Skip navigation links
A B C D E F G H I L M N O P R S T U V W X Z 

A

accepts(Object) - Method in class com.affymetrix.genoviz.demo.adapter.AnnotationAdapter
 
accepts(Object) - Method in class com.affymetrix.genoviz.demo.adapter.AssemblyAdapter
 
accepts(Object) - Method in class com.affymetrix.genoviz.demo.adapter.ScoredAnnotAdapter
 
accepts(Object) - Method in class com.affymetrix.genoviz.demo.adapter.SequenceAnnotAdapter
 
actionPerformed(ActionEvent) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
ActionListener Implementation
actionPerformed(ActionEvent) - Method in class com.affymetrix.genoviz.demo.NeoMapDemo
ActionListener interface implementation
actionPerformed(ActionEvent) - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo
 
actionPerformed(ActionEvent) - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo2
 
actionPerformed(ActionEvent) - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
ActionListener Implementation
actionPerformed(ActionEvent) - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
 
actionPerformed(ActionEvent) - Method in class com.affymetrix.genoviz.demo.TieredMapDemo
 
actionPerformed(ActionEvent) - Method in class com.affymetrix.genoviz.tutorial.GlyphTestMap
 
actionPerformed(ActionEvent) - Method in class com.affymetrix.genoviz.tutorial.NeoDraw
 
actionPerformed(ActionEvent) - Method in class com.affymetrix.genoviz.tutorial.SimpleMap
 
actionPerformed(ActionEvent) - Method in class com.affymetrix.genoviz.tutorial.SimpleMap0
 
actionPerformed(ActionEvent) - Method in class com.affymetrix.genoviz.tutorial.TutorialQualler
 
actionPerformed(ActionEvent) - Method in class com.affymetrix.genoviz.tutorial.TutorialTracer
 
addAlign(Mapping) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
addAlignment() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
addBackAnnotB - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
 
addBackgroundAnnotation() - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 
addBackgroundAnnotation() - Method in class com.affymetrix.genoviz.demo.ShadowDemo
 
addBases(Mapping) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
addBases() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
addConsensus() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
addFileMenuItems(Frame) - Method in class com.affymetrix.genoviz.tutorial.SimpleMap
 
addFileMenuItems(Frame) - Method in class com.affymetrix.genoviz.tutorial.SimpleMap0
 
addGaps(Mapping) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
addGaps() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
addItemsDirectly() - Method in class com.affymetrix.genoviz.demo.NeoMapDemo
 
addItemsWithDataAdapter() - Method in class com.affymetrix.genoviz.demo.NeoMapDemo
----------------- Data Adapters ----------------- Adding items directly to the map or through the map's factories by specifying a start and end position works for simple annotations.
addItemsWithFactory() - Method in class com.affymetrix.genoviz.demo.NeoMapDemo
------------------- Factories ------------------- Different configurations for adding items to maps can be stored in the map as factories.
addMap(String, NeoMap) - Method in class com.affymetrix.genoviz.tutorial.MapHandler
Adds an alias for the "map" tag.
addNeg() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
addNext() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
addOutlineAnnotation() - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 
addSequence() - Method in class com.affymetrix.genoviz.demo.NeoMapDemo
Creating a sequence item, and adding visible annotations to it
addTextAnnotB - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
 
addTheRest() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
addUniAlignment(Mapping) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
Trying to get improved speed and memory usage.
AlignmentParser - Class in com.affymetrix.genoviz.demo.parser
parses "Helt Format" sequence alignment data.
AlignmentParser() - Constructor for class com.affymetrix.genoviz.demo.parser.AlignmentParser
 
Annotation - Class in com.affymetrix.genoviz.demo.datamodel
 
Annotation() - Constructor for class com.affymetrix.genoviz.demo.datamodel.Annotation
 
Annotation(int, int) - Constructor for class com.affymetrix.genoviz.demo.datamodel.Annotation
 
AnnotationAdapter - Class in com.affymetrix.genoviz.demo.adapter
an almost trivial example of a DataAdapter most of the work is done by a MapGlyphFactory the one thing this adapter knows is that the datamodel objects implement the AnnotationI interface, and therefore can create the proper glyph and add it to the map by: MapGlyphFactory.makeGlyph(AnnotationI.getStart(), AnnotationI.getEnd());
AnnotationAdapter() - Constructor for class com.affymetrix.genoviz.demo.adapter.AnnotationAdapter
 
AnnotationI - Interface in com.affymetrix.genoviz.demo.datamodel
 
annotations - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
 
arrowMenuItem - Variable in class com.affymetrix.genoviz.tutorial.NeoDraw
 
AssemblyAdapter - Class in com.affymetrix.genoviz.demo.adapter
 
AssemblyAdapter(NeoAssembler) - Constructor for class com.affymetrix.genoviz.demo.adapter.AssemblyAdapter
Need a constructor that takes a NeoAssembler as a constructor this is really just a usability convenience

B

back_annot_color - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
 
BedFileParser - Class in com.affymetrix.genoviz.demo.parser
 
BedFileParser(String) - Constructor for class com.affymetrix.genoviz.demo.parser.BedFileParser
 
BedSequence - Class in com.affymetrix.genoviz.demo.datamodel
 
BedSequence() - Constructor for class com.affymetrix.genoviz.demo.datamodel.BedSequence
 
BedSequenceDemo - Class in com.affymetrix.genoviz.tutorial
 
BedSequenceDemo() - Constructor for class com.affymetrix.genoviz.tutorial.BedSequenceDemo
 
bg_painter - Variable in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
blackMenuItem - Variable in class com.affymetrix.genoviz.tutorial.NeoDraw
 
blueMenuItem - Variable in class com.affymetrix.genoviz.tutorial.NeoDraw
 
boundedPointMenuItem - Variable in class com.affymetrix.genoviz.tutorial.NeoDraw
 
buttonSetup() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo2
puts buttons on a panel so the user can instigate actions.

