de.unibi.techfak.jpredictor
Class jPREdictor

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Panel
              java.applet.Applet
                  javax.swing.JApplet
                      de.unibi.techfak.jpredictor.jPREdictor

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.RootPaneContainer

public class jPREdictor
extends javax.swing.JApplet

The main pogram. It is designed to work either as command line tool (type '-h' as parameter to get help), as well as GUI (if no parameters are given), as well as an applet in a browser window.

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JApplet

javax.swing.JApplet.AccessibleJApplet

Nested classes/interfaces inherited from class java.applet.Applet

java.applet.Applet.AccessibleApplet

Nested classes/interfaces inherited from class java.awt.Panel

java.awt.Panel.AccessibleAWTPanel

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.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

(package private) static ICommunicator	comm The global communicator, used to 'talk' to the operator, what means, doing all settings and gettings through.
private static int	FLAG_BS Flag, if the background file is a sequence rather than a table file.
private static int	FLAG_DONTUSEPREDEFINED Flag for using the predefined motifs in no case.
private static int	FLAG_FORCE Flag for marking a general force.
private static int	FLAG_FORCE_CCC Flag for forcing the jPREdictor into performing a cutoff calculation.
private static int	FLAG_FORCE_CLUSTERING Flag for forcing the jPREdictor into performing a motif clustering.
private static int	FLAG_FORCE_EVOLUTION Flag for forcing the jPREdictor into performing a motif evolution.
private static int	FLAG_FORCE_GUI Flag for forcing the jPREdictor to read all options and set all commnunicators fields and then starts the GUI.
private static int	FLAG_FORCE_SCORING Flag for forcing the jPREdictor to perform a score sequence operation, and nothing else.
private static int	FLAG_FORCE_SEARCHING Flag for forcing the jPREdictor to perform a search motifs operation.
private static int	FLAG_FORCE_WEIGHTING Flag for forcing the jPREdictor to perform a weight motifs operation.
private static int	FLAG_MS Flag, if the model file is a sequence rather than a table file.
private static int	FLAG_T Flag for single occurrence output, when searching motifs.
private static int	FLAG_U Flag for printing only the best score, when scoring sequences.
private static int	FLAG_USEPREDEFINED Flag for using the predefined motifs in any case.
(package private) static int	flags The local bit array for flags.
(package private) static Operator	op The global operator, which performs all tasks on the sequences by using the motifs.
private static java.lang.String	progInfo Informations on and description of the program.
private static java.lang.String	serialVersionDate Version date.
private static long	serialVersionUID Version number.
private static java.lang.String	version Version string.

Fields inherited from class javax.swing.JApplet

accessibleContext, rootPane, rootPaneCheckingEnabled

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

jPREdictor()

Method Summary

static boolean	commandLineInterpreter(java.lang.String[] args) The command line interpreter tool.
static java.util.Vector	cutoffCalc(ICommunicator comm, boolean out) Performs a cutoff calculation on scores received through the given communicator.
void	destroy() Called, short before the applet is about to be destroyed.
(package private) static void	errorExit(int exitCode) Writes a user message to the error stream of the communicator and exits.
java.lang.String	getAppletInfo() Returns the version info of this program.
(package private) static int	getOccurrencesFromFile(java.lang.String filename, MotifList ml, java.util.Vector[] occ, boolean norm, boolean out) Reads a file and stores the occurrences of the motifs named in the file to the vector array.
static java.lang.String	getProgramInfo() Returns a description of the program.
static java.lang.String	getVersionInfo() Returns the version info of this program.
static java.lang.String	History() Prints the help for specialized tasks the jPREdictor can perform.
void	init() Inits the communicator and the operator.
static void	main(java.lang.String[] args) The main program
(package private) static void	print(boolean verify, java.lang.String s) Prints the string via comm.out().print(), if verify is true.
(package private) static void	processScores() Takes the file given by option '-f' and comprises the scores in it to bands for many cutoffs.
void	stop() Does nothing, because the user might want the applet to work if he is gone.
(package private) static void	taskCutoffCalc(boolean out) Starts the cutoff-calculation task.
(package private) static void	taskScoreSequence() Starts the score-sequence task.
(package private) static void	taskSearchSequence() Starts the search-motifs-on-sequence task.
(package private) static void	taskWeightMotifs(boolean output) Starts the weight-motifs task.
private static void	test(java.lang.String[] args) A method for testing purposed.
static java.lang.String	Usage()
static java.lang.String	UsageHidden()
static java.lang.String	UsageOptionFile() Prints the help for writing an option file.
static java.lang.String	UsageSpec()
(package private) static void	weightMotifs(MotifList ml, ICommunicator comm) This method calculates the motifs weights from two table files.

