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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.stem.ST
public class ST
Class implementing the main input interface
Nested Class Summary | |
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class |
ST.Downloadfile
Inner class controlling the downloading of external files |
class |
ST.Progressdownload
Inner class rendering the progress download display |
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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ST()
Constructor for running STEM through the normal input interface Renders the interace |
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ST(java.lang.String szBatchInputDir,
java.lang.String szBatchOutputDir)
Constructor for running STEM in batch mode |
Method Summary | |
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void |
actionPerformed(java.awt.event.ActionEvent e)
Manages the responds to actions on the interface |
static STEM_DataSet |
buildset(java.lang.String szchromval,
java.lang.String szxrefval,
java.lang.String szexp1val,
java.lang.String szgoval,
java.lang.String szgocategoryval,
int nmaxmissing,
double dexpressedval,
double dmincorrelation,
double dlbcorrelationclust,
double dalphaval,
double dpercentile,
int nmaxchange,
int nnumberprofiles,
double dcorrmodel,
int nsamplesgene,
int nsamplespval,
long nsamplesmodel,
int nmingo,
int nfdr,
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 bkmeans,
boolean bmaxminval,
boolean ballpermuteval,
java.lang.String szorganismsourceval,
java.lang.String szxrefsourceval,
java.lang.String szchromsourceval)
Calls buildsetwithOrig but only returns the data set, not the pre-filtered gene list |
static edu.cmu.cs.sb.stem.ST.DataSetOrigRec |
buildsetwithOrig(java.lang.String szchromval,
java.lang.String szxrefval,
java.lang.String szexp1val,
java.lang.String szgoval,
java.lang.String szgocategoryval,
int nmaxmissing,
double dexpressedval,
double dmincorrelation,
double dlbcorrelationclust,
double dalphaval,
double dpercentile,
int nmaxchange,
int nnumberprofiles,
double dcorrmodel,
int nsamplesgene,
int nsamplespval,
long nsamplesmodel,
int nmingo,
int nfdr,
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 bkmeans,
boolean bmaxminval,
boolean ballpermuteval,
java.lang.String szorganismsourceval,
java.lang.String szxrefsourceval,
java.lang.String szchromsourceval)
A driver method calling procedures to pre-process the data, and computer profile significance |
void |
clusterscript(java.lang.String szchromval,
java.lang.String szxrefval,
java.lang.String szexp1val,
java.lang.String szexp2val,
java.lang.String szgoval,
java.lang.String szgocategoryval,
java.lang.String szmaxmissingval,
java.lang.String szexpressedval,
java.lang.String szfilterthresholdval,
java.lang.String szlbval,
java.lang.String szalphaval,
java.lang.String szpercentile,
java.lang.String szmaxchange,
java.lang.String sznumberprofiles,
java.lang.String szcorrmodel,
java.lang.String szsamplegene,
java.lang.String szsamplepval,
java.lang.String szsamplemodel,
java.lang.String szmingoval,
int nfdr,
java.lang.String szmingolevelval,
java.lang.String szextraval,
boolean balltime,
java.util.Vector repeatnames,
boolean btakelog,
boolean bgetchromval,
boolean bgetxref,
boolean bgetgoann,
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,
boolean ballpermuteval)
The method which drives the execution after the execute button is pressed getting the input and buiding the data sets |
static void |
errorcheck(STEM_DataSet theDataSet1,
STEM_DataSet theOtherSet)
Makes sure repeat data sets agree with each other on the number of rows, columns, and the name of the genes |
static void |
errorcheck(java.lang.String[] origgenes,
java.lang.String[] repeatgenes,
int norigcols,
int nrepeatcols)
Makes sure repeat data sets agree with each other on the number of columns and the name of the genes |
boolean |
getFile(java.lang.String szURL,
java.lang.String szoutfile,
int ntype)
Responsible for downloading the file. |
void |
handlechromval()
Responds to changes in the gene location field on the input interface |
void |
handleclusteringmethod()
Responds to changes in the desired clustering method on the interface |
void |
handlendbval()
Handles changes to changes in GO or cross-reference data sources |
void |
handlenxrefval()
Responds to changes in the gene annotation cross reference field on the main interface |
static void |
initializeDefaults()
Initializes the default settings of all the variables |
static void |
main(java.lang.String[] args)
The main method which launches STEM |
protected javax.swing.JComponent |
makeAnnotationPanel()
Renders the option panel about gene annotations |
protected javax.swing.JComponent |
makeClusteringPanel()
Makes panel of options for the clustering model profiles |
protected javax.swing.JComponent |
makeFilterPanel()
Makes panel of gene filtering options |
protected javax.swing.JComponent |
makeGOAnalysisPanel()
Render the GO Analysis options panels |
void |
makeHelpDialog(java.awt.Component esource)
Renders help information for the various help buttons on the interface |