C

calculateColors(Color[], String, String, int, int) - Method in class com.affymetrix.genoviz.demo.ResiduePainterExample
 
calculateColors(Object, Color[], String, String, int, int) - Method in class com.affymetrix.genoviz.demo.ResiduePainterExample
 
calculateColors(Color[], String, String, int, int) - Method in class com.affymetrix.genoviz.demo.StartCodonPainter
sets the start codons' color.
calculateColors(Object, Color[], String, String, int, int) - Method in class com.affymetrix.genoviz.demo.StartCodonPainter
sets the start codons' color.
centerAtBase(int) - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo
 
centerAtBase(int) - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo2
 
centerAtBase(int) - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
 
centerAtBase(int) - Method in class com.affymetrix.genoviz.tutorial.TutorialQualler
 
centerAtBase(int) - Method in class com.affymetrix.genoviz.tutorial.TutorialTracer
 
centeredCircleMenuItem - Variable in class com.affymetrix.genoviz.tutorial.NeoDraw
 
changeSequence() - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 
characters(char[], int, int) - Method in class com.affymetrix.genoviz.tutorial.MapHandler
 
clearMap() - Method in class com.affymetrix.genoviz.tutorial.NeoDraw
 
clearMenuItem - Variable in class com.affymetrix.genoviz.tutorial.NeoDraw
 
clearSelection() - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo
 
clearSelection() - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo2
 
clearSelection() - Method in class com.affymetrix.genoviz.tutorial.TutorialQualler
 
clipTrace(int, int) - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
 
cloneWidget() - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo
 
cloneWidget() - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
 
col - Variable in class com.affymetrix.genoviz.demo.adapter.ScoredAnnotAdapter
 
colorMenu - Variable in class com.affymetrix.genoviz.tutorial.NeoDraw
 
com.affymetrix.genoviz.demo - package com.affymetrix.genoviz.demo
 
com.affymetrix.genoviz.demo.adapter - package com.affymetrix.genoviz.demo.adapter
 
com.affymetrix.genoviz.demo.datamodel - package com.affymetrix.genoviz.demo.datamodel
 
com.affymetrix.genoviz.demo.parser - package com.affymetrix.genoviz.demo.parser
 
com.affymetrix.genoviz.tutorial - package com.affymetrix.genoviz.tutorial
 
componentHidden(ComponentEvent) - Method in class com.affymetrix.genoviz.demo.GraphDemo
 
componentHidden(ComponentEvent) - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
 
componentMoved(ComponentEvent) - Method in class com.affymetrix.genoviz.demo.GraphDemo
 
componentMoved(ComponentEvent) - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
 
componentResized(ComponentEvent) - Method in class com.affymetrix.genoviz.demo.GraphDemo
 
componentResized(ComponentEvent) - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
 
componentShown(ComponentEvent) - Method in class com.affymetrix.genoviz.demo.GraphDemo
 
componentShown(ComponentEvent) - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
 
configure(String) - Method in class com.affymetrix.genoviz.demo.adapter.AnnotationAdapter
 
configure(Hashtable) - Method in class com.affymetrix.genoviz.demo.adapter.AnnotationAdapter
 
configure(String) - Method in class com.affymetrix.genoviz.demo.adapter.AssemblyAdapter
 
configure(Hashtable) - Method in class com.affymetrix.genoviz.demo.adapter.AssemblyAdapter
 
configure(String) - Method in class com.affymetrix.genoviz.demo.adapter.ScoredAnnotAdapter
 
configure(Hashtable) - Method in class com.affymetrix.genoviz.demo.adapter.ScoredAnnotAdapter
 
configure(String) - Method in class com.affymetrix.genoviz.demo.adapter.SequenceAnnotAdapter
 
configure(Hashtable) - Method in class com.affymetrix.genoviz.demo.adapter.SequenceAnnotAdapter
 
constructControlPanel() - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo
 
constructControlPanel() - Method in class com.affymetrix.genoviz.tutorial.TutorialQualler
 
count - Variable in class com.affymetrix.genoviz.tutorial.ScaleText
 
createBedSequenceList() - Method in class com.affymetrix.genoviz.tutorial.BedSequenceDemo
 
createGlyph(Object) - Method in class com.affymetrix.genoviz.demo.adapter.AnnotationAdapter
 
createGlyph(Object) - Method in class com.affymetrix.genoviz.demo.adapter.AssemblyAdapter
For NeoAssemblyAdapter, multiple glyphs on multiple "inner" scenes are being created.
createGlyph(Object) - Method in class com.affymetrix.genoviz.demo.adapter.ScoredAnnotAdapter
 
createGlyph(Object) - Method in class com.affymetrix.genoviz.demo.adapter.SequenceAnnotAdapter
 
createMapPanel(int) - Method in class com.affymetrix.genoviz.tutorial.BedSequenceDemo
 
createSeqMap() - Method in class com.affymetrix.genoviz.demo.datamodel.BedSequence
 

