de.mpg.biochem.mars.util

Class MarsPosition

java.lang.Object

de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord

de.mpg.biochem.mars.util.MarsPosition

All Implemented Interfaces:

JsonConvertibleRecord

public class MarsPosition
extends AbstractJsonConvertibleRecord
implements JsonConvertibleRecord

This class provides a simple position definition. Usually this is a position in time or slice that is of interest for further analysis. Molecules and MarsMetadatas can contain a list of these positions.

Position definitions include the name, value, column (Time (s) or slice or otherwise), and color (in hex). These values are used by mars-fx to draw position on plots based value and color.

Constructor Summary

Constructors

Constructor and Description
MarsPosition(com.fasterxml.jackson.core.JsonParser jParser) Constructor for creating a plot position given a json stream.
MarsPosition(java.lang.String name) Constructor for creating a plot position of a given name with default settings.
MarsPosition(java.lang.String name, java.lang.String column, double position, java.lang.String color, double stroke) Constructor for creating a plot region using known parameters.

Method Summary

Modifier and Type	Method and Description
protected void	createIOMaps() Must be implemented in subclasses to define how fields, objects, arrays should be saved based on the Jackson streaming API.
java.lang.String	getColor() Get the string color of the region in hex.
java.lang.String	getColumn() Get the name of the column the position value refers to.
java.lang.String	getName() Get position name.
double	getPosition() Get the position value.
double	getStroke() Get the stroke value (line thickness).
void	setColor(java.lang.String color) Set the hex color string.
void	setColumn(java.lang.String column) Set the name of the column the position value refers to.
void	setName(java.lang.String name) Set position name.
void	setPosition(double position) Set the position value in units of column.
void	setStroke(double stroke) Set the stroke value (line thickness).

Methods inherited from class de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord

dumpJSON, fromJSON, getJsonGenerator, getJsonParser, setJsonField, setShowWarnings, toJSON

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.mpg.biochem.mars.molecule.JsonConvertibleRecord

dumpJSON, fromJSON, getJsonGenerator, getJsonParser, setJsonField, setShowWarnings, toJSON

Constructor Detail

MarsPosition

public MarsPosition(java.lang.String name)

Constructor for creating a plot position of a given name with default settings. This has a default black color and position value = 0. The position can then be changed in the gui.

Parameters:

name - Name of the MarsPosition to create.

MarsPosition

public MarsPosition(com.fasterxml.jackson.core.JsonParser jParser)
             throws java.io.IOException

Constructor for creating a plot position given a json stream. Used when loading objects from file.

Parameters:

jParser - Json stream used to build the object.

Throws:

java.io.IOException - Thrown if unable to parse Json from JsonParser.

MarsPosition

public MarsPosition(java.lang.String name,
                    java.lang.String column,
                    double position,
                    java.lang.String color,
                    double stroke)

Constructor for creating a plot region using known parameters.

Parameters:

name - Name of the region.

column - Name of column the region refers to.

position - Location of the position in unit of column.

color - Color string in hex format.

stroke - Line thickness.

Method Detail

createIOMaps

protected void createIOMaps()

Description copied from class: AbstractJsonConvertibleRecord

Must be implemented in subclasses to define how fields, objects, arrays should be saved based on the Jackson streaming API.

Specified by:

createIOMaps in class AbstractJsonConvertibleRecord

getName

public java.lang.String getName()

Get position name.

Returns:

Position name.

setName

public void setName(java.lang.String name)

Set position name.

Parameters:

name - Position name.

getColumn

public java.lang.String getColumn()

Get the name of the column the position value refers to.

Returns:

The column name.

setColumn

public void setColumn(java.lang.String column)

Set the name of the column the position value refers to.

Parameters:

column - Name of the column that defines the position units.

getColor

public java.lang.String getColor()

Get the string color of the region in hex.

Returns:

Color string in hex.

setColor

public void setColor(java.lang.String color)

Set the hex color string.

Parameters:

color - The hex color string.

getPosition

public double getPosition()

Get the position value.

Returns:

Position value.

setPosition

public void setPosition(double position)

Set the position value in units of column.

Parameters:

position - Position value.

getStroke

public double getStroke()

Get the stroke value (line thickness).

Returns:

Stroke (line thickness).

setStroke

public void setStroke(double stroke)

Set the stroke value (line thickness). Default is 1.0.

Parameters:

stroke - Line thickness.