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 Details
- KaplanMeierFigure
  
  public KaplanMeierFigure()
Method Details
- 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

Class KaplanMeierFigure

Nested Class Summary

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

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

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

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

Field Summary

Fields inherited from class javax.swing.JComponent

Fields inherited from class java.awt.Component

Fields inherited from interface java.awt.image.ImageObserver

Constructor Summary

Method Summary

Methods inherited from class javax.swing.JPanel

Methods inherited from class javax.swing.JComponent

Methods inherited from class java.awt.Container

Methods inherited from class java.awt.Component

Methods inherited from class java.lang.Object

Constructor Details

KaplanMeierFigure

Method Details

getGroups

getSurvivalTimePercentile

setKMFigureInfo

getKMFigureInfo

setFigureLineInfo

setCoxInfo

fmt

getSurvivalFitInfo

setSurvivalData

setSurvivalData

setSurvivalData

saveSurvivalData

paintComponent

getFileName

getTop

getBottom

getLeft

getRight

getxAxisTimeValues

getxAxisTimeCoordinates

getTimeAxisIncrementPercentage

savePNGKMNumRisk

savePNG

main