D

defineGlyphStyle(NeoMap, String, String, Integer) - Method in class com.affymetrix.genoviz.tutorial.MapHandler
defines a glyph style.
deselectColorMenu(JCheckBoxMenuItem) - Method in class com.affymetrix.genoviz.tutorial.NeoDraw
 
deselectGlyphMenu(JCheckBoxMenuItem) - Method in class com.affymetrix.genoviz.tutorial.NeoDraw
 
destroy() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
destroy() - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 
destroy() - Method in class com.affymetrix.genoviz.demo.ShadowDemo
 
doExternalSort() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
An example of arbitrary sorting of alignments -- in this case, just reverse the order in which they are currently sorted General method for arbitrary sorting is: call NeoAssembler.getAlignmentGlyphs() to get vector of all alignment glyphs, ordered from top to bottom of NeoAssembler rearrange ordering in vector call NeoAssembler.pack() to repack from top to bottom as ordered in the vector
draw(ViewI) - Method in class com.affymetrix.genoviz.tutorial.RoundedRect
 
draw(ViewI) - Method in class com.affymetrix.genoviz.tutorial.ScaleText
 

E

editMenu - Variable in class com.affymetrix.genoviz.tutorial.NeoDraw
 
end - Variable in class com.affymetrix.genoviz.demo.datamodel.Annotation
 
endDocument() - Method in class com.affymetrix.genoviz.tutorial.MapHandler
Handle the end of the document.
endElement(String, String, String) - Method in class com.affymetrix.genoviz.tutorial.MapHandler
Handle the end of an element.
exportContent(OutputStream, Object) - Method in class com.affymetrix.genoviz.tutorial.MapHandler
exportContent needed to implement ContentParser Here the signature is empty because we are only interested in providing the importContent functionality associated with ContentParser.
exportContent(OutputStream, Object) - Method in class com.affymetrix.genoviz.tutorial.NarcissusParser
 
exportSequenceFasta() - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 

F

factory - Variable in class com.affymetrix.genoviz.demo.adapter.AnnotationAdapter
 
factory - Variable in class com.affymetrix.genoviz.demo.adapter.ScoredAnnotAdapter
 
factory - Variable in class com.affymetrix.genoviz.demo.adapter.SequenceAnnotAdapter
 
featureTypes - Variable in class com.affymetrix.genoviz.tutorial.NarcissusParser
 
featureTypes - Variable in class com.affymetrix.genoviz.tutorial.SimpleMap4
 
fg_painter - Variable in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
fillOvalMenuItem - Variable in class com.affymetrix.genoviz.tutorial.NeoDraw
 
fillRectMenuItem - Variable in class com.affymetrix.genoviz.tutorial.NeoDraw
 
firstL - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
 
fontC - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
 
fontL - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
 
forward - Variable in class com.affymetrix.genoviz.demo.datamodel.Annotation
forward is defined by (start <= end) so forward field is really just a convenience Also, because of this, setForward() should adjust the start and end as well

G

getAlignment(BufferedReader) - Static method in class com.affymetrix.genoviz.demo.parser.BedFileParser
 
getAlignments(URL) - Static method in class com.affymetrix.genoviz.demo.parser.AlignmentParser
gets the alignment data from the net.
getAlignments(BufferedReader) - Static method in class com.affymetrix.genoviz.demo.parser.AlignmentParser
gets the alignment data by parsing a stream of characters.
getAlignments(URL, Hashtable) - Static method in class com.affymetrix.genoviz.demo.parser.AlignmentParser
gets the alignment data from the net.
getAlignments(BufferedReader, Hashtable) - Static method in class com.affymetrix.genoviz.demo.parser.AlignmentParser
gets the alignment data by parsing a stream of bytes.
getAlignments(URL) - Method in class com.affymetrix.genoviz.demo.parser.BedFileParser
 
getAppletContext() - Method in class com.affymetrix.genoviz.demo.GraphDemo
 
getAppletContext() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
getAppletContext() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo2
 
getAppletContext() - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo
 
getAppletContext() - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo2
 
getAppletContext() - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 
getAppletContext() - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
 
getAppletInfo() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
getAppletInfo() - Method in class com.affymetrix.genoviz.demo.NeoMapDemo
 
getAppletInfo() - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo
 
getAppletInfo() - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo2
 
getAppletInfo() - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 
getAppletInfo() - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
 
getAppletInfo() - Method in class com.affymetrix.genoviz.demo.ShadowDemo
 
getAppletInfo() - Method in class com.affymetrix.genoviz.tutorial.NeoDraw
 
getAppletInfo() - Method in class com.affymetrix.genoviz.tutorial.SequenceMap0
 
getAppletInfo() - Method in class com.affymetrix.genoviz.tutorial.SequenceMap1
 
getAppletInfo() - Method in class com.affymetrix.genoviz.tutorial.SimpleMap
 
getAppletInfo() - Method in class com.affymetrix.genoviz.tutorial.SimpleMap0
 
getAppletInfo() - Method in class com.affymetrix.genoviz.tutorial.SimpleSelectableMap
 
getAppletInfo() - Method in class com.affymetrix.genoviz.tutorial.TutorialQualler
 
getAppletInfo() - Method in class com.affymetrix.genoviz.tutorial.TutorialTracer
 
getChr() - Method in class com.affymetrix.genoviz.demo.datamodel.BedSequence
 
getChromosome(String) - Method in class com.affymetrix.genoviz.tutorial.BedSequenceDemo
 
getCodeBase() - Method in class com.affymetrix.genoviz.demo.GraphDemo
 
getCodeBase() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
getCodeBase() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo2
 
