Serialized Form

Package AFLPcore

Class AFLPcore.DataList implements Serializable

Serialized Fields

isSearchable

boolean isSearchable

Class AFLPcore.ListNotSearchableError implements Serializable

Class AFLPcore.MissingParameterError implements Serializable

Class AFLPcore.NoBrowserException implements Serializable

Class AFLPcore.NoDataError implements Serializable

Class AFLPcore.PrettyInsignificantError implements Serializable

Class AFLPcore.ScanCalcError implements Serializable

Class AFLPcore.ScoringFailure implements Serializable

Package AFLPgui

Class AFLPgui.AboutDialog implements Serializable

Serialized Fields

infoTA

java.awt.TextArea infoTA

okB

java.awt.Button okB

Class AFLPgui.AnalysisView implements Serializable

Serialized Fields

outputArea

java.awt.TextArea outputArea

buttonBar

ButtonBar buttonBar

infoBar

Bar infoBar

infoLabel

java.awt.Label infoLabel

methodChoice

java.awt.Choice methodChoice

selection

java.lang.String selection

output

java.lang.String output

gel

Gel gel

topWindow

java.awt.Frame topWindow

Class AFLPgui.Bar implements Serializable

Serialized Fields

drawTop

boolean drawTop

drawBottom

boolean drawBottom

Class AFLPgui.BinDialog implements Serializable

Serialized Fields

okButton

java.awt.Button okButton

cancelButton

java.awt.Button cancelButton

newButton

java.awt.Button newButton

deleteButton

java.awt.Button deleteButton

delAllButton

java.awt.Button delAllButton

helpButton

java.awt.Button helpButton

enterButton

java.awt.Button enterButton

scoreOptionButton

java.awt.Button scoreOptionButton

scoreAllCheck

java.awt.Checkbox scoreAllCheck

binList

java.awt.List binList

scoreChoice

java.awt.Choice scoreChoice

nameField

java.awt.TextField nameField

locationField

java.awt.TextField locationField

rangeField

java.awt.TextField rangeField

bins

DataList bins

savedBins

DataList savedBins

currentBin

Bin currentBin

index

int index

allMode

boolean allMode

scoreNames

java.lang.String[] scoreNames

scoreFn

ScoreFunction scoreFn

parent

java.awt.Frame parent

Class AFLPgui.ButtonBar implements Serializable

Serialized Fields

newButton

ImgButton newButton

openButton

ImgButton openButton

saveButton

ImgButton saveButton

printButton

ImgButton printButton

buttonCount

int buttonCount

adjustments

int adjustments

Class AFLPgui.ControlBar implements Serializable

Serialized Fields

BUTTON_WIDTH

int BUTTON_WIDTH

BUTTON_HEIGHT

int BUTTON_HEIGHT

BUTTON_VSPACE

int BUTTON_VSPACE

BUTTON_HSPACE

int BUTTON_HSPACE

BUTTON_INIT_VSPACE

int BUTTON_INIT_VSPACE

PANEL_WIDTH

int PANEL_WIDTH

PANEL_HEIGHT

int PANEL_HEIGHT

gelButton

java.awt.Button gelButton

thumbnailButton

java.awt.Button thumbnailButton

graphButton

java.awt.Button graphButton

analysisButton

java.awt.Button analysisButton

traceButton

java.awt.Button traceButton

parent

FragmentMap parent

Class AFLPgui.CutoffDialog implements Serializable

Serialized Fields

okButton

java.awt.Button okButton

cancelButton

java.awt.Button cancelButton

newButton

java.awt.Button newButton

deleteButton

java.awt.Button deleteButton

defaultButton

java.awt.Button defaultButton

helpButton

java.awt.Button helpButton

enterButton

java.awt.Button enterButton

cutoffList

java.awt.List cutoffList

heightField

java.awt.TextField heightField

currentCutoff

Cutoff currentCutoff

lanes

DataList lanes

index

int index

size

double size

parent

java.awt.Frame parent

Class AFLPgui.CutoffSlider implements Serializable

Serialized Fields

cutoff

Cutoff cutoff

applyToLanes

DataList applyToLanes

message

java.lang.String message

arrow

java.awt.Polygon arrow

currentFunction

CutoffFunction currentFunction

scale

double scale

size

double size

type

int type

currentLevel

int currentLevel

