Tutorials peakml.jar

The peakml Java library defines the common application programming interface for writing tools in the mzmatch framework and consists of many elements that ease development. In this tutorial an overview of the most important elements is given. For more information see the javadoc documentation.

This tutorial contains:

• Prerequisites
• I/O classes
• PeakML files
• Thermo RAW files
• Waters RAW files
• MassChromatogram

Prerequisites

The peakml library can be downloaded from the files menu. The peakml.jar then needs to be linked to your project and it is ready for use (i.e. there exist no external dependencies).

I/O classes

In order to use the library, the most used classes need to be imported.

import peakml.*;
import peakml.io.*;
			

The Header class contains the following elements:

• ApplicationInfo
• FileInfo
• MeasurementInfo
• ParseResult
• SampleInfo
• ScanInfo
• SetInfo

PeakML files

Access to PeakML files is provided by the class PeakMLParser, which provides parse functions, and the class PeakMLWriter, which provides write functions. Both classes provide static functions to do the operations and do not need to be initialized. The example below loads a file, of which the contents is unknown. The second parameter indicates that the complete contents of the file needs to be loaded into memory. The class ParseResult will contain the two elements Header and Measurement. The measurement instance in the case of the PeakML files will always be an instance of IPeakSet.

ParseResult result = PeakMLParser.parse(new FileInputStream("[FILENAME].peakml"), true);
Header header = result.header;
IPeakSet<? extends IPeak> peakset = (IPeakSet<? extends IPeak>) result.measurement;
			

if (peakset.getContainerClass().equals(IPeakSet.class))
	System.out.println("IPeakSet");
else if (peakset.getContainerClass().equals(BackgroundIon.class))
	System.out.println("BackgroundIon");
else if (peakset.getContainerClass().equals(MassChromatogram.class))
	System.out.println("MassChromatogram");
			

java.util.Vector<? extends IPeak> unpacked = IPeak.unpack(peakset);
			

public static void recursive(IPeak peak)
{
  Class<? extends IPeak> cls = peak.getClass();
  if (cls.equals(IPeakSet.class))
  {
    for (IPeak p : (IPeakSet) peak)
      recursive(p);
  }
  else if (cls.equals(MassChromatogram.class))
    ;
  else if (cls.equals(BackgroundIon.class))
    ;
}
			

For a complete overview of all the functions see the OpenPeakML snippet.

Thermo RAW files

Java programmatic access to Thermo RAW files is provided by the class IXRawfile, which uses the Microsoft Windows OLE specific mechanism for providing a 1-to-1 mapping to Thermo's IXRawfile.DLL. This means this class will only work on the windows platform with a valid installation of Xcalibur or the Thermo MSFileReader. Please note! this is truly a 1-to-1 mapping and the DLL does not implement a standardized scheme with regards to the indices. Read the documentation of the methods.

Before access to the raw files can be obtained, the instance needs to be initialized and the file opened. Do not forget to close and dispose the connection when you are done. Especially in cases where multiple files need to be opened, it's important to dispose every time because of a bug in the Thermo library, which will result in an error-message when opening over 9 files. This means it's a good idea to keep the needed data in memory.

IXRawfile raw = new IXRawfile();
raw.init();
raw.open("[FILENAME].raw");
  // do your operations
raw.close();
raw.dispose();
			

int nrcontrollers = raw.getNumberOfControllersOfType(IXRawfile.CONTROLLER_MS);
for (int i=1; i<=raw.getNumberOfControllers(); ++i)
{
  raw.setCurrentController(IXRawfile.CONTROLLER_MS, i);
  // do your operations
}
			

System.out.println("Filename: " + raw.getFileName());
System.out.println("Created by: " + raw.getCreatorID());
System.out.println("File version: " + raw.getVersionNumber());
System.out.println("Created: " + raw.getCreationDate());
			

Waters RAW files

Java programmatic access to Waters RAW files is provided by the classes in the package peakml.io.dac, which uses the Microsoft Windows OLE specific mechanism for providing a 1-to-1 mapping to Waters' Data Access Component. This means this class will only work on the windows platform with a valid installation of MassLynx.

The required library for setting up the link between the Waters DLL and peakml is automatically ejected from the peakml.jar upon first use. There is no need to take care of anything with this regard.

This package consists of the classes DACHeader, DACSpectrum, DACCalibrationInfo, DACScanStats, DACExScanStats, DACFunctionInfo, DACExperimentInfo, and DACProcessInfo which are direct mappings to the classes defined in the DAC DLL of Waters. The data is gathered by the 'dac.dll', which is integrated into the library and automatically exported outside the jar when needed. For each of the classes an instance needs to be created and then the method open(java.lang.String) called to fill the instance (analogous to the setup of Waters).

In the example below some header information is printed.

DACHeader hdr = new DACHeader();
hdr.open(filename);
System.out.println(hdr);
			

DACSpectrum spectrum = new DACSpectrum();
spectrum.open(filename, 1, 0, 120);
System.out.println(spectrum);
			

MassChromatogram

The class MassChromatogram contains the data points collected in a 2D setup (LC or GC), making up the chromatographic feature. In order to specify whether the chromatographic feature is built up out off profile or centroid data generics are used.

MassChromatogram mc;