getCodeBase() - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo
 
getCodeBase() - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo2
 
getCodeBase() - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 
getCodeBase() - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
 
getDescription() - Method in class com.affymetrix.genoviz.demo.datamodel.BedSequence
 
getDocumentBase() - Method in class com.affymetrix.genoviz.demo.GraphDemo
 
getDocumentBase() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
getDocumentBase() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo2
 
getDocumentBase() - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo
 
getDocumentBase() - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo2
 
getDocumentBase() - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 
getDocumentBase() - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
 
getEnd() - Method in class com.affymetrix.genoviz.demo.datamodel.Annotation
 
getEnd() - Method in interface com.affymetrix.genoviz.demo.datamodel.AnnotationI
 
getEnd() - Method in class com.affymetrix.genoviz.demo.datamodel.BedSequence
 
getGlyphFactory() - Method in class com.affymetrix.genoviz.demo.adapter.AnnotationAdapter
 
getGlyphFactory() - Method in class com.affymetrix.genoviz.demo.adapter.ScoredAnnotAdapter
 
getGoing() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
getGoing() - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 
getHRef(GlyphI) - Method in class com.affymetrix.genoviz.tutorial.MapHandler
 
getImage(URL, String) - Method in class com.affymetrix.genoviz.demo.GraphDemo
 
getLaG() - Method in class com.affymetrix.genoviz.demo.datamodel.BedSequence
 
getMapLength() - Static method in class com.affymetrix.genoviz.demo.parser.BedFileParser
 
getName() - Method in class com.affymetrix.genoviz.demo.datamodel.BedSequence
 
getParameter(String) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
getParameter(String) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo2
 
getParameter(String) - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo
 
getParameter(String) - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo2
 
getParameter(String) - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 
getParameter(String) - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
 
getpG() - Method in class com.affymetrix.genoviz.demo.datamodel.BedSequence
 
getResidues() - Method in class com.affymetrix.genoviz.demo.datamodel.SequenceAnnotation
 
getResidues() - Method in interface com.affymetrix.genoviz.demo.datamodel.SequenceAnnotationI
 
getResults() - Method in class com.affymetrix.genoviz.demo.parser.BedFileParser
 
getScore() - Method in class com.affymetrix.genoviz.demo.datamodel.ScoredAnnotation
 
getScore(int) - Method in class com.affymetrix.genoviz.demo.datamodel.ScoredAnnotation
 
getScore() - Method in interface com.affymetrix.genoviz.demo.datamodel.ScoredAnnotationI
 
getScore(int) - Method in interface com.affymetrix.genoviz.demo.datamodel.ScoredAnnotationI
 
getSelectedGlyph(NeoAssembler) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
getSelectedGlyph(NeoAssembler) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo2
 
getSelectedRange(AlignmentGlyph) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
getSelectedRange(AlignmentGlyph) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo2
 
getSelectedResidues(AlignmentGlyph) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
getSelectedResidues(AlignmentGlyph) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo2
 
getSeqG() - Method in class com.affymetrix.genoviz.demo.datamodel.BedSequence
 
getSeqMap() - Method in class com.affymetrix.genoviz.demo.datamodel.BedSequence
 
getSequences(URL) - Static method in class com.affymetrix.genoviz.demo.parser.SequenceParser
gets and parses data from somewhere on the net.
getSequences(BufferedReader) - Static method in class com.affymetrix.genoviz.demo.parser.SequenceParser
parsers the data coming from a stream of characters.
getStart() - Method in class com.affymetrix.genoviz.demo.datamodel.Annotation
 
getStart() - Method in interface com.affymetrix.genoviz.demo.datamodel.AnnotationI
 
getStart() - Method in class com.affymetrix.genoviz.demo.datamodel.BedSequence
 
getStrand() - Method in class com.affymetrix.genoviz.demo.datamodel.BedSequence
 
getTarget(GlyphI) - Method in class com.affymetrix.genoviz.tutorial.MapHandler
 
getType() - Method in class com.affymetrix.genoviz.demo.datamodel.Annotation
 
glyphMenu - Variable in class com.affymetrix.genoviz.tutorial.NeoDraw
 
GlyphTestMap - Class in com.affymetrix.genoviz.tutorial
 
GlyphTestMap() - Constructor for class com.affymetrix.genoviz.tutorial.GlyphTestMap
 
GraphDemo - Class in com.affymetrix.genoviz.demo
 
GraphDemo() - Constructor for class com.affymetrix.genoviz.demo.GraphDemo
 
grayMenuItem - Variable in class com.affymetrix.genoviz.tutorial.NeoDraw
 

H

HairMap - Class in com.affymetrix.genoviz.tutorial
 
HairMap() - Constructor for class com.affymetrix.genoviz.tutorial.HairMap
 
heardEvent(Event) - Method in class com.affymetrix.genoviz.tutorial.TutorialQualler
 
