Serialized Form

Package de.unibi.techfak.jpredictor

Class de.unibi.techfak.jpredictor.jPREdictor extends javax.swing.JApplet implements Serializable

serialVersionUID: 122L

Package de.unibi.techfak.jpredictor.gui

Class de.unibi.techfak.jpredictor.gui.CutoffCalculator extends javax.swing.JDialog implements Serializable

Serialized Fields

owner

java.awt.Window owner

The parent of this JDialog.

buttonTexts

java.lang.String[] buttonTexts

The text of all buttons

comm

ICommunicator comm

The communicator which holds all settings.

op

IOperator op

The operator to perform the operations through.

bExit

javax.swing.JButton bExit

The buttons.

bCancel

javax.swing.JButton bCancel

bStartCalc

javax.swing.JButton bStartCalc

bGetDistr

javax.swing.JButton bGetDistr

tfEValue

javax.swing.JTextField tfEValue

the textfields

tfSequLen

javax.swing.JTextField tfSequLen

tfSampleSize

javax.swing.JTextField tfSampleSize

tfProgress

javax.swing.JTextField tfProgress

tfCutoff

javax.swing.JTextField tfCutoff

generatingCharacters

char[] generatingCharacters

The characters used to generate the random sequences.

generatingDistribution

double[] generatingDistribution

The probabilities for the single characters. It is used when the random sequences are generated. It is set in the constructor, either the communicators background distribution or as { 0.283, 0.217, 0.217, 0.283 }.

t

CutoffCalculator.CutoffCalcThread t

The thread how it was started.

Class de.unibi.techfak.jpredictor.gui.MainPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

comm

ICommunicator comm

The saved communicator, used to 'talk' to the operator, what means, doing all settings and gettings through it. Given to and set by the constructor.

op

Operator op

The saved operator, which performs all tasks on the sequences by using the motifs. Set by the constructor.

motifMaker

MotifMaker motifMaker

The motif maker to be used by this class. Should only be instanciated if it is null.

parent

java.awt.Window parent

The parent of this panel. If it is an applet it is null.

buttonTexts

java.lang.String[] buttonTexts

The text for the buttons.

bSequSet

javax.swing.JButton bSequSet

Some global buttons for sequences.

bPosSet

javax.swing.JButton bPosSet

bNegSet

javax.swing.JButton bNegSet

bSequBrowse

javax.swing.JButton bSequBrowse

bPosBrowse

javax.swing.JButton bPosBrowse

bNegBrowse

javax.swing.JButton bNegBrowse

bOutBrowse

javax.swing.JButton bOutBrowse

bCancel

javax.swing.JButton bCancel

bMotifMaker

javax.swing.JButton bMotifMaker

The global action buttons.

bSearchMotifs

javax.swing.JButton bSearchMotifs

bWeightMotifs

javax.swing.JButton bWeightMotifs

bScoreSequ

javax.swing.JButton bScoreSequ

bCutoffCalc

javax.swing.JButton bCutoffCalc

tfSequFile

javax.swing.JTextField tfSequFile

The textfields.

tfPosFile

javax.swing.JTextField tfPosFile

tfNegFile

javax.swing.JTextField tfNegFile

tfOutFile

javax.swing.JTextField tfOutFile

tfWindowWidth

javax.swing.JTextField tfWindowWidth

tfWindowShift

javax.swing.JTextField tfWindowShift

tfCutoff

javax.swing.JTextField tfCutoff

cbSequFile

javax.swing.JCheckBox cbSequFile

Checkboxes.

cbPosFile

javax.swing.JCheckBox cbPosFile

cbNegFile

javax.swing.JCheckBox cbNegFile

cbLengthNorm

javax.swing.JCheckBox cbLengthNorm

cbMotifOcc

javax.swing.JCheckBox cbMotifOcc

cbAppend

javax.swing.JCheckBox cbAppend

cbOverwrite

javax.swing.JCheckBox cbOverwrite

cbTextOutput

javax.swing.JCheckBox cbTextOutput

cbGraphOutput

javax.swing.JCheckBox cbGraphOutput

cbSelectSingle

javax.swing.JCheckBox cbSelectSingle

cbSelectMulti

javax.swing.JCheckBox cbSelectMulti

taOutput

javax.swing.JTextArea taOutput

The text area for the output.

taError

javax.swing.JTextArea taError

The text area for the error messages.

motifTree

MotifCheckTree motifTree

The tree of motifs in a panel.

fileChooser

javax.swing.JFileChooser fileChooser

The file chooser used in this window, its always used the same filechooser when browsing for files. This garantees, that the user works always in the directory he changed into for the first time.

sequenceInput

TextInsertDialog sequenceInput

The input form for the sequences.

menuBar

javax.swing.JMenuBar menuBar

Global setting whether a menu is already created or not. Per default menuBar is set in the constructor. If not, it is null and no menu will be drawn.

