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AFLPgui
Class FragmentMap

java.lang.Object
  |
  +--java.awt.Component
        |
        +--java.awt.Container
              |
              +--java.awt.Window
                    |
                    +--java.awt.Frame
                          |
                          +--AFLPgui.FragmentMap
All Implemented Interfaces:
javax.accessibility.Accessible, java.awt.event.ActionListener, java.util.EventListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.awt.event.WindowListener
public class FragmentMap
extends java.awt.Frame
implements java.awt.event.ActionListener, java.awt.event.WindowListener

This is the main GenoGrapher program window. It displays all of the data and manages the classes. It takes care of all of the menu items and switches between different data view. It can display the data as a standard gel image, as a set of thumbnails for the current bin, a graph of the bin, a trace, or as text analysis. These view are actually created in seperate classes. Each of these views has it's own button bar and info bar, but this class picks which one to display.

It also handles the printing of the views as well as saving, opening, importing, and exporting files. Most of the views do a lot of work in their respective classes, but this one manages them all.

See Also:
Serialized Form

Inner classes inherited from class java.awt.Frame
java.awt.Frame.AccessibleAWTFrame
 
Inner classes inherited from class java.awt.Window
java.awt.Window.AccessibleAWTWindow
 
Inner classes inherited from class java.awt.Container
java.awt.Container.AccessibleAWTContainer
 
Inner classes inherited from class java.awt.Component
java.awt.Component.AccessibleAWTComponent
 
Field Summary
protected  java.awt.MenuItem aboutItem
           
protected  AnalysisView analysis
           
static int ANALYSIS
           
protected static int BAR_HEIGHT
           
protected  java.awt.MenuItem[] binOpItem
           
protected  java.awt.MenuItem binRedrawItem
           
protected  java.awt.Panel bottomP
           
protected  ButtonBar buttonBar
           
protected  Bin currentBin
           
protected  java.lang.String currentDir
           
protected  java.lang.String currentFile
           
protected  int currentView
           
protected  double defaultCutoff
           
protected  AFLPgui.ErrorDialog errorDialog
           
protected  java.awt.MenuItem exitItem
           
protected  java.awt.MenuItem exportItem
           
protected  java.awt.FileDialog fileDialog
           
protected  Gel gel
           
static int GEL
           
protected  java.awt.MenuItem[] gelOpItem
           
protected  java.awt.MenuItem gelRedrawItem
           
protected  GelView gelView
           
protected  GraphView graph
           
static int GRAPH
           
protected  java.awt.MenuItem helpItem
           
protected  MultiFileDialog importDialog
           
protected  java.awt.MenuItem importItem
           
protected  Bar infoBar
           
protected  java.awt.MenuItem laneDeleteItem
           
protected  java.awt.MenuItem[] laneOpItem
           
protected  java.awt.ScrollPane mainPanel
           
protected  boolean modified
           
protected  java.awt.Button newButton
           
protected  java.awt.MenuItem newItem
           
protected  java.awt.Button openButton
           
protected  java.awt.MenuItem openItem
           
protected  java.awt.Button printButton
           
protected  java.awt.MenuItem printItem
           
protected  java.awt.MenuItem saveAsItem
           
protected  java.awt.Button saveButton
           
protected  java.awt.MenuItem saveItem
           
protected  Bar statusBar
           
protected  java.awt.Label statusLabel
           
protected  Thumbnail thumbnail
           
static int THUMBNAIL
           
protected  TraceView trace
           
static int TRACE
           
protected  java.awt.MenuItem viewAnalysisItem
           
protected  java.awt.MenuItem viewGelItem
           
protected  java.awt.MenuItem viewGraphItem
           
protected  java.awt.MenuItem viewThumbnailItem
           
protected  java.awt.MenuItem viewTraceItem
           
 
Fields inherited from class java.awt.Frame
CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, 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 java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
 
Constructor Summary
FragmentMap()
          Create a new FragmentMap.
FragmentMap(java.lang.String[] argv)
          Create a new FragmentMap.
 
