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java.lang.Objectjava.awt.Component
java.awt.Container
java.awt.Window
java.awt.Frame
javax.swing.JFrame
edu.cmu.cs.sb.drem.DREM_IO
public class DREM_IO
Class implementing the main input interface
Nested Class Summary | |
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class |
DREM_IO.Downloadfile
A runnable class used for controlling the downloading of files |
class |
DREM_IO.Progressdownload
Runnable class used to display the download progress and also starts the download of a file |
Nested classes/interfaces inherited from class javax.swing.JFrame |
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javax.swing.JFrame.AccessibleJFrame |
Nested classes/interfaces inherited from class java.awt.Frame |
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java.awt.Frame.AccessibleAWTFrame |
Nested classes/interfaces inherited from class java.awt.Window |
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java.awt.Window.AccessibleAWTWindow |
Nested classes/interfaces inherited from class java.awt.Container |
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java.awt.Container.AccessibleAWTContainer |
Nested classes/interfaces inherited from class java.awt.Component |
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java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy |
Field Summary |
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Fields inherited from class javax.swing.JFrame |
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accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled |
Fields inherited from class java.awt.Frame |
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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 |
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BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT |
Fields inherited from interface javax.swing.WindowConstants |
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DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE |
Fields inherited from interface java.awt.image.ImageObserver |
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ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH |
Constructor Summary | |
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DREM_IO()
Class constructor - builds the input interface calls parseDefaults to get the initial settings from a default settings file if specified |
Method Summary | |
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void |
actionPerformed(java.awt.event.ActionEvent e)
Responds to buttons being pressed on the main input interface |
static DREM_DataSet |
buildset(java.lang.String szorganismsourceval,
java.lang.String szxrefsourceval,
java.lang.String szxrefval,
java.lang.String szexp1val,
java.lang.String szgoval,
java.lang.String szgocategoryval,
int nmaxmissing,
double dexpressedval,
double dmincorrelation,
int nsamplespval,
int nmingo,
int nmingolevel,
java.lang.String szextraval,
boolean balltime,
java.util.Vector repeatnames,
boolean btakelog,
boolean bspotincluded,
boolean badd0,
java.lang.String szcategoryIDval,
java.lang.String szevidenceval,
java.lang.String sztaxonval,
boolean bpontoval,
boolean bcontoval,
boolean bfontoval,
boolean brandomgoval,
boolean bmaxminval)
Returns a DREM_DataSet based on the provided input parameters |
void |
clusterscript(java.lang.String szstaticFieldval,
java.lang.String szxrefval,
java.lang.String szexp1val,
java.lang.String szgoval,
java.lang.String szgocategoryval,
java.lang.String szmaxmissingval,
java.lang.String szexpressedval,
java.lang.String szfilterthresholdval,
java.lang.String szsamplepval,
java.lang.String szmingoval,
java.lang.String szmingolevelval,
java.lang.String szextraval,
boolean balltime,
java.util.Vector repeatnames,
boolean btakelog,
boolean bgetxref,
boolean bgetgoann,
boolean bspotincluded,
boolean badd0,
java.lang.String szcategoryIDval,
java.lang.String szinitfileval,
java.lang.String szevidenceval,
java.lang.String sztaxonval,
boolean bpontoval,
boolean bcontoval,
boolean bfontoval,
boolean brandomgoval,
boolean bmaxminval)
A control method that handles the response for when the execute button on the interface is pressed including building the data set, running the DREM modeling procedure, and displaying the results |
static void |
errorcheck(DREM_DataSet theDataSet1,
DREM_DataSet theOtherSet)
Checks if the two data sets have the same number of rows, time points, and the gene name matches. |
static void |
errorcheck(java.lang.String[] origgenes,
java.lang.String[] repeatgenes,
int norigcols,
int nrepeatcols)
Checks if origcols and nrepeat cols are the same value, the length of origgenes and repeatgenes is the same, and the gene names are the same |
boolean |
getFile(java.lang.String szURL,
java.lang.String szoutfile,
int ntype)
Download the data at the location of szURL into a file szoutfile ntype is used for updating the download progress percentages |
void |
handlendbval()
Updates the interface and internal values for the GO cross reference input |
void |
handlenxrefval()
Updates the interface and internal values for the GO cross reference input |
void |
handlestaticsource()
Updates the interface and internal values for the static TF-gene input |
static void |
main(java.lang.String[] args)