Class de.unibi.techfak.jpredictor.gui.MainWindow extends javax.swing.JFrame implements Serializable

Class de.unibi.techfak.jpredictor.gui.MotifMaker extends javax.swing.JDialog implements Serializable

Serialized Fields

toolkit

java.awt.Toolkit toolkit

A toolkit to do something useful, like beep

owner

java.awt.Window owner

The parent of this JDialog.

buttonTexts

java.lang.String[] buttonTexts

bOk

javax.swing.JButton bOk

Global buttons list.

bCancel

javax.swing.JButton bCancel

bEditMotif

javax.swing.JButton bEditMotif

bRemoveMotif

javax.swing.JButton bRemoveMotif

bClearMotifList

javax.swing.JButton bClearMotifList

bClearMotifSel

javax.swing.JButton bClearMotifSel

bReplaceMotif

javax.swing.JButton bReplaceMotif

bRegisterMotif

javax.swing.JButton bRegisterMotif

bOverwriteMotif

javax.swing.JButton bOverwriteMotif

bClearMotifFields

javax.swing.JButton bClearMotifFields

bClearAllFields

javax.swing.JButton bClearAllFields

bRecalcPSPM

javax.swing.JButton bRecalcPSPM

bRecalcPSSM

javax.swing.JButton bRecalcPSSM

bPastePSPM

javax.swing.JButton bPastePSPM

bPastePSSM

javax.swing.JButton bPastePSSM

bMultiGT

javax.swing.JButton bMultiGT

bMultiGTGT

javax.swing.JButton bMultiGTGT

bMultiLT

javax.swing.JButton bMultiLT

bMultiDel

javax.swing.JButton bMultiDel

bMultiClr

javax.swing.JButton bMultiClr

bDoubleBuild

javax.swing.JButton bDoubleBuild

bMultiAddDist

javax.swing.JButton bMultiAddDist

rbSDSequPlus

javax.swing.JRadioButton rbSDSequPlus

The check boxes for the search direction

rbSDRegEPlus

javax.swing.JRadioButton rbSDRegEPlus

rbSDPSPMPlus

javax.swing.JRadioButton rbSDPSPMPlus

rbSDPSSMPlus

javax.swing.JRadioButton rbSDPSSMPlus

rbSDSequMinus

javax.swing.JRadioButton rbSDSequMinus

rbSDRegEMinus

javax.swing.JRadioButton rbSDRegEMinus

rbSDPSPMMinus

javax.swing.JRadioButton rbSDPSPMMinus

rbSDPSSMMinus

javax.swing.JRadioButton rbSDPSSMMinus

rbSDSequBoth

javax.swing.JRadioButton rbSDSequBoth

rbSDRegEBoth

javax.swing.JRadioButton rbSDRegEBoth

rbSDPSPMBoth

javax.swing.JRadioButton rbSDPSPMBoth

rbSDPSSMBoth

javax.swing.JRadioButton rbSDPSSMBoth

tablePSPM

javax.swing.JTable tablePSPM

The both tables, one for PSPM and one for PSSM

tablePSSM

javax.swing.JTable tablePSSM

ACTUAL_PANE

int ACTUAL_PANE

The actual selected tabbed pane.

tfName

javax.swing.JTextField[] tfName

For all tabbed panes: name, description, weight

tfDesc

javax.swing.JTextField[] tfDesc

tfWeight

javax.swing.JTextField[] tfWeight

tfMotifSequ

javax.swing.JTextField tfMotifSequ

for SequenceMotif and RegExpMotif pane

tfMotifRegE

javax.swing.JTextField tfMotifRegE

tfErrorsSequ

javax.swing.JTextField tfErrorsSequ

tfErrorsRegE

javax.swing.JTextField tfErrorsRegE

tfThresholdPSPM

javax.swing.JTextField tfThresholdPSPM

for PSPM motif pane and PSSM motif pane

tfThresholdPSSM

javax.swing.JTextField tfThresholdPSSM

cbSelf

javax.swing.JCheckBox cbSelf

The checkboxes and textfields shown in the multimotif pane

tfMinDist

javax.swing.JTextField tfMinDist

tfMaxDist

javax.swing.JTextField tfMaxDist

tabbedPane

javax.swing.JTabbedPane tabbedPane

The global tabbed pane.

