MDACC
Biostatistics

org.mdanderson.biostat.geneclust
Class Settings

java.lang.Object
  extended byorg.mdanderson.biostat.geneclust.Settings

public class Settings
extends Object

Settings - Load and store settings for user interface values.


Constructor Summary
Settings()
          Class constructor
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

Settings

public Settings()
Class constructor


Settings

public Settings(boolean isDemoEnabled)
Class constructor specifying if demo enabled

Parameters:
isDemoEnabled - if true, set demo enabled; otherwise, disable it
Method Detail

read

public void read(File file)
          throws org.mdanderson.biostat.geneclust.FileVersionMismatchException,
                 FileNotFoundException
Reads the settings file and updates the associated GUI components with those values.

Parameters:
file - abstract pathname containing properties to read
Throws:
FileNotFoundException - if file could not be located
org.mdanderson.biostat.geneclust.FileVersionMismatchException - if file created by more recent version of this software

write

public void write(File file)
Writes the current GUI component values to a settings file.

Parameters:
file - abstract pathname where properties are to be saved

isDemoMode

public boolean isDemoMode()
Returns the selected simulation mode.

Returns:
true if demo mode selected; otherwise, false (raw data mode)
See Also:
setSelectedMode(boolean)

getSelectedMode

public String getSelectedMode()
Returns the selected simulation mode.

Returns:
string representing the selected mode
See Also:
setSelectedMode(boolean)

getIsDisplayGenesGraph

public boolean getIsDisplayGenesGraph()
Returns the flag used to determine if genes graph should be displayed.

Returns:
true if genes graph should be displayed
See Also:
setIsDisplayGenesGraph(boolean)

getIsDisplaySamplesGraph

public boolean getIsDisplaySamplesGraph()
Returns the flag used to determine if samples graph should be displayed.

Returns:
true if samples graph should be displayed
See Also:
setIsDisplaySamplesGraph(boolean)

getIsDisplayDataMatrix

public boolean getIsDisplayDataMatrix()
Returns the flag used to determine if samples graph should be displayed.

Returns:
true if samples graph should be displayed
See Also:
setIsDisplaySamplesGraph(boolean)

getIsDisplayShaving

public boolean getIsDisplayShaving()
Returns the flag used to determine if samples graph should be displayed.

Returns:
true if samples graph should be displayed
See Also:
setIsDisplaySamplesGraph(boolean)

getIsPerformSupervised

public boolean getIsPerformSupervised()
Returns the flag used to determine if supervised shaving should be performed.

Returns:
true if supervised shaving enabled; otherwise, false if supervised shaving disabled
See Also:
setIsPerformSupervised(boolean)

getPercentSupervision

public String getPercentSupervision()
Returns the supervision percentage.

Returns:
string containing percent supervision
See Also:
setPercentSupervision(java.lang.String)

getClassificationFileName

public String getClassificationFileName()
Returns the classification file to use for supervised shaving.

Returns:
string containing classification file name
See Also:
setClassificationFileName(java.lang.String)

getNumExtClusters

public String getNumExtClusters()
Returns the number of clusters to extract.

Returns:
string containing number of clusters to extract
See Also:
setNumExtClusters(java.lang.String)

getPercentToShave

public String getPercentToShave()
Returns the percent to shave.

Returns:
string containing percent to shave
See Also:
setPercentToShave(java.lang.String)

getNumPermutations

public String getNumPermutations()
Returns the number of permutations to find optimal cluster.

Returns:
string containing number of permutations
See Also:
setNumPermutations(java.lang.String)

getGapTolerance

public String getGapTolerance()
Returns the gap tolerance.

Returns:
string containing gap tolerance
See Also:
setGapTolerance(java.lang.String)

getRawDataFileName

public String getRawDataFileName()
Returns the raw data file to process.

Returns:
string containing raw data file name
See Also:
setRawDataFileName(java.lang.String)

getNumRows

public String getNumRows()
Returns the number of rows in the gene expression matrix (genes)

Returns:
string containing number of rows
See Also:
setNumRows(java.lang.String)

getNumColumns

public String getNumColumns()
Returns the number of samples in the gene expression matrix (cell lines)

Returns:
string containing number of columns
See Also:
setNumColumns(java.lang.String)

getAmplitude

public String getAmplitude()
Returns the maximum value of signal used when generating matrix

Returns:
string containing amplitude
See Also:
setAmplitude(java.lang.String)

getModel

public String getModel()
Returns the model to use when generating matrix

Returns:
string containing model (data generation type)
See Also:
setModel(java.lang.String)

getNoise

public String getNoise()
Returns the type of noise to use when generating matrix

Returns:
string containing noise to generate (none, Gaussian, Chi-square, or T)
See Also:
setNoise(java.lang.String)

getDegreesFreedom

public String getDegreesFreedom()
Returns the degrees of freedom needed by certain algorithms for noise generation

Returns:
string containing degrees of freedom
See Also:
setDegreesFreedom(java.lang.String), setNoise(java.lang.String)

setSelectedMode

public void setSelectedMode(boolean isDemoEnabled)
Sets the selected simulation mode.