The main method which when executed will have the input interface created |
protected javax.swing.JComponent |
makeAdditionalSearchPanel()
Makes the panel showing the model selection options |
protected javax.swing.JComponent |
makeAnnotationPanel()
Makes the GO annotation options panel |
protected javax.swing.JComponent |
makeFilterPanel()
Makes the option panel on the input interface controlling gene filtering. |
protected javax.swing.JComponent |
makeGOAnalysisPanel()
Makes the GO analysis options panel |
void |
makeHelpDialog(java.awt.Component esource)
Renders a help dialog based on the specific help button pressed |
void |
makeOptionsDialog()
Renders the tabbed set of option window panes |
protected javax.swing.JComponent |
makeSearchPanel()
Makes the option panel on the input interface controlling the search options |
static void |
parseDefaults()
Assigns the initial settings of the parameters based on the contents of szDefaultFile |
static void |
renderDialog(javax.swing.JDialog thedialog,
java.lang.String szMessage,
int noffsetx,
int noffsety)
Places szMessage in thedialog window with the title 'Help' |
static void |
renderDialog(javax.swing.JDialog thedialog,
java.lang.String szMessage,
int noffsetx,
int noffsety,
java.lang.String szTitle)
Places szMessage in thedialog window with the title szTitle |
void |
stateChanged(javax.swing.event.ChangeEvent e)
Responds to a change in the radio button selection specifying the model selection criteria |
Methods inherited from class javax.swing.JFrame |
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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 |
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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 |
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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 |
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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 |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface java.awt.MenuContainer |
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getFont, postEvent |
Constructor Detail |
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public DREM_IO() throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException
Method Detail |
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public static void parseDefaults() throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException
public static void errorcheck(DREM_DataSet theDataSet1, DREM_DataSet theOtherSet)
public static void errorcheck(java.lang.String[] origgenes, java.lang.String[] repeatgenes, int norigcols, int nrepeatcols)
public static DREM_DataSet buildset(java.lang.String szorganismsourceval, java.lang.String szxrefsourceval, java.lang.String szxrefval, java.lang.String szexp1val, java.lang.String szgoval, java.lang.String szgocategoryval, int nmaxmissing, double dexpressedval, double dmincorrelation, int nsamplespval, int nmingo, int nmingolevel, java.lang.String szextraval, boolean balltime, java.util.Vector repeatnames, boolean btakelog, boolean bspotincluded, boolean badd0, java.lang.String szcategoryIDval, java.lang.String szevidenceval, java.lang.String sztaxonval, boolean bpontoval, boolean bcontoval, boolean bfontoval, boolean brandomgoval, boolean bmaxminval) throws java.lang.Exception
java.lang.Exception
public void clusterscript(java.lang.String szstaticFieldval, java.lang.String szxrefval, java.lang.String szexp1val, java.lang.String szgoval, java.lang.String szgocategoryval, java.lang.String szmaxmissingval, java.lang.String szexpressedval, java.lang.String szfilterthresholdval, java.lang.String szsamplepval, java.lang.String szmingoval, java.lang.String szmingolevelval, java.lang.String szextraval, boolean balltime, java.util.Vector repeatnames, boolean btakelog, boolean bgetxref, boolean bgetgoann, boolean bspotincluded, boolean badd0, java.lang.String szcategoryIDval, java.lang.String szinitfileval, java.lang.String szevidenceval, java.lang.String sztaxonval, boolean bpontoval, boolean bcontoval, boolean bfontoval, boolean brandomgoval, boolean bmaxminval) throws java.lang.Exception
java.lang.Exception
public void handlestaticsource()
public void handlenxrefval()
public void handlendbval()
public void stateChanged(javax.swing.event.ChangeEvent e)
stateChanged
in interface javax.swing.event.ChangeListener
public void actionPerformed(java.awt.event.ActionEvent e)
actionPerformed
in interface java.awt.event.ActionListener
public boolean getFile(java.lang.String szURL, java.lang.String szoutfile, int ntype)
public void makeHelpDialog(java.awt.Component esource)
public static void renderDialog(javax.swing.JDialog thedialog, java.lang.String szMessage, int noffsetx, int noffsety)
public static void renderDialog(javax.swing.JDialog thedialog, java.lang.String szMessage, int noffsetx, int noffsety, java.lang.String szTitle)
public void makeOptionsDialog()
protected javax.swing.JComponent makeAnnotationPanel()
protected javax.swing.JComponent makeGOAnalysisPanel()
protected javax.swing.JComponent makeAdditionalSearchPanel()
protected javax.swing.JComponent makeSearchPanel()
protected javax.swing.JComponent makeFilterPanel()
public static void main(java.lang.String[] args) throws java.lang.Exception
java.lang.Exception
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