Package org.biojava.nbio.survival.kaplanmeier.figure

Class KaplanMeierFigure

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JPanel

org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable, Accessible

public class KaplanMeierFigure
extends JPanel

Author:

Scooter Willis

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JPanel

JPanel.AccessibleJPanel

Nested classes/interfaces inherited from class javax.swing.JComponent

JComponent.AccessibleJComponent

Nested classes/interfaces inherited from class java.awt.Container

Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

Fields inherited from class javax.swing.JComponent

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

accessibleContext, 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

Constructors

Constructor	Description
KaplanMeierFigure()

Method Summary

Modifier and Type	Method	Description
static String	fmt(Double d, int precision, int pad)
int	getBottom()
String	getFileName()
ArrayList<String>	getGroups()	Get the name of the groups that are being plotted in the figure
KMFigureInfo	getKMFigureInfo()
int	getLeft()
int	getRight()
SurvFitInfo	getSurvivalFitInfo()
Double	getSurvivalTimePercentile(String group, double percentile)	To get the median percentile for a particular group pass the value of .50.
Double	getTimeAxisIncrementPercentage()	Get the percentage increment for the time axis
int	getTop()
ArrayList<Integer>	getxAxisTimeCoordinates()
ArrayList<Double>	getxAxisTimeValues()
static void	main(String[] args)
void	paintComponent(Graphics g)
void	savePNG(String fileName)
void	savePNGKMNumRisk(String fileName)	Combine the KM and Num risk into one image
void	saveSurvivalData(String fileName)	Save data from survival curve to text file
void	setCoxInfo(ArrayList<String> title, CoxInfo ci, String strataVariable, LinkedHashMap<String,String> legendMap, Boolean useWeighted)
void	setFigureLineInfo(ArrayList<String> lineInfoList)
void	setKMFigureInfo(KMFigureInfo kmfi)
void	setSurvivalData(ArrayList<String> title, LinkedHashMap<String,ArrayList<CensorStatus>> survivalData, Boolean useWeighted)	The data will set the max time which will result in off time points for tick marks
void	setSurvivalData(ArrayList<String> title, LinkedHashMap<String,ArrayList<CensorStatus>> survivalData, Double userSetMaxTime, Boolean useWeighted)
void	setSurvivalData(ArrayList<String> title, SurvFitInfo sfi, Double userSetMaxTime)	Allow setting of points in the figure where weighted correction has been done and percentage has already been calculated.

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, 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, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, 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, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, 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, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setMixingCutoutShape, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

KaplanMeierFigure

public KaplanMeierFigure()

Method Detail

getGroups

public ArrayList<String> getGroups()

Get the name of the groups that are being plotted in the figure

Returns:

getSurvivalTimePercentile

public Double getSurvivalTimePercentile(String group,
                                        double percentile)

To get the median percentile for a particular group pass the value of .50.

Parameters:

group -

percentile -

Returns:

setKMFigureInfo

public void setKMFigureInfo(KMFigureInfo kmfi)

Parameters:

kmfi -

getKMFigureInfo

public KMFigureInfo getKMFigureInfo()

setFigureLineInfo

public void setFigureLineInfo(ArrayList<String> lineInfoList)

Parameters:

lineInfoList -

setCoxInfo

public void setCoxInfo(ArrayList<String> title,
                       CoxInfo ci,
                       String strataVariable,
                       LinkedHashMap<String,String> legendMap,
                       Boolean useWeighted)
                throws Exception

Parameters:

title - Title of figures

ci -

strataVariable - The column that based on value will do a figure line

legendMap - Map the value in the column to something readable

useWeighted -

Throws:

Exception

fmt

public static String fmt(Double d,
                         int precision,
                         int pad)

Parameters:

d -

precision -

pad -

Returns:

getSurvivalFitInfo

public SurvFitInfo getSurvivalFitInfo()

Returns:

setSurvivalData

public void setSurvivalData(ArrayList<String> title,
                            SurvFitInfo sfi,
                            Double userSetMaxTime)

Allow setting of points in the figure where weighted correction has been done and percentage has already been calculated.

Parameters:

title -

sfi -

userSetMaxTime -

setSurvivalData

public void setSurvivalData(ArrayList<String> title,
                            LinkedHashMap<String,ArrayList<CensorStatus>> survivalData,
                            Boolean useWeighted)
                     throws Exception

The data will set the max time which will result in off time points for tick marks

Parameters:

title -

survivalData -

useWeighted -

Throws:

Exception

setSurvivalData

public void setSurvivalData(ArrayList<String> title,
                            LinkedHashMap<String,ArrayList<CensorStatus>> survivalData,
                            Double userSetMaxTime,
                            Boolean useWeighted)
                     throws Exception

Parameters:

title -

survivalData -

userSetMaxTime -

useWeighted -

Throws:

Exception

saveSurvivalData

public void saveSurvivalData(String fileName)
                      throws Exception

Save data from survival curve to text file

Parameters:

fileName -

Throws:

Exception

paintComponent

public void paintComponent(Graphics g)

Overrides:

paintComponent in class JComponent

getFileName

public String getFileName()

Returns:

the fileName

getTop

public int getTop()

Returns:

the top

getBottom

public int getBottom()

Returns:

the bottom

getLeft

public int getLeft()

Returns:

the left

getRight

public int getRight()

Returns:

the right

getxAxisTimeValues

public ArrayList<Double> getxAxisTimeValues()

Returns:

the xAxisTimeValues

getxAxisTimeCoordinates

public ArrayList<Integer> getxAxisTimeCoordinates()

Returns:

the xAxisTimeValues

getTimeAxisIncrementPercentage

public Double getTimeAxisIncrementPercentage()

Get the percentage increment for the time axis

Returns:

savePNGKMNumRisk

public void savePNGKMNumRisk(String fileName)

Combine the KM and Num risk into one image

Parameters:

fileName -

savePNG

public void savePNG(String fileName)

Parameters:

fileName -

main

public static void main(String[] args)

Parameters:

args - the command line arguments