edu.cmu.cs.sb.drem
Class DREMGui

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.umd.cs.piccolox.PFrame
                          extended by edu.cmu.cs.sb.drem.DREMGui
All Implemented Interfaces:
java.awt.event.ComponentListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class DREMGui
extends edu.umd.cs.piccolox.PFrame
implements java.awt.event.ComponentListener

Class for the main interface window of a DREM regulatory map

See Also:
Serialized Form

Nested Class Summary
static class DREMGui.SigInfoRec
          Record for information about significant transcription factors
 
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
DREMGui(DREM_Timeiohmm theTimeiohmm, edu.cmu.cs.sb.drem.DREM_Timeiohmm.Treenode treecopy, boolean brealXaxisDEF, double dYaxisDEF, double dXaxisDEF, int nKeyInputTypeDEF, double dKeyInputXDEF, double dpercentDEF, java.lang.String szFinal, double dnodekDEF)
          Class constructor
 
Method Summary
 void beforeInitialize()
          Sets the screen size
 void closeWindows()
          Closes the frame windows
 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)
          Calls drawmain
 void componentShown(java.awt.event.ComponentEvent e)
          Calls drawmain
 void drawmain()
          Responsible for laying out the main interface window
 edu.umd.cs.piccolo.event.PBasicInputEventHandler drawNodes(edu.cmu.cs.sb.drem.DREM_Timeiohmm.Treenode ptr, int ndepth, double parentx, double parenty, int ncurrscore, int nchild, java.awt.Color currColor, java.awt.Color prevColor, int nprevcolorID, int ncurrparentcolorindex, int nprevminparentlevel)
          Draws nodes on the interface screen
 void hidelabels()
          Hides all annotation labels
 void initialize()
          calls drawmain
 void renderFilterText()
          Controls the display of the tex showing the filter information
 java.lang.String saveColors()
          Saves the edge color selections to an ouput file
 void selectGO(java.lang.String szSelectedGO)
          Changes the gene visibility based on the selected GO category szSelectedGO
 void setFilterText()
          Generates the string in filterText which displays information as to how the genes were selecte
 void setGeneColors()
          Sets the colors of the individual genes
 void setSigText(java.util.TreeSet tsSigTF, edu.umd.cs.piccolo.nodes.PText theSigText, int ntype)
          Sets the text for the significant transcription factors
 void showlabels()
          Shows all annotation labels
 void unselectGO()
          Undo gene display based on the GO selection
 
Methods inherited from class edu.umd.cs.piccolox.PFrame
addEscapeFullScreenModeListener, chooseBestDisplayMode, getBestDisplayMode, getCanvas, getDefaultFrameBounds, getPreferredDisplayModes, main, PFrameHelper, removeEscapeFullScreenModeListener, setFullScreenMode
 
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, paint, 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

DREMGui

public DREMGui(DREM_Timeiohmm theTimeiohmm,
               edu.cmu.cs.sb.drem.DREM_Timeiohmm.Treenode treecopy,
               boolean brealXaxisDEF,
               double dYaxisDEF,
               double dXaxisDEF,
               int nKeyInputTypeDEF,
               double dKeyInputXDEF,
               double dpercentDEF,
               java.lang.String szFinal,
               double dnodekDEF)
Class constructor

Method Detail

setGeneColors

public void setGeneColors()
Sets the colors of the individual genes


closeWindows

public void closeWindows()
Closes the frame windows


saveColors

public java.lang.String saveColors()
Saves the edge color selections to an ouput file


unselectGO

public void unselectGO()
Undo gene display based on the GO selection


selectGO

public void selectGO(java.lang.String szSelectedGO)
Changes the gene visibility based on the selected GO category szSelectedGO


setFilterText

public void setFilterText()
Generates the string in filterText which displays information as to how the genes were selecte


renderFilterText

public void renderFilterText()
Controls the display of the tex showing the filter information


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

componentShown

public void componentShown(java.awt.event.ComponentEvent e)
Calls drawmain

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

componentResized

public void componentResized(java.awt.event.ComponentEvent e)
Calls drawmain

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

beforeInitialize

public void beforeInitialize()
Sets the screen size

Overrides:
beforeInitialize in class edu.umd.cs.piccolox.PFrame

initialize

public void initialize()
calls drawmain

Overrides:
initialize in class edu.umd.cs.piccolox.PFrame

drawmain

public void drawmain()
Responsible for laying out the main interface window


hidelabels

public void hidelabels()
Hides all annotation labels


showlabels

public void showlabels()
Shows all annotation labels


setSigText

public void setSigText(java.util.TreeSet tsSigTF,
                       edu.umd.cs.piccolo.nodes.PText theSigText,
                       int ntype)
Sets the text for the significant transcription factors


drawNodes

public edu.umd.cs.piccolo.event.PBasicInputEventHandler drawNodes(edu.cmu.cs.sb.drem.DREM_Timeiohmm.Treenode ptr,
                                                                  int ndepth,
                                                                  double parentx,
                                                                  double parenty,
                                                                  int ncurrscore,
                                                                  int nchild,
                                                                  java.awt.Color currColor,
                                                                  java.awt.Color prevColor,
                                                                  int nprevcolorID,
                                                                  int ncurrparentcolorindex,
                                                                  int nprevminparentlevel)
Draws nodes on the interface screen