HelloMap - Class in com.affymetrix.genoviz.tutorial
 
HelloMap() - Constructor for class com.affymetrix.genoviz.tutorial.HelloMap
 
hider - Variable in class com.affymetrix.genoviz.tutorial.TutorialQualler
 
hider - Variable in class com.affymetrix.genoviz.tutorial.TutorialTracer
 

I

ignorableWhitespace(char[], int, int) - Method in class com.affymetrix.genoviz.tutorial.MapHandler
Handle ignorable whitespace.
importContent(Reader) - Method in class com.affymetrix.genoviz.tutorial.MapHandler
importContent parses an xml formated stream and creates and returns a NeoMap object that contains the objects specified by the stream.
importContent(InputStream) - Method in class com.affymetrix.genoviz.tutorial.MapHandler
converts an InputStream to a Reader and then parses.
importContent(URL) - Method in class com.affymetrix.genoviz.tutorial.NarcissusParser
imports Narcissus format data from an internet.
importContent(Reader) - Method in class com.affymetrix.genoviz.tutorial.NarcissusParser
 
importContent(InputStream) - Method in class com.affymetrix.genoviz.tutorial.NarcissusParser
converts an InputStream to a Reader and then parses.
init() - Method in class com.affymetrix.genoviz.demo.GraphDemo
 
init() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo2
 
init() - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo
 
init(URL, URL) - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo
 
init(ReadConfidence) - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo
 
init(String, ReadConfidence) - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo
 
init() - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo2
 
init() - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 
init() - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
 
init() - Method in class com.affymetrix.genoviz.demo.ShadowDemo
 
init() - Method in class com.affymetrix.genoviz.demo.TieredMapDemo
 
init() - Method in class com.affymetrix.genoviz.demo.VerticalMapDemo
 
init() - Method in class com.affymetrix.genoviz.tutorial.SimpleMap
 
init() - Method in class com.affymetrix.genoviz.tutorial.SimpleMap0
 
init() - Method in class com.affymetrix.genoviz.tutorial.SimpleMap5
 
init() - Method in class com.affymetrix.genoviz.tutorial.SimpleMap6
 
init() - Method in class com.affymetrix.genoviz.tutorial.TutorialAssmblr
 
init() - Method in class com.affymetrix.genoviz.tutorial.TutorialGlyphDemo
 
init() - Method in class com.affymetrix.genoviz.tutorial.TutorialGlyphDemo2
 
init() - Method in class com.affymetrix.genoviz.tutorial.TutorialQualler
 
init(URL, URL) - Method in class com.affymetrix.genoviz.tutorial.TutorialQualler
 
init(ReadConfidence) - Method in class com.affymetrix.genoviz.tutorial.TutorialQualler
 
init(String, ReadConfidence) - Method in class com.affymetrix.genoviz.tutorial.TutorialQualler
 
init() - Method in class com.affymetrix.genoviz.tutorial.TutorialTracer
 
isApplet - Variable in class com.affymetrix.genoviz.tutorial.SimpleSelectableMap
 
isForward() - Method in class com.affymetrix.genoviz.demo.datamodel.Annotation
 
itemStateChanged(ItemEvent) - Method in class com.affymetrix.genoviz.demo.NeoMapDemo
 
itemStateChanged(ItemEvent) - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
ItemListener Implementation
itemStateChanged(ItemEvent) - Method in class com.affymetrix.genoviz.tutorial.NeoDraw
 

L

labelFactory - Variable in class com.affymetrix.genoviz.tutorial.NarcissusParser
 
lastL - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
 
lineContainerMenuItem - Variable in class com.affymetrix.genoviz.tutorial.NeoDraw
 
loadData() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
loadData(URL, URL) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
loadData(URL, URL) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo2
 
loadSequence(String) - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
loads a sequence from over the network.
loadSequence(String) - Method in class com.affymetrix.genoviz.tutorial.ParseOne
 

M

magentaMenuItem - Variable in class com.affymetrix.genoviz.tutorial.NeoDraw
 
main(String[]) - Static method in class com.affymetrix.genoviz.demo.GraphDemo
 
main(String[]) - Static method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
main(String[]) - Static method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo2
 
main(String[]) - Static method in class com.affymetrix.genoviz.demo.NeoMapDemo
 
main(String[]) - Static method in class com.affymetrix.genoviz.demo.NeoQuallerDemo
 
main(String[]) - Static method in class com.affymetrix.genoviz.demo.NeoQuallerDemo2
 
main(String[]) - Static method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 
main(String[]) - Static method in class com.affymetrix.genoviz.demo.NeoTracerDemo
 
main(String[]) - Static method in class com.affymetrix.genoviz.demo.ShadowDemo
 
main(String[]) - Static method in class com.affymetrix.genoviz.demo.TieredMapDemo
 
main(String[]) - Static method in class com.affymetrix.genoviz.demo.VerticalMapDemo
 
main(String[]) - Static method in class com.affymetrix.genoviz.tutorial.BedSequenceDemo
 
main(String[]) - Static method in class com.affymetrix.genoviz.tutorial.GlyphTestMap
 
main(String[]) - Static method in class com.affymetrix.genoviz.tutorial.HairMap
 
main(String[]) - Static method in class com.affymetrix.genoviz.tutorial.HelloMap
 
main(String[]) - Static method in class com.affymetrix.genoviz.tutorial.NarcissusParser
for testing.
main(String[]) - Static method in class com.affymetrix.genoviz.tutorial.NeoDraw
main method wrapper for NeoDraw (which is a JApplet), so can be used as both an applet and a standalone program
main(String[]) - Static method in class com.affymetrix.genoviz.tutorial.SequenceMap0
 
main(String[]) - Static method in class com.affymetrix.genoviz.tutorial.SequenceMap1
 
main(String[]) - Static method in class com.affymetrix.genoviz.tutorial.SimpleMap
 
main(String[]) - Static method in class com.affymetrix.genoviz.tutorial.SimpleMap0
 
main(String[]) - Static method in class com.affymetrix.genoviz.tutorial.SimpleMap1
 
main(String[]) - Static method in class com.affymetrix.genoviz.tutorial.SimpleMap2
 
main(String[]) - Static method in class com.affymetrix.genoviz.tutorial.SimpleMap3
 
