Merge pull request #545 from SteffenHeu/SingleMassListProcessing

DataPoint/Spectra processing

src/main/java/net/sf/mzmine/main/MZmineModulesList.java

@@ -121,6 +121,10 @@
 import net.sf.mzmine.modules.visualization.scatterplot.ScatterPlotVisualizerModule;
 import net.sf.mzmine.modules.visualization.spectra.msms.MsMsVisualizerModule;
 import net.sf.mzmine.modules.visualization.spectra.simplespectra.SpectraVisualizerModule;
+import net.sf.mzmine.modules.visualization.spectra.simplespectra.datapointprocessing.DataPointProcessingManager;
+import net.sf.mzmine.modules.visualization.spectra.simplespectra.datapointprocessing.identification.sumformulaprediction.DPPSumFormulaPredictionModule;
+import net.sf.mzmine.modules.visualization.spectra.simplespectra.datapointprocessing.isotopes.deisotoper.DPPIsotopeGrouperModule;
+import net.sf.mzmine.modules.visualization.spectra.simplespectra.datapointprocessing.massdetection.DPPMassDetectionModule;
 import net.sf.mzmine.modules.visualization.spectra.simplespectra.spectraidentification.customdatabase.CustomDBSpectraSearchModule;
 import net.sf.mzmine.modules.visualization.spectra.simplespectra.spectraidentification.lipidsearch.LipidSpectraSearchModule;
 import net.sf.mzmine.modules.visualization.spectra.simplespectra.spectraidentification.onlinedatabase.OnlineDBSpectraSearchModule;
@@ -214,7 +218,9 @@ public class MZmineModulesList {
       // all other regular MZmineRunnableModule (not MZmineProcessingModule) NOT LISTED IN MENU
       SpectraIdentificationSpectralDatabaseModule.class, LibrarySubmitModule.class,
       CustomDBSpectraSearchModule.class, LipidSpectraSearchModule.class,
-      OnlineDBSpectraSearchModule.class, SumFormulaSpectraSearchModule.class
+      OnlineDBSpectraSearchModule.class, SumFormulaSpectraSearchModule.class,
 
+      // Data point processing
+      DataPointProcessingManager.class, DPPMassDetectionModule.class, DPPSumFormulaPredictionModule.class, DPPIsotopeGrouperModule.class
   };
 }

src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/lipididentification/LipidSearchTask.java

@@ -251,12 +251,12 @@ private void searchMsmsFragments(PeakListRow row, double lipidIonMass, LipidIden
             massDetector = new CentroidMassDetector();
             CentroidMassDetectorParameters parametersMSMS = new CentroidMassDetectorParameters();
             CentroidMassDetectorParameters.noiseLevel.setValue(noiseLevelMSMS);
-            massList = massDetector.getMassValues(msmsScan, parametersMSMS);
+            massList = massDetector.getMassValues(msmsScan.getDataPoints(), parametersMSMS);
           } else {
             massDetector = new ExactMassDetector();
             ExactMassDetectorParameters parametersMSMS = new ExactMassDetectorParameters();
             ExactMassDetectorParameters.noiseLevel.setValue(noiseLevelMSMS);
-            massList = massDetector.getMassValues(msmsScan, parametersMSMS);
+            massList = massDetector.getMassValues(msmsScan.getDataPoints(), parametersMSMS);
           }
         }
         MSMSLipidTools msmsLipidTools = new MSMSLipidTools();

src/main/java/net/sf/mzmine/modules/rawdatamethods/peakpicking/massdetection/MassDetector.java

@@ -31,6 +31,8 @@ public interface MassDetector extends MZmineModule {
   /**
    * Returns mass and intensity values detected in given scan
    */
+  public DataPoint[] getMassValues(DataPoint[] dp, ParameterSet parameters);
+
   public DataPoint[] getMassValues(Scan scan, ParameterSet parameters);
 
 }

src/main/java/net/sf/mzmine/modules/rawdatamethods/peakpicking/massdetection/centroid/CentroidMassDetector.java

