com.affymetrix.genoviz.tutorial

Class MapHandler

java.lang.Object

org.xml.sax.helpers.DefaultHandler

com.affymetrix.genoviz.tutorial.MapHandler

All Implemented Interfaces:

com.affymetrix.genoviz.parser.ContentParser, ContentHandler, DTDHandler, EntityResolver, ErrorHandler

public class MapHandler
extends DefaultHandler
implements com.affymetrix.genoviz.parser.ContentParser

Version:

$Id: MapHandler.java 5443 2010-03-05 19:58:52Z sgblanch $

Field Summary

Fields

Modifier and Type	Field and Description
protected com.affymetrix.genoviz.widget.NeoMap	map
protected XMLReader	xmlParser

Constructor Summary

Constructors

Constructor and Description
MapHandler()

Method Summary

Modifier and Type	Method and Description
void	addMap(String theName, com.affymetrix.genoviz.widget.NeoMap theMap) Adds an alias for the "map" tag.
void	characters(char[] ch, int start, int length)
void	defineGlyphStyle(com.affymetrix.genoviz.widget.NeoMap theMap, String name, String config, Integer labelPlacement) defines a glyph style.
void	endDocument() Handle the end of the document.
void	endElement(String uri, String localName, String name) Handle the end of an element.
void	exportContent(OutputStream theOutput, Object o) exportContent needed to implement ContentParser Here the signature is empty because we are only interested in providing the importContent functionality associated with ContentParser.
String	getHRef(com.affymetrix.genoviz.bioviews.GlyphI theGlyph)
String	getTarget(com.affymetrix.genoviz.bioviews.GlyphI theGlyph)
void	ignorableWhitespace(char[] ch, int start, int length) Handle ignorable whitespace.
Object	importContent(InputStream theInput) converts an InputStream to a Reader and then parses.
Object	importContent(Reader theInput) importContent parses an xml formated stream and creates and returns a NeoMap object that contains the objects specified by the stream.
void	processingInstruction(String target, String data) Handle a processing instruction.
void	setWidget(com.affymetrix.genoviz.widget.NeoAbstractWidget theWidget) sets the widget (in our case a NeoMap).
void	startDocument() Handle the start of the document.
void	startElement(String uri, String localName, String name, Attributes attributes) Handle the start of an element.

Methods inherited from class org.xml.sax.helpers.DefaultHandler

endPrefixMapping, error, fatalError, notationDecl, resolveEntity, setDocumentLocator, skippedEntity, startPrefixMapping, unparsedEntityDecl, warning

Methods inherited from class java.lang.Object

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

Field Detail

map

protected com.affymetrix.genoviz.widget.NeoMap map

xmlParser

protected XMLReader xmlParser

Constructor Detail

MapHandler

public MapHandler()

Method Detail

importContent

public Object importContent(Reader theInput)
                     throws IOException

importContent parses an xml formated stream and creates and returns a NeoMap object that contains the objects specified by the stream.

Throws:

IOException

importContent

public Object importContent(InputStream theInput)
                     throws IOException

converts an InputStream to a Reader and then parses.

Specified by:

importContent in interface com.affymetrix.genoviz.parser.ContentParser

Throws:

IOException

exportContent

public void exportContent(OutputStream theOutput,
                          Object o)
                   throws IOException

exportContent needed to implement ContentParser Here the signature is empty because we are only interested in providing the importContent functionality associated with ContentParser.

Specified by:

exportContent in interface com.affymetrix.genoviz.parser.ContentParser

Throws:

IOException

setWidget

public void setWidget(com.affymetrix.genoviz.widget.NeoAbstractWidget theWidget)

sets the widget (in our case a NeoMap).

Parameters:

theWidget -

addMap

public void addMap(String theName,
                   com.affymetrix.genoviz.widget.NeoMap theMap)

Adds an alias for the "map" tag. You can call this multiple times thereby directing glyphs to multiple maps.

Parameters:

theName - a unique name.

theMap - on which glyphs are to be placed.

startDocument

public void startDocument()

Handle the start of the document.

Specified by:

startDocument in interface ContentHandler

Overrides:

startDocument in class DefaultHandler

See Also:

DocumentHandler.startDocument()

endDocument

public void endDocument()

Handle the end of the document.

Specified by:

endDocument in interface ContentHandler

Overrides:

endDocument in class DefaultHandler

See Also:

DocumentHandler.endDocument()

startElement

public void startElement(String uri,
                         String localName,
                         String name,
                         Attributes attributes)

Handle the start of an element.

Specified by:

startElement in interface ContentHandler

Overrides:

startElement in class DefaultHandler

Parameters:

uri -

localName -

name -

attributes -

See Also:

DocumentHandler.startElement(java.lang.String, org.xml.sax.AttributeList)

getHRef

public String getHRef(com.affymetrix.genoviz.bioviews.GlyphI theGlyph)

Parameters:

theGlyph -

Returns:

a URL if an href attribute was specified for this glyph. null otherwise.

getTarget

public String getTarget(com.affymetrix.genoviz.bioviews.GlyphI theGlyph)

Parameters:

theGlyph -

Returns:

a target if one was specified for this glyph. null otherwise.

defineGlyphStyle

public void defineGlyphStyle(com.affymetrix.genoviz.widget.NeoMap theMap,
                             String name,
                             String config,
                             Integer labelPlacement)

defines a glyph style.

Parameters:

theMap -

name - of the style

config - string to pass to the glyph factory

labelPlacement - LEFT, RIGHT, ABOVE, BELOW, or CENTER

endElement

public void endElement(String uri,
                       String localName,
                       String name)

Handle the end of an element.

Specified by:

endElement in interface ContentHandler

Overrides:

endElement in class DefaultHandler

Parameters:

uri -

localName -

name -

See Also:

DocumentHandler.endElement(java.lang.String)

characters

public void characters(char[] ch,
                       int start,
                       int length)

Specified by:

characters in interface ContentHandler

Overrides:

characters in class DefaultHandler

Parameters:

ch -

start -

length -

ignorableWhitespace

public void ignorableWhitespace(char[] ch,
                                int start,
                                int length)

Handle ignorable whitespace.

Specified by:

ignorableWhitespace in interface ContentHandler

Overrides:

ignorableWhitespace in class DefaultHandler

Parameters:

ch -

start -

length -

See Also:

DocumentHandler.ignorableWhitespace(char[], int, int)

processingInstruction

public void processingInstruction(String target,
                                  String data)

Handle a processing instruction.

Specified by:

processingInstruction in interface ContentHandler

Overrides:

processingInstruction in class DefaultHandler

Parameters:

target -

data -

See Also:

DocumentHandler.processingInstruction(java.lang.String, java.lang.String)