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<!DOCTYPE html>
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<title>MZmine 3 - Module Development Tutorial</title>
<meta name="description" content="MZmine 3 is an open-source software for mass spectrometry data processing.">
<meta name="author" content="Thomas F. Dyrlund">
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<h2>Module <strong>Development Tutorial</strong></h2>
Let's demonstrate MZmine 2 module development by making a simple centroiding module. This module will take a continuous mode spectra represented by a continuous stream of data points which form m/z peaks, and convert it to centroided spectra, where each m/z peak is represened by a single data point (m/z and intensity pair). The algorithm used for centroiding is very simple: the intensity of all data points is summed over certain m/z interval and replaced with a single (centroid) data point. The width of this m/z interval will be the only parameter of our method.
<br/><br/>
We need to create 3 Java classes:<br/>
<ul>
<li><a href="#Centroider"><strong>Centroider.java</strong></a> - this class is the core of the module and implements the MZmineModule interface</li>
<li><a href="#CentroiderParameters"><strong>CentroiderParameters.java</strong></a> - this class contains the parameters of our method and implements the StorableParameterSet interface</li>
<li><a href="#CentroiderTask"><strong>CentroiderTask.java</strong></a> - this class contains the actual data processing logic (executed by the task controller) and implements the Task interface</li>
</ul>
Once compiled, the module has to be installed into the conf/config.xml file, for example by adding the following line in the <modules> section:
<br/>
<script type="syntaxhighlighter" class="brush: java">
<![CDATA[
<modules>
<module class="net.sf.mzmine.modules.centroider.Centroider" />
...
</modules>
]]>
</script>
The commented source codes of these three classes follow:
<br/><br/>
<span class="anchor" id="Centroider"></span>
<h2>Centroider.java source</h2>
<script type="syntaxhighlighter" class="brush: java">
<![CDATA[
package net.sf.mzmine.modules.centroider;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.KeyEvent;
import net.sf.mzmine.data.ParameterSet;
import net.sf.mzmine.data.RawDataFile;
import net.sf.mzmine.desktop.Desktop;
import net.sf.mzmine.desktop.MZmineMenu;
import net.sf.mzmine.main.MZmineCore;
import net.sf.mzmine.main.MZmineModule;
import net.sf.mzmine.taskcontrol.Task;
import net.sf.mzmine.util.dialogs.ExitCode;
import net.sf.mzmine.util.dialogs.ParameterSetupDialog;
/**
* This code is a demonstration of MZmine 2 module development.
* It represents a simple module for converting continuous
* (profile) mode data into centroided data. This class is the
* main class of the module, which implements MZmineModule
* interface.
*/
public class Centroider implements ActionListener, MZmineModule {
private CentroiderParameters parameters;
/**
* Module initialization. This method is called only once,
* during MZmine 2 startup sequence.
*/
public void initModule() {
// Create a new instance of our parameters class
parameters = new CentroiderParameters();
// Obtain a reference to MZmine 2 Desktop
Desktop desktop = MZmineCore.getDesktop();
// Create a menu item for our module
desktop.addMenuItem(MZmineMenu.RAWDATAFILTERING,
"Centroider", "Module to transform continuous "
+ "data into centroid mode",
KeyEvent.VK_C, false, this, null);
}
/**
* Method defined by the ActionListener interface. This
* method is called when user activates our menu item.
*/
public void actionPerformed(ActionEvent e) {
// Obtain a reference to MZmine 2 Desktop
Desktop desktop = MZmineCore.getDesktop();
// Obtain selected data files
RawDataFile[] dataFiles = desktop.getSelectedDataFiles();
// If no data file is selected, exit
if (dataFiles.length == 0) {
MZmineCore.getDesktop().displayErrorMessage(
"Please select a data file");
return;
}
// Show the parameter setup dialog with our parameter
// class
ParameterSetupDialog dialog = new ParameterSetupDialog(
"Please set parameter values for Centroider",
parameters);
dialog.setVisible(true);
// If user clicked cancel, just exit
if (dialog.getExitCode() != ExitCode.OK)
return;
// Create a copy of our parameters. The copy will be used
// for one processing session. This way we avoid sharing
// the same instance of the parameters by many threads -
// that would cause trouble because user may run the same
// method with different parameters later.