@@ -34,14 +34,16 @@
 public class CentroidMassDetector implements MassDetector {
 
   public DataPoint[] getMassValues(Scan scan, ParameterSet parameters) {
+    return getMassValues(scan.getDataPoints(), parameters);
+  }
+
+  public DataPoint[] getMassValues(DataPoint dataPoints[], ParameterSet parameters) {
 
     double noiseLevel =
         parameters.getParameter(CentroidMassDetectorParameters.noiseLevel).getValue();
 
     ArrayList<DataPoint> mzPeaks = new ArrayList<DataPoint>();
 
-    DataPoint dataPoints[] = scan.getDataPoints();
-
     // Find possible mzPeaks
     for (int j = 0; j < dataPoints.length; j++) {
 

src/main/java/net/sf/mzmine/modules/rawdatamethods/peakpicking/massdetection/exactmass/ExactMassDetector.java

@@ -33,10 +33,14 @@
 
 public class ExactMassDetector implements MassDetector {
 
+  public DataPoint[] getMassValues(Scan scan, ParameterSet parameters) {
+    return getMassValues(scan.getDataPoints(), parameters);
+  }
+
   /**
    * @see net.sf.mzmine.modules.peakpicking.threestep.massdetection.MassDetector#getMassValues(net.sf.mzmine.datamodel.Scan)
    */
-  public DataPoint[] getMassValues(Scan scan, ParameterSet parameters) {
+  public DataPoint[] getMassValues(DataPoint dataPoints[], ParameterSet parameters) {
 
     double noiseLevel = parameters.getParameter(ExactMassDetectorParameters.noiseLevel).getValue();
 
@@ -50,7 +54,7 @@ public DataPoint[] getMassValues(Scan scan, ParameterSet parameters) {
         new DataPointSorter(SortingProperty.Intensity, SortingDirection.Descending));
 
     // First get all candidate peaks (local maximum)
-    getLocalMaxima(scan, candidatePeaks, noiseLevel);
+    getLocalMaxima(dataPoints, candidatePeaks, noiseLevel);
 
     // We calculate the exact mass for each peak,
     // starting with biggest intensity peak and so on
@@ -83,10 +87,9 @@ public DataPoint[] getMassValues(Scan scan, ParameterSet parameters) {
    * @param scan
    * @return
    */
-  private void getLocalMaxima(Scan scan, TreeSet<ExactMzDataPoint> candidatePeaks,
+  private void getLocalMaxima(DataPoint scanDataPoints[], TreeSet<ExactMzDataPoint> candidatePeaks,
       double noiseLevel) {
 
-    DataPoint[] scanDataPoints = scan.getDataPoints();
     if (scanDataPoints.length == 0)
       return;
     DataPoint localMaximum = scanDataPoints[0];

src/main/java/net/sf/mzmine/modules/rawdatamethods/peakpicking/massdetection/localmaxima/LocalMaxMassDetector.java

@@ -31,17 +31,19 @@
  * This class detects all local maxima in a given scan.
  */
 public class LocalMaxMassDetector implements MassDetector {
-
+  
   public DataPoint[] getMassValues(Scan scan, ParameterSet parameters) {
+    return getMassValues(scan.getDataPoints(), parameters);
+  }
+
+  public DataPoint[] getMassValues(DataPoint dataPoints[], ParameterSet parameters) {
 
     double noiseLevel =
         parameters.getParameter(LocalMaxMassDetectorParameters.noiseLevel).getValue();
 
     // List of found mz peaks
     ArrayList<DataPoint> mzPeaks = new ArrayList<DataPoint>();
 
-    DataPoint dataPoints[] = scan.getDataPoints();
-
     // All data points of current m/z peak
 
     // Top data point of current m/z peak

src/main/java/net/sf/mzmine/modules/rawdatamethods/peakpicking/massdetection/recursive/RecursiveMassDetector.java

