Serialized Form

Package org.strbio.app

Class org.strbio.app.JThread extends ProfileGUIApp implements Serializable

Serialized Fields

saveProteins

javax.swing.Action saveProteins

saveLog

javax.swing.Action saveLog

clearLog

javax.swing.Action clearLog

threadProteins

javax.swing.Action threadProteins

print

javax.swing.Action print

quit

javax.swing.Action quit

nextProtein

javax.swing.Action nextProtein

prevProtein

javax.swing.Action prevProtein

showOptions

javax.swing.Action showOptions

loadProteinsB

javax.swing.JButton loadProteinsB

threadProteinsB

javax.swing.JButton threadProteinsB

greenBorder

javax.swing.border.Border greenBorder

buttonBorder

javax.swing.border.Border buttonBorder

directions

PrintfJTextArea directions

tabbedPane

javax.swing.JTabbedPane tabbedPane

frPane

org.strbio.app.JThread.FRPane frPane

frScrollPane

javax.swing.JScrollPane frScrollPane

alignmentPane

org.strbio.app.JThread.AlignmentPane alignmentPane

alScrollPane

javax.swing.JScrollPane alScrollPane

splitPane

javax.swing.JSplitPane splitPane

library

FoldLibrary library

standardFoldLibrary

FoldLibrary standardFoldLibrary

userFoldLibrary

FoldLibrary userFoldLibrary

useTomRB

javax.swing.JRadioButton useTomRB

loadLibPD

ProfileGUIApp.LoadProgressDialog loadLibPD

wrapLines

boolean wrapLines

wrapPos

int wrapPos

graphPrediction

boolean graphPrediction

showScore

boolean showScore

show2ary

boolean show2ary

frColumnWidth

int[] frColumnWidth

expert

boolean expert

showAlignmentPane

boolean showAlignmentPane

blastServer

int blastServer

blastURL

java.lang.String blastURL

threadThread

org.strbio.app.JThread.ThreadThread threadThread

threadPD

org.strbio.app.JThread.ThreadProgressDialog threadPD

loadLibThread

org.strbio.app.JThread.LoadUserLibraryThread loadLibThread

optionsDialog

org.strbio.app.JThread.OptionsDialog optionsDialog

alAP

AlignmentParametersEA alAP

pdbInfoClass

java.lang.Class<T> pdbInfoClass

cathInfoClass

java.lang.Class<T> cathInfoClass

doAlCutoff

double doAlCutoff

shownProf

int shownProf

profile currently being shown in top thread window.

shownAl

int shownAl

alignment being shown in the bottom thread window.

tr

ThreadResults[] tr

Thread results on current protein set.

numBuffer

char[] numBuffer

Class org.strbio.app.NSPred2ary extends java.awt.Frame implements Serializable

Serialized Fields

frame

NSPred2ary frame

frameSize

java.awt.Dimension frameSize

frameLoc

java.awt.Point frameLoc

logText

PrintfTextArea logText

proteinPane

org.strbio.app.NSPred2ary.ProteinPane proteinPane

pda

ProfileDisplayArea pda

scrollPanel

java.awt.ScrollPane scrollPanel

aboutDialog

org.strbio.app.NSPred2ary.AboutDialog aboutDialog

helpDialog

org.strbio.app.NSPred2ary.HelpDialog helpDialog

progressDialog

org.strbio.app.NSPred2ary.ProgressDialog progressDialog

tabbedPane

java.awt.Panel tabbedPane

label

java.awt.Label label

p

PredictionSet p

currentJury

Jury currentJury

fontSize

int fontSize

networkLabel

java.awt.Label networkLabel

chooseSequenceB

java.awt.Button chooseSequenceB

printB

java.awt.Button printB

saveProteinsB

java.awt.Button saveProteinsB

loadProteinsB

java.awt.Button loadProteinsB

predictProteinsB

java.awt.Button predictProteinsB

saveProteinsMI

java.awt.MenuItem saveProteinsMI

loadProteinsMI

java.awt.MenuItem loadProteinsMI

numBuffer

char[] numBuffer

Class org.strbio.app.NSPred2ary.AboutMessage extends java.awt.Canvas implements Serializable