treeView

MotifTree treeView

The tree of motifs to the left side.

treeViewMultiMotif

MotifDistanceTree treeViewMultiMotif

The tree of motifs in the multi motif panel.

cbAddMotifsListTexts

java.lang.String[] cbAddMotifsListTexts

The strings for the combo box to insert.

cbAddMotifsList

javax.swing.JComboBox cbAddMotifsList

Contains a list of motif lists to be added, just like 'Add PREdictor motifs'.

rawPosProbs

java.lang.Integer[] rawPosProbs

The positions in the PSPM table.

rawPosScores

java.lang.Integer[] rawPosScores

The positions in the PSSM table.

rawDataScores

java.lang.Double[][] rawDataScores

The raw data for the tables either in the PSSM tab. All positions are scores.

rawDataProbs

java.lang.Double[][] rawDataProbs

The raw data for the tables in the PSPM tab. All positions are probabilities.

backData

java.lang.Double[][] backData

The background probabilities for the table in the PSSM tab.

initialMotifList

MotifList initialMotifList

The initial MotifList, this class was created with. Set in the constructor. This list is only changed, if the user clicks on the exit/ok-button.

generatingSequences

java.lang.String generatingSequences

The sequences pasted for the PSPM and PSSM motif. If the tables are edited, this sequences are set to null again.

generatingBackground

boolean generatingBackground

If the actual PSSM was generated using a valid background, this variable is set to true. When registering the motif, the background can be saved together with the motif. It is used only together with the generatingSequences.

stateChangedByUser

boolean stateChangedByUser

If the tabbed pane is selected by the user and not by the methods of this class.

Class de.unibi.techfak.jpredictor.gui.ScorePlotBrowser extends javax.swing.JPanel implements Serializable

Serialized Fields

parent

javax.swing.JFrame parent

Parent window that holds the panel.

menuBar

javax.swing.JMenuBar menuBar

Global setting whether a menu is present or not. Per default menuBar is null. This means, that no menu will be drawn and all buttons are present on the panels surface. If the class is constructed by wishing a menu to be present, only rudimentary buttons are shown on the panel and all other buttons are banned to the menu.

fileChooser

javax.swing.JFileChooser fileChooser

The file chooser used in this window, its always used the same filechooser.

scorePlotArea

ScorePlotBrowser.ScorePlotArea scorePlotArea

The global area to draw the score plot. Set by method getPlotPane

sequencePlotArea

ScorePlotBrowser.SequencePlotArea sequencePlotArea

The global area to draw the sequence. Set by method getMotifPane

statusBar

StatusBar statusBar

The status bar with the different labels. The first label is for hint texts, the next is for the mouse coordinates, then comes the x-zoom and y-zoom. The last label is the clock.

bTexts

java.lang.String[] bTexts

The text for the buttons.

bNoBar

javax.swing.AbstractButton bNoBar

The button to disable the bar.

bNoHLine

javax.swing.AbstractButton bNoHLine

The button to disable the horizontal line.

bMin

javax.swing.AbstractButton bMin

The radio button for the comprised minimum.

bMax

javax.swing.AbstractButton bMax

The radio button for the comprised maximum.

bMean

javax.swing.AbstractButton bMean

The radio button for the comprised mean.

results

java.util.Vector<E> results

Here the result vector from the communicator is stored. If the graphical output is not activated, the vector is null.

resultNumber

int resultNumber

The number of results stored in the result vector. Note, that one "result" may consist of more than one object and that only fully completed "results" are counted. If number of results changes due to updates made to the result vector the minimum and maximum must be recalculated, in fact beginning with this number. This value is recognized and set in paint-method of the ScorePlotArea class.

resultMin

double resultMin

The minimal number stored in the result vector. It is set from the paint-method of the ScorePlotArea class and used to draw the y-axis.

resultMax

double resultMax

The maximal number stored in the result vector. It is set from the paint-method of the ScorePlotArea class and used to draw the y-axis.

spinnerNumberModel

javax.swing.SpinnerNumberModel spinnerNumberModel

The model used for the spinner which in turn is responsible for choosing the horizontal line's y-axis. The horizontal line has a minimal and maximal range dependent on the score data. It is stored here in this class, because minimum and maximum will be dynamically adjusted by ScorePlotArea-class, when the result vector is updated.

