Serialized Form

Package com.objex.panywhere

Class com.objex.panywhere.AddEvent extends java.util.EventObject implements Serializable

Serialized Fields

addedIndividual

Individual addedIndividual

Class com.objex.panywhere.Allele extends java.lang.Object implements Serializable

Serialized Fields

ID

java.lang.String ID

The Allele's ID

type

java.lang.String type

The Allele type designates the type of the Allele. Common Allele types are HLA-A, HLA-B, HLA-DR etc

color

java.awt.Paint color

The Allele's color use to draw the Allele Icon on the Pedigree

colorManuallyAssigned

boolean colorManuallyAssigned

paternity

java.lang.String paternity

The partenity of the Allele inheritance. Possible types are Allele.MATERNAL and Allele.PATERNAL

iconX

double iconX

The position in Graphics2D space of the Allele's data. This is where the Allele bar will be drawn starting from

x

double x

The position in Graphics2D space of the Allele's data. This is where the Allele bar will be drawn starting from

iconY

double iconY

The position in Graphics2D space of the Allele's data. This is where the Allele bar will be drawn starting from

y

double y

The position in Graphics2D space of the Allele's data. This is where the Allele bar will be drawn starting from

width

double width

height

double height

Class com.objex.panywhere.BooleanDataType extends DataType implements Serializable

Serialized Fields

sampleProperty

java.lang.String sampleProperty

propertySupport

java.beans.PropertyChangeSupport propertySupport

Class com.objex.panywhere.Chromosome extends java.lang.Object implements Serializable

Serialized Fields

markers

java.util.Map<K,V> markers

The markers that make up this chromosome. A chromosome will have any number of markers. If all the Maternal markers of a chromosome have been inherited from one parent then the result is a linked set of Alleles inherited together making up a Haplotype. Each marker in the markers map is retrivable using the marker ID/name.

name

java.lang.String name

nextMarkerSequence

int nextMarkerSequence

Class com.objex.panywhere.ChromosomeMarker extends java.lang.Object implements Serializable

Serialized Fields

maternalAllele

Allele maternalAllele

paternalAllele

Allele paternalAllele

name

java.lang.String name

sequence

int sequence

genetic_distance

double genetic_distance

location

double location

Class com.objex.panywhere.Data extends java.lang.Object implements Serializable

Serialized Fields

fieldname

java.lang.String fieldname

fieldid

int fieldid

value

java.lang.Object value

subdata

java.util.Map<K,V> subdata

data

java.lang.Object data

Class com.objex.panywhere.DatabaseField extends java.lang.Object implements Serializable

Serialized Fields

fieldname

java.lang.String fieldname

datatype

DataType datatype

ID

java.lang.String ID

fieldid

int fieldid

subfields

java.util.Map<K,V> subfields

Class com.objex.panywhere.DatabaseTable extends java.lang.Object implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream stream)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Overide readobject so that the transient members are set before reading of serilizable members commences

Throws:

java.io.IOException

java.lang.ClassNotFoundException

Serialized Fields

tableid

int tableid

tablename

java.lang.String tablename

fields

java.util.Map<K,V> fields

Class com.objex.panywhere.DataDictionary extends java.lang.Object implements Serializable

Serialized Fields

tables

java.util.Map<K,V> tables

Class com.objex.panywhere.DataType extends java.lang.Object implements Serializable

Serialized Fields

typename

java.lang.String typename

attributes

java.util.Map<K,V> attributes

dataTypeClass

java.lang.Class<T> dataTypeClass

typeid

int typeid

Class com.objex.panywhere.DateDataType extends DataType implements Serializable

Serialized Fields

sampleProperty

java.lang.String sampleProperty

propertySupport

java.beans.PropertyChangeSupport propertySupport

Class com.objex.panywhere.DeleteEvent extends java.util.EventObject implements Serializable

Serialized Fields

deletedIndividual

Individual deletedIndividual

Class com.objex.panywhere.DropDownDataType extends DataType implements Serializable

Class com.objex.panywhere.EventListeners extends java.lang.Object implements Serializable

Class com.objex.panywhere.Family extends java.lang.Object implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream stream)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Overide readobject so that the transient members are set before reading of serilizable members commences

Throws:

java.io.IOException

java.lang.ClassNotFoundException

Serialized Fields

familyID

java.lang.String familyID

familyName

java.lang.String familyName

members

java.util.Map<K,V> members

A list of family members stored in a hashmap

siblinglist

java.util.Map<K,V> siblinglist

NOT USED -- Reserved for version 1.1 Key = sibgroup, Value = ArrayList of UPN's of all individuals who are siblings of one another as well as kids of of a certain pair of parents or some parent of he/she has no spouse.