Method Summary
 void actionPerformed(java.awt.event.ActionEvent e)
          Handles the events from buttons and menu items.
 java.awt.MenuItem[] addMenu(java.awt.Menu menu, Manager mgr)
          Adds Operations from the specified Manager to the specified menu and stores the menu items.
 void exportView(int view)
          This will export the specified data view out to a file.
 void readFile(java.lang.String fileName)
          Reads the specified file in to the program.
protected  void showAbout()
          Displays an about dialog box for the program.
 void switchTo(java.lang.String value)
          Change the program display so that it displays the type specified.
 void windowActivated(java.awt.event.WindowEvent e)
          Unused
 void windowClosed(java.awt.event.WindowEvent e)
          Unused
 void windowClosing(java.awt.event.WindowEvent e)
          exits the program when the window is closed.
 void windowDeactivated(java.awt.event.WindowEvent e)
          Unused
 void windowDeiconified(java.awt.event.WindowEvent e)
          Unused
 void windowIconified(java.awt.event.WindowEvent e)
          Unused
 void windowOpened(java.awt.event.WindowEvent e)
          Unused
 void writeFile(java.lang.String fileName)
          Writes the gel out to the specified file name.
 
Methods inherited from class java.awt.Frame
addNotify, finalize, getAccessibleContext, getCursorType, getFrames, getIconImage, getMenuBar, getState, getTitle, isResizable, paramString, remove, removeNotify, setCursor, setIconImage, setMenuBar, setResizable, setState, setTitle
 
Methods inherited from class java.awt.Window
addWindowListener, applyResourceBundle, applyResourceBundle, dispose, getFocusOwner, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getOwnedWindows, getOwner, getToolkit, getWarningString, hide, isShowing, pack, postEvent, processEvent, processWindowEvent, removeWindowListener, setCursor, show, toBack, toFront
 
Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, addImpl, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getInsets, getLayout, getMaximumSize, getMinimumSize, getPreferredSize, insets, invalidate, isAncestorOf, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, remove, removeAll, removeContainerListener, setFont, setLayout, update, validate, validateTree
 
Methods inherited from class java.awt.Component
action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addPropertyChangeListener, addPropertyChangeListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, getBackground, getBounds, getBounds, getColorModel, getComponentOrientation, getCursor, getDropTarget, getFont, getFontMetrics, getForeground, getGraphics, getHeight, getInputMethodRequests, getLocation, getLocation, getLocationOnScreen, getName, getParent, getPeer, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isDisplayable, isDoubleBuffered, isEnabled, isFocusTraversable, isLightweight, isOpaque, 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, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, reshape, resize, resize, setBackground, setBounds, setBounds, setComponentOrientation, setDropTarget, setEnabled, setForeground, setLocale, setLocation, setLocation, setName, setSize, setSize, setVisible, show, size, toString, transferFocus
 
Methods inherited from class java.lang.Object
clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface java.awt.MenuContainer
getFont, postEvent
 

