com.affymetrix.genoviz.tutorial

Class NarcissusParser

java.lang.Object

com.affymetrix.genoviz.tutorial.NarcissusParser

All Implemented Interfaces:

com.affymetrix.genoviz.parser.ContentParser

public class NarcissusParser
extends Object
implements com.affymetrix.genoviz.parser.ContentParser

parses Narcissus format data for a NeoMap.

Field Summary

Fields

Modifier and Type	Field and Description
protected Hashtable	featureTypes
protected com.affymetrix.genoviz.bioviews.MapGlyphFactory	labelFactory
protected Hashtable	positions
protected Adjustable	zoomer

Constructor Summary

Constructors

Constructor and Description
NarcissusParser() constructs a parser

Method Summary

Modifier and Type	Method and Description
void	exportContent(OutputStream s, Object o)
Object	importContent(InputStream theInput) converts an InputStream to a Reader and then parses.
Object	importContent(Reader theInput)
Object	importContent(URL url) imports Narcissus format data from an internet.
static void	main(String[] argv) for testing.
protected int[]	parseDirectedRange(StreamTokenizer theTokens) parses a pair if integers representing the beginning and end of a directed range of integers.
protected void	parseFeatureType(StreamTokenizer theTokens) parses a feature type and adds it to a list of such types.
protected boolean	parseLabel(StreamTokenizer theTokens, Object theLabeledGlyph) parses a label.
protected void	parseLine(int theLineNumber, StreamTokenizer theTokens)
protected com.affymetrix.genoviz.datamodel.Range	parseRange(StreamTokenizer theTokens) parses a pair if integers representing the beginning and end of a range of integers.
protected String	parseString(StreamTokenizer theTokens)

Methods inherited from class java.lang.Object

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

Field Detail

positions

protected Hashtable positions

labelFactory

protected com.affymetrix.genoviz.bioviews.MapGlyphFactory labelFactory

featureTypes

protected Hashtable featureTypes

zoomer

protected Adjustable zoomer

Constructor Detail

NarcissusParser

public NarcissusParser()

constructs a parser

Method Detail

importContent

public Object importContent(URL url)

imports Narcissus format data from an internet.

Parameters:

url - the Uniform Resourse Locator pointing to the data.

Returns:

a map.

importContent

public Object importContent(Reader theInput)
                     throws IOException

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

parseLabel

protected boolean parseLabel(StreamTokenizer theTokens,
                             Object theLabeledGlyph)
                      throws IOException

parses a label.

Throws:

IOException

parseRange

protected com.affymetrix.genoviz.datamodel.Range parseRange(StreamTokenizer theTokens)
                                                     throws IOException

parses a pair if integers representing the beginning and end of a range of integers.

Returns:

a Range

Throws:

IOException

See Also:

Range

parseDirectedRange

protected int[] parseDirectedRange(StreamTokenizer theTokens)
                            throws IOException

parses a pair if integers representing the beginning and end of a directed range of integers. The range is "directed" in that the beginning may be greater than the end. This is useful for cofiguring directed glyphs like the ArrowGlyph.

Returns:

an array of two integers

Throws:

IOException

parseString

protected String parseString(StreamTokenizer theTokens)
                      throws IOException

Throws:

IOException

parseLine

protected void parseLine(int theLineNumber,
                         StreamTokenizer theTokens)
                  throws IOException

Throws:

IOException

parseFeatureType

protected void parseFeatureType(StreamTokenizer theTokens)
                         throws IOException

parses a feature type and adds it to a list of such types. Once added, the feature type becomes a keyword.

Throws:

IOException

exportContent

public void exportContent(OutputStream s,
                          Object o)

Specified by:

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

main

public static void main(String[] argv)

for testing.