com.objex.progeny.anywhere.data
Class MarkerLegendItem

java.lang.Object
  com.objex.progeny.anywhere.data.MarkerLegendItem

All Implemented Interfaces:

java.io.Serializable

public class MarkerLegendItem
extends java.lang.Object
implements java.io.Serializable

A MarkerLegendItem is the equivalent of a chromosome marker in the marker legend. It has the same ID and name as a ChromosomeMarker but also has an alias and legend display text, both of which can be used
when rendering marker legend below the person's icon.

See Also:

MarkerLegend, ChromosomeLegendItem, Serialized Form

Constructor Summary

MarkerLegendItem()
Creates a new MarkerLegendItem instance

Method Summary

java.lang.String	getAlias()
double	getBasePairs()
double	getCM()
int	getFieldid()
java.lang.String	getLegendDisplayText()
java.lang.String	getName() Getter for property name.
int	getSequence() Getter for property sequence.
int	getType()
void	setAlias(java.lang.String alias) Sets a new alias for the marker legend item.
void	setBasePairs(double basePairs) Set the genetic distance for this marker base pairs
void	setCM(double cM) Set the genetic distance for of the marker to which this legend item is linked.
void	setFieldid(int ai_fieldid) Set the ID of the marker to which this legend item is linked.
void	setLegendDisplayText(java.lang.String as_legendDisplayText) Set the text that will be displayed on the legend.
void	setName(java.lang.String rhs) Setter for property name.
void	setSequence(int rhs) Setter for property sequence.
void	setType(int ai_type) Set the new marker type.
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

MarkerLegendItem

public MarkerLegendItem()

Creates a new MarkerLegendItem instance

Method Detail

getName

public java.lang.String getName()

Getter for property name.

Returns:

Value of property name.

setName

public void setName(java.lang.String rhs)

Setter for property name.

Parameters:

rhs - New value of property name.

getAlias

public java.lang.String getAlias()

Returns:

The alias for this marker legend item. This can be used as legend display text when rendering the marker legend

setAlias

public void setAlias(java.lang.String alias)

Sets a new alias for the marker legend item. This can be used as legend display text when rendering the marker legend

Parameters:

alias - The new alias of the marker legend item.

getCM

public double getCM()

Returns:

The genetic distance in cM of the marker to which this legend item is linked.

setCM

public void setCM(double cM)

Set the genetic distance for of the marker to which this legend item is linked.

Parameters:

cM - The genetic distance in cM of the marker to which this legend item is linked.

getBasePairs

public double getBasePairs()

Returns:

The genetic distance in basePairs

setBasePairs

public void setBasePairs(double basePairs)

Set the genetic distance for this marker base pairs

Parameters:

basePairs - The genetic distance in bP

getFieldid

public int getFieldid()

Returns:

The ID of the marker of the marker to which this legend item is linked.

setFieldid

public void setFieldid(int ai_fieldid)

Set the ID of the marker to which this legend item is linked.

Parameters:

ai_fieldid - The new fieldid of the marker to which this legend item is linked.

getLegendDisplayText

public java.lang.String getLegendDisplayText()

Returns:

The text that will be displayed on the legend. If not set then the name or alias of the marker will be used instead.

setLegendDisplayText

public void setLegendDisplayText(java.lang.String as_legendDisplayText)

Set the text that will be displayed on the legend. If not set then the name or alias of the marker will be used instead.

Parameters:

as_legendDisplayText - THe new text that will be displayed on the legend. If not set then the name or alias of the marker will be used instead.

getType

public int getType()

Returns:

The marker type. Can be 0 for microsattelites and 1 for SNP's

setType

public void setType(int ai_type)

Set the new marker type. Can be 0 for microsattelites and 1 for SNP's

Parameters:

type - The new marker type. Can be 0 for microsattelites and 1 for SNP's

getSequence

public int getSequence()

Getter for property sequence. The sequencing must be automatically determined depending on the location of the marker on the haplotype in question. So if you have a hpalotype with 10 markes and marker rs200 is on position 10 then the seuqnec is 10.

**NOTE** This seuqnece is within the haplotype of which this marker is part and not within the chromosome

Returns:

Value of property sequence.

setSequence

public void setSequence(int rhs)

Setter for property sequence. The sequencing must be automatically determined depending on the location of the marker on the haplotype in question. So if you have a haplotype with 10 markes and marker rs200 is on position 10 then the seuqnec is 1.

**NOTE** This seuqnece is within the haplotype of which this marker is part and not within the chromosome

Sequence must be set only if it is unset i.e. if getSequence return -1

Parameters:

rhs - New value of property sequence.

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object