Serialized Fields

titleFont

java.awt.Font titleFont

versionFont

java.awt.Font versionFont

creditFont

java.awt.Font creditFont

icon

java.awt.Image icon

maxX

int maxX

maxY

int maxY

imageWidth

int imageWidth

imageHeight

int imageHeight

Class org.strbio.app.Pred2ary extends javax.swing.JFrame implements Serializable

Serialized Fields

frame

Pred2ary frame

frameSize

java.awt.Dimension frameSize

frameLoc

java.awt.Point frameLoc

helpFrameSize

java.awt.Dimension helpFrameSize

helpFrameLoc

java.awt.Point helpFrameLoc

logText

PrintfJTextArea logText

proteinPane

org.strbio.app.Pred2ary.ProteinPane proteinPane

pda

ProfileDisplayArea pda

proteinScrollPane

javax.swing.JScrollPane proteinScrollPane

tabbedPane

javax.swing.JTabbedPane tabbedPane

popup

javax.swing.JPopupMenu popup

aboutDialog

org.strbio.app.Pred2ary.AboutDialog aboutDialog

helpFrame

HelpFrame helpFrame

blastDialog

org.strbio.app.Pred2ary.BlastDialog blastDialog

predictionPD

org.strbio.app.Pred2ary.PredictionProgressDialog predictionPD

predictionThread

org.strbio.app.Pred2ary.PredictionThread predictionThread

blastPD

org.strbio.app.Pred2ary.BlastProgressDialog blastPD

blastThread

org.strbio.app.Pred2ary.BlastThread blastThread

loadPD

org.strbio.app.Pred2ary.LoadProgressDialog loadPD

loadThread

org.strbio.app.Pred2ary.LoadThread loadThread

loadFile

java.io.File loadFile

label

PrintfJLabel label

p

PredictionSet p

currentJury

Jury currentJury

loadDir

java.io.File loadDir

blastType

int blastType

blastServer

int blastServer

blastURL

java.lang.String blastURL

fontSize

int fontSize

loadProteins

javax.swing.Action loadProteins

saveProteins

javax.swing.Action saveProteins

saveLog

javax.swing.Action saveLog

clearLog

javax.swing.Action clearLog

predictProteins

javax.swing.Action predictProteins

print

javax.swing.Action print

blast

javax.swing.Action blast

quit

javax.swing.Action quit

chooseSequence

javax.swing.Action chooseSequence

showProfileMI

javax.swing.JMenuItem showProfileMI

showSingleMI

javax.swing.JMenuItem showSingleMI

showProfileRB

javax.swing.JRadioButton showProfileRB

showSingleRB

javax.swing.JRadioButton showSingleRB

networkLabel

javax.swing.JLabel networkLabel

wrapCHB

javax.swing.JCheckBox wrapCHB

numBuffer

char[] numBuffer

Package org.strbio.io

Class org.strbio.io.OldBufferedPrintfTextArea extends java.awt.TextArea implements Serializable

Serialized Fields

stringBuffer

java.lang.StringBuffer stringBuffer

Class org.strbio.io.OldPrintfJLabel extends javax.swing.JLabel implements Serializable

Serialized Fields

charbuffer

char[] charbuffer

i

int i

Class org.strbio.io.OldPrintfJTextArea extends javax.swing.JTextArea implements Serializable

Class org.strbio.io.OldPrintfTextArea extends java.awt.TextArea implements Serializable

Class org.strbio.io.PrintfJLabel extends javax.swing.JLabel implements Serializable

Serialized Fields

charbuffer

char[] charbuffer

i

int i

Class org.strbio.io.PrintfJTextArea extends javax.swing.JTextArea implements Serializable

Class org.strbio.io.PrintfTextArea extends java.awt.TextArea implements Serializable

Package org.strbio.math

Class org.strbio.math.DVectorSet extends java.util.Vector implements Serializable

Serialized Fields

minDimension

int minDimension

Package org.strbio.mol

Class org.strbio.mol.PolymerSet extends java.util.Vector implements Serializable

Class org.strbio.mol.ProfilePSISet extends ProfileSet implements Serializable

Class org.strbio.mol.ProfileSet extends ProteinSet implements Serializable

Class org.strbio.mol.ProteinSet extends PolymerSet implements Serializable

Package org.strbio.mol.lib

Class org.strbio.mol.lib.FoldLibrary extends ProfilePSISet implements Serializable

Class org.strbio.mol.lib.TOMFoldLibrary extends FoldLibrary implements Serializable

Class org.strbio.mol.lib.UserFoldLibrary extends FoldLibrary implements Serializable

Package org.strbio.mol.lib.pred2ary

Class org.strbio.mol.lib.pred2ary.PCPSet extends ProfileSet implements Serializable

Class org.strbio.mol.lib.pred2ary.Pred2aryApplet extends java.applet.Applet implements Serializable

Serialized Fields

frame

Pred2aryAppletFrame frame

Class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame extends java.awt.Frame implements Serializable

