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Serialized Form

Package gnu.jpdf

Class gnu.jpdf.BoundingBox extends java.awt.Rectangle implements Serializable

Serialized Fields

drawingPoint

java.awt.Point drawingPoint

The point to use for Graphics.drawString()

absoluteLocation

java.awt.Point absoluteLocation

The absolute, world location of the box

parent

BoundingBox parent

Link to parent box

stringArray

java.lang.String[] stringArray

If this box was the result of a getStringBounds call, this array will hold the broken strings

fullString

java.lang.String fullString

The string specified in getStringBounds

Class gnu.jpdf.PDFAnnot extends PDFObject implements Serializable

Serialized Fields

subtype

java.lang.String subtype

The subtype of the outline, ie text, note, etc

l

int l

The size of the annotation

b

int b

The size of the annotation

r

int r

The size of the annotation

t

int t

The size of the annotation

s

java.lang.String s

The text of a text annotation

dest

PDFObject dest

Link to the Destination page

fl

int fl

If fl!=FULL_PAGE then this is the region of the destination page shown. Otherwise they are ignored.

fb

int fb

If fl!=FULL_PAGE then this is the region of the destination page shown. Otherwise they are ignored.

fr

int fr

If fl!=FULL_PAGE then this is the region of the destination page shown. Otherwise they are ignored.

ft

int ft

If fl!=FULL_PAGE then this is the region of the destination page shown. Otherwise they are ignored.

border

PDFBorder border

the border for this annotation

Class gnu.jpdf.PDFBorder extends PDFObject implements Serializable

Serialized Fields

style

short style

The style of the border

width

double width

The width of the border

dash

double[] dash

This array allows the definition of a dotted line for the border

Class gnu.jpdf.PDFCatalog extends PDFObject implements Serializable

Serialized Fields

pdfPageList

PDFPageList pdfPageList

The pages of the document

outlines

PDFOutline outlines

The outlines of the document

pagemode

int pagemode

The initial page mode

Class gnu.jpdf.PDFDocument extends java.lang.Object implements Serializable

Serialized Fields

objser

int objser

This is used to allocate objects a unique serial number in the document.

objects

java.util.Vector<E> objects

This vector contains each indirect object within the document.

catalog

PDFCatalog catalog

This is the Catalog object, which is required by each PDF Document

info

PDFInfo info

This is the info object. Although this is an optional object, we include it.

pdfPageList

PDFPageList pdfPageList

This is the Pages object, which is required by each PDF Document

outline

PDFOutline outline

This is the Outline object, which is optional

defaultOutlineBorder

PDFObject defaultOutlineBorder

This holds a PDFObject describing the default border for annotations. It's only used when the document is being written.

fontid

int fontid

This is used to provide a unique name for a font

imageid

int imageid

This is used to provide a unique name for an image

fonts

java.util.Vector<E> fonts

This holds the current fonts

Class gnu.jpdf.PDFFont extends PDFObject implements Serializable

Serialized Fields

name

java.lang.String name

The PDF document name of the font

type

java.lang.String type

The PDF type of the font, usually /Type1

font

java.lang.String font

The font's real name

javaFont

java.lang.String javaFont

The name of the equivalent Java font

style

int style

The PDF Style, ie: BOLD, ITALIC, etc

Class gnu.jpdf.PDFGraphics extends java.awt.Graphics implements Serializable

Serialized Fields

media

java.awt.Rectangle media

This is the media we are working with

mediaRot

int mediaRot

The media's rotation, either 0,90,180 or 270.

trax

int trax

This is used to translate coordinates

tray

int tray

This is used to translate coordinates

pre_np

java.lang.String pre_np

Part of the optimiser: This is written to the stream when the newPath() is called. np then clears this value.

inStroke

boolean inStroke

Part of the optimiser: When true, we are drawing a path.