nextsibgroupid

int nextsibgroupid

Class com.objex.panywhere.IconClickEvent extends java.awt.event.MouseEvent implements Serializable

Serialized Fields

owner

Individual owner

Class com.objex.panywhere.ImageEvent extends java.util.EventObject implements Serializable

Serialized Fields

image

java.awt.image.BufferedImage image

Class com.objex.panywhere.ImportEvent extends java.util.EventObject implements Serializable

Serialized Fields

importedIndividual

Individual importedIndividual

ii_num_inds

int ii_num_inds

is_message

java.lang.String is_message

Class com.objex.panywhere.Individual extends java.lang.Object implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream stream)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Overide readobject so that the transient members are set before reading of serilizable members commences

Throws:

java.io.IOException

java.lang.ClassNotFoundException

Serialized Fields

siblinggroup

java.lang.String siblinggroup

NOT USED -- Reserved for ver 1.1. for memory streamlining Will be used as the key into the Family.siblinglist hashmap. An Individual with no siblings will have a siblinggroup = "0".

kidgroups

java.util.List<E> kidgroups

NOT USED - Reserved for ver 1.1 for memory streamlining For each parent with kids. If a parent has one or no spouse and has one set of kids, then a single entry of Individual.siblinggroup will be found in kidgroups list. If a parent has two sets of kids then two entries of sibling group will be found in the kidgroups list as an a link to the list Family.siblinglist where Family if the object representing the family to which this Individual belongs.

upn

java.lang.String upn

Instance Variables

tag

java.lang.String tag

Instance Variables

fatherid

java.lang.String fatherid

Instance Variables

motherid

java.lang.String motherid

Instance Variables

gender

java.lang.String gender

Instance Variables

markedby

java.lang.String markedby

Instance Variables

firstName

java.lang.String firstName

Instance Variables

lastName

java.lang.String lastName

Instance Variables

familyID

java.lang.String familyID

Instance Variables

icontext

java.lang.String icontext

Instance Variables

iconsubtext

java.lang.String iconsubtext

Instance Variables

tree

java.lang.String tree

Instance Variables

shadowupn

java.lang.String shadowupn

The UPN of a the Individual to whom this Individual is a shadow. If this value is anyhting other than the default "0", the the individual's isShadow method must return true. shadow.

shadow

boolean shadow

A boolean indcating whether this Individual is a shadow or not. If he is, his UPN will be the same as The shadowupn property of some Individual in this family.

deceased

boolean deceased

Main properies of the Individual bean

changed

boolean changed

Main properies of the Individual bean

adopted

boolean adopted

Main properies of the Individual bean

adoptedIn

boolean adoptedIn

Main properies of the Individual bean

adoptedOut

boolean adoptedOut

Main properies of the Individual bean

SAB

boolean SAB

Main properies of the Individual bean

noissue

boolean noissue

Main properies of the Individual bean

highlighted

boolean highlighted

Main properies of the Individual bean

genderunknown

boolean genderunknown

Main properies of the Individual bean

infertile

boolean infertile

Main properies of the Individual bean

proband

boolean proband

Main properies of the Individual bean

monozygotic

boolean monozygotic

Main properies of the Individual bean

twintypeunknown

boolean twintypeunknown

Main properies of the Individual bean

dizygotic

boolean dizygotic

Main properies of the Individual bean

generation

int generation

The generation of the Individual. This figure defaults to "999999" for every individual and increases as you go up the ancestral line while it decreases as you go down the descendant line. A bit of a misnomer but works anyway.

xcoordinate

double xcoordinate

X and Y Coordinate values for the location of this Individual's Icon is 2D space on the pedigree

ycoordinate

double ycoordinate

X and Y Coordinate values for the location of this Individual's Icon is 2D space on the pedigree

pageNo

double pageNo

X and Y Coordinate values for the location of this Individual's Icon is 2D space on the pedigree

childlineRL

RelationshipLine childlineRL

Relationship line instance members

siblinglineRL

RelationshipLine siblinglineRL

Relationship line instance members

twinlineRL

RelationshipLine twinlineRL

Relationship line instance members

relationships

java.util.Hashtable<K,V> relationships

siblings

java.util.Hashtable<K,V> siblings

spouses

java.util.Hashtable<K,V> spouses

kids

java.util.Hashtable<K,V> kids

spouselines

java.util.Hashtable<K,V> spouselines

parentlines

java.util.Hashtable<K,V> parentlines

spouseindex

java.util.Hashtable<K,V> spouseindex

Special Relationship tables -- updated when a spouse is added and when a twin brother / sister is added

twinindex

java.util.Hashtable<K,V> twinindex

Special Relationship tables -- updated when a spouse is added and when a twin brother / sister is added

symbol

Symbol symbol

Encapsulates the symbol elements and quadrants color values for this Individual. Supercedes the use of the property Individual.legendItems which is effectively DEPRECATED.

