Fixed showing of isotope patterns

src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/formulaprediction/ResultWindow.java

@@ -30,6 +30,7 @@
 import java.io.File;
 import java.io.FileWriter;
 import java.util.Map;
+import java.util.logging.Logger;
 
 import javax.swing.BorderFactory;
 import javax.swing.BoxLayout;
@@ -53,20 +54,22 @@
 import net.sf.mzmine.datamodel.RawDataFile;
 import net.sf.mzmine.datamodel.impl.SimplePeakIdentity;
 import net.sf.mzmine.main.MZmineCore;
+import net.sf.mzmine.modules.peaklistmethods.isotopes.isotopeprediction.IsotopePatternCalculator;
 import net.sf.mzmine.modules.visualization.spectra.simplespectra.SpectraVisualizerModule;
 import net.sf.mzmine.modules.visualization.spectra.simplespectra.SpectraVisualizerWindow;
 import net.sf.mzmine.taskcontrol.Task;
 import net.sf.mzmine.taskcontrol.TaskStatus;
 import net.sf.mzmine.util.ExceptionUtils;
+import net.sf.mzmine.util.FormulaUtils;
 import net.sf.mzmine.util.GUIUtils;
 import net.sf.mzmine.util.components.PercentageCellRenderer;
 
 public class ResultWindow extends JFrame implements ActionListener {
 
-  /**
-   * 
-   */
   private static final long serialVersionUID = 1L;
+
+  private Logger logger = Logger.getLogger(this.getClass().getName());
+
   private final JTable resultsTable;
   private final ResultTableModel resultsTableModel;
   private final TableRowSorter<ResultTableModel> resultsTableSorter;
@@ -226,6 +229,7 @@ public void actionPerformed(ActionEvent e) {
 
     if (command.equals("SHOW_ISOTOPES")) {
 
+      logger.finest("Showing isotope pattern for formula " + formula.getFormulaAsString());
       IsotopePattern predictedPattern = formula.getPredictedIsotopes();
 
       if (predictedPattern == null)

src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/formulaprediction/SingleRowPredictionTask.java

@@ -204,24 +204,23 @@ private void checkConstraints(IMolecularFormula cdkFormula) {
     }
 
     // Calculate isotope similarity score
-    IsotopePattern detectedPattern = peakListRow.getBestIsotopePattern();
-    IsotopePattern predictedIsotopePattern = null;
-    Double isotopeScore = null;
-    if ((checkIsotopes) && (detectedPattern != null)) {
+    final IsotopePattern detectedPattern = peakListRow.getBestIsotopePattern();
 
-      String stringFormula = MolecularFormulaManipulator.getString(cdkFormula);
+    final String stringFormula = MolecularFormulaManipulator.getString(cdkFormula);
 
-      String adjustedFormula = FormulaUtils.ionizeFormula(stringFormula, ionType, charge);
+    final String adjustedFormula = FormulaUtils.ionizeFormula(stringFormula, ionType, charge);
 
-      final double isotopeNoiseLevel = isotopeParameters
-          .getParameter(IsotopePatternScoreParameters.isotopeNoiseLevel).getValue();
+    final double isotopeNoiseLevel =
+        isotopeParameters.getParameter(IsotopePatternScoreParameters.isotopeNoiseLevel).getValue();
 
-      final double detectedPatternHeight = detectedPattern.getHighestDataPoint().getIntensity();
+    // Fixed min abundance
+    final double minPredictedAbundance = 0.00001;
 
-      final double minPredictedAbundance = isotopeNoiseLevel / detectedPatternHeight;
+    final IsotopePattern predictedIsotopePattern = IsotopePatternCalculator.calculateIsotopePattern(
+        adjustedFormula, minPredictedAbundance, charge, ionType.getPolarity());
 
-      predictedIsotopePattern = IsotopePatternCalculator.calculateIsotopePattern(adjustedFormula,
-          minPredictedAbundance, charge, ionType.getPolarity());
+    Double isotopeScore = null;
+    if ((checkIsotopes) && (detectedPattern != null)) {
 
       isotopeScore = IsotopePatternScoreCalculator.getSimilarityScore(detectedPattern,
           predictedIsotopePattern, isotopeParameters);