lx

int lx

Part of the optimiser: The last known moveto/lineto x coordinate

See Also:: PDFGraphics.moveto(int, int), PDFGraphics.lineto(int, int)

ly

int ly

Part of the optimiser: The last known moveto/lineto y coordinate

See Also:: PDFGraphics.moveto(int, int), PDFGraphics.lineto(int, int)

inText

boolean inText

Part of the optimiser: When true, we are within a Text Block.

newFont

boolean newFont

Part of the optimiser: When true, the font has changed.

tx

int tx

Part of the optimiser: The last x coordinate when rendering text

ty

int ty

Part of the optimiser: The last y coordinate when rendering text

color

java.awt.Color color

This is the current pen/fill color

pdffont

PDFFont pdffont

This is the current font (in PDF format)

font

java.awt.Font font

This is the current font (in Java format)

pw

java.io.PrintWriter pw

This is the PrintWriter used to write PDF drawing commands to the Stream

page

PDFPage page

This is a reference to the PDFPage we are rendering to.

child

boolean child

This is true for any Graphics instance that didn't create the stream.

See Also:: PDFGraphics.create()

clipRectangle

java.awt.Rectangle clipRectangle

This holds the current clipRectangle

Class gnu.jpdf.PDFImage extends PDFStream implements Serializable

Serialized Fields

objwidth

int objwidth

objheight

int objheight

width

int width

height

int height

img

java.awt.Image img

name

java.lang.String name

Class gnu.jpdf.PDFInfo extends PDFObject implements Serializable

Serialized Fields

author

java.lang.String author

creator

java.lang.String creator

title

java.lang.String title

subject

java.lang.String subject

keywords

java.lang.String keywords

Class gnu.jpdf.PDFJob extends java.awt.PrintJob implements Serializable

Serialized Fields

pdfDocument

PDFDocument pdfDocument

This is the PDF file being constructed

page

PDFPage page

This is the current page being constructed by the last getGraphics() call

pagenum

int pagenum

This is the page number of the current page

Class gnu.jpdf.PDFObject extends java.lang.Object implements Serializable

Serialized Fields

type

java.lang.String type

This is the object's PDF Type

objser

int objser

This is the unique serial number for this object.

pdfDocument

PDFDocument pdfDocument

This allows any PDF object to refer to the document being constructed.

Class gnu.jpdf.PDFOutline extends PDFObject implements Serializable

Serialized Fields

outlines

java.util.Vector<E> outlines

This holds any outlines below us

parent

PDFOutline parent

For subentries, this points to it's parent outline

title

java.lang.String title

This is this outlines Title

dest

PDFPage dest

The destination page

l

int l

The region on the destination page

b

int b

The region on the destination page

r

int r

The region on the destination page

t

int t

The region on the destination page

destMode

boolean destMode

How the destination is handled

Class gnu.jpdf.PDFPage extends PDFObject implements Serializable

Serialized Fields

mediabox

java.awt.Rectangle mediabox

This is this pages media box, ie the size of the page

pdfPageList

PDFObject pdfPageList

This is the pages object id that this page belongs to. It is set by the pages object when it is added to it.

java.util.Vector<E> contents

This holds the contents of the page.

rotate

int rotate

Specifies the number of degrees the page should be rotated clockwise when it is displayed. This value must be zero (the default), or a multiple of 90.

See Also:: PDFPage.PORTRAIT, PDFPage.LANDSCAPE, PDFPage.INVERTEDPORTRAIT, PDFPage.SEASCAPE

thumbnail

PDFObject thumbnail

Object ID that contains a thumbnail sketch of the page. -1 indicates no thumbnail.

annotations

java.util.Vector<E> annotations

This holds any Annotations contained within this page.

resources

java.util.Vector<E> resources

This holds any resources for this page

imageResources

java.util.Vector<E> imageResources

fonts

java.util.Vector<E> fonts

The fonts associated with this page

hasImageB

boolean hasImageB

These handle the procset for this page. Refer to page 140 of the PDF Reference manual NB: Text is handled when the fonts Vector is null, and a font is created refer to getFont() to see where it's defined

hasImageC

boolean hasImageC

hasImageI

boolean hasImageI

procset

PDFPage.procset procset

xobjects

java.util.Vector<E> xobjects

Contains the text strings for the xobjects.