father

Individual father

The father reference for this Individual

mother

Individual mother

The mother reference for this Individual

spouse

Individual spouse

The spouse reference for this Individual

dataitems

java.util.Map<K,V> dataitems

Data items holder for this Individual

chromosome

Chromosome chromosome

Only one chromosome shall be displayed on the pedigree so only one chromsome field shall be stored in the Individual Bean This is the chromosome being displayed

Since:

Ver1.01

symbols

java.util.List<E> symbols

subtext

Subtext subtext

Class com.objex.panywhere.Legend extends java.lang.Object implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream stream)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Overide readobject so that the transient members are set before reading of serilizable members commences

Throws:

java.io.IOException

java.lang.ClassNotFoundException

Serialized Fields

legendHeight

double legendHeight

minimumX

double minimumX

minimumY

double minimumY

legendWidth

double legendWidth

legendPosX

double legendPosX

legendPosY

double legendPosY

legendItems

java.util.Map<K,V> legendItems

A hashtable containing the current Legend Items for this Pedigree

Class com.objex.panywhere.LegendChangeEvent extends java.util.EventObject implements Serializable

Serialized Fields

m_item

LegendItem m_item

m_olditem

LegendItem m_olditem

m_changingProperty

java.lang.String m_changingProperty

m_newValue

java.lang.Object m_newValue

m_oldValue

java.lang.Object m_oldValue

Class com.objex.panywhere.LegendCondition extends java.lang.Object implements Serializable

Serialized Fields

conditionFieldid

int conditionFieldid

operator

java.lang.String operator

compareValue

java.lang.Object compareValue

sampleProperty

java.lang.String sampleProperty

propertySupport

java.beans.PropertyChangeSupport propertySupport

Class com.objex.panywhere.LegendItem extends java.lang.Object implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream stream)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Overide readobject so that the transient members are set before reading of serilizable members commences

Throws:

java.io.IOException

java.lang.ClassNotFoundException

Serialized Fields

ID

java.lang.String ID

legendText

java.lang.String legendText

quadOneColor

java.awt.Color quadOneColor

quadTwoColor

java.awt.Color quadTwoColor

quadThreeColor

java.awt.Color quadThreeColor

quadFourColor

java.awt.Color quadFourColor

centerCircleColor

java.awt.Color centerCircleColor

centerSquareColor

java.awt.Color centerSquareColor

vLine

boolean vLine

hLine

boolean hLine

quad1Dot

boolean quad1Dot

quad2Dot

boolean quad2Dot

quad3Dot

boolean quad3Dot

quad4Dot

boolean quad4Dot

quad1DotColor

java.awt.Color quad1DotColor

quad2DotColor

java.awt.Color quad2DotColor

quad3DotColor

java.awt.Color quad3DotColor

quad4DotColor

java.awt.Color quad4DotColor

quadOnePaint

java.awt.Paint quadOnePaint

quadTwoPaint

java.awt.Paint quadTwoPaint

quadThreePaint

java.awt.Paint quadThreePaint

quadFourPaint

java.awt.Paint quadFourPaint

centerCirclePaint

java.awt.Paint centerCirclePaint

centerSquarePaint

java.awt.Paint centerSquarePaint

x

double x

y

double y

questionMark

boolean questionMark

symHeight

double symHeight

symWidth

double symWidth

legendItemConditions

java.util.List<E> legendItemConditions

Class com.objex.panywhere.LineClickEvent extends java.awt.event.MouseEvent implements Serializable

Serialized Fields

rline

java.awt.geom.Line2D rline

rel1

Individual rel1

rel2

Individual rel2

Class com.objex.panywhere.MarkerDataType extends DataType implements Serializable

Serialized Fields

sampleProperty

java.lang.String sampleProperty

propertySupport

java.beans.PropertyChangeSupport propertySupport

Class com.objex.panywhere.NumberDataType extends DataType implements Serializable

Serialized Fields

sampleProperty

java.lang.String sampleProperty

propertySupport

java.beans.PropertyChangeSupport propertySupport

Class com.objex.panywhere.Pedigree extends javax.swing.JPanel implements Serializable