Class AFLPgui.EntryDialog implements Serializable

Serialized Fields

okButton

java.awt.Button okButton

cancelButton

java.awt.Button cancelButton

entryField

java.awt.TextField entryField

message1

java.awt.Label message1

message2

java.awt.Label message2

message3

java.awt.Label message3

parent

java.awt.Frame parent

entry

java.lang.String entry

mode

int mode

Class AFLPgui.FragmentMap implements Serializable

Serialized Fields

ICON

java.lang.String ICON

newItem

java.awt.MenuItem newItem

openItem

java.awt.MenuItem openItem

saveItem

java.awt.MenuItem saveItem

saveAsItem

java.awt.MenuItem saveAsItem

importItem

java.awt.MenuItem importItem

exportItem

java.awt.MenuItem exportItem

printItem

java.awt.MenuItem printItem

exitItem

java.awt.MenuItem exitItem

laneDeleteItem

java.awt.MenuItem laneDeleteItem

laneOpItem

java.awt.MenuItem[] laneOpItem

binRedrawItem

java.awt.MenuItem binRedrawItem

binOpItem

java.awt.MenuItem[] binOpItem

gelRedrawItem

java.awt.MenuItem gelRedrawItem

gelOpItem

java.awt.MenuItem[] gelOpItem

viewGelItem

java.awt.MenuItem viewGelItem

viewThumbnailItem

java.awt.MenuItem viewThumbnailItem

viewGraphItem

java.awt.MenuItem viewGraphItem

viewTraceItem

java.awt.MenuItem viewTraceItem

viewAnalysisItem

java.awt.MenuItem viewAnalysisItem

helpItem

java.awt.MenuItem helpItem

aboutItem

java.awt.MenuItem aboutItem

newButton

java.awt.Button newButton

openButton

java.awt.Button openButton

saveButton

java.awt.Button saveButton

printButton

java.awt.Button printButton

gel

Gel gel

gelView

GelView gelView

thumbnail

Thumbnail thumbnail

graph

GraphView graph

trace

TraceView trace

analysis

AnalysisView analysis

mainPanel

java.awt.ScrollPane mainPanel

buttonBar

ButtonBar buttonBar

infoBar

Bar infoBar

statusBar

Bar statusBar

bottomP

java.awt.Panel bottomP

statusLabel

java.awt.Label statusLabel

defaultCutoff

double defaultCutoff

currentView

int currentView

currentBin

Bin currentBin

importDialog

MultiFileDialog importDialog

fileDialog

java.awt.FileDialog fileDialog

errorDialog

AFLPgui.ErrorDialog errorDialog

currentFile

java.lang.String currentFile

currentDir

java.lang.String currentDir

modified

boolean modified

Class AFLPgui.GelView implements Serializable

Serialized Fields

offDimension

java.awt.Dimension offDimension

offImage

java.awt.Image offImage

offGraphics

java.awt.Graphics offGraphics

gelBar

ButtonBar gelBar

infoBar

Bar infoBar

infoLabel

java.awt.Label infoLabel

zoomSelect

java.awt.Choice zoomSelect

minSizeField

java.awt.TextField minSizeField

maxSizeField

java.awt.TextField maxSizeField

intensityField

java.awt.TextField intensityField

refreshButton

ImgButton refreshButton

binButton

ImgButton binButton

binDialog

BinDialog binDialog

entryDialog

EntryDialog entryDialog

errorDialog

AFLPgui.ErrorDialog errorDialog

gel

Gel gel

gelLength

int gelLength

gelWidth

int gelWidth

pixel

int[] pixel

gelImage

java.awt.Image gelImage

imgSource

java.awt.image.MemoryImageSource imgSource

zoomFactor

double zoomFactor

previousZoom

double previousZoom

zoomIndex

int zoomIndex

sizeLoc

double sizeLoc

laneLoc

int laneLoc

overType

int overType

currentBin

Bin currentBin

selectedBin

Bin selectedBin

dragMode

int dragMode

dragged

boolean dragged

dragStart

java.awt.Point dragStart

oldBin

Bin oldBin

standardCursor

java.awt.Cursor standardCursor

resizeCursor

java.awt.Cursor resizeCursor

moveCursor

java.awt.Cursor moveCursor

topWindow

java.awt.Frame topWindow

sizeSet

boolean sizeSet

Class AFLPgui.GraphView implements Serializable

Serialized Fields

offDimension

java.awt.Dimension offDimension

offImage

java.awt.Image offImage

offGraphics

java.awt.Graphics offGraphics

buttonBar

ButtonBar buttonBar

infoBar

Bar infoBar

