Class 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
    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method 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, 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 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 -
      • 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