Serialized Fields

applet

Pred2aryApplet applet

frame

Pred2aryAppletFrame frame

aboutDialog

Pred2aryAppletFrame.AboutDialog aboutDialog

progressDialog

Pred2aryAppletFrame.ProgressDialog progressDialog

saveWindow

Pred2aryAppletFrame.SaveWindow saveWindow

loadWindow

Pred2aryAppletFrame.LoadWindow loadWindow

logText

OldBufferedPrintfTextArea logText

proteinPane

Pred2aryAppletFrame.ProteinPane proteinPane

pda

ProfileDisplayArea pda

scrollPanel

JMCScrollPane scrollPanel

tabbedPane

java.awt.Panel tabbedPane

mainLabel

java.awt.Label mainLabel

p

PredictionSet p

currentJury

AppletJury currentJury

fontSize

int fontSize

networkLabel

java.awt.Label networkLabel

chooseSequenceB

java.awt.Button chooseSequenceB

loadProteinsB

java.awt.Button loadProteinsB

loadProteinsMI

java.awt.MenuItem loadProteinsMI

saveProteinsB

java.awt.Button saveProteinsB

predictProteinsB

java.awt.Button predictProteinsB

saveProteinsMI

java.awt.MenuItem saveProteinsMI

numBuffer

char[] numBuffer

icon

java.awt.Image icon

Class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.AboutDialog extends java.awt.Frame implements Serializable

Class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.AboutMessage extends java.awt.Canvas implements Serializable

Serialized Fields

titleFont

java.awt.Font titleFont

versionFont

java.awt.Font versionFont

creditFont

java.awt.Font creditFont

maxX

int maxX

maxY

int maxY

imageWidth

int imageWidth

imageHeight

int imageHeight

Class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.LoadWindow extends java.awt.Frame implements Serializable

Serialized Fields

textArea

java.awt.TextArea textArea

Class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.ProgressDialog extends java.awt.Frame implements Serializable

Serialized Fields

label

java.awt.Label label

ofN

java.lang.String ofN

Class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.ProteinPane extends java.awt.Canvas implements Serializable

Serialized Fields

pd

ProfileDisplayArea pd

Class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.SaveWindow extends java.awt.Frame implements Serializable

Serialized Fields

textArea

OldBufferedPrintfTextArea textArea

Class org.strbio.mol.lib.pred2ary.PredictionSet extends TPSet implements Serializable

Serialized Fields

t_set

TrainingSet t_set

Class org.strbio.mol.lib.pred2ary.TPSet extends PCPSet implements Serializable

Serialized Fields

nstats

int nstats

r_SM

SimMatrix r_SM

SM

SimMatrix SM

CSM

SimMatrix CSM

CSM1

CorrectMatrix[] CSM1

cutoff_2ary

double cutoff_2ary

cutoff_lvl2

double cutoff_lvl2

cutoff_class

double[] cutoff_class

vars

TPSet.NetVars vars

Class org.strbio.mol.lib.pred2ary.TrainingSet extends TPSet implements Serializable

Serialized Fields

p_set

PredictionSet p_set

net

NeuralNet net

net_2

NeuralNet net_2

cnet4

NeuralNet cnet4

cnet1

NeuralNet[] cnet1

weight_2ary

java.lang.String weight_2ary

weight_lvl2

java.lang.String weight_lvl2

weight_class

java.lang.String weight_class

done_2ary

boolean done_2ary

done_lvl2

boolean done_lvl2

done_class

boolean done_class

nsets

int nsets

child_set

TrainingSet[] child_set

parent_set

TrainingSet parent_set

j_set

int j_set

r_set

int r_set

Package org.strbio.util

Class org.strbio.util.ActionJButton extends javax.swing.JButton implements Serializable

Serialized Fields

myAction

javax.swing.Action myAction

Class org.strbio.util.BarLegend extends javax.swing.JComponent implements Serializable

Serialized Fields

colorScale

ColorScale colorScale

min

double min

max

double max

format

java.lang.String format

charbuffer

char[] charbuffer

formatFont

java.awt.Font formatFont

charWidth

int charWidth

charHeight

int charHeight

minWidth

int minWidth

maxWidth

int maxWidth

Class org.strbio.util.DensityPlot extends javax.swing.JComponent implements Serializable

Serialized Fields

colorScale

ColorScale colorScale

matrix

DMatrix matrix

The matrix that is being shown. It is private for now, but might later be made public, so it can be changed by the user, for greater efficiency. This would have be done with care, by calling matrixChanged() if values in the matrix have been changed without calling the functions here.