main(String[]) - Static method in class com.affymetrix.genoviz.tutorial.SimpleMap4
 
main(String[]) - Static method in class com.affymetrix.genoviz.tutorial.SimpleSelectableMap
 
map - Variable in class com.affymetrix.genoviz.demo.adapter.AssemblyAdapter
 
map - Variable in class com.affymetrix.genoviz.tutorial.MapHandler
 
map - Variable in class com.affymetrix.genoviz.tutorial.SimpleMap
 
map - Variable in class com.affymetrix.genoviz.tutorial.SimpleMap0
 
mapframe - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
 
MapHandler - Class in com.affymetrix.genoviz.tutorial
 
MapHandler() - Constructor for class com.affymetrix.genoviz.tutorial.MapHandler
 
mapview - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
 
MAX_SIZE - Static variable in class com.affymetrix.genoviz.tutorial.ScaleText
 
ml - Variable in class com.affymetrix.genoviz.tutorial.SimpleSelectableMap
 
mouse_offset - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
 
mouseClicked(MouseEvent) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
MouseListener implelementation and collecting mouse events
mouseClicked(MouseEvent) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo2
 
mouseClicked(MouseEvent) - Method in class com.affymetrix.genoviz.demo.NeoMapDemo
MouseListener interface implementation
mouseClicked(MouseEvent) - Method in class com.affymetrix.genoviz.demo.ShadowDemo
MouseListener Implementation
mouseClicked(MouseEvent) - Method in class com.affymetrix.genoviz.demo.TieredMapDemo
 
mouseDragged(MouseEvent) - Method in class com.affymetrix.genoviz.demo.ShadowDemo
MouseMotionListener Implementation
mouseEntered(MouseEvent) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
mouseEntered(MouseEvent) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo2
 
mouseEntered(MouseEvent) - Method in class com.affymetrix.genoviz.demo.NeoMapDemo
 
mouseEntered(MouseEvent) - Method in class com.affymetrix.genoviz.demo.ShadowDemo
 
mouseEntered(MouseEvent) - Method in class com.affymetrix.genoviz.demo.TieredMapDemo
 
mouseExited(MouseEvent) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
mouseExited(MouseEvent) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo2
 
mouseExited(MouseEvent) - Method in class com.affymetrix.genoviz.demo.NeoMapDemo
 
mouseExited(MouseEvent) - Method in class com.affymetrix.genoviz.demo.ShadowDemo
 
mouseExited(MouseEvent) - Method in class com.affymetrix.genoviz.demo.TieredMapDemo
 
mouseMoved(MouseEvent) - Method in class com.affymetrix.genoviz.demo.ShadowDemo
 
mousePressed(MouseEvent) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
mousePressed(MouseEvent) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo2
 
mousePressed(MouseEvent) - Method in class com.affymetrix.genoviz.demo.NeoMapDemo
 
mousePressed(MouseEvent) - Method in class com.affymetrix.genoviz.demo.ShadowDemo
 
mousePressed(MouseEvent) - Method in class com.affymetrix.genoviz.demo.TieredMapDemo
 
mouser - Variable in class com.affymetrix.genoviz.tutorial.SequenceMap1
 
mouser - Variable in class com.affymetrix.genoviz.tutorial.TutorialQualler
 
mouser - Variable in class com.affymetrix.genoviz.tutorial.TutorialTracer
 
mouseReleased(MouseEvent) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
mouseReleased(MouseEvent) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo2
 
mouseReleased(MouseEvent) - Method in class com.affymetrix.genoviz.demo.NeoMapDemo
 
mouseReleased(MouseEvent) - Method in class com.affymetrix.genoviz.demo.ShadowDemo
 
mouseReleased(MouseEvent) - Method in class com.affymetrix.genoviz.demo.TieredMapDemo
 

N

NarcissusParser - Class in com.affymetrix.genoviz.tutorial
parses Narcissus format data for a NeoMap.
NarcissusParser() - Constructor for class com.affymetrix.genoviz.tutorial.NarcissusParser
constructs a parser
NeoAssemblerDemo - Class in com.affymetrix.genoviz.demo
A demo of the NeoAssembler widget.
NeoAssemblerDemo() - Constructor for class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
NeoAssemblerDemo() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
NeoAssemblerDemo2 - Class in com.affymetrix.genoviz.demo
This is a reworking of the old NeoAssemblerDemo It adds a button to clear and reload the NeoAssembler.
NeoAssemblerDemo2() - Constructor for class com.affymetrix.genoviz.demo.NeoAssemblerDemo2
 
NeoDraw - Class in com.affymetrix.genoviz.tutorial
 
NeoDraw() - Constructor for class com.affymetrix.genoviz.tutorial.NeoDraw
 
NeoMapDemo - Class in com.affymetrix.genoviz.demo
 
NeoMapDemo() - Constructor for class com.affymetrix.genoviz.demo.NeoMapDemo
 
neoMouseClicked(NeoMouseEvent) - Method in class com.affymetrix.genoviz.tutorial.SequenceMap1
 
NeoQuallerDemo - Class in com.affymetrix.genoviz.demo
 
NeoQuallerDemo() - Constructor for class com.affymetrix.genoviz.demo.NeoQuallerDemo
 
NeoQuallerDemo2 - Class in com.affymetrix.genoviz.demo
 
NeoQuallerDemo2() - Constructor for class com.affymetrix.genoviz.demo.NeoQuallerDemo2
 