CentroiderParameters pCopy = (CentroiderParameters) parameters
.clone();
// Process each data file in a separate task
for (int i = 0; i < dataFiles.length; i++) {
// Create a new task
Task task = new CentroiderTask(dataFiles[i], pCopy);
// Submit the task to the task controller
MZmineCore.getTaskController().addTask(task);
}
}
/**
* This method returns our parameter set, for example when
* parameters are being saved to a configuration file.
*
*/
public ParameterSet getParameterSet() {
return parameters;
}
/**
* This method sets new parameters, for example when these
* are loaded from a configuration file.
*/
public void setParameters(ParameterSet parameters) {
this.parameters = (CentroiderParameters) parameters;
}
}
]]>
</script>
<hr>
<span class="anchor" id="CentroiderParameters"></span>
<h2>CentroiderParameters.java source</h2>
<script type="syntaxhighlighter" class="brush: java">
<![CDATA[
package net.sf.mzmine.modules.centroider;
import net.sf.mzmine.data.Parameter;
import net.sf.mzmine.data.ParameterType;
import net.sf.mzmine.data.impl.SimpleParameter;
import net.sf.mzmine.data.impl.SimpleParameterSet;
import net.sf.mzmine.main.MZmineCore;
/**
* This class defines the parameters of our module. We have only
* one parameter (mzStepWidth). This class must implement the
* StorableParameterSet interface, so MZmine 2 can save our
* parameter values on exit and reload them when restarted. The
* easiest way to implement the StorableParameterSet interface is
* to extend the SimpleParameterSet class.
*
*/
public class CentroiderParameters extends SimpleParameterSet {
/**
* Here we define our only parameter, the width of the m/z
* interval which will be centroided into single peak. We
* must set the type of the parameter (DOUBLE), name,
* description, units, default value, minimum value, maximum
* value (set to null), and formatting of the values (we use
* default format for m/z values).
*/
public static final Parameter mzStepWidth = new SimpleParameter(
ParameterType.DOUBLE, "m/z step width",
"width of the m/z interval that will "
+ " be replaced by a single peak", "m/z",
new Double(1.0), new Double(0.0), null, MZmineCore
.getMZFormat());
/**
* Constructor which provides our parameter (only one) to the
* SimpleParameterSet constructor.
*/
public CentroiderParameters() {
super(new Parameter[] { mzStepWidth });
}
}
]]>
</script>
<hr>
<span class="anchor" id="CentroiderTask"></span>
<h2>CentroiderTask.java source</h2>
<script type="syntaxhighlighter" class="brush: java">
<![CDATA[
package net.sf.mzmine.modules.centroider;
import java.util.ArrayList;
import net.sf.mzmine.data.DataPoint;
import net.sf.mzmine.data.RawDataFile;
import net.sf.mzmine.data.RawDataFileWriter;
import net.sf.mzmine.data.Scan;
import net.sf.mzmine.data.impl.SimpleDataPoint;
import net.sf.mzmine.data.impl.SimpleScan;
import net.sf.mzmine.main.MZmineCore;
import net.sf.mzmine.taskcontrol.Task;
import net.sf.mzmine.taskcontrol.TaskStatus;
/**
* This class implements the Task interface. It represents the
* main logic of the data processing module, which is executed by
* passing this task to the TaskController.
*/
class CentroiderTask implements Task {
// Original data file and newly created centroided file
private RawDataFile origDataFile, centroidedDataFile;
// Task status, initially set to WAITING
private TaskStatus status = TaskStatus.WAITING;
// Error message, in case error happens
private String errorMessage;
// Counters of scans
private int centroidedScans, totalScans;
// Our only parameter - m/z window width
private double mzStepWidth;
/**
* Constructor
*/
CentroiderTask(RawDataFile origDataFile,
CentroiderParameters parameters) {
this.origDataFile = origDataFile;
mzStepWidth = (Double) parameters
.getParameterValue(CentroiderParameters.mzStepWidth);
}
/**
* Returns task description. This is shown in the task list
* in the GUI.
*/
public String getTaskDescription() {
return "Centroiding " + origDataFile;
}
/**
* Returns a double value in the range 0.0-1.0, representing
* how much of the task has been completed. This is shown in
* the task list in the GUI.
*/
public double getFinishedPercentage() {
if (totalScans == 0)
return 0;
return (double) centroidedScans / totalScans;
}
/**
* Returns the task status. This is shown in the task list in
* the GUI.
