- ScaleText - Class in com.affymetrix.genoviz.tutorial
-
- ScaleText() - Constructor for class com.affymetrix.genoviz.tutorial.ScaleText
-
- scene - Variable in class com.affymetrix.genoviz.demo.adapter.AnnotationAdapter
-
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])
- scene - Variable in class com.affymetrix.genoviz.demo.adapter.ScoredAnnotAdapter
-
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])
- scene - Variable in class com.affymetrix.genoviz.demo.adapter.SequenceAnnotAdapter
-
- ScoredAnnotAdapter - Class in com.affymetrix.genoviz.demo.adapter
-
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
- ScoredAnnotAdapter() - Constructor for class com.affymetrix.genoviz.demo.adapter.ScoredAnnotAdapter
-
- ScoredAnnotation - Class in com.affymetrix.genoviz.demo.datamodel
-
- ScoredAnnotation(int, int, double) - Constructor for class com.affymetrix.genoviz.demo.datamodel.ScoredAnnotation
-
- ScoredAnnotationI - Interface in com.affymetrix.genoviz.demo.datamodel
-
- selectAnnotation() - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
-
- selectedB - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
-
- seq - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
-
- seq - Variable in class com.affymetrix.genoviz.tutorial.SequenceMap0
-
- seq2 - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
-
- seq3 - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
-
- seqFrame - Variable in class com.affymetrix.genoviz.tutorial.SequenceMap0
-
- SequenceAnnotAdapter - Class in com.affymetrix.genoviz.demo.adapter
-
- SequenceAnnotAdapter() - Constructor for class com.affymetrix.genoviz.demo.adapter.SequenceAnnotAdapter
-
- SequenceAnnotation - Class in com.affymetrix.genoviz.demo.datamodel
-
- SequenceAnnotation(int, String) - Constructor for class com.affymetrix.genoviz.demo.datamodel.SequenceAnnotation
-
- SequenceAnnotationI - Interface in com.affymetrix.genoviz.demo.datamodel
-
- SequenceMap0 - Class in com.affymetrix.genoviz.tutorial
-
- SequenceMap0() - Constructor for class com.affymetrix.genoviz.tutorial.SequenceMap0
-
- SequenceMap1 - Class in com.affymetrix.genoviz.tutorial
-
- SequenceMap1() - Constructor for class com.affymetrix.genoviz.tutorial.SequenceMap1
-
- SequenceParser - Class in com.affymetrix.genoviz.demo.parser
-
parses "Helt Format" sequence data.
- SequenceParser() - Constructor for class com.affymetrix.genoviz.demo.parser.SequenceParser
-
- seqview - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
-
- setAnnotColors(Color) - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
-
- setBasesBackground(Color) - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
-
- setChr(String) - Method in class com.affymetrix.genoviz.demo.datamodel.BedSequence
-
- setDescription(String) - Method in class com.affymetrix.genoviz.demo.datamodel.BedSequence
-
- setEnd(int) - Method in class com.affymetrix.genoviz.demo.datamodel.Annotation
-
- setEnd(int) - Method in class com.affymetrix.genoviz.demo.datamodel.BedSequence
-
- setForward(boolean) - Method in class com.affymetrix.genoviz.demo.datamodel.Annotation
-
- setLaG(String[]) - Method in class com.affymetrix.genoviz.demo.datamodel.BedSequence
-
- setName(String) - Method in class com.affymetrix.genoviz.demo.datamodel.BedSequence
-
- setpG(String[]) - Method in class com.affymetrix.genoviz.demo.datamodel.BedSequence
-
- setResidues(String) - Method in class com.affymetrix.genoviz.demo.datamodel.SequenceAnnotation
-
- setScene(Scene) - Method in class com.affymetrix.genoviz.demo.adapter.AnnotationAdapter
-
- setScene(Scene) - Method in class com.affymetrix.genoviz.demo.adapter.AssemblyAdapter
-
need to maintain setScene for backward compatibility with NeoDataAdapterI
interface
- setScene(Scene) - Method in class com.affymetrix.genoviz.demo.adapter.ScoredAnnotAdapter
-
- setScene(Scene) - Method in class com.affymetrix.genoviz.demo.adapter.SequenceAnnotAdapter
-
- setScore(double) - Method in class com.affymetrix.genoviz.demo.datamodel.ScoredAnnotation
-
- setSeqG(String[]) - Method in class com.affymetrix.genoviz.demo.datamodel.BedSequence
-
- setSeqMap(Map) - Method in class com.affymetrix.genoviz.demo.datamodel.BedSequence
-
- setStart(int) - Method in class com.affymetrix.genoviz.demo.datamodel.Annotation
-
- setStart(int) - Method in class com.affymetrix.genoviz.demo.datamodel.BedSequence
-
- setStrand(String) - Method in class com.affymetrix.genoviz.demo.datamodel.BedSequence
-
- setTrace(TraceI) - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
-
- setTrace(TraceI) - Method in class com.affymetrix.genoviz.tutorial.TutorialTracer
-
- setTraceColors(Color[]) - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
-
- setTraceLabel(String) - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
-
- setTraceLabel(String) - Method in class com.affymetrix.genoviz.tutorial.TutorialTracer
-
- setTracesBackground(Color) - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
-
- setType(String) - Method in class com.affymetrix.genoviz.demo.datamodel.Annotation
-
- setUpMap(String) - Method in class com.affymetrix.genoviz.demo.ShadowDemo
-
- setupMenus(Frame) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
-
- setupMenus() - Method in class com.affymetrix.genoviz.demo.NeoMapDemo
-
- setupMenus(Frame) - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
-
- setUpShadowRect(NeoSeq, NeoMap) - Method in class com.affymetrix.genoviz.demo.ShadowDemo
-
Sets up a shadow of the source on the destination
- setWidget(NeoAbstractWidget) - Method in class com.affymetrix.genoviz.tutorial.MapHandler
-
sets the widget (in our case a NeoMap).