Methods inherited from class javax.swing.JApplet

addImpl, createRootPane, getAccessibleContext, getContentPane, getGlassPane, getJMenuBar, getLayeredPane, getRootPane, isRootPaneCheckingEnabled, paramString, remove, setContentPane, setGlassPane, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, update

Methods inherited from class java.applet.Applet

getAppletContext, getAudioClip, getAudioClip, getCodeBase, getDocumentBase, getImage, getImage, getLocale, getParameter, getParameterInfo, isActive, newAudioClip, play, play, resize, resize, setStub, showStatus, start

Methods inherited from class java.awt.Panel

addNotify

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getInsets, getLayout, getListeners, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, processEvent, remove, removeAll, removeContainerListener, removeNotify, setComponentZOrder, setFocusCycleRoot, 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, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getToolkit, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, setBackground, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

serialVersionUID

private static final long serialVersionUID

Version number. Note, that 1.02 is translated into an "1.2" version string.

See Also:

Constant Field Values

serialVersionDate

private static final java.lang.String serialVersionDate

Version date.

See Also:

Constant Field Values

comm

static ICommunicator comm

The global communicator, used to 'talk' to the operator, what means, doing all settings and gettings through.

op

static Operator op

The global operator, which performs all tasks on the sequences by using the motifs.

version

private static java.lang.String version

Version string. It is created either by the main method or by the init method, depending on how the program was started.

progInfo

private static java.lang.String progInfo

Informations on and description of the program.

flags

static int flags

The local bit array for flags.

FLAG_BS

private static final int FLAG_BS

Flag, if the background file is a sequence rather than a table file. Note, that multiple files given as background are always treated as to contain sequences.

See Also:

Constant Field Values

FLAG_MS

private static final int FLAG_MS

Flag, if the model file is a sequence rather than a table file. Note, that multiple files given as model are always treated as to contain sequences.

See Also:

Constant Field Values

FLAG_USEPREDEFINED

private static final int FLAG_USEPREDEFINED

Flag for using the predefined motifs in any case. If neither this flag nor FLAG_USEPREDEFINED is set in flags the program decides from whether motifs are given whether it adds the predefined ones or not.

See Also:

Constant Field Values

FLAG_DONTUSEPREDEFINED

private static final int FLAG_DONTUSEPREDEFINED

Flag for using the predefined motifs in no case. If neither this flag nor FLAG_USEPREDEFINED is set in flags the program decides from whether motifs are given whether it adds the predefined ones or not.

See Also:

Constant Field Values

FLAG_T

private static final int FLAG_T

Flag for single occurrence output, when searching motifs.

See Also:

Constant Field Values

FLAG_U

private static final int FLAG_U

Flag for printing only the best score, when scoring sequences.

See Also:

Constant Field Values

FLAG_FORCE_SEARCHING

private static final int FLAG_FORCE_SEARCHING

Flag for forcing the jPREdictor to perform a search motifs operation. This flag might be useful when the user gives all training sets but only wishes a motif search.

See Also:

Constant Field Values

FLAG_FORCE_WEIGHTING

private static final int FLAG_FORCE_WEIGHTING

Flag for forcing the jPREdictor to perform a weight motifs operation. This flag might prove useful when the user gives all sequences but only wishes to obtain the motifs weights.

See Also:

Constant Field Values

FLAG_FORCE_SCORING

private static final int FLAG_FORCE_SCORING

Flag for forcing the jPREdictor to perform a score sequence operation, and nothing else.

See Also:

Constant Field Values

FLAG_FORCE_CCC

private static final int FLAG_FORCE_CCC

Flag for forcing the jPREdictor into performing a cutoff calculation.

See Also:

Constant Field Values

FLAG_FORCE_GUI

private static final int FLAG_FORCE_GUI

Flag for forcing the jPREdictor to read all options and set all commnunicators fields and then starts the GUI. With this the GUI can be started despite any arguments are given. This might be useful to give an option file to the GUI.

See Also:

Constant Field Values

FLAG_FORCE_CLUSTERING

private static final int FLAG_FORCE_CLUSTERING

Flag for forcing the jPREdictor into performing a motif clustering.

See Also:

Constant Field Values

FLAG_FORCE_EVOLUTION

private static final int FLAG_FORCE_EVOLUTION

Flag for forcing the jPREdictor into performing a motif evolution.

See Also:

Constant Field Values

FLAG_FORCE

private static final int FLAG_FORCE

Flag for marking a general force. Its value is the disjunction of all FORCE_FLAGS.

See Also:

Constant Field Values

Constructor Detail

jPREdictor

public jPREdictor()

Method Detail

Usage

public static java.lang.String Usage()

Returns:

The usage text for this program and all available flags as one big string.

UsageSpec

public static java.lang.String UsageSpec()

Returns:

The help for specialized tasks the jPREdictor can perform in one big string.

UsageHidden

public static java.lang.String UsageHidden()

Returns:

The help for hidden tasks the jPREdictor can perform in one big string.

UsageOptionFile

public static java.lang.String UsageOptionFile()

Prints the help for writing an option file.

