edu.cmu.cs.sb.stem
Class ProfileGui

java.lang.Object
  extended by java.awt.Component
      extended by java.awt.Container
          extended by java.awt.Window
              extended by java.awt.Frame
                  extended by javax.swing.JFrame
                      extended by edu.cmu.cs.sb.stem.ProfileGui
All Implemented Interfaces:
java.awt.event.ComponentListener, java.awt.event.MouseListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class ProfileGui
extends javax.swing.JFrame
implements java.awt.event.MouseListener, java.awt.event.ComponentListener

Class for interface display for all the genes assigned to the same profile

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from class javax.swing.JFrame
javax.swing.JFrame.AccessibleJFrame
 
Nested classes/interfaces inherited from class java.awt.Frame
java.awt.Frame.AccessibleAWTFrame
 
Nested classes/interfaces inherited from class java.awt.Window
java.awt.Window.AccessibleAWTWindow
 
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.JFrame
accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled
 
Fields inherited from class java.awt.Frame
CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR
 
Fields inherited from class java.awt.Component
BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT
 
Fields inherited from interface javax.swing.WindowConstants
DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE
 
Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
 
Constructor Summary
ProfileGui(STEM_DataSet theDataSet, int nprofile, int[] ranklookup, java.util.HashSet inames, int ncompareprofile, java.lang.String szIntersect, java.lang.String szGene, java.lang.String szSpot, GenePlotPanel thegeneplotpanel, ChromFrame cf)
          Constructor renders the display interface
 
Method Summary
static java.lang.String clusterArrayToString(java.util.ArrayList alcprofiles)
          Static method that returns an array of profiles, a string with their profile IDs
 void componentHidden(java.awt.event.ComponentEvent e)
          Empty method
 void componentMoved(java.awt.event.ComponentEvent e)
          Empty method
 void componentResized(java.awt.event.ComponentEvent e)
          Empty method
 void componentShown(java.awt.event.ComponentEvent e)
          Empty method
 void drawintersectgo(java.awt.Color fillColor)
          Draws button for GO table for set of genes in a comparison intersection
 java.lang.String enrichedToSz(double dexpected)
          Converts the number of genes enriched as a double to a string representation
 void init()
          Initializes the colors
 void mouseClicked(java.awt.event.MouseEvent e)
          Responds to mouse clicked events
 void mouseEntered(java.awt.event.MouseEvent e)
          Empty constructor method
 void mouseExited(java.awt.event.MouseEvent e)
          Empty constructor method
 void mousePressed(java.awt.event.MouseEvent e)
          Empty constructor method
 void mouseReleased(java.awt.event.MouseEvent e)
          Empty constructor method
 void paint(java.awt.Graphics g)
          Renders the interface by getting the interface option settings and then calling plotgenevalues
 void plotgenevalues(java.awt.Graphics2D g2, double numassigned, double numexpected, double pvalue, double[][] genevalues, int[][] missing, java.util.ArrayList[] bestAssignments, double[] profilevals, boolean[] sig, java.util.ArrayList currProfileAssignments)
          Responsible for rendering the profile window interface
 
Methods inherited from class javax.swing.JFrame
addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getGraphics, getJMenuBar, getLayeredPane, getRootPane, getTransferHandler, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, repaint, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setIconImage, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, setTransferHandler, update
 
Methods inherited from class java.awt.Frame
addNotify, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setResizable, setState, setTitle, setUndecorated
 
Methods inherited from class java.awt.Window
addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getGraphicsConfiguration, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOwnedWindows, getOwner, getOwnerlessWindows, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isShowing, pack, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImages, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setVisible, show, toBack, toFront
 
Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, 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, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resize, resize, setBackground, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusUpCycle
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface java.awt.MenuContainer
getFont, postEvent
 

Constructor Detail

ProfileGui

public ProfileGui(STEM_DataSet theDataSet,
                  int nprofile,
                  int[] ranklookup,
                  java.util.HashSet inames,
                  int ncompareprofile,
                  java.lang.String szIntersect,
                  java.lang.String szGene,
                  java.lang.String szSpot,
                  GenePlotPanel thegeneplotpanel,
                  ChromFrame cf)
Constructor renders the display interface

Method Detail

componentHidden

public void componentHidden(java.awt.event.ComponentEvent e)
Empty method

Specified by:
componentHidden in interface java.awt.event.ComponentListener

componentMoved

public void componentMoved(java.awt.event.ComponentEvent e)
Empty method

Specified by:
componentMoved in interface java.awt.event.ComponentListener

componentResized

public void componentResized(java.awt.event.ComponentEvent e)
Empty method

Specified by:
componentResized in interface java.awt.event.ComponentListener

componentShown

public void componentShown(java.awt.event.ComponentEvent e)
Empty method

Specified by:
componentShown in interface java.awt.event.ComponentListener

enrichedToSz

public java.lang.String enrichedToSz(double dexpected)
Converts the number of genes enriched as a double to a string representation


init

public void init()
Initializes the colors


mousePressed

public void mousePressed(java.awt.event.MouseEvent e)
Empty constructor method

Specified by:
mousePressed in interface java.awt.event.MouseListener

mouseReleased

public void mouseReleased(java.awt.event.MouseEvent e)
Empty constructor method

Specified by:
mouseReleased in interface java.awt.event.MouseListener

mouseEntered

public void mouseEntered(java.awt.event.MouseEvent e)
Empty constructor method

Specified by:
mouseEntered in interface java.awt.event.MouseListener

mouseExited

public void mouseExited(java.awt.event.MouseEvent e)
Empty constructor method

Specified by:
mouseExited in interface java.awt.event.MouseListener

drawintersectgo

public void drawintersectgo(java.awt.Color fillColor)
Draws button for GO table for set of genes in a comparison intersection


mouseClicked

public void mouseClicked(java.awt.event.MouseEvent e)
Responds to mouse clicked events

Specified by:
mouseClicked in interface java.awt.event.MouseListener

clusterArrayToString

public static java.lang.String clusterArrayToString(java.util.ArrayList alcprofiles)
Static method that returns an array of profiles, a string with their profile IDs


plotgenevalues

public void plotgenevalues(java.awt.Graphics2D g2,
                           double numassigned,
                           double numexpected,
                           double pvalue,
                           double[][] genevalues,
                           int[][] missing,
                           java.util.ArrayList[] bestAssignments,
                           double[] profilevals,
                           boolean[] sig,
                           java.util.ArrayList currProfileAssignments)
Responsible for rendering the profile window interface


paint

public void paint(java.awt.Graphics g)
Renders the interface by getting the interface option settings and then calling plotgenevalues

Overrides:
paint in class java.awt.Container