@@ -34,6 +34,10 @@
 public class RecursiveMassDetector implements MassDetector {
 
   public DataPoint[] getMassValues(Scan scan, ParameterSet parameters) {
+    return getMassValues(scan.getDataPoints(), parameters);
+  }
+
+  public DataPoint[] getMassValues(DataPoint dataPoints[], ParameterSet parameters) {
 
     double noiseLevel =
         parameters.getParameter(RecursiveMassDetectorParameters.noiseLevel).getValue();
@@ -42,7 +46,6 @@ public DataPoint[] getMassValues(Scan scan, ParameterSet parameters) {
     double maximumMZPeakWidth =
         parameters.getParameter(RecursiveMassDetectorParameters.maximumMZPeakWidth).getValue();
 
-    DataPoint dataPoints[] = scan.getDataPoints();
     TreeSet<DataPoint> mzPeaks =
         new TreeSet<DataPoint>(new DataPointSorter(SortingProperty.MZ, SortingDirection.Ascending));
 

src/main/java/net/sf/mzmine/modules/rawdatamethods/peakpicking/massdetection/wavelet/WaveletMassDetector.java

@@ -38,6 +38,10 @@
  * to detect possible peaks in the original raw datapoints.
  */
 public class WaveletMassDetector implements MassDetector {
+
+  public DataPoint[] getMassValues(Scan scan, ParameterSet parameters) {
+    return getMassValues(scan.getDataPoints(), parameters);
+  }
 
   /**
    * Parameters of the wavelet, NPOINTS is the number of wavelet values to use The WAVELET_ESL &
@@ -47,15 +51,13 @@ public class WaveletMassDetector implements MassDetector {
   private static final int WAVELET_ESL = -5;
   private static final int WAVELET_ESR = 5;
 
-  public DataPoint[] getMassValues(Scan scan, ParameterSet parameters) {
+  public DataPoint[] getMassValues(DataPoint originalDataPoints[] , ParameterSet parameters) {
     double noiseLevel =
         parameters.getParameter(WaveletMassDetectorParameters.noiseLevel).getValue();
     int scaleLevel = parameters.getParameter(WaveletMassDetectorParameters.scaleLevel).getValue();
     double waveletWindow =
         parameters.getParameter(WaveletMassDetectorParameters.waveletWindow).getValue();
 
-    DataPoint originalDataPoints[] = scan.getDataPoints();
-
     DataPoint waveletDataPoints[] = performCWT(originalDataPoints, waveletWindow, scaleLevel);
 
     DataPoint mzPeaks[] = getMzPeaks(noiseLevel, originalDataPoints, waveletDataPoints);

src/main/java/net/sf/mzmine/modules/visualization/spectra/simplespectra/SpectraBottomPanel.java

@@ -22,20 +22,21 @@
 import java.awt.Color;
 import java.awt.Font;
 import java.util.logging.Logger;
-
 import javax.swing.Box;
 import javax.swing.BoxLayout;
 import javax.swing.JButton;
+import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JPanel;
 import javax.swing.SwingConstants;
 import javax.swing.event.TreeModelEvent;
 import javax.swing.event.TreeModelListener;
 import javax.swing.tree.DefaultMutableTreeNode;
-
 import net.sf.mzmine.datamodel.PeakList;
 import net.sf.mzmine.datamodel.RawDataFile;
 import net.sf.mzmine.main.MZmineCore;
+import net.sf.mzmine.modules.visualization.spectra.simplespectra.datapointprocessing.DataPointProcessingManager;
+import net.sf.mzmine.parameters.ParameterSet;
 import net.sf.mzmine.util.GUIUtils;
 
 /**
@@ -56,6 +57,8 @@ class SpectraBottomPanel extends JPanel implements TreeModelListener {
   private JPanel topPanel, bottomPanel;
   private JComboBox<String> msmsSelector;
   private JComboBox<PeakList> peakListSelector;
+  private JCheckBox processingCbx;
+  private JButton processingParametersBtn ;
 
   private RawDataFile dataFile;
   private SpectraVisualizerWindow masterFrame;
@@ -97,6 +100,19 @@ class SpectraBottomPanel extends JPanel implements TreeModelListener {
     peakListSelector.setActionCommand("PEAKLIST_CHANGE");
     topPanel.add(peakListSelector);
 