Class gnu.jpdf.PDFPage.procset extends PDFObject implements Serializable

Serialized Fields

set

java.util.Vector<E> set

Class gnu.jpdf.PDFPageList extends PDFObject implements Serializable

Serialized Fields

pages

java.util.Vector<E> pages

This holds the pages

Class gnu.jpdf.PDFStream extends PDFObject implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException

This implements our own special Serialization for this object

Here we read the length of the stream's contents, then a byte array of the contents. Then we recreate a new ByteArrayOutputStream. We have to do this, as ByteArrayOutputStream is not serializable (hence the transient tag).

Throws:: java.io.IOException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

This implements our own special Serialization for this object.

Here we write the length of the stream's contents, then a byte array of the contents. We have to do this, as ByteArrayOutputStream is not serializable (hence the transient tag).

Throws:: java.io.IOException

Serialized Fields

deflate

boolean deflate

True if we will compress the stream in the pdf file

Class gnu.jpdf.PDFTest extends javax.swing.JFrame implements Serializable

Serialized Fields

pane

javax.swing.JPanel pane

Main content pane

documentDimension

java.awt.Dimension documentDimension

All sizes will be derived from the desired pdf document size

currentPage

int currentPage

job

PDFJob job

pdfDocumentAlreadyDone

boolean pdfDocumentAlreadyDone

drawingArea

gnu.jpdf.TestPanel drawingArea

A JPanel used for drawing the document on the screen The source is included in this file at the bottom

menuBar

gnu.jpdf.TestMenuBar menuBar

The menu bar

Class gnu.jpdf.StringTooLongException extends java.lang.Exception implements Serializable

Serialized Fields

msg

java.lang.String msg

Package gov.lbl.genome.common

Class gov.lbl.genome.common.BadCoordinateTypeException extends java.lang.Exception implements Serializable

Class gov.lbl.genome.common.GeneNotFoundException extends java.lang.Exception implements Serializable

Class gov.lbl.genome.common.VGBException extends java.lang.Exception implements Serializable

Serialized Fields

code

int code

Package gov.lbl.genome.common.features

Class gov.lbl.genome.common.features.ChromSegments extends java.util.Vector implements Serializable

Package gov.lbl.genome.gui

Class gov.lbl.genome.gui.GeneralGraphComp extends VistaPanel implements Serializable

Serialized Fields

view

GeneralGraphView view

isLoading

boolean isLoading

marginLeft

int marginLeft

marginRight

int marginRight

marginTop

int marginTop

width

int width

Class gov.lbl.genome.gui.GeneralGraphView extends VGBPanel implements Serializable

Serialized Fields

model

GeneralGraphModel model

graph

GeneralGraphComp graph

graphs

GeneralGraphComp[] graphs

newGraphView

GeneralGraphView newGraphView

curveViews

java.util.Collection<E> curveViews

dp

DisplayPanel dp

x

int x

y

int y

parent

GeneralGraphView parent

children

java.util.Vector<E> children

image

java.awt.image.BufferedImage image

minProc

java.lang.String minProc

maxProc

java.lang.String maxProc

GGV

GeneralGraphView GGV

visible

boolean visible

onMML

java.awt.event.MouseMotionListener onMML

onML

java.awt.event.MouseListener onML

pnlName

VGBPanel pnlName

pnlYAxis

VGBPanel pnlYAxis

pnlNames

VGBPanel[] pnlNames

pnlYAxiss

VGBPanel[] pnlYAxiss

pnlGraph

VGBPanel pnlGraph

pnlGraphs

VGBPanel[] pnlGraphs

pnlContig

VGBPanel pnlContig

pnlContainer

VGBPanel pnlContainer

lblName

VistaLabel lblName

lblMinY

VistaLabel lblMinY

lblMaxY

VistaLabel lblMaxY

axisPanel

AxisPanel axisPanel

contigPanel

ContigPanel contigPanel

yUnitsFormat

java.text.NumberFormat yUnitsFormat

N

int N

line

int line

selected

boolean selected

Class gov.lbl.genome.gui.InvalidDataEntryException extends java.lang.Exception implements Serializable