Serialized Fields

autodraw

boolean autodraw

System-wide Control Properties

showgrid

boolean showgrid

System-wide Control Properties

snaptogrid

boolean snaptogrid

System-wide Control Properties

showpagebreaks

boolean showpagebreaks

System-wide Control Properties

livedragging

boolean livedragging

System-wide Control Properties

showlegend

boolean showlegend

System-wide Control Properties

showheader

boolean showheader

System-wide Control Properties

showfooter

boolean showfooter

System-wide Control Properties

importshadow

boolean importshadow

System-wide Control Properties

oneclickadd

boolean oneclickadd

System-wide Control Properties

showhaplotypes

boolean showhaplotypes

System-wide Control Properties

minimumX

double minimumX

minimumY

double minimumY

siblingnumxvalue

int siblingnumxvalue

siblingnumyvalue

int siblingnumyvalue

nextupn

int nextupn

minupn

int minupn

nextFamilyID

int nextFamilyID

nextTreeID

int nextTreeID

individualoffset

double individualoffset

iconwidth

double iconwidth

iconheight

double iconheight

generationoffset

double generationoffset

childlineheight

double childlineheight

subtextyvalue

double subtextyvalue

creationDate

java.util.Date creationDate

Date on which this particular pedigree was first created

family

Family family

The current Pedigree family. The family is the main data storage model for the Pedigree as all Individuals are stored in the Family bean.

m_GenerationPosMarkers

java.util.Hashtable<K,V> m_GenerationPosMarkers

Keeps track of snapshots of generations and their Y coordianates and the rightmost Individuals' X-Coordinates per genetion. Used during drawing.

legend

Legend legend

The legend containing legend items for this Pedigree

pedigreeAdjusted

boolean pedigreeAdjusted

m_UserPrefs

java.util.prefs.Preferences m_UserPrefs

Preferences object for setting user preferences

commandkeydown

boolean commandkeydown

Flag used to keep track of when the Command Key (in mac env) is pressed down or not

licensevalidator

com.objex.panywhere.LicenseValidator licensevalidator

Registration and Licencing Properties

datadictionary

DataDictionary datadictionary

Datadictionary property. Used to carry the database meta data if and when the Pedigree has Individuals with data attributes as part of their properties.

fastsearchtable

java.util.Map<K,V> fastsearchtable

used to store those individuals whose icons are currently visible or within the VisibleRect of this canvas This is done to allow fast search in the event that there vast numbers of Individuals on this pedigree.

individualRenderer

IndividualRenderer individualRenderer

The Renderer object whose responsibility is to render Individual Icons on the Pedigree

pedigreescale

java.lang.String pedigreescale

Pedigree Scale use dto control the scale of rendering. This will be passed on to the Graphics context

header

java.lang.String header

Pedigree Scale use dto control the scale of rendering. This will be passed on to the Graphics context

footer

java.lang.String footer

Pedigree Scale use dto control the scale of rendering. This will be passed on to the Graphics context

showhooks

boolean showhooks

showblueid

boolean showblueid

showDate

boolean showDate

matchspouses

boolean matchspouses

changeverticalpos

boolean changeverticalpos

pulllonerelatives

boolean pulllonerelatives

recalculatepos

boolean recalculatepos

horizontalgridspacing

int horizontalgridspacing

verticalgridspacing

int verticalgridspacing

iconsubtextfont

java.awt.Font iconsubtextfont

linewidth

float linewidth

imageZoomFactor

double imageZoomFactor

Determines the default size of images created from the pedigree since teh system can only generate images up to a certain size

drawingcontext

DrawingContext drawingcontext

smartCalcLegend

boolean smartCalcLegend

When set, the legend is smartDrawn otherwise drawn in position

legendboxadjusted

boolean legendboxadjusted

Set to true when a manual attempt has been made to resize the legend bounding box and reset the second time the legend is redrawn

subtextLegend

SubtextLegend subtextLegend

ib_symbols_linkedtodata

boolean ib_symbols_linkedtodata

showSubtextLegend

boolean showSubtextLegend

useStandardProbandArrow

boolean useStandardProbandArrow

is_proband_arrowpos

java.lang.String is_proband_arrowpos

markerDisplayHeight

double markerDisplayHeight

markerDisplayWidth

double markerDisplayWidth

alleleDisplayWidth

double alleleDisplayWidth

ib_deleteonkeydown

boolean ib_deleteonkeydown

m_deleteConfirmCompListener

java.awt.event.ComponentListener m_deleteConfirmCompListener

Class com.objex.panywhere.PedigreePrintEvent extends java.util.EventObject implements Serializable