- ShadowDemo - Class in com.affymetrix.genoviz.demo
-
Demo of "shadowing" a NeoSeq on a NeoMap via RangeChangeEvents and
TransientGlyphs
- ShadowDemo() - Constructor for class com.affymetrix.genoviz.demo.ShadowDemo
-
- shadowRect - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
-
- showProperties() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
-
- showProperties() - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo
-
- showProperties() - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo2
-
- showProperties() - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
-
- showStatus(String) - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
-
- SimpleMap - Class in com.affymetrix.genoviz.tutorial
-
- SimpleMap() - Constructor for class com.affymetrix.genoviz.tutorial.SimpleMap
-
- SimpleMap0 - Class in com.affymetrix.genoviz.tutorial
-
- SimpleMap0() - Constructor for class com.affymetrix.genoviz.tutorial.SimpleMap0
-
- SimpleMap1 - Class in com.affymetrix.genoviz.tutorial
-
- SimpleMap1() - Constructor for class com.affymetrix.genoviz.tutorial.SimpleMap1
-
- SimpleMap2 - Class in com.affymetrix.genoviz.tutorial
-
- SimpleMap2() - Constructor for class com.affymetrix.genoviz.tutorial.SimpleMap2
-
- SimpleMap3 - Class in com.affymetrix.genoviz.tutorial
-
- SimpleMap3() - Constructor for class com.affymetrix.genoviz.tutorial.SimpleMap3
-
- SimpleMap4 - Class in com.affymetrix.genoviz.tutorial
-
- SimpleMap4() - Constructor for class com.affymetrix.genoviz.tutorial.SimpleMap4
-
- SimpleMap5 - Class in com.affymetrix.genoviz.tutorial
-
- SimpleMap5() - Constructor for class com.affymetrix.genoviz.tutorial.SimpleMap5
-
- SimpleMap6 - Class in com.affymetrix.genoviz.tutorial
-
- SimpleMap6() - Constructor for class com.affymetrix.genoviz.tutorial.SimpleMap6
-
- SimpleSelectableMap - Class in com.affymetrix.genoviz.tutorial
-
- SimpleSelectableMap() - Constructor for class com.affymetrix.genoviz.tutorial.SimpleSelectableMap
-
- simulateTrimmedEdges - Variable in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
-
- sizeL - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
-
- sizeT - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
-
- spacingL - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
-
- spacingT - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
-
- squiggleMenuItem - Variable in class com.affymetrix.genoviz.tutorial.NeoDraw
-
- start - Variable in class com.affymetrix.genoviz.demo.datamodel.Annotation
-
- start() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
-
- start() - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo
-
- start() - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo2
-
- start() - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
-
- start() - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
-
- start() - Method in class com.affymetrix.genoviz.demo.ShadowDemo
-
- start() - Method in class com.affymetrix.genoviz.demo.TieredMapDemo
-
- start() - Method in class com.affymetrix.genoviz.tutorial.SequenceMap0
-
- start() - Method in class com.affymetrix.genoviz.tutorial.TutorialQualler
-
- start() - Method in class com.affymetrix.genoviz.tutorial.TutorialTracer
-
- StartCodonPainter - Class in com.affymetrix.genoviz.demo
-
another simple ResiduePainter.
- StartCodonPainter(Color) - Constructor for class com.affymetrix.genoviz.demo.StartCodonPainter
-
- StartCodonPainter() - Constructor for class com.affymetrix.genoviz.demo.StartCodonPainter
-
constructs a painter that paints start codons red.
- startDocument() - Method in class com.affymetrix.genoviz.tutorial.MapHandler
-
Handle the start of the document.
- startElement(String, String, String, Attributes) - Method in class com.affymetrix.genoviz.tutorial.MapHandler
-
Handle the start of an element.
- stop() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
-
- stop() - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo
-
- stop() - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo2
-
- stop() - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
-
- stop() - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
-
- stop() - Method in class com.affymetrix.genoviz.demo.ShadowDemo
-
- stop() - Method in class com.affymetrix.genoviz.demo.TieredMapDemo
-
- stop() - Method in class com.affymetrix.genoviz.tutorial.SequenceMap0
-
- stop() - Method in class com.affymetrix.genoviz.tutorial.TutorialQualler
-
- stop() - Method in class com.affymetrix.genoviz.tutorial.TutorialTracer
-
- stripeL - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
-
- stripeT - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
-
- switchFontSize() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
-
- switchFontStyle() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
-
- switchFontType() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
-