*/
public TaskStatus getStatus() {
return status;
}
/**
* Returns the error message, if the task status has been set
* to ERROR
*/
public String getErrorMessage() {
return errorMessage;
}
/**
* This method is called by the GUI when the user cancels the
* task. We only set the task status to CANCELED. The task
* status is periodically checked during processing in the
* run() method.
*/
public void cancel() {
status = TaskStatus.CANCELED;
}
/**
* This method contains the actual data processing. It is
* called by the TaskController when a new thread is
* allocated for this task.
*/
public void run() {
// Update the status of this task
status = TaskStatus.PROCESSING;
// Use the try/catch block to catch any exceptions and in
// case of an exception, set the status and errorMessage
// accordingly
try {
// Create a new file
String newName = origDataFile.getName()
+ " centroided";
RawDataFileWriter rawDataFileWriter = MZmineCore
.createNewFile(newName);
// Get scan numbers from original file
int[] scanNumbers = origDataFile.getScanNumbers();
// Set the counter of all scans
totalScans = scanNumbers.length;
// Loop through all scans
for (int scanIndex = 0; scanIndex < totalScans; scanIndex++) {
// If this task was canceled, stop processing
if (status == TaskStatus.CANCELED)
return;
// Get original continuous scan
Scan oldScan = origDataFile
.getScan(scanNumbers[scanIndex]);
// Get data points (m/z and intensity pairs) of
// the original scan
DataPoint oldDataPoints[] = oldScan
.getDataPoints();
// Convert the data points to centroid using our
// algorithm
DataPoint newDataPoints[] = doCentroid(oldDataPoints);
// Create centroided scan
SimpleScan newScan = new SimpleScan(oldScan);
newScan.setCentroided(true);
newScan.setDataPoints(newDataPoints);
// Write the centroided scan to new file
rawDataFileWriter.addScan(newScan);
// Update the counter of already centroided scans
centroidedScans++;
}
// Finalize writing
centroidedDataFile = rawDataFileWriter
.finishWriting();
// Add the newly created file to the project
MZmineCore.getCurrentProject().addFile(
centroidedDataFile);
// Set task status to FINISHED
status = TaskStatus.FINISHED;
} catch (Exception e) {
status = TaskStatus.ERROR;
errorMessage = e.toString();
return;
}
}
/**
* This method implements the actual centroiding algorithm.
* It takes the original continuous data points as argument
* and returns an array of centroided data points.
*/
private DataPoint[] doCentroid(DataPoint oldDataPoints[]) {
// If there is are no data points in the original array,
// just return original array
if (oldDataPoints.length == 0)
return oldDataPoints;
// Create an ArrayList for new, centroided data points
ArrayList<DataPoint> newDataPoints = new ArrayList<DataPoint>();
// This variable represents the m/z of each
// centroided peak
double mz = oldDataPoints[0].getMZ() + (mzStepWidth / 2);
// This variable represents the intensity of
// each centroided peak
double intensitySum = 0;
// Loop through all original data points
for (DataPoint dp : oldDataPoints) {
// If we reached the end of the interval <mz;
// mz+mzStepWidth/2> then finish this centroided peak
// and start a new interval
if (dp.getMZ() > mz + (mzStepWidth / 2)) {
if (intensitySum > 0) {
// Create a new centroided peak
DataPoint newDP = new SimpleDataPoint(mz,
intensitySum);
newDataPoints.add(newDP);
}
// Move the m/z to the start of new interval,
// which contains the current data point (dp)
while (dp.getMZ() > mz + (mzStepWidth / 2)) {
mz += mzStepWidth;
}
// Start new interval with zero intensity
intensitySum = 0;
}
// Keep summing the intensity of data points in the
// current interval
intensitySum += dp.getIntensity();
}
// Don't forget to add a peak for the last interval
if (intensitySum > 0) {
DataPoint newDP = new SimpleDataPoint(mz,
intensitySum);
newDataPoints.add(newDP);
}
return newDataPoints.toArray(new DataPoint[0]);
}
/**
* Returns the objects newly created by this task. This
* method is used during batch processing, when newly created
* objects are automatically used as input for next step of
* the batch. In case of this module, only new centroided
* data file is created.
*/
public Object[] getCreatedObjects() {
return new Object[] { centroidedDataFile };
}
}
]]>
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