MDACC
Biostatistics

org.mdanderson.biostat.geneclust
Class GeneClustPanel

java.lang.Object
  extended byjava.awt.Component
      extended byjava.awt.Container
          extended byjavax.swing.JComponent
              extended byjavax.swing.JPanel
                  extended byorg.mdanderson.biostat.geneclust.GeneClustPanel
All Implemented Interfaces:
Accessible, GeneClustKeys, ImageObserver, MenuContainer, Serializable

public class GeneClustPanel
extends JPanel
implements GeneClustKeys

GeneClustPanel - Implements the user interface of the application.

See Also:
Serialized Form

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 org.mdanderson.biostat.geneclust.GeneClustKeys
ABOUT_DIALOG_CONTACT_EMAIL_ADDRESS, ABOUT_DIALOG_CONTACT_EMAIL_ADDRESS_DESCRIPTION, ABOUT_DIALOG_CONTACT_EMAIL_LABEL, ABOUT_DIALOG_CONTACT_PANEL_TITLE, ABOUT_DIALOG_CONTACT_USPS_ADDRESS_CITY_STATE, ABOUT_DIALOG_CONTACT_USPS_ADDRESS_NAME, ABOUT_DIALOG_CONTACT_USPS_ADDRESS_STREET, ABOUT_DIALOG_CONTACT_USPS_LABEL, ABOUT_DIALOG_CONTACT_WEB_ADDRESS, ABOUT_DIALOG_CONTACT_WEB_ADDRESS_DESCRIPTION, ABOUT_DIALOG_CONTACT_WEB_LABEL, ABOUT_DIALOG_CREDITS_COLLABORATOR_LABEL, ABOUT_DIALOG_CREDITS_DEVELOPER_LABEL, ABOUT_DIALOG_CREDITS_RESEARCHER_LABEL, ABOUT_DIALOG_TITLE, ABOUT_MENUITEM_DESCRIPTION, ABOUT_MENUITEM_LABEL, ABOUT_MENUITEM_MNEMONIC, ABOUT_MENUITEM_TOOLTIP, AMPLITUDE_LABEL, AMPLITUDE_TEXTFIELD_COLUMNS, AMPLITUDE_TEXTFIELD_DEFAULT_VALUE, AMPLITUDE_TEXTFIELD_DESCRIPTION, AMPLITUDE_TEXTFIELD_MAXIMUM_VALUE, AMPLITUDE_TEXTFIELD_MINIMUM_VALUE, AMPLITUDE_TEXTFIELD_TOOLTIP, APPLICATION_COPYRIGHT, APPLICATION_DESCRIPTION, APPLICATION_LEGALITIES, APPLICATION_NAME, APPLICATION_RELEASE_DATE, APPLICATION_USAGE, APPLICATION_VERSION, APPLICATION_WINDOW_TITLE, CHOOSE_CLASSIFICATION_FILE_SELECTION_DIALOG_TITLE, CHOOSE_DATA_FILE_SELECTION_DIALOG_TITLE, CHOOSE_FILE_SELECTION_DIALOG_OK_BUTTON_LABEL, CHOOSE_FILE_SELECTION_DIALOG_OK_BUTTON_TOOLTIP, CLASSIFICATION_FILENAME_CHOOSER_BUTTON_DESCRIPTION, CLASSIFICATION_FILENAME_CHOOSER_BUTTON_LABEL, CLASSIFICATION_FILENAME_CHOOSER_BUTTON_TOOLTIP, CLASSIFICATION_FILENAME_LABEL, CLASSIFICATION_FILENAME_TEXTFIELD_COLUMNS, CLASSIFICATION_FILENAME_TEXTFIELD_DEFAULT_VALUE, CLASSIFICATION_FILENAME_TEXTFIELD_DESCRIPTION, CLASSIFICATION_FILENAME_TEXTFIELD_TOOLTIP, DEGREES_FREEDOM_LABEL, DEGREES_FREEDOM_TEXTFIELD_COLUMNS, DEGREES_FREEDOM_TEXTFIELD_DEFAULT_VALUE, DEGREES_FREEDOM_TEXTFIELD_DESCRIPTION, DEGREES_FREEDOM_TEXTFIELD_MAXIMUM_VALUE, DEGREES_FREEDOM_