Merge pull request #1 from robinschmid/isotoprefinement

Update master, simplify isotope scorer

Author: Sonja-analytik

Dockerfile

@@ -25,17 +25,42 @@
 
 package io.github.mzmine.datamodel.features.types.numbers;
 
-import io.github.mzmine.datamodel.features.types.numbers.abstr.FloatType;
+import io.github.mzmine.datamodel.MZmineProject;
+import io.github.mzmine.datamodel.RawDataFile;
+import io.github.mzmine.datamodel.features.ModularFeature;
+import io.github.mzmine.datamodel.features.ModularFeatureList;
+import io.github.mzmine.datamodel.features.ModularFeatureListRow;
+import io.github.mzmine.datamodel.features.types.numbers.abstr.IntegerType;
 import java.text.DecimalFormat;
 import java.text.NumberFormat;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
 import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
 
-public class PotentialType extends FloatType {
+public class PotentialType extends IntegerType {
 
-  private static final DecimalFormat format = new DecimalFormat("0.00");
+  private static final DecimalFormat format = new DecimalFormat("0");
 
   public PotentialType() {
-    super(format);
+    super();
+  }
+
+  @Override
+  public Object loadFromXML(@NotNull XMLStreamReader reader, @NotNull MZmineProject project,
+      @NotNull ModularFeatureList flist, @NotNull ModularFeatureListRow row,
+      @Nullable ModularFeature feature, @Nullable RawDataFile file) throws XMLStreamException {
+    String str = reader.getElementText();
+    if (str == null || str.isEmpty()) {
+      return null;
+    }
+    try {
+      return Integer.parseInt(str);
+    } catch (NumberFormatException e) {
+      // silent, still V value from old projects.
+    }
+
+    return (int) (Float.parseFloat(str) * 1000);
   }
 
   @Override
@@ -45,7 +70,7 @@ public PotentialType() {
 
   @Override
   public @NotNull String getHeaderString() {
-    return "Potential / V";
+    return "Potential / mV";
   }
 
   @Override

src/main/java/io/github/mzmine/datamodel/features/types/numbers/PotentialType.java

@@ -36,14 +36,9 @@ public class CalcEcmsPotentialParameters extends SimpleParameterSet {
 
   public static final FeatureListsParameter flists = new FeatureListsParameter();
 
-  public static final DoubleParameter tubingLengthMM = new DoubleParameter("Tubing length / mm",
-      "Tubing length between EC-Cell and ESI-Needle.", new DecimalFormat("0.0"), 750d);
-
-  public static final DoubleParameter tubingIdMM = new DoubleParameter("Tubing inner diameter / mm",
-      "Inner diameter of the tubing.", new DecimalFormat("0.000"), 0.127d);
-
-  public static final DoubleParameter flowRateMicroLiterPerMin = new DoubleParameter(
-      "Flow rate / μL/min", "Tubing length between EC-Cell and ESI-Needle.", new DecimalFormat("0.0"));
+  public static final DoubleParameter delayTime = new DoubleParameter("Delay Time / s",
+      "Delay time before analytes from the EC cell reach the mass spectrometer",
+      new DecimalFormat("0.0"), 30d);
 
   public static final DoubleParameter potentialRampSpeed = new DoubleParameter(
       "Potential ramp / mV/s", "Potential ramp speed in mV/s.");
@@ -53,7 +48,7 @@ public class CalcEcmsPotentialParameters extends SimpleParameterSet {
       "Percentage of the maximum metabolite intensity that will be used to assign the formation potential to a metabolite.");
 
   public CalcEcmsPotentialParameters() {
-    super(new Parameter[]{flists, tubingLengthMM, tubingIdMM, flowRateMicroLiterPerMin, potentialRampSpeed,
+    super(new Parameter[]{flists, delayTime, potentialRampSpeed,
         potentialAssignmentIntensityPercentage});
   }
 }

src/main/java/io/github/mzmine/modules/dataprocessing/id_ecmscalcpotential/CalcEcmsPotentialParameters.java

@@ -43,23 +43,10 @@
 
 public class CalcEcmsPotentialTask extends AbstractTask {
 
-  /**
-   * tubing length in mm
-   */
-  private final double tubingLength;
-  /**
-   * tubing id in mm
-   */
-  private final double tubingId;
-  /**
-   * flow rate in uL/min
-   */
-  private final double flowRate;
-  /**
-   * potential ramp speed in mV/s
-   */
+
   private final double potentialRampSpeed;
   private final double potentialAssignmentPercentage;
+  private final double delayTimeSeconds;
   private final ModularFeatureList[] flists;
 
   private final ParameterSet parameters;
@@ -74,11 +61,10 @@ protected CalcEcmsPotentialTask(@NotNull MZmineProject project, @NotNull Paramet
     this.project = project;
 
     flists = parameters.getValue(CalcEcmsPotentialParameters.flists).getMatchingFeatureLists();
-    tubingLength = parameters.getValue(CalcEcmsPotentialParameters.tubingLengthMM);
-    tubingId = parameters.getValue(CalcEcmsPotentialParameters.tubingIdMM);
-    flowRate = parameters.getValue(CalcEcmsPotentialParameters.flowRateMicroLiterPerMin);
+    delayTimeSeconds = parameters.getValue(CalcEcmsPotentialParameters.delayTime);
     potentialRampSpeed = parameters.getValue(CalcEcmsPotentialParameters.potentialRampSpeed);
-    potentialAssignmentPercentage = parameters.getValue(CalcEcmsPotentialParameters.potentialAssignmentIntensityPercentage);
+    potentialAssignmentPercentage = parameters.getValue(
+        CalcEcmsPotentialParameters.potentialAssignmentIntensityPercentage);
     numRows = Arrays.stream(flists).mapToInt(ModularFeatureList::getNumberOfRows).sum();
   }
 
@@ -96,9 +82,6 @@ public double getFinishedPercentage() {
   public void run() {
     setStatus(TaskStatus.PROCESSING);
 
-    final double tubingVolumeMicroL = EcmsUtils.getTubingVolume(tubingLength, tubingId);
-    final double delayTimeSeconds = EcmsUtils.getDelayTime(flowRate / 60d, tubingVolumeMicroL);
-
     for (ModularFeatureList flist : flists) {
       for (FeatureListRow row : flist.getRows()) {
         final Feature f = row.getBestFeature();
@@ -126,7 +109,7 @@ public void run() {
             // potential in mV
             final double potential = EcmsUtils.getPotentialAtRt(eic.getRetentionTime(i),
                 delayTimeSeconds, potentialRampSpeed);
-            row.set(PotentialType.class, (float) potential / 1000);
+            row.set(PotentialType.class, (int) potential);
             break;
           }
         }

src/main/java/io/github/mzmine/modules/dataprocessing/id_ecmscalcpotential/CalcEcmsPotentialTask.java

@@ -50,7 +50,7 @@ public static double getDelayTime(final double flowRate, final double volume) {
    * @param rt                 Retention time in minutes.
    * @param potentialRampSpeed Potential ramp speed in mV/s.
    * @param delayTime          Delay time in s.
-   * @return The potential at the given retention time.
+   * @return The potential at the given retention time in mV.
    */
   public static double getPotentialAtRt(final float rt, final double delayTime,
       final double potentialRampSpeed) {