Field Detail

GEL

public static final int GEL

THUMBNAIL

public static final int THUMBNAIL

GRAPH

public static final int GRAPH

TRACE

public static final int TRACE

ANALYSIS

public static final int ANALYSIS

BAR_HEIGHT

protected static int BAR_HEIGHT

newItem

protected java.awt.MenuItem newItem

openItem

protected java.awt.MenuItem openItem

saveItem

protected java.awt.MenuItem saveItem

saveAsItem

protected java.awt.MenuItem saveAsItem

importItem

protected java.awt.MenuItem importItem

exportItem

protected java.awt.MenuItem exportItem

printItem

protected java.awt.MenuItem printItem

exitItem

protected java.awt.MenuItem exitItem

laneDeleteItem

protected java.awt.MenuItem laneDeleteItem

laneOpItem

protected java.awt.MenuItem[] laneOpItem

binRedrawItem

protected java.awt.MenuItem binRedrawItem

binOpItem

protected java.awt.MenuItem[] binOpItem

gelRedrawItem

protected java.awt.MenuItem gelRedrawItem

gelOpItem

protected java.awt.MenuItem[] gelOpItem

viewGelItem

protected java.awt.MenuItem viewGelItem

viewThumbnailItem

protected java.awt.MenuItem viewThumbnailItem

viewGraphItem

protected java.awt.MenuItem viewGraphItem

viewTraceItem

protected java.awt.MenuItem viewTraceItem

viewAnalysisItem

protected java.awt.MenuItem viewAnalysisItem

helpItem

protected java.awt.MenuItem helpItem

aboutItem

protected java.awt.MenuItem aboutItem

newButton

protected java.awt.Button newButton

openButton

protected java.awt.Button openButton

saveButton

protected java.awt.Button saveButton

printButton

protected java.awt.Button printButton

gel

protected Gel gel

gelView

protected GelView gelView

thumbnail

protected Thumbnail thumbnail

graph

protected GraphView graph

trace

protected TraceView trace

analysis

protected AnalysisView analysis

mainPanel

protected java.awt.ScrollPane mainPanel

buttonBar

protected ButtonBar buttonBar

infoBar

protected Bar infoBar

statusBar

protected Bar statusBar

bottomP

protected java.awt.Panel bottomP

statusLabel

protected java.awt.Label statusLabel

defaultCutoff

protected double defaultCutoff

currentView

protected int currentView

currentBin

protected Bin currentBin

importDialog

protected MultiFileDialog importDialog

fileDialog

protected java.awt.FileDialog fileDialog

errorDialog

protected AFLPgui.ErrorDialog errorDialog

currentFile

protected java.lang.String currentFile

currentDir

protected java.lang.String currentDir

modified

protected boolean modified
Constructor Detail

FragmentMap

public FragmentMap()
Create a new FragmentMap. This is the main program window.

FragmentMap

public FragmentMap(java.lang.String[] argv)
Create a new FragmentMap. This is the main program window.
Parameters:
command - line parameters. The only value accepted is the path for the program files. It should be the same as the startup directory.
Method Detail

switchTo

public void switchTo(java.lang.String value)
Change the program display so that it displays the type specified. Possible values are: "Gel" "Thumbnail" "Graph" "Trace" and "Analysis". This will handle switching the button bars as well as the main window.
Parameters:
value - the view to switch the display to.

readFile

public void readFile(java.lang.String fileName)
Reads the specified file in to the program. The file should be the result of writing out a gel. This is the format used by the program. This is the result of an open operation.
Parameters:
fileName - the name of a gel file written by the program.
See Also:
Gel.read(java.io.DataInputStream), writeFile(java.lang.String)

writeFile

public void writeFile(java.lang.String fileName)
Writes the gel out to the specified file name. This will write all of the information in the program session. In other words, it saves the session. The file can be restored with the readFile method.
Parameters:
fileName - the name of the file to write to.
See Also:
Gel.write(java.io.DataOutputStream), readFile(java.lang.String)

exportView

public void exportView(int view)
This will export the specified data view out to a file. A dialog box will be presented to allow the user to select a file name. Only the gel and analysis currently support exporting. The gel is exported as a PNG file, which can be read by several graphics programs. The analysis is exported as a simple text file.
Parameters:
view - corresponds to one of the constants declared in this class: GEL, THUMBNAIL, GRAPH, TRACE, or ANALYSIS. Only GEL and ANALYSIS are currently supported.

showAbout

protected void showAbout()
Displays an about dialog box for the program.

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent e)
Handles the events from buttons and menu items.
Specified by:
actionPerformed in interface java.awt.event.ActionListener

windowClosing

public void windowClosing(java.awt.event.WindowEvent e)
exits the program when the window is closed.
Specified by:
windowClosing in interface java.awt.event.WindowListener

addMenu

public java.awt.MenuItem[] addMenu(java.awt.Menu menu,
                                   Manager mgr)
Adds Operations from the specified Manager to the specified menu and stores the menu items. If the manager contains anything, the mehtod will add a separator to the menu before it adds any of the items.
Parameters:
menu - the menu to add the items to.
mgr - the manager to retrieve the operations from
Returns:
an array containing all of the menu items added.
See Also:
Manager

windowOpened

public void windowOpened(java.awt.event.WindowEvent e)
Unused
Specified by:
windowOpened in interface java.awt.event.WindowListener

windowClosed

public void windowClosed(java.awt.event.WindowEvent e)
Unused
Specified by:
windowClosed in interface java.awt.event.WindowListener

windowIconified

public void windowIconified(java.awt.event.WindowEvent e)
Unused
Specified by:
windowIconified in interface java.awt.event.WindowListener

windowDeiconified

public void windowDeiconified(java.awt.event.WindowEvent e)
Unused
Specified by:
windowDeiconified in interface java.awt.event.WindowListener

windowActivated

public void windowActivated(java.awt.event.WindowEvent e)
Unused
Specified by:
windowActivated in interface java.awt.event.WindowListener

windowDeactivated

public void windowDeactivated(java.awt.event.WindowEvent e)
Unused
Specified by:
windowDeactivated in interface java.awt.event.WindowListener
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