Parameters:
isDemoEnabled - if true, set demo mode; otherwise, raw data mode
See Also:
setSelectedMode(String), getSelectedMode(), isDemoMode()

setSelectedMode

public void setSelectedMode(String mode)
Sets the selected simulation mode.

Parameters:
mode - string representing the selected mode
See Also:
setSelectedMode(boolean), getSelectedMode(), isDemoMode()

setIsDisplayGenesGraph

public void setIsDisplayGenesGraph(boolean isDisplayGenesGraph)
Sets the flag used to determine if genes graph should be displayed.

Parameters:
isDisplayGenesGraph - if true, enable genes graph display
See Also:
getIsDisplayGenesGraph()

setIsDisplaySamplesGraph

public void setIsDisplaySamplesGraph(boolean isDisplaySamplesGraph)
Sets the flag used to determine if samples graph should be displayed.

Parameters:
isDisplaySamplesGraph - if true, enable samples graph display
See Also:
getIsDisplaySamplesGraph()

setIsDisplayDataMatrix

public void setIsDisplayDataMatrix(boolean isDisplayDataMatrix)
Sets the flag used to determine if samples graph should be displayed.

Parameters:
isDisplayDataMatrix - if true, enable samples graph display
See Also:
getIsDisplayDataMatrix()

setIsDisplayShaving

public void setIsDisplayShaving(boolean isDisplayShaving)
Sets the flag used to determine if samples graph should be displayed.

Parameters:
isDisplayShaving - if true, enable samples graph display
See Also:
getIsDisplayShaving()

setIsPerformSupervised

public void setIsPerformSupervised(boolean isPerformSupervised)
Sets the flag used to determine if supervised shaving should be performed

Parameters:
isPerformSupervised - if true, enable supervised shaving
See Also:
getIsPerformSupervised()

setPercentSupervision

public void setPercentSupervision(String percentSupervision)
Sets the supervision percentage.

Parameters:
percentSupervision - string containing percent to supervise
See Also:
getPercentSupervision()

setClassificationFileName

public void setClassificationFileName(String classificationFileName)
Sets the classification file to use for supervised shaving.

Parameters:
classificationFileName - string containing classification file name
See Also:
getClassificationFileName()

setNumExtClusters

public void setNumExtClusters(String numExtClusters)
Sets the number of clusters to extract.

Parameters:
numExtClusters - string containing number of clusters to extract
See Also:
getNumExtClusters()

setPercentToShave

public void setPercentToShave(String percentToShave)
Sets the percent to shave.

Parameters:
percentToShave - string containing percent to shave
See Also:
getPercentToShave()

setNumPermutations

public void setNumPermutations(String numPermutations)
Sets the number of permutations to find optimal cluster.

Parameters:
numPermutations - string containing number of permutations
See Also:
getNumPermutations()

setGapTolerance

public void setGapTolerance(String gapTolerance)
Sets the gap tolerance.

Parameters:
gapTolerance - string containing gap tolerance
See Also:
getGapTolerance()

setRawDataFileName

public void setRawDataFileName(String rawDataFileName)
Sets the raw data file to process.

Parameters:
rawDataFileName - string containing raw data file name
See Also:
getRawDataFileName()

setNumRows

public void setNumRows(String numRows)
Sets the number of rows in the gene expression matrix (genes)

Parameters:
numRows - string containing number of rows
See Also:
getNumRows()

setNumColumns

public void setNumColumns(String numColumns)
Sets the number of samples in the gene expression matrix (cell lines)

Parameters:
numColumns - string containing number of columns
See Also:
getNumColumns()

setAmplitude

public void setAmplitude(String amplitude)
Sets the maximum value of signal used when generating matrix

Parameters:
amplitude - string containing amplitude
See Also:
getAmplitude()

setModel

public void setModel(String model)
Sets the model to use when generating matrix

Parameters:
model - string containing model (data generation type)
See Also:
getModel()

setNoise

public void setNoise(String noise)
Sets the type of noise to use when generating matrix

Parameters:
noise - string containing noise to generate (none, Gaussian, Chi-square, or T)
See Also:
getNoise()

setDegreesFreedom

public void setDegreesFreedom(String degreesFreedom)
Sets the degrees of freedom nneded by certain algorithms for noise generation

Parameters:
degreesFreedom - string containing degrees of freedom
See Also:
getDegreesFreedom(), setNoise(java.lang.String)

MDACC
Biostatistics

Copyright © 2002 M.D. Anderson Cancer Center. All Rights Reserved.