NeoSeqDemo - Class in com.affymetrix.genoviz.demo
 
NeoSeqDemo() - Constructor for class com.affymetrix.genoviz.demo.NeoSeqDemo
 
NeoTracerDemo - Class in com.affymetrix.genoviz.demo
 
NeoTracerDemo() - Constructor for class com.affymetrix.genoviz.demo.NeoTracerDemo
 
newseq - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
 
no_reverse - Variable in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
num_left - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
 

O

orientC - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
 
orientL - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
 
outlineRectMenuItem - Variable in class com.affymetrix.genoviz.tutorial.NeoDraw
 

P

paint(Graphics) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
paint(Graphics) - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 
paint(Graphics) - Method in class com.affymetrix.genoviz.demo.TieredMapDemo
 
pan - Variable in class com.affymetrix.genoviz.tutorial.ParseOne
 
pan - Variable in class com.affymetrix.genoviz.tutorial.SequenceMap0
 
pan - Variable in class com.affymetrix.genoviz.tutorial.SimpleMap0
 
pan - Variable in class com.affymetrix.genoviz.tutorial.SimpleMap5
 
pan - Variable in class com.affymetrix.genoviz.tutorial.SimpleMap6
 
parseDirectedRange(StreamTokenizer) - Method in class com.affymetrix.genoviz.tutorial.NarcissusParser
parses a pair if integers representing the beginning and end of a directed range of integers.
parseDirectedRange(StreamTokenizer) - Method in class com.affymetrix.genoviz.tutorial.SimpleMap0
parses a pair of integers representing the beginning and end of a directed range of integers.
parseFeatureType(StreamTokenizer) - Method in class com.affymetrix.genoviz.tutorial.NarcissusParser
parses a feature type and adds it to a list of such types.
parseFeatureType(StreamTokenizer) - Method in class com.affymetrix.genoviz.tutorial.SimpleMap4
 
parseInput(Reader) - Method in class com.affymetrix.genoviz.tutorial.SimpleMap1
 
parseInput(Reader) - Method in class com.affymetrix.genoviz.tutorial.TutorialAssmblr
 
parseInputString(String) - Method in class com.affymetrix.genoviz.tutorial.SimpleMap
 
parseInputString(String) - Method in class com.affymetrix.genoviz.tutorial.SimpleMap0
 
parseInputString(String) - Method in class com.affymetrix.genoviz.tutorial.SimpleMap5
 
parseInputString(String) - Method in class com.affymetrix.genoviz.tutorial.SimpleMap6
 
parseInputString(String) - Method in class com.affymetrix.genoviz.tutorial.TutorialAssmblr
 
parseLabel(StreamTokenizer, Object) - Method in class com.affymetrix.genoviz.tutorial.NarcissusParser
parses a label.
parseLabel(StreamTokenizer, Object) - Method in class com.affymetrix.genoviz.tutorial.SimpleMap2
 
parseLine(int, StreamTokenizer) - Method in class com.affymetrix.genoviz.tutorial.NarcissusParser
 
parseLine(int, StreamTokenizer) - Method in class com.affymetrix.genoviz.tutorial.SimpleMap0
 
parseLine(int, StreamTokenizer) - Method in class com.affymetrix.genoviz.tutorial.SimpleMap2
 
ParseOne - Class in com.affymetrix.genoviz.tutorial
 
ParseOne() - Constructor for class com.affymetrix.genoviz.tutorial.ParseOne
 
parser - Variable in class com.affymetrix.genoviz.tutorial.ParseOne
 
parser - Variable in class com.affymetrix.genoviz.tutorial.SimpleMap5
 
parser - Variable in class com.affymetrix.genoviz.tutorial.SimpleMap6
 
parseRange(StreamTokenizer) - Method in class com.affymetrix.genoviz.tutorial.NarcissusParser
parses a pair if integers representing the beginning and end of a range of integers.
parseRange(StreamTokenizer) - Method in class com.affymetrix.genoviz.tutorial.SimpleMap0
parses a pair of integers representing the beginning and end of a range of integers.
parseSequence(StreamTokenizer) - Method in class com.affymetrix.genoviz.tutorial.SequenceMap0
 
parseString(StreamTokenizer) - Method in class com.affymetrix.genoviz.tutorial.NarcissusParser
 
parseString(StreamTokenizer) - Method in class com.affymetrix.genoviz.tutorial.SimpleMap0
 
positions - Variable in class com.affymetrix.genoviz.tutorial.NarcissusParser
 
printSelectionOverlappers() - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 
processingInstruction(String, String) - Method in class com.affymetrix.genoviz.tutorial.MapHandler
Handle a processing instruction.

R

rangeChanged(NeoRangeEvent) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
RangeListener implelementation
rangeChanged(NeoRangeEvent) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo2
RangeListener implelementation
rangeChanged(NeoRangeEvent) - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo
 
rangeChanged(NeoRangeEvent) - Method in class com.affymetrix.genoviz.demo.NeoQuallerDemo2
 
rangeChanged(NeoRangeEvent) - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
 
rangeChanged(NeoRangeEvent) - Method in class com.affymetrix.genoviz.demo.ShadowDemo
RangeListener Implementation
rangeChanged(NeoRangeEvent) - Method in class com.affymetrix.genoviz.tutorial.SequenceMap1
 
redMenuItem - Variable in class com.affymetrix.genoviz.tutorial.NeoDraw
 
removeAnnotB - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
 
removeSeq() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
renderGeneModels(String, String) - Method in class com.affymetrix.genoviz.tutorial.BedSequenceDemo
 
repackMenuItem - Variable in class com.affymetrix.genoviz.tutorial.NeoDraw
 
report(String) - Method in class com.affymetrix.genoviz.tutorial.SimpleSelectableMap
 
reportSelectedResidues() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
reportSelectedResidues() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo2
 
