taskspaces.rna
Class MotifsParser

taskspaces.rna.MotifsParser

public class MotifsParser

Parses XML (using Apache Xerces SAX parser) documents conforming to Motifs.dtd definition and creates java.util.ArrayList of DatabaseEntry objects.

Version:

1.0

Author:

Rob Markel

Field Summary

private int[]	constraint Holds entry constraint values.
private java.util.ArrayList	constraints Holds entry constraint arrays.
private java.lang.String	elementName Holds name of the current element.
private static java.util.ArrayList	entries Holds the parsed entries.
private java.util.ArrayList	modules Holds entry sequence modules.
private java.lang.String	motifName Holds name of the motif.
private java.util.ArrayList	structures Holds entry structures.

Constructor Summary

MotifsParser(java.lang.String xmlFile)
Parses Entry XML file.

Method Summary

void	characters(char[] text, int start, int length) Catches data from element.
void	endElement(java.lang.String uri, java.lang.String local, java.lang.String qName) Catches end element event.
static java.util.ArrayList	getEntries() Returns the parsed entries.
static void	reset() Resets the entries ArrayList.
void	startElement(java.lang.String uri, java.lang.String local, java.lang.String qName, taskspaces.rna.Attributes atts) Catches a start element event.

Field Detail

motifName

private java.lang.String motifName

Holds name of the motif.

elementName

private java.lang.String elementName

Holds name of the current element.

entries

private static java.util.ArrayList entries

Holds the parsed entries.

modules

private java.util.ArrayList modules

Holds entry sequence modules.

structures

private java.util.ArrayList structures

Holds entry structures.

constraints

private java.util.ArrayList constraints

Holds entry constraint arrays.

constraint

private int[] constraint

Holds entry constraint values.

Constructor Detail

MotifsParser

public MotifsParser(java.lang.String xmlFile)

Parses Entry XML file.

Parameters:

xmlFile - path or URL of the XML file.

Method Detail

startElement

public void startElement(java.lang.String uri,
                         java.lang.String local,
                         java.lang.String qName,
                         taskspaces.rna.Attributes atts)

Catches a start element event.

Returns:

void

characters

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

Catches data from element.

Returns:

void

endElement

public void endElement(java.lang.String uri,
                       java.lang.String local,
                       java.lang.String qName)

Catches end element event.

Returns:

void

getEntries

public static java.util.ArrayList getEntries()

Returns the parsed entries.

Returns:

the DatabaseEntry objects.

reset

public static void reset()

Resets the entries ArrayList.

Returns:

void