edu.cmu.cs.sb.stem
Class ST

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.ST
All Implemented Interfaces:
java.awt.event.ActionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class ST
extends javax.swing.JFrame
implements java.awt.event.ActionListener

Class implementing the main input interface

See Also:
Serialized Form

Nested Class Summary
 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
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
ST()
          Constructor for running STEM through the normal input interface Renders the interace
ST(java.lang.String szBatchInputDir, java.lang.String szBatchOutputDir)
          Constructor for running STEM in batch mode
 
Method Summary
 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
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

ST

public ST(java.lang.String szBatchInputDir,
          java.lang.String szBatchOutputDir)
Constructor for running STEM in batch mode


ST

public ST()
   throws java.io.FileNotFoundException,
          java.io.IOException
Constructor for running STEM through the normal input interface Renders the interace

Throws:
java.io.FileNotFoundException
java.io.IOException
Method Detail

validVariable

public static boolean validVariable(java.lang.String sztype)
Returns true iff sztype is a valid variable for the defaults file


initializeDefaults

public static void initializeDefaults()
Initializes the default settings of all the variables


runBatchDir

public void runBatchDir()
Runs STEM on a batch set of default files in szBatchInputDir


parseDefaults

public static void parseDefaults(java.lang.String szDefaultFile)
                          throws java.io.FileNotFoundException,
                                 java.io.IOException
Parse the contents of a defaults file

Throws:
java.io.FileNotFoundException
java.io.IOException

errorcheck

public 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


errorcheck

public 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


buildset

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
Calls buildsetwithOrig but only returns the data set, not the pre-filtered gene list

Throws:
java.lang.Exception

buildsetwithOrig

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
A driver method calling procedures to pre-process the data, and computer profile significance

Throws:
java.lang.Exception

printBatchOutputProfileTable

public void printBatchOutputProfileTable(STEM_DataSet theDataSet)
                                  throws java.io.IOException
Prints a table for batch output about each profile or k-means cluster

Throws:
java.io.IOException

printBatchOutputGeneTable

public void printBatchOutputGeneTable(STEM_DataSet theDataSet)
                               throws java.io.IOException
Prints a table for batch output showing for each gene the profile to which it was assigned

Throws:
java.io.IOException

clusterscript

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
The method which drives the execution after the execute button is pressed getting the input and buiding the data sets

Throws:
java.lang.Exception

handleclusteringmethod

public void handleclusteringmethod()
Responds to changes in the desired clustering method on the interface


handlenxrefval

public void handlenxrefval()
Responds to changes in the gene annotation cross reference field on the main interface


handlechromval

public void handlechromval()
Responds to changes in the gene location field on the input interface


handlendbval

public void handlendbval()
Handles changes to changes in GO or cross-reference data sources


actionPerformed

public void actionPerformed(java.awt.event.ActionEvent e)
Manages the responds to actions on the interface

Specified by:
actionPerformed in interface java.awt.event.ActionListener

makeHelpDialog

public void makeHelpDialog(java.awt.Component esource)
Renders help information for the various help buttons on the interface


makeOptionsDialog

public void makeOptionsDialog()
Manages the rendering of the set of option tabbed panels


updateSettings

public void updateSettings()
Makes sure all the settings displayed on the interface correspond to the variables internal values.


makeAnnotationPanel

protected javax.swing.JComponent makeAnnotationPanel()
Renders the option panel about gene annotations


makeGOAnalysisPanel

protected javax.swing.JComponent makeGOAnalysisPanel()
Render the GO Analysis options panels


getFile

public boolean getFile(java.lang.String szURL,
                       java.lang.String szoutfile,
                       int ntype)
Responsible for downloading the file. ntype specifies the type of file we are downloading.


makeClusteringPanel

protected javax.swing.JComponent makeClusteringPanel()
Makes panel of options for the clustering model profiles


makeModelPanel

protected javax.swing.JComponent makeModelPanel()
Makes panel of options related to the selection and significance of model profiles


makeFilterPanel

protected javax.swing.JComponent makeFilterPanel()
Makes panel of gene filtering options


main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception
The main method which launches STEM

Throws:
java.lang.Exception