Serialized Fields

ii_page

int ii_page

Class com.objex.panywhere.Relationship extends java.lang.Object implements Serializable

Serialized Fields

upn

java.lang.String upn

type

java.lang.String type

Class com.objex.panywhere.RelationshipLine extends java.lang.Object implements Serializable

Serialized Fields

x1

double x1

y1

double y1

x2

double x2

y2

double y2

dotted

boolean dotted

parentlineAnchorX

double parentlineAnchorX

parentlineAnchorY

double parentlineAnchorY

Class com.objex.panywhere.SpouseRelationship extends Relationship implements Serializable

Serialized Fields

consanguineous

boolean consanguineous

divorced

boolean divorced

married

boolean married

separated

boolean separated

casual

boolean casual

noissue

boolean noissue

infertile

boolean infertile

Class com.objex.panywhere.Subtext extends java.lang.Object implements Serializable

Serialized Fields

sampleProperty

java.lang.String sampleProperty

propertySupport

java.beans.PropertyChangeSupport propertySupport

subtextItems

java.util.Map<K,V> subtextItems

Class com.objex.panywhere.Subtext.SubtextItem extends java.lang.Object implements Serializable

Serialized Fields

text

java.lang.String text

x

double x

y

double y

fieldid

int fieldid

computed

boolean computed

Class com.objex.panywhere.SubtextEvent extends java.util.EventObject implements Serializable

Serialized Fields

m_item

SubtextLegendItem m_item

Class com.objex.panywhere.SubtextLegend extends java.lang.Object implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream stream)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Overide readobject so that the transient members are set before reading of serializable members commences

Throws:

java.io.IOException

java.lang.ClassNotFoundException

Serialized Fields

sampleProperty

java.lang.String sampleProperty

propertySupport

java.beans.PropertyChangeSupport propertySupport

subtextLegendItems

java.util.Map<K,V> subtextLegendItems

width

double width

height

double height

Class com.objex.panywhere.SubtextLegendItem extends java.lang.Object implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream stream)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Overide readobject so that the transient members are set before reading of serilizable members commences

Throws:

java.io.IOException

java.lang.ClassNotFoundException

Serialized Fields

sampleProperty

java.lang.String sampleProperty

propertySupport

java.beans.PropertyChangeSupport propertySupport

fieldid

int fieldid

order

int order

legendDisplayText

java.lang.String legendDisplayText

subtextconditions

java.util.List<E> subtextconditions

Class com.objex.panywhere.Symbol extends java.lang.Object implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream stream)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Overide readobject so that the transient members are set before reading of serilizable members commences

Throws:

java.io.IOException

java.lang.ClassNotFoundException

Serialized Fields

ownerID

java.lang.String ownerID

quadOneColor

java.awt.Color quadOneColor

quadTwoColor

java.awt.Color quadTwoColor

quadThreeColor

java.awt.Color quadThreeColor

quadFourColor

java.awt.Color quadFourColor

centerCircleColor

java.awt.Color centerCircleColor

centerSquareColor

java.awt.Color centerSquareColor

vLine

boolean vLine

hLine

boolean hLine

quad1Dot

boolean quad1Dot

quad2Dot

boolean quad2Dot

quad3Dot

boolean quad3Dot

quad4Dot

boolean quad4Dot

quad1DotColor

java.awt.Color quad1DotColor

quad2DotColor

java.awt.Color quad2DotColor

quad3DotColor

java.awt.Color quad3DotColor

quad4DotColor

java.awt.Color quad4DotColor

questionMark

boolean questionMark

Class com.objex.panywhere.SymbolChangeEvent extends java.util.EventObject implements Serializable

Serialized Fields

RGB

int RGB

quadrant

int quadrant

Class com.objex.panywhere.SymbolSelectionEvent extends java.util.EventObject implements Serializable

Serialized Fields

selectedSymbol

int selectedSymbol

Class com.objex.panywhere.TableField extends DatabaseField implements Serializable

Serialized Fields

subfields

java.util.Map<K,V> subfields

sampleProperty

java.lang.String sampleProperty

propertySupport

java.beans.PropertyChangeSupport propertySupport

Class com.objex.panywhere.TextDataType extends DataType implements Serializable

Class com.objex.panywhere.TwinRelationship extends Relationship implements Serializable

Serialized Fields

dizygotic

boolean dizygotic

monozygotic

boolean monozygotic

unknown

boolean unknown

Class com.objex.panywhere.YesNoDataType extends DataType implements Serializable