TEXTFIELD_MINIMUM_VALUE, DEGREES_FREEDOM_TEXTFIELD_TOOLTIP, DEMO_DATA_TAB_TITLE, DISPLAY_BUTTON_DESCRIPTION, DISPLAY_BUTTON_LABEL, DISPLAY_BUTTON_TOOLTIP, DISPLAY_DATA_MATRIX_CHECKBOX_DEFAULT_VALUE, DISPLAY_DATA_MATRIX_CHECKBOX_DESCRIPTION, DISPLAY_DATA_MATRIX_CHECKBOX_LABEL, DISPLAY_DATA_MATRIX_CHECKBOX_TOOLTIP, DISPLAY_GENES_GRAPH_CHECKBOX_DEFAULT_VALUE, DISPLAY_GENES_GRAPH_CHECKBOX_DESCRIPTION, DISPLAY_GENES_GRAPH_CHECKBOX_LABEL, DISPLAY_GENES_GRAPH_CHECKBOX_TOOLTIP, DISPLAY_PANEL_TITLE, DISPLAY_SAMPLES_GRAPH_CHECKBOX_DEFAULT_VALUE, DISPLAY_SAMPLES_GRAPH_CHECKBOX_DESCRIPTION, DISPLAY_SAMPLES_GRAPH_CHECKBOX_LABEL, DISPLAY_SAMPLES_GRAPH_CHECKBOX_TOOLTIP, DISPLAY_SHAVING_CLUSTERS_CHECKBOX_DEFAULT_VALUE, DISPLAY_SHAVING_CLUSTERS_CHECKBOX_DESCRIPTION, DISPLAY_SHAVING_CLUSTERS_CHECKBOX_LABEL, DISPLAY_SHAVING_CLUSTERS_CHECKBOX_TOOLTIP, ENABLE_DEMO_CHECKBOX_DESCRIPTION, ENABLE_DEMO_CHECKBOX_TOOLTIP, ENABLE_DEMO_LABEL, ERR_EXTRACT_CLUSTERS_TOO_BIG, ERR_FILE_VERSION_MISMATCH, ERR_JVM_PREREQUISITE, ERR_LOAD_FILE, ERR_NO_PROPERTY_ITEMS_FOUND, ERR_SIMULATION_FAILED, ERROR_DIALOG_TITLE, EXIT_MENUITEM_DESCRIPTION, EXIT_MENUITEM_LABEL, EXIT_MENUITEM_MNEMONIC, EXIT_MENUITEM_TOOLTIP, FILE_MENU_DESCRIPTION, FILE_MENU_LABEL, GAP_TOLERANCE_LABEL, GAP_TOLERANCE_TEXTFIELD_COLUMNS, GAP_TOLERANCE_TEXTFIELD_DEFAULT_VALUE, GAP_TOLERANCE_TEXTFIELD_DESCRIPTION, GAP_TOLERANCE_TEXTFIELD_MAXIMUM_VALUE, GAP_TOLERANCE_TEXTFIELD_MINIMUM_VALUE, GAP_TOLERANCE_TEXTFIELD_TOOLTIP, HELP_MENU_DESCRIPTION, HELP_MENU_LABEL, INFO_LOAD_FILE, INFO_STARTUP, LOGO_DESCRIPTION, MENUBAR_DESCRIPTION, MODEL_COMBOBOX_DESCRIPTION, MODEL_COMBOBOX_ITEM_LABEL_1, MODEL_COMBOBOX_ITEM_LABEL_10, MODEL_COMBOBOX_ITEM_LABEL_2, MODEL_COMBOBOX_ITEM_LABEL_3, MODEL_COMBOBOX_ITEM_LABEL_4, MODEL_COMBOBOX_ITEM_LABEL_5, MODEL_COMBOBOX_ITEM_LABEL_6, MODEL_COMBOBOX_ITEM_LABEL_7, MODEL_COMBOBOX_ITEM_LABEL_8, MODEL_COMBOBOX_ITEM_LABEL_9, MODEL_COMBOBOX_TOOLTIP, MODEL_LABEL, NO_EXCEPTION_DETAIL_MESSAGE, NOISE_COMBOBOX_DESCRIPTION, NOISE_COMBOBOX_ITEM_LABEL_1, NOISE_COMBOBOX_ITEM_LABEL_2, NOISE_COMBOBOX_ITEM_LABEL_3, NOISE_COMBOBOX_ITEM_LABEL_4, NOISE_COMBOBOX_TOOLTIP, NOISE_LABEL, NUM_CLUSTERS_TO_EXTRACT_LABEL, NUM_CLUSTERS_TO_EXTRACT_TEXTFIELD_COLUMNS, NUM_CLUSTERS_TO_EXTRACT_TEXTFIELD_DEFAULT_VALUE, NUM_CLUSTERS_TO_EXTRACT_TEXTFIELD_DESCRIPTION, NUM_CLUSTERS_TO_EXTRACT_TEXTFIELD_MAXIMUM_VALUE, NUM_CLUSTERS_TO_EXTRACT_TEXTFIELD_MINIMUM_VALUE, NUM_CLUSTERS_TO_EXTRACT_TEXTFIELD_TOOLTIP, NUM_COLUMNS_LABEL, NUM_COLUMNS_