Class gov.lbl.genome.gui.LinkLabel extends javax.swing.JLabel implements Serializable

Serialized Fields

defaultCursor

java.awt.Cursor defaultCursor

handCursor

java.awt.Cursor handCursor

linkURL

java.net.URL linkURL

link

java.lang.String link

linkColor

java.awt.Color linkColor

overColor

java.awt.Color overColor

currentColor

java.awt.Color currentColor

va

VistaApp va

Class gov.lbl.genome.gui.SplashWindow extends javax.swing.JDialog implements Serializable

Serialized Fields

va

VistaApp va

panel

javax.swing.JPanel panel

okPanel

javax.swing.JPanel okPanel

verPanel

javax.swing.JPanel verPanel

picPanel

javax.swing.JPanel picPanel

btnOK

javax.swing.JButton btnOK

Class gov.lbl.genome.gui.VistaApp extends javax.swing.JApplet implements Serializable

Serialized Fields

va

VistaApp va

resource

Resource resource

This public parameter provides access to the default section of the resource file.

history

History history

dataPuller

java.lang.Thread dataPuller

parameters

java.util.HashMap<K,V> parameters

codebaseURL

java.lang.String codebaseURL

saveURL

java.lang.String saveURL

uploadURL

java.lang.String uploadURL

servletURL

java.lang.String servletURL

textbrowserURL

java.lang.String textbrowserURL

clientWidth

int clientWidth

clientHeight

int clientHeight

boundary

java.lang.String boundary

fileNameHeader

java.lang.String fileNameHeader

preHeader

java.lang.String preHeader

postHeader

java.lang.String postHeader

connection

java.net.HttpURLConnection connection

Runs

java.lang.String Runs

Pos

java.lang.String Pos

BG

java.lang.String BG

minConsIdentity

int minConsIdentity

minConsWidth

int minConsWidth

dataInterval

int dataInterval

window

int window

min_y

int min_y

max_y

int max_y

mode

java.lang.String mode

cu

CommUnit cu

minX

long minX

maxX

long maxX

chrom

java.lang.String chrom

posHistory

java.util.Vector<E> posHistory

errorHandler

ErrorHandler errorHandler

newWidth

int newWidth

newHeight

int newHeight

dangerous

boolean dangerous

corner

javax.swing.JPanel corner

This panel is used to draw small black triangle in the right bottom corner when "autoResize" checkbox is disabled.

mainPanel

javax.swing.JPanel mainPanel

This panel contains all visible content of the program

framedPanel

javax.swing.JPanel framedPanel

This transparent panel is used to simulate resize window functionality in the applet when "autoResize" checkbox is disabled

redBorder

javax.swing.border.Border redBorder

matteBorder

javax.swing.border.MatteBorder matteBorder

emptyBorder

javax.swing.border.Border emptyBorder

currentCursor

java.awt.Cursor currentCursor

SECursor

java.awt.Cursor SECursor

ECursor

java.awt.Cursor ECursor

SCursor

java.awt.Cursor SCursor

defaultCursor

java.awt.Cursor defaultCursor

cornerRect

java.awt.Rectangle cornerRect

eastRect

java.awt.Rectangle eastRect

southRect

java.awt.Rectangle southRect

resize

boolean resize

addFramedPane

boolean addFramedPane

toolBar

javax.swing.JToolBar toolBar

menuBar

javax.swing.JMenuBar menuBar

splitPane

javax.swing.JSplitPane splitPane

progressPanel

javax.swing.JPanel progressPanel

toolsPanel

javax.swing.JPanel toolsPanel

animation

javax.swing.JPanel animation

progressAnimationPanel

javax.swing.JPanel progressAnimationPanel