+
+    processingCbx = GUIUtils.addCheckbox(topPanel, "Enable Processing", masterFrame,
+        "ENABLE_PROCESSING", "Enables quick scan processing.");
+    processingCbx.setBackground(Color.white);
+    processingCbx.setFont(smallFont);
+    updateProcessingCheckbox();
+
+    processingParametersBtn = GUIUtils.addButton(topPanel, "Spectra processing", null,
+        masterFrame, "SET_PROCESSING_PARAMETERS", "Set the parameters for quick spectra processing.");
+    processingParametersBtn.setBackground(Color.white);
+    processingParametersBtn.setFont(smallFont);
+    updateProcessingButton();
+
     topPanel.add(Box.createHorizontalGlue());
 
     JButton nextScanBtn = GUIUtils.addButton(topPanel, rightArrow, null, masterFrame, "NEXT_SCAN");
@@ -214,4 +230,11 @@ public void treeStructureChanged(TreeModelEvent event) {
       rebuildPeakListSelector();
   }
 
+  public void updateProcessingCheckbox() {
+    processingCbx.setSelected(DataPointProcessingManager.getInst().isEnabled());
+  }
+
+  public void updateProcessingButton() {
+    processingParametersBtn.setEnabled(DataPointProcessingManager.getInst().isEnabled()); 
+  }
 }

src/main/java/net/sf/mzmine/modules/visualization/spectra/simplespectra/SpectraPlot.java

@@ -34,6 +34,7 @@
 import org.jfree.chart.JFreeChart;
 import org.jfree.chart.axis.NumberAxis;
 import org.jfree.chart.block.BlockBorder;
+import org.jfree.chart.labels.XYItemLabelGenerator;
 import org.jfree.chart.plot.DatasetRenderingOrder;
 import org.jfree.chart.plot.PlotOrientation;
 import org.jfree.chart.plot.XYPlot;
@@ -47,13 +48,15 @@
 import net.sf.mzmine.datamodel.MassSpectrumType;
 import net.sf.mzmine.datamodel.Scan;
 import net.sf.mzmine.main.MZmineCore;
+import net.sf.mzmine.modules.visualization.spectra.simplespectra.datapointprocessing.DataPointProcessingController;
+import net.sf.mzmine.modules.visualization.spectra.simplespectra.datapointprocessing.DataPointProcessingManager;
+import net.sf.mzmine.modules.visualization.spectra.simplespectra.datapointprocessing.datamodel.results.DPPResultsDataSet;
 import net.sf.mzmine.modules.visualization.spectra.simplespectra.datasets.IsotopesDataSet;
 import net.sf.mzmine.modules.visualization.spectra.simplespectra.datasets.PeakListDataSet;
 import net.sf.mzmine.modules.visualization.spectra.simplespectra.datasets.ScanDataSet;
 import net.sf.mzmine.modules.visualization.spectra.simplespectra.renderers.ContinuousRenderer;
 import net.sf.mzmine.modules.visualization.spectra.simplespectra.renderers.PeakRenderer;
 import net.sf.mzmine.modules.visualization.spectra.simplespectra.renderers.SpectraItemLabelGenerator;
-import net.sf.mzmine.modules.visualization.spectra.simplespectra.spectraidentification.SpectraDatabaseSearchLabelGenerator;
 import net.sf.mzmine.util.GUIUtils;
 import net.sf.mzmine.util.SaveImage;
 import net.sf.mzmine.util.SaveImage.FileType;
@@ -94,7 +97,11 @@ public class SpectraPlot extends EChartPanel {
   // increasing even when we remove old data sets
   private int numOfDataSets = 0;
 
-  public SpectraPlot(ActionListener masterPlot) {
+  // Spectra processing
+  DataPointProcessingController controller;
+  private boolean processingAllowed;
+
+  public SpectraPlot(ActionListener masterPlot, boolean processingAllowed) {
 
     super(ChartFactory.createXYLineChart("", // title
         "m/z", // x-axis label
@@ -217,6 +224,13 @@ public SpectraPlot(ActionListener masterPlot) {
     ZoomHistory history = getZoomHistory();
     if (history != null)
       history.clear();
+
+    // set processingAllowed
+    setProcessingAllowed(processingAllowed);
+  }
+
+  public SpectraPlot(ActionListener masterPlot) {
+    this(masterPlot, false);
   }
 
