com.affymetrix.genoviz.demo.adapter

Class ScoredAnnotAdapter

java.lang.Object

com.affymetrix.genoviz.demo.adapter.ScoredAnnotAdapter

All Implemented Interfaces:

com.affymetrix.genoviz.bioviews.NeoDataAdapterI

public class ScoredAnnotAdapter
extends Object
implements com.affymetrix.genoviz.bioviews.NeoDataAdapterI

a data adapter that colors glyphs based on the score of an annotation like AnnotationAdapter, most of the work is done by a MapGlyphFactory MapGlyphFactory is not necessarily well suited for this purpose, but they are adequate

Field Summary

Fields

Modifier and Type	Field and Description
protected Color	col
protected com.affymetrix.genoviz.bioviews.MapGlyphFactory	factory
protected com.affymetrix.genoviz.bioviews.Scene	scene need a Scene to set up MapGlyphFactory (which needs to know which scene it is building glyphs for, in order to pack the glyph relative to other glyphs [actually, should really need to know the View that it should base its packing on, but for now we consider the simpler case where it packs to the first view of the scene])

Constructor Summary

Constructors

Constructor and Description
ScoredAnnotAdapter()

Method Summary

Modifier and Type	Method and Description
boolean	accepts(Object obj)
void	configure(Hashtable options)
void	configure(String options)
com.affymetrix.genoviz.bioviews.GlyphI	createGlyph(Object obj)
com.affymetrix.genoviz.bioviews.MapGlyphFactory	getGlyphFactory()
void	setScene(com.affymetrix.genoviz.bioviews.Scene scene)

Methods inherited from class java.lang.Object

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

Field Detail

factory

protected com.affymetrix.genoviz.bioviews.MapGlyphFactory factory

col

protected Color col

scene

protected com.affymetrix.genoviz.bioviews.Scene scene

need a Scene to set up MapGlyphFactory (which needs to know which scene it is building glyphs for, in order to pack the glyph relative to other glyphs [actually, should really need to know the View that it should base its packing on, but for now we consider the simpler case where it packs to the first view of the scene])

Constructor Detail

ScoredAnnotAdapter

public ScoredAnnotAdapter()

Method Detail

getGlyphFactory

public com.affymetrix.genoviz.bioviews.MapGlyphFactory getGlyphFactory()

setScene

public void setScene(com.affymetrix.genoviz.bioviews.Scene scene)

Specified by:

setScene in interface com.affymetrix.genoviz.bioviews.NeoDataAdapterI

configure

public void configure(String options)

Specified by:

configure in interface com.affymetrix.genoviz.bioviews.NeoDataAdapterI

configure

public void configure(Hashtable options)

Specified by:

configure in interface com.affymetrix.genoviz.bioviews.NeoDataAdapterI

accepts

public boolean accepts(Object obj)

Specified by:

accepts in interface com.affymetrix.genoviz.bioviews.NeoDataAdapterI

createGlyph

public com.affymetrix.genoviz.bioviews.GlyphI createGlyph(Object obj)

Specified by:

createGlyph in interface com.affymetrix.genoviz.bioviews.NeoDataAdapterI