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MDACC Biostatistics |
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java.lang.Objectjava.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JPanel
org.mdanderson.biostat.geneclust.GeneClustPanel
GeneClustPanel - Implements the user interface of the application.
Nested Class Summary |
Nested classes inherited from class javax.swing.JPanel |
JPanel.AccessibleJPanel |
Nested classes inherited from class javax.swing.JComponent |
JComponent.AccessibleJComponent |
Nested classes inherited from class java.awt.Container |
Container.AccessibleAWTContainer |
Nested classes inherited from class java.awt.Component |
Component.AccessibleAWTComponent, Component.BltBufferStrategy, Component.FlipBufferStrategy |
Field Summary |
Fields inherited from class javax.swing.JComponent |
accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW |
Fields inherited from class java.awt.Component |
BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT |
Fields inherited from interface java.awt.image.ImageObserver |
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH |
Constructor Summary | |
GeneClustPanel(JFrame frame)
Class constructor |
Method Summary | |
double |
getAmplitude()
Returns the maximum value of signal used when generating matrix |
String |
getClassificationFileName()
Returns the string representing the classification filename |
int |
getDegreesFreedom()
Returns the degrees of freedom (used by certain noise distributions) |
int |
getGapTolerance()
Returns the gap tolerance |
String |
getModel(boolean removeWhitespace)
Returns the string representing the data model |
String |
getNoise()
Returns the string representing the noise |
int |
getNoiseIndex()
Returns the index of the selected noise |
int |
getNumClustersToExtract()
Returns the number of clusters to extract |
int |
getNumColumns()
Returns the number of samples in the gene expression matrix (cell lines) |
int |
getNumPermutations()
Returns the number of permutations to find optimal |
int |
getNumRows()
Returns the number of rows in the gene expression matrix (genes) |
int |
getPercentSupervision()
Returns the percent supervision |
int |
getPercentToShave()
Returns the percent to shave |
String |
getRawDataFileName()
Returns the string representing the filename |
boolean |
isDemoEnabled()
Returns boolean that tells whether data should be generated or not. |
boolean |
isDisplayDataMatrix()
Returns boolean that tells whether to display graph of hierarchial clustering of samples should be performed or not. |
boolean |
isDisplayGenesGraph()
Returns boolean that tells whether to display graph of hierarchial clustering of genes should be performed or not. |
boolean |
isDisplaySamplesGraph()
Returns boolean that tells whether to display graph of hierarchial clustering of samples should be performed or not. |
boolean |
isDisplayShaving()
Returns boolean that tells whether to display graph of hierarchial clustering of samples should be performed or not. |
boolean |
isPerformSupervised()
Returns boolean that tells whether supervised shaving should be performed or not. |
boolean |
isWriteMatrix()
Returns boolean that tells whether original matrix should be written to disk or not. |
Methods inherited from class javax.swing.JPanel |
getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
public GeneClustPanel(JFrame frame)
frame
- parent componentMethod Detail |
public boolean isWriteMatrix()
public boolean isDisplayGenesGraph()
public boolean isDisplaySamplesGraph()
public boolean isDisplayDataMatrix()
public boolean isDisplayShaving()
public boolean isPerformSupervised()
public int getPercentSupervision()
public String getClassificationFileName()
public int getNumClustersToExtract()
public int getNumPermutations()
public int getGapTolerance()
public int getPercentToShave()
public int getNumRows()
public int getNumColumns()
public double getAmplitude()
public String getModel(boolean removeWhitespace)
removeWhitespace
- if true, remove any whitespace from entry
public String getNoise()
public int getNoiseIndex()
public int getDegreesFreedom()
public String getRawDataFileName()
public boolean isDemoEnabled()
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MDACC Biostatistics |
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