History

public static java.lang.String History()

Prints the help for specialized tasks the jPREdictor can perform.

taskSearchSequence

static void taskSearchSequence()

Starts the search-motifs-on-sequence task. Prints an error message, if the search could not be started.

taskWeightMotifs

static void taskWeightMotifs(boolean output)

Starts the weight-motifs task. Prints an error message, if the search could not be started.

taskScoreSequence

static void taskScoreSequence()

Starts the score-sequence task. Test first, whether all motifs are properly weighted. Sends error messages to comm.err().

taskCutoffCalc

static void taskCutoffCalc(boolean out)

Starts the cutoff-calculation task. Test first, whether all motifs are properly weighted. Sends error messages to comm.err().

Parameters:

out - Whether progress informations are to be sent to stderr

errorExit

static void errorExit(int exitCode)

Writes a user message to the error stream of the communicator and exits. The message is 'Use parameter '-h' to get help!'. Then System.exit( exitCode ) is called.

Parameters:

exitCode - The program leaves with this code.

print

static void print(boolean verify,
                  java.lang.String s)

Prints the string via comm.out().print(), if verify is true.

Parameters:

verify - Decides whether to print the string or not.

s - The String to get printed.

weightMotifs

static void weightMotifs(MotifList ml,
                         ICommunicator comm)

This method calculates the motifs weights from two table files. Both files must contain the occurrences of the motifs in any given sequence, a previous call to the jPREdictor without '-b' or '-m' creates such a file. The table file given through parameter '-b' means the negative training set (background) searched, the one given through parameter '-m' means the positive training set (model) searched. Both corresponding filenames are taken from the communicator.

Prints first the motifs occurrences in the positive training set, second the ones of the negative training set. Note, that the calculated weights of the motifs are not output.

Parameters:

ml - The list of motifs to set the weigths for.

comm - The communicator to get some settings.

getOccurrencesFromFile

static int getOccurrencesFromFile(java.lang.String filename,
                                  MotifList ml,
                                  java.util.Vector[] occ,
                                  boolean norm,
                                  boolean out)

Reads a file and stores the occurrences of the motifs named in the file to the vector array. The file has to be of the form the parameter '-f' produces as output (without '-v'). The motif list is used to compare the names found in the file to, thus the vector of occurrences has the same order than the motif list.

Parameters:

filename - The name of the file.

ml - The motif lsit the names found in the file are compared to.

occ - The vector array to be filled. One vector for every motif, thus must be in length of the size of ml.

norm - Normalize the occurrences by sequence length or do it not.

out - Output the occurrences or not.

Returns:

Returns 0, if the vector array is valid.

processScores

static void processScores()

Takes the file given by option '-f' and comprises the scores in it to bands for many cutoffs. The width of the sequence window is taken from the static communicator. If a valid cutoff is set in the communicator no cutoff calculation is performed but the bands above that cutoff are output in the form: 'seq#:start-end:max;min;mean'.

cutoffCalc

public static java.util.Vector cutoffCalc(ICommunicator comm,
                                          boolean out)

Performs a cutoff calculation on scores received through the given communicator. A cutoff calculation means that the number of bands are calculated for every possible cutoff (in steps of one). The scores as well as the width are taken from the given communicator. Since all calculations are done by the scoring factory, the table returned upon completion is the vector received from the ScoringFactory.getCutoffTable()-method.

Parameters:

comm - The communicator the results are received from.

out - true, if the function should print some progress notes to comm.err().

Returns:

A table of integers in vector format as received by a call to ScoringFactory.getCutoffTable().

See Also:

ScoringFactory.getCutoffTable()

commandLineInterpreter

public static boolean commandLineInterpreter(java.lang.String[] args)

The command line interpreter tool.

Parameters:

args - Runtime arguments, parameters.

Returns:

If the parameter '--GUI' was given, true, in all other cases (especially error cases), false

main

public static void main(java.lang.String[] args)

The main program

Parameters:

args - Runtime arguments, parameters

init

public void init()

Inits the communicator and the operator. Builds the gui.

Overrides:

init in class java.applet.Applet

stop

public void stop()

Does nothing, because the user might want the applet to work if he is gone.

Overrides:

stop in class java.applet.Applet

destroy

public void destroy()

Called, short before the applet is about to be destroyed. Puts stop to the threads previously started.

Overrides:

destroy in class java.applet.Applet

getAppletInfo

public java.lang.String getAppletInfo()

Returns the version info of this program.

Overrides:

getAppletInfo in class java.applet.Applet

Returns:

A short text with infos about this applet.

getVersionInfo

public static java.lang.String getVersionInfo()

Returns the version info of this program.

Returns:

A short text with infos about this program.

getProgramInfo

public static java.lang.String getProgramInfo()

Returns a description of the program.

Returns:

A short text with infos about this program.

test

private static void test(java.lang.String[] args)

A method for testing purposed. Called first in the main method. In a stable version this method does nothing but to return.