TEXTFIELD_COLUMNS, NUM_COLUMNS_TEXTFIELD_DEFAULT_VALUE, NUM_COLUMNS_TEXTFIELD_DESCRIPTION, NUM_COLUMNS_TEXTFIELD_MAXIMUM_VALUE, NUM_COLUMNS_TEXTFIELD_MINIMUM_VALUE, NUM_COLUMNS_TEXTFIELD_TOOLTIP, NUM_PERMUTATIONS_LABEL, NUM_PERMUTATIONS_TEXTFIELD_COLUMNS, NUM_PERMUTATIONS_TEXTFIELD_DEFAULT_VALUE, NUM_PERMUTATIONS_TEXTFIELD_DESCRIPTION, NUM_PERMUTATIONS_TEXTFIELD_MAXIMUM_VALUE, NUM_PERMUTATIONS_TEXTFIELD_MINIMUM_VALUE, NUM_PERMUTATIONS_TEXTFIELD_TOOLTIP, NUM_ROWS_LABEL, NUM_ROWS_TEXTFIELD_COLUMNS, NUM_ROWS_TEXTFIELD_DEFAULT_VALUE, NUM_ROWS_TEXTFIELD_DESCRIPTION, NUM_ROWS_TEXTFIELD_MAXIMUM_VALUE, NUM_ROWS_TEXTFIELD_MINIMUM_VALUE, NUM_ROWS_TEXTFIELD_TOOLTIP, OPEN_MENUITEM_DESCRIPTION, OPEN_MENUITEM_LABEL, OPEN_MENUITEM_MNEMONIC, OPEN_MENUITEM_TOOLTIP, OPEN_SETTINGS_FILE_SELECTION_DIALOG_TITLE, OVERVIEW_DIALOG_MESSAGE, OVERVIEW_DIALOG_TITLE, OVERVIEW_MENUITEM_DESCRIPTION, OVERVIEW_MENUITEM_LABEL, OVERVIEW_MENUITEM_MNEMONIC, OVERVIEW_MENUITEM_TOOLTIP, OVERWRITE_DIALOG_MESSAGE, OVERWRITE_DIALOG_TITLE, PACKAGE_NAME, PERCENT_SUPERVISION_LABEL, PERCENT_SUPERVISION_TEXTFIELD_COLUMNS, PERCENT_SUPERVISION_TEXTFIELD_DEFAULT_VALUE, PERCENT_SUPERVISION_TEXTFIELD_DESCRIPTION, PERCENT_SUPERVISION_TEXTFIELD_MAXIMUM_VALUE, PERCENT_SUPERVISION_TEXTFIELD_MINIMUM_VALUE, PERCENT_SUPERVISION_TEXTFIELD_TOOLTIP, PERCENT_TO_SHAVE_LABEL, PERCENT_TO_SHAVE_TEXTFIELD_COLUMNS, PERCENT_TO_SHAVE_TEXTFIELD_DEFAULT_VALUE, PERCENT_TO_SHAVE_TEXTFIELD_DESCRIPTION, PERCENT_TO_SHAVE_TEXTFIELD_MAXIMUM_VALUE, PERCENT_TO_SHAVE_TEXTFIELD_MINIMUM_VALUE, PERCENT_TO_SHAVE_TEXTFIELD_TOOLTIP, PERFORM_SUPERVISED_CHECKBOX_DEFAULT_VALUE, PERFORM_SUPERVISED_CHECKBOX_DESCRIPTION, PERFORM_SUPERVISED_CHECKBOX_LABEL, PERFORM_SUPERVISED_CHECKBOX_TOOLTIP, RAW_DATA_FILENAME_CHOOSER_BUTTON_DESCRIPTION, RAW_DATA_FILENAME_CHOOSER_BUTTON_LABEL, RAW_DATA_FILENAME_CHOOSER_BUTTON_TOOLTIP, RAW_DATA_FILENAME_LABEL, RAW_DATA_FILENAME_TEXTFIELD_COLUMNS, RAW_DATA_FILENAME_TEXTFIELD_DEFAULT_VALUE, RAW_DATA_FILENAME_TEXTFIELD_DESCRIPTION, RAW_DATA_FILENAME_TEXTFIELD_TOOLTIP, RAW_DATA_TAB_TITLE, SAVE_MENUITEM_DESCRIPTION, SAVE_MENUITEM_LABEL, SAVE_MENUITEM_MNEMONIC, SAVE_MENUITEM_TOOLTIP, SAVE_SETTINGS_FILE_SELECTION_DIALOG_TITLE, SHAVING_PANEL_TITLE, SIMULATION_DIALOG_BUTTON_LABEL, SIMULATION_DIALOG_MESSAGE, SIMULATION_DIALOG_TITLE, USER_GUIDE_DIALOG_TITLE, USER_GUIDE_FILE_URL, USER_GUIDE_HTTP_URL, USER_GUIDE_MENUITEM_DESCRIPTION, USER_GUIDE_MENUITEM_LABEL, USER_GUIDE_MENUITEM_MNEMONIC, USER_GUIDE_MENUITEM_TOOLTIP
 