infoLabel

java.awt.Label infoLabel

graphChoice

java.awt.Choice graphChoice

previousButton

ImgButton previousButton

nextButton

ImgButton nextButton

addCutoffButton

ImgButton addCutoffButton

cutoffDialogButton

ImgButton cutoffDialogButton

ctDialog

CutoffDialog ctDialog

slider

CutoffSlider slider

currentBin

Bin currentBin

height

int height

width

int width

h_inset

int h_inset

v_inset

int v_inset

graph_width

int graph_width

maxSize

double maxSize

minSize

double minSize

scale

double scale

tickInc

double tickInc

maxIntensity

double maxIntensity

lanes

DataList lanes

bins

DataList bins

graph

Graph[] graph

graphIndex

int graphIndex

topWindow

java.awt.Frame topWindow

Class AFLPgui.ImgButton implements Serializable

Serialized Fields

image

java.awt.Image image

pos_x

int pos_x

pos_y

int pos_y

Class AFLPgui.MultiFileDialog implements Serializable

Serialized Fields

pathLabel

java.awt.Label pathLabel

directoryList

java.awt.List directoryList

openList

java.awt.List openList

fileType

java.awt.Choice fileType

addButton

java.awt.Button addButton

removeButton

java.awt.Button removeButton

addAllButton

java.awt.Button addAllButton

clearButton

java.awt.Button clearButton

importButton

java.awt.Button importButton

cancelButton

java.awt.Button cancelButton

parentItem

java.lang.String parentItem

directory

java.lang.String directory

file

java.lang.String file

constantFiles

java.io.File[] constantFiles

currentFile

java.io.File currentFile

fileList

java.io.File[] fileList

importFiles

java.util.Vector importFiles

importList

java.io.File[] importList

filter

ImportFilter filter

Class AFLPgui.OptionDialog implements Serializable

Serialized Fields

optionPane

java.awt.Panel optionPane

okButton

java.awt.Button okButton

cancelButton

java.awt.Button cancelButton

optUIComponent

java.awt.Component[] optUIComponent

opts

Option[] opts

numRequired

int numRequired

canceled

boolean canceled

parentWin

java.awt.Frame parentWin

Class AFLPgui.Thumbnail implements Serializable

Serialized Fields

offDimension

java.awt.Dimension offDimension

offImage

java.awt.Image offImage

offGraphics

java.awt.Graphics offGraphics

lanes

DataList lanes

bins

DataList bins

buttonBar

ButtonBar buttonBar

infoBar

Bar infoBar

infoLabel

java.awt.Label infoLabel

invertButton

ImgButton invertButton

previousButton

ImgButton previousButton

nextButton

ImgButton nextButton

addCutoffButton

ImgButton addCutoffButton

cutoffDialogButton

ImgButton cutoffDialogButton

ctDialog

CutoffDialog ctDialog

slider

CutoffSlider slider

currentBin

Bin currentBin

height

int height

width

int width

hspace

int hspace

vspace

int vspace

sliderSpace

int sliderSpace

scoreWidth

int scoreWidth

printViewWidth

int printViewWidth

numColumns

int numColumns

numRows

int numRows

overType

int overType

size

double size

intensity

double intensity

laneNum

int laneNum

minSize

double minSize

maxSize

double maxSize

hScale

double hScale

vScale

double vScale

maxIntensity

double maxIntensity

parent

java.awt.ScrollPane parent

topWindow

java.awt.Frame topWindow

Class AFLPgui.TraceView implements Serializable

Serialized Fields

offDimension

java.awt.Dimension offDimension

offImage

java.awt.Image offImage

offGraphics

java.awt.Graphics offGraphics

buttonBar

ButtonBar buttonBar

infoBar

Bar infoBar

infoLabel

java.awt.Label infoLabel

previousButton

ImgButton previousButton

nextButton

ImgButton nextButton

topWindow

java.awt.Frame topWindow

lanes

DataList lanes

lane

Lane lane

h_inset

int h_inset

v_inset

int v_inset

width

int width

height

int height

maxIntensity

double maxIntensity

hScale

double hScale

vScale

double vScale

minSize

double minSize

maxSize

double maxSize