mask

boolean[][] mask

A 2-d array of booleans showing which positions to draw and which not to.

min

double min

max

double max

autoscaleMin

boolean autoscaleMin

autoscaleMax

boolean autoscaleMax

maxX

int maxX

maxY

int maxY

flipY

boolean flipY

flipX

boolean flipX

Class org.strbio.util.JMCScrollPane extends java.awt.Panel implements Serializable

Serialized Fields

xoffset

int xoffset

yoffset

int yoffset

viewportSize

java.awt.Dimension viewportSize

hbar

java.awt.Scrollbar hbar

vbar

java.awt.Scrollbar vbar

viewport

org.strbio.util.JMCScrollPane.Viewport viewport

child

java.awt.Component child

Package org.strbio.util.db

Class org.strbio.util.db.Data extends java.util.Vector implements Serializable

Package org.strbio.util.graph

Class org.strbio.util.graph.Graph2D extends javax.swing.JComponent implements Serializable

Serialized Fields

listener

Graph2D.ClickListener listener

minX

double minX

minY

double minY

maxX

double maxX

maxY

double maxY

autoscaleMaxX

boolean autoscaleMaxX

autoscaleMaxY

boolean autoscaleMaxY

autoscaleMinX

boolean autoscaleMinX

autoscaleMinY

boolean autoscaleMinY

graphPos

java.awt.Rectangle graphPos

totalWidth

int totalWidth

totalHeight

int totalHeight

leftMargin

int leftMargin

rightMargin

int rightMargin

topMargin

int topMargin

bottomMargin

int bottomMargin

XAxisLabel

java.lang.String XAxisLabel

YAxisLabel

java.lang.String YAxisLabel

title

java.lang.String title

XScale

XAxisScale XScale

YScale

YAxisScale YScale

graphs

java.util.Vector<E> graphs

drawBox

int drawBox

BOX_NONE

int BOX_NONE

Don't draw a box around the graph region.

BOX_LEFT

int BOX_LEFT

Draw line on left side of graph region.

BOX_RIGHT

int BOX_RIGHT

Draw line on right side of graph region.

BOX_TOP

int BOX_TOP

Draw line on top side of graph region.

BOX_BOTTOM

int BOX_BOTTOM

Draw line on bottom side of graph region.

BOX_ALL

int BOX_ALL

Draw box completely around graph region (default).

flipY

boolean flipY

flipX

boolean flipX

labelFont

java.awt.Font labelFont

labelFontMetrics

java.awt.FontMetrics labelFontMetrics

charWidth

int charWidth

charHeight

int charHeight

Package org.strbio.util.ui

Class org.strbio.util.ui.AboutDialog extends javax.swing.JFrame implements Serializable

Serialized Fields

parent

GUIApp parent

Parent app for this dialog.

Class org.strbio.util.ui.GUIApp extends javax.swing.JFrame implements Serializable

Serialized Fields

mainFrame

GUIApp mainFrame

aboutDialog

AboutDialog aboutDialog

helpFrame

HelpFrame helpFrame

statusLine

PrintfJLabel statusLine

mainFrameSize

java.awt.Dimension mainFrameSize

mainFrameLoc

java.awt.Point mainFrameLoc

helpFrameSize

java.awt.Dimension helpFrameSize

helpFrameLoc

java.awt.Point helpFrameLoc

fontSize

int fontSize

Class org.strbio.util.ui.HelpFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

index

java.net.URL index

This is the index url.

frame

HelpFrame frame

A pointer to this frame, for "quit" button to access.

editor

javax.swing.JEditorPane editor

the editor pane that shows stuff.

history

java.util.Stack<E> history

history list of things clicked on.

back

javax.swing.JButton back

button to go back 1 page in the history list.

Class org.strbio.util.ui.ProfileGUIApp extends GUIApp implements Serializable

Serialized Fields

p

ProfileSet p

loadThread

org.strbio.util.ui.ProfileGUIApp.LoadThread loadThread

loadFile

java.io.File loadFile

loadPD

ProfileGUIApp.LoadProgressDialog loadPD

loadProteins

javax.swing.Action loadProteins

loadDir

java.io.File loadDir

logText

PrintfJTextArea logText

Class org.strbio.util.ui.ProfileGUIApp.LoadFormats extends javax.swing.JPanel implements Serializable

Serialized Fields

combine

boolean combine

Class org.strbio.util.ui.ProfileGUIApp.LoadProgressDialog extends javax.swing.JFrame implements Serializable

Serialized Fields

label

PrintfJLabel label