNotFoundException
- if file could not be located
org.mdanderson.biostat.geneclust.FileVersionMismatchException
- if file created by more recent
version of this softwarepublic void write(File file)
file
- abstract pathname where properties are to be savedpublic boolean isDemoMode()
setSelectedMode(boolean)
public String getSelectedMode()
setSelectedMode(boolean)
public boolean getIsDisplayGenesGraph()
setIsDisplayGenesGraph(boolean)
public boolean getIsDisplaySamplesGraph()
setIsDisplaySamplesGraph(boolean)
public boolean getIsDisplayDataMatrix()
setIsDisplaySamplesGraph(boolean)
public boolean getIsDisplayShaving()
setIsDisplaySamplesGraph(boolean)
public boolean getIsPerformSupervised()
setIsPerformSupervised(boolean)
public String getPercentSupervision()
setPercentSupervision(java.lang.String)
public String getClassificationFileName()
setClassificationFileName(java.lang.String)
public String getNumExtClusters()
setNumExtClusters(java.lang.String)
public String getPercentToShave()
setPercentToShave(java.lang.String)
public String getNumPermutations()
setNumPermutations(java.lang.String)
public String getGapTolerance()
setGapTolerance(java.lang.String)
public String getRawDataFileName()
setRawDataFileName(java.lang.String)
public String getNumRows()
setNumRows(java.lang.String)
public String getNumColumns()
setNumColumns(java.lang.String)
public String getAmplitude()
setAmplitude(java.lang.String)
public String getModel()
setModel(java.lang.String)
public String getNoise()
setNoise(java.lang.String)
public String getDegreesFreedom()
setDegreesFreedom(java.lang.String)
,
setNoise(java.lang.String)
public void setSelectedMode(boolean isDemoEnabled)
isDemoEnabled
- if true, set demo mode; otherwise, raw data modesetSelectedMode(String)
,
getSelectedMode()
,
isDemoMode()
public void setSelectedMode(String mode)
mode
- string representing the selected modesetSelectedMode(boolean)
,
getSelectedMode()
,
isDemoMode()
public void setIsDisplayGenesGraph(boolean isDisplayGenesGraph)
isDisplayGenesGraph
- if true, enable genes graph displaygetIsDisplayGenesGraph()
public void setIsDisplaySamplesGraph(boolean isDisplaySamplesGraph)
isDisplaySamplesGraph
- if true, enable samples graph displaygetIsDisplaySamplesGraph()
public void setIsDisplayDataMatrix(boolean isDisplayDataMatrix)
isDisplayDataMatrix
- if true, enable samples graph displaygetIsDisplayDataMatrix()
public void setIsDisplayShaving(boolean isDisplayShaving)
isDisplayShaving
- if true, enable samples graph displaygetIsDisplayShaving()
public void setIsPerformSupervised(boolean isPerformSupervised)
isPerformSupervised
- if true, enable supervised shavinggetIsPerformSupervised()
public void setPercentSupervision(String percentSupervision)
percentSupervision
- string containing percent to supervisegetPercentSupervision()
public void setClassificationFileName(String classificationFileName)
classificationFileName
- string containing classification file namegetClassificationFileName()
public void setNumExtClusters(String numExtClusters)
numExtClusters
- string containing number of clusters to extractgetNumExtClusters()
public void setPercentToShave(String percentToShave)
percentToShave
- string containing percent to shavegetPercentToShave()
public void setNumPermutations(String numPermutations)
numPermutations
- string containing number of permutationsgetNumPermutations()
public void setGapTolerance(String gapTolerance)
gapTolerance
- string containing gap tolerancegetGapTolerance()
public void setRawDataFileName(String rawDataFileName)
rawDataFileName
- string containing raw data file namegetRawDataFileName()
public void setNumRows(String numRows)
numRows
- string containing number of rowsgetNumRows()
public void setNumColumns(String numColumns)
numColumns
- string containing number of columnsgetNumColumns()
public void setAmplitude(String amplitude)
amplitude
- string containing amplitudegetAmplitude()
public void setModel(String model)
model
- string containing model (data generation type)getModel()
public void setNoise(String noise)
noise
- string containing noise to generate
(none, Gaussian, Chi-square, or T)getNoise()
public void setDegreesFreedom(String degreesFreedom)
degreesFreedom
- string containing degrees of freedomgetDegreesFreedom()
,
setNoise(java.lang.String)
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MDACC Biostatistics |
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