Package org.monarchinitiative.lirical.io.output.svg

Class Lirical2Svg

java.lang.Object

org.monarchinitiative.lirical.io.output.svg.Lirical2Svg

Direct Known Subclasses:

Lr2Svg, Posttest2Svg, Sparkline2Svg

public class Lirical2Svg
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
protected static final String	BLACK
protected static final String	BLUE
protected static final int	BOX_HEIGHT
protected static final int	BOX_OFFSET	distance between two adjacent "boxes"
protected static final String	BRIGHT_GREEN
protected static final String	BROWN
protected static final String	DARKBLUE
protected static final String	GREEN
protected static final int	MIN_VERTICAL_OFFSET	minimum distance to top of image of graphic elements
protected static final String	ORANGE
protected static final String	RED
protected static final String	VIOLET

Constructor Summary

Constructors

Constructor	Description
Lirical2Svg()

Method Summary

Modifier and Type	Method	Description
protected String	prettifyDiseaseName(String originalDiseaseName)	This method shortens items such as #101200 APERT SYNDROME;;ACROCEPHALOSYNDACTYLY, TYPE I; ACS1;;ACS IAPERT-CROUZON DISEASE, INCLUDED;; to simply APERT SYNDROME
protected static <K, V extends Comparable<? super V>> Map<K,V>	sortByValue(Map<K,V> map)
protected void	writeDiamond(Writer writer, int X, int Y)	We use a diamond symbol to show a value that would be too small to appear as a visible box.
protected void	writeDiamond(Writer writer, int X, int Y, String msg)	We use a diamond symbol to show a value that would be too small to appear as a visible box.
protected void	writeFooter(Writer writer)

Methods inherited from class java.lang.Object

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

Field Details

MIN_VERTICAL_OFFSET

protected static final int MIN_VERTICAL_OFFSET

minimum distance to top of image of graphic elements

See Also:

• Constant Field Values

BOX_OFFSET

protected static final int BOX_OFFSET

distance between two adjacent "boxes"

See Also:

• Constant Field Values

BOX_HEIGHT

protected static final int BOX_HEIGHT

See Also:

• Constant Field Values

BLUE

protected static final String BLUE

See Also:

• Constant Field Values

RED

protected static final String RED

See Also:

• Constant Field Values

BROWN

protected static final String BROWN

See Also:

• Constant Field Values

DARKBLUE

protected static final String DARKBLUE

See Also:

• Constant Field Values

VIOLET

protected static final String VIOLET

See Also:

• Constant Field Values

ORANGE

protected static final String ORANGE

See Also:

• Constant Field Values

BLACK

protected static final String BLACK

See Also:

• Constant Field Values

GREEN

protected static final String GREEN

See Also:

• Constant Field Values

BRIGHT_GREEN

protected static final String BRIGHT_GREEN

See Also:

• Constant Field Values

Constructor Details

Lirical2Svg

public Lirical2Svg()

Method Details

writeFooter

protected void writeFooter(Writer writer)
                    throws IOException

Throws:

IOException

prettifyDiseaseName

protected String prettifyDiseaseName(String originalDiseaseName)

This method shortens items such as #101200 APERT SYNDROME;;ACROCEPHALOSYNDACTYLY, TYPE I; ACS1;;ACS IAPERT-CROUZON DISEASE, INCLUDED;; to simply APERT SYNDROME

Parameters:

originalDiseaseName - original String from HPO database, derived from OMIM and potentially historic

Returns:

simplified and prettified name

writeDiamond

protected void writeDiamond(Writer writer,
 int X,
 int Y,
 String msg)
                     throws IOException

We use a diamond symbol to show a value that would be too small to appear as a visible box. We do this bothfor the likelihood ratio as well as for the post-test probability

Throws:

IOException

writeDiamond

protected void writeDiamond(Writer writer,
 int X,
 int Y)
                     throws IOException

We use a diamond symbol to show a value that would be too small to appear as a visible box. We do this bothfor the likelihood ratio as well as for the post-test probability

Throws:

IOException

sortByValue

protected static <K,
V extends Comparable<? super V>>
Map<K,V> sortByValue(Map<K,V> map)