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:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible
```
public class KaplanMeierFigure
extends javax.swing.JPanel
```
Author:

Scooter Willis

See Also:

Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from class javax.swing.JPanel
  javax.swing.JPanel.AccessibleJPanel
- Nested classes/interfaces inherited from class javax.swing.JComponent
  javax.swing.JComponent.AccessibleJComponent
- Nested classes/interfaces inherited from class java.awt.Container
  java.awt.Container.AccessibleAWTContainer
- Nested classes/interfaces inherited from class java.awt.Component
  java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.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 and Description

KaplanMeierFigure()

Constructors
Constructor and Description
`KaplanMeierFigure()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static java.lang.String`	`fmt(java.lang.Double d, int precision, int pad)`
`int`	`getBottom()`
`java.lang.String`	`getFileName()`
`java.util.ArrayList<java.lang.String>`	`getGroups()` Get the name of the groups that are being plotted in the figure
`KMFigureInfo`	`getKMFigureInfo()`
`int`	`getLeft()`
`int`	`getRight()`
`SurvFitInfo`	`getSurvivalFitInfo()`
`java.lang.Double`	`getSurvivalTimePercentile(java.lang.String group, double percentile)` To get the median percentile for a particular group pass the value of .50.
`java.lang.Double`	`getTimeAxisIncrementPercentage()` Get the percentage increment for the time axis
`int`	`getTop()`
`java.util.ArrayList<java.lang.Integer>`	`getxAxisTimeCoordinates()`
`java.util.ArrayList<java.lang.Double>`	`getxAxisTimeValues()`
`static void`	`main(java.lang.String[] args)`
`void`	`paintComponent(java.awt.Graphics g)`
`void`	`savePNG(java.lang.String fileName)`
`void`	`savePNGKMNumRisk(java.lang.String fileName)` Combine the KM and Num risk into one image
`void`	`saveSurvivalData(java.lang.String fileName)` Save data from survival curve to text file
`void`	`setCoxInfo(java.util.ArrayList<java.lang.String> title, CoxInfo ci, java.lang.String strataVariable, java.util.LinkedHashMap<java.lang.String,java.lang.String> legendMap, java.lang.Boolean useWeighted)`
`void`	`setFigureLineInfo(java.util.ArrayList<java.lang.String> lineInfoList)`
`void`	`setKMFigureInfo(KMFigureInfo kmfi)`
`void`	`setSurvivalData(java.util.ArrayList<java.lang.String> title, java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<CensorStatus>> survivalData, java.lang.Boolean useWeighted)` The data will set the max time which will result in off time points for tick marks
`void`	`setSurvivalData(java.util.ArrayList<java.lang.String> title, java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<CensorStatus>> survivalData, java.lang.Double userSetMaxTime, java.lang.Boolean useWeighted)`
`void`	`setSurvivalData(java.util.ArrayList<java.lang.String> title, SurvFitInfo sfi, java.lang.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, getPeer, 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, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, 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 java.util.ArrayList<java.lang.String> getGroups()
```
Get the name of the groups that are being plotted in the figure

Returns:

getSurvivalTimePercentile

public java.lang.Double getSurvivalTimePercentile(java.lang.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(java.util.ArrayList<java.lang.String> lineInfoList)

Parameters:: lineInfoList -

setCoxInfo

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

fmt

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

Parameters:: d -; precision -; pad -
Returns:

getSurvivalFitInfo

public SurvFitInfo getSurvivalFitInfo()

Returns:

setSurvivalData

public void setSurvivalData(java.util.ArrayList<java.lang.String> title,
                            SurvFitInfo sfi,
                            java.lang.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(java.util.ArrayList<java.lang.String> title,
                            java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<CensorStatus>> survivalData,
                            java.lang.Boolean useWeighted)
                     throws java.lang.Exception

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

Parameters:: title -; survivalData -; useWeighted -
Throws:: java.lang.Exception

setSurvivalData

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

Parameters:: title -; survivalData -; userSetMaxTime -; useWeighted -
Throws:: java.lang.Exception

saveSurvivalData

public void saveSurvivalData(java.lang.String fileName)
                      throws java.lang.Exception

Save data from survival curve to text file

Parameters:: fileName -
Throws:: java.lang.Exception

paintComponent
```
public void paintComponent(java.awt.Graphics g)
```
Overrides:

paintComponent in class javax.swing.JComponent

getFileName
```
public java.lang.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 java.util.ArrayList<java.lang.Double> getxAxisTimeValues()

Returns:: the xAxisTimeValues

getxAxisTimeCoordinates

public java.util.ArrayList<java.lang.Integer> getxAxisTimeCoordinates()

Returns:: the xAxisTimeValues

getTimeAxisIncrementPercentage
```
public java.lang.Double getTimeAxisIncrementPercentage()
```
Get the percentage increment for the time axis

Returns:

savePNGKMNumRisk
```
public void savePNGKMNumRisk(java.lang.String fileName)
```
Combine the KM and Num risk into one image

Parameters:

fileName -

savePNG

public void savePNG(java.lang.String fileName)

Parameters:: fileName -

main

public static void main(java.lang.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 Detail

KaplanMeierFigure

Method Detail

getGroups

getSurvivalTimePercentile

setKMFigureInfo

getKMFigureInfo

setFigureLineInfo

setCoxInfo

fmt

getSurvivalFitInfo

setSurvivalData

setSurvivalData

setSurvivalData

saveSurvivalData

paintComponent

getFileName

getTop

getBottom

getLeft

getRight

getxAxisTimeValues

getxAxisTimeCoordinates

getTimeAxisIncrementPercentage

savePNGKMNumRisk

savePNG

main