ResiduePainterExample - Class in com.affymetrix.genoviz.demo
a simple ResiduePainter just ignores consensus, and colors all the residues white except that it colors AG and GT blue/green (potential splice sites?) (not that I'm recommending this as a good way of displaying splice sites -- I just needed an example that didn't require a more sophisticated datamodel external to the widgets)
ResiduePainterExample() - Constructor for class com.affymetrix.genoviz.demo.ResiduePainterExample
 
RoundedRect - Class in com.affymetrix.genoviz.tutorial
 
RoundedRect() - Constructor for class com.affymetrix.genoviz.tutorial.RoundedRect
 
rubberBandChanged(NeoRubberBandEvent) - Method in class com.affymetrix.genoviz.demo.NeoMapDemo
NeoRubberBandListener interface implementation
rubberBandChanged(NeoRubberBandEvent) - Method in class com.affymetrix.genoviz.tutorial.NeoDraw
 
rubberBandChanged(NeoRubberBandEvent) - Method in class com.affymetrix.genoviz.tutorial.SimpleSelectableMap
 

S

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
 

T

testMap(int) - Method in class com.affymetrix.genoviz.demo.VerticalMapDemo
 
testSelectedVisibility() - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 
text - Variable in class com.affymetrix.genoviz.tutorial.ScaleText
 
text_annot_color - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
 
TieredMapDemo - Class in com.affymetrix.genoviz.demo
This applet, as its name implies, demonstrates some of the capabilities of the TieredNeoMap widget.
TieredMapDemo() - Constructor for class com.affymetrix.genoviz.demo.TieredMapDemo
 
toFrontSelectionOverlappers() - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 
toggleExternalFontColoring() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
toggleExternalRectColoring() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
toString() - Method in class com.affymetrix.genoviz.demo.datamodel.Annotation
 
toString() - Method in class com.affymetrix.genoviz.demo.datamodel.ScoredAnnotation
 
triangleMenuItem - Variable in class com.affymetrix.genoviz.tutorial.NeoDraw
 
triBarGlyphMenuItem - Variable in class com.affymetrix.genoviz.tutorial.NeoDraw
 
tryUniString - Variable in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
turnOffAddAlignMenus() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
TutorialAssmblr - Class in com.affymetrix.genoviz.tutorial
 
TutorialAssmblr() - Constructor for class com.affymetrix.genoviz.tutorial.TutorialAssmblr
 
TutorialGlyphDemo - Class in com.affymetrix.genoviz.tutorial
 
TutorialGlyphDemo() - Constructor for class com.affymetrix.genoviz.tutorial.TutorialGlyphDemo
 
TutorialGlyphDemo2 - Class in com.affymetrix.genoviz.tutorial
 
TutorialGlyphDemo2() - Constructor for class com.affymetrix.genoviz.tutorial.TutorialGlyphDemo2
 
TutorialQualler - Class in com.affymetrix.genoviz.tutorial
 
TutorialQualler() - Constructor for class com.affymetrix.genoviz.tutorial.TutorialQualler
 
TutorialTracer - Class in com.affymetrix.genoviz.tutorial
 
TutorialTracer() - Constructor for class com.affymetrix.genoviz.tutorial.TutorialTracer
 
type - Variable in class com.affymetrix.genoviz.demo.datamodel.Annotation
 

U

updateProgress(long, int, int) - Method in class com.affymetrix.genoviz.tutorial.BedSequenceDemo
 

V

VerticalMapDemo - Class in com.affymetrix.genoviz.demo
Demonstrates using the vertical map option WARNING: currently many glyphs do not display correctly on vertical maps!
VerticalMapDemo() - Constructor for class com.affymetrix.genoviz.demo.VerticalMapDemo
 
visibleB - Variable in class com.affymetrix.genoviz.demo.ShadowDemo
 

W

widget - Variable in class com.affymetrix.genoviz.demo.NeoTracerDemo
 
widget - Variable in class com.affymetrix.genoviz.tutorial.ParseOne
 
windowActivated(WindowEvent) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
WindowListener Implementation
windowActivated(WindowEvent) - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
WindowListener Implementation
windowClosed(WindowEvent) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
windowClosed(WindowEvent) - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 
windowClosing(WindowEvent) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
windowClosing(WindowEvent) - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 
windowDeactivated(WindowEvent) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
windowDeactivated(WindowEvent) - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 
windowDeiconified(WindowEvent) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
windowDeiconified(WindowEvent) - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 
windowIconified(WindowEvent) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
windowIconified(WindowEvent) - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 
windowOpened(WindowEvent) - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
windowOpened(WindowEvent) - Method in class com.affymetrix.genoviz.demo.NeoSeqDemo
 

X

xmlParser - Variable in class com.affymetrix.genoviz.tutorial.MapHandler
 

Z

zoomer - Variable in class com.affymetrix.genoviz.tutorial.NarcissusParser
 
zoomFrameSetup() - Method in class com.affymetrix.genoviz.demo.NeoAssemblerDemo
 
zoomFrameSetup() - Method in class com.affymetrix.genoviz.demo.NeoTracerDemo
Testing external zoom controls
A B C D E F G H I L M N O P R S T U V W X Z 
Skip navigation links

Copyright © 2021. All rights reserved.