de.mpg.biochem.mars.util

Class MarsRegion

java.lang.Object

de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord

de.mpg.biochem.mars.util.MarsRegion

All Implemented Interfaces:

JsonConvertibleRecord

public class MarsRegion
extends AbstractJsonConvertibleRecord
implements JsonConvertibleRecord

This class provides a simple region definition. Usually this a region in time or slice that is of interest for further analysis. Molecules and MarsMetadatas can contain a list of these regions, which are used when running several commands including KCPCommand, SigmaCalculatorCommand, KCPCommand, RegionDifferenceCalculatorCommand, VarianceCalculatorCommand.

Region definitions include name, start value, end value, column (Time (s) or slice or otherwise), color (in hex), and opacity (range 0 to 1). These values are used by mars-fx to draw regions on plots based on the start, end color and opacity.

Opacity specified in the hex code is ignored. The opacity setting overrides the value in the hex string.

Constructor Summary

Constructors

Constructor and Description
MarsRegion(com.fasterxml.jackson.core.JsonParser jParser) Constructor for creating a plot region given a json stream.
MarsRegion(java.lang.String name) Constructor for creating a plot region of a given name with default settings.
MarsRegion(java.lang.String name, java.lang.String column, double start, double end, java.lang.String color, double opacity) 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 start and end values refer to.
double	getEnd() Get the upper bound of the region.
java.lang.String	getName() Get the name of the region.
double	getOpacity() Get the opacity of the region.
double	getStart() Get lower bound of the region.
void	setColor(java.lang.String color) Set the hex color string.
void	setColumn(java.lang.String column) Set the name of the column the start and end values refer to.
void	setEnd(double end) Set the upper bound of the region.
void	setName(java.lang.String name) Set the region name.
void	setOpacity(double opacity) Set the opacity of the region.
void	setStart(double start) Set the lower bound of the region.

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

MarsRegion

public MarsRegion(java.lang.String name)

Constructor for creating a plot region of a given name with default settings. This has a default light blue color and start = end = 0. The bounds can then be changed in the gui.

Parameters:

name - Name of the region.

MarsRegion

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

Constructor for creating a plot region 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 the JsonParser stream.

MarsRegion

public MarsRegion(java.lang.String name,
                  java.lang.String column,
                  double start,
                  double end,
                  java.lang.String color,
                  double opacity)

Constructor for creating a plot region using known parameters.

Parameters:

name - Name of the region.

column - Name of column the region refers to.

start - Starting value of the region.

end - Ending value of the region.

color - Color string in hex format.

opacity - Opacity of the region between 0 and 1.

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 the name of the region.

Returns:

The region name.

setName

public void setName(java.lang.String name)

Set the region name.

Parameters:

name - The region name.

getColumn

public java.lang.String getColumn()

Get the name of the column the start and end values refer to.

Returns:

The column name.

setColumn

public void setColumn(java.lang.String column)

Set the name of the column the start and end values refer to.

Parameters:

column - The column name.

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.

getStart

public double getStart()

Get lower bound of the region.

Returns:

Lower bound of the region.

setStart

public void setStart(double start)

Set the lower bound of the region.

Parameters:

start - The lower bound of the region.

getEnd

public double getEnd()

Get the upper bound of the region.

Returns:

The upper bound of the region.

setEnd

public void setEnd(double end)

Set the upper bound of the region.

Parameters:

end - The upper bound of the region.

setOpacity

public void setOpacity(double opacity)

Set the opacity of the region. Range is 0 to 1. Used by the javafx gui when drawing regions on plots.

Parameters:

opacity - The opacity of the region.

getOpacity

public double getOpacity()

Get the opacity of the region. Range is 0 to 1. Used by the javafx gui when drawing regions on plots.

Returns:

The opacity of the region.