org.systemsbiology.jrap.stax
Class MSXMLParser

java.lang.Object
  org.systemsbiology.jrap.stax.MSXMLParser

public final class MSXMLParser
extends java.lang.Object

A generic utility class for reading an MSXML file in a random access fashion and utilizing a stored scan index for fast reads.

Field Summary

protected long	chrogramIndex
protected java.lang.String	fileName The file we are in charge of reading
protected boolean	isML
protected boolean	isXML
protected int	maxScan
protected java.util.Map<java.lang.Integer,java.lang.Long>	offsets The indexes

Constructor Summary

MSXMLParser(java.lang.String fileName)

Method Summary

int	getMaxScanNumber()
int	getScanCount() Get the total number of scans in the mzXMLfile handled by this parser.
long	getScanOffset(int scanNumber) get scan offset, scan number is 1 based.
Scan	rap(int scanNumber) Read a particular scan from a MSXML file and return a generic Scan object with it's data.
MZXMLFileInfo	rapFileHeader() this gives back the file header (info before scan)
ScanHeader	rapHeader(int scanNumber)

Methods inherited from class java.lang.Object

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

Field Detail

fileName

protected java.lang.String fileName

The file we are in charge of reading

offsets

protected java.util.Map<java.lang.Integer,java.lang.Long> offsets

The indexes

maxScan

protected int maxScan

chrogramIndex

protected long chrogramIndex

isXML

protected boolean isXML

isML

protected boolean isML

Constructor Detail

MSXMLParser

public MSXMLParser(java.lang.String fileName)

Method Detail

rapFileHeader

public MZXMLFileInfo rapFileHeader()

this gives back the file header (info before scan)

Returns:

the file header info (MZXMLFileInfo)

rapHeader

public ScanHeader rapHeader(int scanNumber)

Returns:

a scan header object without peaks information.

rap

public Scan rap(int scanNumber)

Read a particular scan from a MSXML file and return a generic Scan object with it's data. Note: scanNumbers are 1-based, so scanNumber must be at least 1 and be not greater than getScanCount() + 1

Returns:

a scan object. It has all the infomation in a scanheader object and also peaks information that doesn't included in scanHeader object.

getScanCount

public int getScanCount()

Get the total number of scans in the mzXMLfile handled by this parser.

Returns:

The number of scans.

getMaxScanNumber

public int getMaxScanNumber()

getScanOffset

public long getScanOffset(int scanNumber)

get scan offset, scan number is 1 based.