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 javax.swing.JComponent
addAncestorListener, addNotify, addPropertyChangeListener, addPropertyChangeListener, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBorder, getBounds, getClientProperty, getComponentGraphics, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getGraphics, getHeight, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPreferredSize, getPropertyChangeListeners, getPropertyChangeListeners, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isOptimizedDrawingEnabled, isPaintingTile, isPreferredSizeSet, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removePropertyChangeListener, removePropertyChangeListener, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFont, setForeground, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update
 
Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, addImpl, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, setLayout, transferFocusBackward, transferFocusDownCycle, validate, validateTree
 
Methods inherited from class java.awt.Component
action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMouseWheelListeners, getName, getParent, getPeer, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusUpCycle
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

GeneClustPanel

public GeneClustPanel(JFrame frame)
Class constructor

Parameters:
frame - parent component
Method Detail

isWriteMatrix

public boolean isWriteMatrix()
Returns boolean that tells whether original matrix should be written to disk or not. Only really needed for demo mode since there is otherwise no means of seeing what got 'created' based on the interface settings on the demo tab. In raw data mode, the data file already exists.

Returns:
true or false

isDisplayGenesGraph

public boolean isDisplayGenesGraph()
Returns boolean that tells whether to display graph of hierarchial clustering of genes should be performed or not.

Returns:
true or false

isDisplaySamplesGraph

public boolean isDisplaySamplesGraph()
Returns boolean that tells whether to display graph of hierarchial clustering of samples should be performed or not.

Returns:
true or false

isDisplayDataMatrix

public boolean isDisplayDataMatrix()
Returns boolean that tells whether to display graph of hierarchial clustering of samples should be performed or not.

Returns:
true or false

isDisplayShaving

public boolean isDisplayShaving()
Returns boolean that tells whether to display graph of hierarchial clustering of samples should be performed or not.

Returns:
true or false

isPerformSupervised

public boolean isPerformSupervised()
Returns boolean that tells whether supervised shaving should be performed or not.

Returns:
true or false

getPercentSupervision

public int getPercentSupervision()
Returns the percent supervision

Returns:
integer in range 1..100

getClassificationFileName

public String getClassificationFileName()
Returns the string representing the classification filename

Returns:
string describing the classification filename

getNumClustersToExtract

public int getNumClustersToExtract()
Returns the number of clusters to extract

Returns:
integer in range 1..128

getNumPermutations

public int getNumPermutations()
Returns the number of permutations to find optimal

Returns:
integer in range 1..100

getGapTolerance

public int getGapTolerance()
Returns the gap tolerance

Returns:
integer in range 1..100

getPercentToShave

public int getPercentToShave()
Returns the percent to shave

Returns:
integer in range 1..99

getNumRows

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

Returns:
integer in range 1..32767

getNumColumns

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

Returns:
integer in range 1..32767

getAmplitude

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

Returns:
double in range 1.0..20.0

getModel

public String getModel(boolean removeWhitespace)
Returns the string representing the data model

Parameters:
removeWhitespace - if true, remove any whitespace from entry
Returns:
string describing the data model

getNoise

public String getNoise()
Returns the string representing the noise

Returns:
string describing the noise

getNoiseIndex

public int getNoiseIndex()
Returns the index of the selected noise

Returns:
index of the selected noise

getDegreesFreedom

public int getDegreesFreedom()
Returns the degrees of freedom (used by certain noise distributions)

Returns:
integer in range 1..10

getRawDataFileName

public String getRawDataFileName()
Returns the string representing the filename

Returns:
string describing the filename

isDemoEnabled

public boolean isDemoEnabled()
Returns boolean that tells whether data should be generated or not.

Returns:
true or false

MDACC
Biostatistics

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