   @Override
@@ -376,6 +390,12 @@ public void mouseClicked(MouseEvent event) {
   }
 
   public synchronized void removeAllDataSets() {
+
+    // if the data sets are removed, we have to cancel the tasks.
+    if (controller != null)
+      controller.cancelTasks();
+    controller = null;
+
     for (int i = 0; i < plot.getDatasetCount(); i++) {
       plot.setDataset(i, null);
     }
@@ -410,11 +430,13 @@ public synchronized void addDataSet(XYDataset dataSet, Color color, boolean tran
     plot.setRenderer(numOfDataSets, newRenderer);
     numOfDataSets++;
 
+    if (dataSet instanceof ScanDataSet)
+      checkAndRunController();
   }
 
   // add Dataset with label generator
   public synchronized void addDataSet(XYDataset dataSet, Color color, boolean transparency,
-      SpectraDatabaseSearchLabelGenerator labelGenerator) {
+      XYItemLabelGenerator labelGenerator) {
 
     XYItemRenderer newRenderer;
 
@@ -445,6 +467,8 @@ public synchronized void addDataSet(XYDataset dataSet, Color color, boolean tran
     plot.setRenderer(numOfDataSets, newRenderer);
     numOfDataSets++;
 
+    if (dataSet instanceof ScanDataSet)
+      checkAndRunController();
   }
 
 
@@ -457,7 +481,7 @@ public synchronized void removePeakListDataSets() {
     }
   }
 
-  ScanDataSet getMainScanDataSet() {
+  public ScanDataSet getMainScanDataSet() {
     for (int i = 0; i < plot.getDatasetCount(); i++) {
       XYDataset dataSet = plot.getDataset(i);
       if (dataSet instanceof ScanDataSet) {
@@ -467,4 +491,50 @@ ScanDataSet getMainScanDataSet() {
     return null;
   }
 
+  /**
+   * Checks if the spectra processing is enabled & allowed and executes the controller if it is.
+   * Processing is forbidden for instances of ParameterSetupDialogWithScanPreviews
+   */
+  public void checkAndRunController() {
+
+    // if controller != null, processing on the current spectra has already been executed. When
+    // loading a new spectrum, the controller is set to null in removeAllDataSets()
+    DataPointProcessingManager inst = DataPointProcessingManager.getInst();
+
+    if (!isProcessingAllowed() || !inst.isEnabled())
+      return;
+
+    if(controller != null)
+      controller = null;
+
+    // if a controller is re-run then delete previous results
+    removeDataPointProcessingResultDataSets();
+
+    // if enabled, do the data point processing as set up by the user
+    XYDataset dataSet = getMainScanDataSet();
+    if (dataSet instanceof ScanDataSet) {
+
+      controller = new DataPointProcessingController(inst.getProcessingQueue(), this,
+          getMainScanDataSet().getDataPoints());
+      inst.addController(controller);
+    }
+  }
+
+  public boolean isProcessingAllowed() {
+    return processingAllowed;
+  }
+
+  public void setProcessingAllowed(boolean processingAllowed) {
+    this.processingAllowed = processingAllowed;
+  }
+
+  public void removeDataPointProcessingResultDataSets() {
+    for (int i = 0; i < plot.getDatasetCount(); i++) {
+      XYDataset dataSet = plot.getDataset(i);
+      if (dataSet instanceof DPPResultsDataSet) {
+         plot.setDataset(i, null);
+      }
+    }
+  }
+
 }

src/main/java/net/sf/mzmine/modules/visualization/spectra/simplespectra/SpectraVisualizerModule.java

@@ -99,7 +99,7 @@ public static SpectraVisualizerWindow showNewSpectrumWindow(RawDataFile dataFile
       return null;
     }
 
-    SpectraVisualizerWindow newWindow = new SpectraVisualizerWindow(dataFile);
+    SpectraVisualizerWindow newWindow = new SpectraVisualizerWindow(dataFile, true);
     newWindow.loadRawData(scan);
 
     if (peak != null)