protected javax.swing.JComponent |
makeModelPanel()
Makes panel of options related to the selection and significance of model profiles |
void |
makeOptionsDialog()
Manages the rendering of the set of option tabbed panels |
static void |
parseDefaults(java.lang.String szDefaultFile)
Parse the contents of a defaults file |
void |
printBatchOutputGeneTable(STEM_DataSet theDataSet)
Prints a table for batch output showing for each gene the profile to which it was assigned |
void |
printBatchOutputProfileTable(STEM_DataSet theDataSet)
Prints a table for batch output about each profile or k-means cluster |
void |
runBatchDir()
Runs STEM on a batch set of default files in szBatchInputDir |
void |
updateSettings()
Makes sure all the settings displayed on the interface correspond to the variables internal values. |
static boolean |
validVariable(java.lang.String sztype)
Returns true iff sztype is a valid variable for the defaults file |
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 ST(java.lang.String szBatchInputDir, java.lang.String szBatchOutputDir)
public ST() throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException
Method Detail |
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public static boolean validVariable(java.lang.String sztype)
public static void initializeDefaults()
public void runBatchDir()
public static void parseDefaults(java.lang.String szDefaultFile) throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException
public static void errorcheck(STEM_DataSet theDataSet1, STEM_DataSet theOtherSet)
public static void errorcheck(java.lang.String[] origgenes, java.lang.String[] repeatgenes, int norigcols, int nrepeatcols)
public static STEM_DataSet buildset(java.lang.String szchromval, java.lang.String szxrefval, java.lang.String szexp1val, java.lang.String szgoval, java.lang.String szgocategoryval, int nmaxmissing, double dexpressedval, double dmincorrelation, double dlbcorrelationclust, double dalphaval, double dpercentile, int nmaxchange, int nnumberprofiles, double dcorrmodel, int nsamplesgene, int nsamplespval, long nsamplesmodel, int nmingo, int nfdr, 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 bkmeans, boolean bmaxminval, boolean ballpermuteval, java.lang.String szorganismsourceval, java.lang.String szxrefsourceval, java.lang.String szchromsourceval) throws java.lang.Exception
java.lang.Exception
public static edu.cmu.cs.sb.stem.ST.DataSetOrigRec buildsetwithOrig(java.lang.String szchromval, java.lang.String szxrefval, java.lang.String szexp1val, java.lang.String szgoval, java.lang.String szgocategoryval, int nmaxmissing, double dexpressedval, double dmincorrelation, double dlbcorrelationclust, double dalphaval, double dpercentile, int nmaxchange, int nnumberprofiles, double dcorrmodel, int nsamplesgene, int nsamplespval, long nsamplesmodel, int nmingo, int nfdr, 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 bkmeans, boolean bmaxminval, boolean ballpermuteval, java.lang.String szorganismsourceval, java.lang.String szxrefsourceval, java.lang.String szchromsourceval) throws java.lang.Exception
java.lang.Exception
public void printBatchOutputProfileTable(STEM_DataSet theDataSet) throws java.io.IOException
java.io.IOException
public void printBatchOutputGeneTable(STEM_DataSet theDataSet) throws java.io.IOException
java.io.IOException
public void clusterscript(java.lang.String szchromval, java.lang.String szxrefval, java.lang.String szexp1val, java.lang.String szexp2val, java.lang.String szgoval, java.lang.String szgocategoryval, java.lang.String szmaxmissingval, java.lang.String szexpressedval, java.lang.String szfilterthresholdval, java.lang.String szlbval, java.lang.String szalphaval, java.lang.String szpercentile, java.lang.String szmaxchange, java.lang.String sznumberprofiles, java.lang.String szcorrmodel, java.lang.String szsamplegene, java.lang.String szsamplepval, java.lang.String szsamplemodel, java.lang.String szmingoval, int nfdr, java.lang.String szmingolevelval, java.lang.String szextraval, boolean balltime, java.util.Vector repeatnames, boolean btakelog, boolean bgetchromval, boolean bgetxref, boolean bgetgoann, 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, boolean ballpermuteval) throws java.lang.Exception
java.lang.Exception
public void handleclusteringmethod()
public void handlenxrefval()
public void handlechromval()
public void handlendbval()
public void actionPerformed(java.awt.event.ActionEvent e)
actionPerformed
in interface java.awt.event.ActionListener
public void makeHelpDialog(java.awt.Component esource)
public void makeOptionsDialog()
public void updateSettings()
protected javax.swing.JComponent makeAnnotationPanel()
protected javax.swing.JComponent makeGOAnalysisPanel()
public boolean getFile(java.lang.String szURL, java.lang.String szoutfile, int ntype)
protected javax.swing.JComponent makeClusteringPanel()
protected javax.swing.JComponent makeModelPanel()
protected javax.swing.JComponent makeFilterPanel()
public static void main(java.lang.String[] args) throws java.lang.Exception
java.lang.Exception
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