peakml.io.mzxml
Class MzXmlParser

java.lang.Object
  peakml.io.mzxml.MzXmlParser

public abstract class MzXmlParser
extends java.lang.Object

Implementation of a parser for the mzXML file format, with additional, hidden support for the mzData file format. As both formats are very comparable a single parse function is provided, which results in an instance of type ChromatographyMS in the ParseResult

Constructor Summary

MzXmlParser()

Method Summary

static ParseResult

parseCMS(java.io.InputStream input) Parse function for loading the data stored in a mzXML or mzData file.

Methods inherited from class java.lang.Object

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

Constructor Detail

MzXmlParser

public MzXmlParser()

Method Detail

parseCMS

public static ParseResult parseCMS(java.io.InputStream input)
                            throws java.io.IOException,
                                   domsax.XmlParserException

Parse function for loading the data stored in a mzXML or mzData file. Only 2-dimensional data is supported and the resulting Measurement is of type ChromatographyMS.

Parameters:

input - The input stream to read from.

minintensity - Minimal intensity for a data-point to be taken into account (when set to 0 all are parsed).

Returns:

The resulting data (ChromatographyMS) and header.

Throws:

java.io.IOException - Thrown when I/O related problems occur

domsax.XmlParserException - Thrown when an interpretation error of the data occurs.