sequenceEnum

SequenceEnumeration sequenceEnum

Holds all sequences to be displayed.

xZoom

double xZoom

Set when the buttons x zoom in and x zoom out are pressed. Every zoom out halfes it, and every zoom in doubles it. In other words, it represents the number of dots, that must be drawn for every score. This value is used by the ScorePlotArea class. It is initialy set to one by the constructor.

yZoom

double yZoom

Set when the buttons y zoom in and y zoom out are pressed. Every zoom out halfes it, and every zoom in doubles it. In other words, it represents the number of dots, that are drawn for every unit of heigth. This value is used by the ScorePlotArea class. It is initialy set to one by the constructor.

xZoomFitToWindow

boolean xZoomFitToWindow

Set to true, if the user has not clicked on one of the buttons for x-zoom . As long as this switch is true, the x-zoom is automatically set the way that the user can see the whole area. This variable is used by the ScorePlotArea-class.

yZoomFitToWindow

boolean yZoomFitToWindow

Set to true, if the user has not clicked on one of the buttons for y-zoom . As long as this switch is true, the y-zoom is automatically set the way that the user can see the whole area. This variable is used by the ScorePlotArea-class.

selectionMid

int selectionMid

Set by methods receiving mouse motion events of the ScorePlotArea. Gives the mid point of the grey bar (displayed in the ScorePlotArea) and the mid of the sequence shown in SequencePlotArea. Set to -1 for no bar (dont't forget to repaint).
This mid point is messured in indices on the score and index arrays.

horizontalLine

int horizontalLine

Set by the spinner and by the methods receiving state change events of it. Gives the y coordinate of the horizontal line to be drawn. Used by the ScorePlotArea class. Set to Integer.MIN_VALUE for no bar (dont't forget to repaint).

drawingStyle

int drawingStyle

The style in which the scores are plotted. Set this variable to BARS, if bars should be drawn, to DOTS, if dots are wished and to LINES, if lines connecting the dots should be drawn. Default is BARS.

drawingChoose

int drawingChoose

If the score plot is zoomed out many scores have to be comprised to one pixel (dot or line). Set this to MINIMUM, MAXIMUM (default) or MEAN, repectively, to tell the draw method what to do with the scores, when they are broken down to one pixel width.

Class de.unibi.techfak.jpredictor.gui.StatusBar extends javax.swing.JPanel implements Serializable

Serialized Fields

labels

javax.swing.JLabel[] labels

All labels. The first one is the message label.

timerTask

java.awt.event.ActionListener timerTask

The task which is called by an installed timer and updates the date and time.

timer

javax.swing.Timer timer

The timer task started if the user wants to have shown date and time.

timeLabel

int timeLabel

The label's number to hold the time (-1 if no time is shown).

dateLabel

int dateLabel

The label's number to hold the date (-1 if no date is shown).

Class de.unibi.techfak.jpredictor.gui.TextInsertDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

taMessage

javax.swing.JTextArea taMessage

textArea

javax.swing.JTextArea textArea

insertedText

java.lang.String insertedText

optionPane

javax.swing.JOptionPane optionPane

options

java.lang.Object[] options

An array specifying the number of dialog buttons and their text. This text should be compared in the propertyChange-method.

Package de.unibi.techfak.jpredictor.motifs

Class de.unibi.techfak.jpredictor.motifs.CycleInMultiMotifExeption extends java.lang.RuntimeException implements Serializable

Class de.unibi.techfak.jpredictor.motifs.MissingCharSequenceException extends java.lang.RuntimeException implements Serializable

Class de.unibi.techfak.jpredictor.motifs.MissingMotifException extends java.lang.RuntimeException implements Serializable

Class de.unibi.techfak.jpredictor.motifs.MotifList extends java.util.Vector implements Serializable

Class de.unibi.techfak.jpredictor.motifs.MotifNotCompleteException extends java.lang.RuntimeException implements Serializable

Package de.unibi.techfak.jpredictor.sequences

Class de.unibi.techfak.jpredictor.sequences.NewSequenceBlockException extends java.io.IOException implements Serializable

Class de.unibi.techfak.jpredictor.sequences.NoMoreSequencesAvailableException extends java.lang.Exception implements Serializable

Class de.unibi.techfak.jpredictor.sequences.ResetNotSupportedException extends java.lang.IndexOutOfBoundsException implements Serializable