Merge branch 'master' into master

du-lab · Sep 18, 2022 · bef89ac · bef89ac
2 parents 3c5f7bc + bb498d0
commit bef89ac
Show file tree

Hide file tree

Showing 82 changed files with 442 additions and 1,711 deletions.
diff --git a/build.gradle b/build.gradle
@@ -247,15 +247,15 @@ javafx {
 
 tasks.withType(JavaCompile) {
     options.encoding = "UTF-8"
-    options.compilerArgs += ['--enable-preview']
+//    options.compilerArgs += ['--enable-preview']
 }
 
 tasks.withType(Test) {
-    jvmArgs += "--enable-preview"
+//    jvmArgs += "--enable-preview"
 }
 
 tasks.withType(JavaExec) {
-    jvmArgs += '--enable-preview'
+//    jvmArgs += '--enable-preview'
 }
 
 /*

diff --git a/src/main/java/io/github/mzmine/datamodel/Frame.java b/src/main/java/io/github/mzmine/datamodel/Frame.java
@@ -47,10 +47,6 @@ default int getFrameId() {
 
   @NotNull MobilityType getMobilityType();
 
-  /**
-   * @return Unsorted set of sub spectrum numbers.
-   */
-//  Set<Integer> getMobilityScanNumbers();
   @NotNull Range<Double> getMobilityRange();
 
   /**

diff --git a/src/main/java/io/github/mzmine/datamodel/data_access/BinningMobilogramDataAccess.java b/src/main/java/io/github/mzmine/datamodel/data_access/BinningMobilogramDataAccess.java
@@ -156,7 +156,8 @@ public BinningMobilogramDataAccess(@NotNull final IMSRawDataFile rawDataFile,
 
   @NotNull
   public static int getRecommendedBinWidth(IMSRawDataFile file) {
-    final Frame frame = file.getFrame(0);
+    // timsTOF data can be empty in the early scans, so we use one from the middle
+    final Frame frame = file.getFrame(file.getNumberOfFrames() / 2);
     switch (frame.getMobilityType()) {
       case NONE, DRIFT_TUBE, TRAVELING_WAVE, FAIMS -> {
         return 1;
@@ -183,30 +184,24 @@ public static Integer getPreviousBinningWith(@NotNull final ModularFeatureList f
       if (method.getModule()
           .equals(MZmineCore.getModuleInstance(IonMobilityTraceBuilderModule.class))) {
         final ParameterSet parameterSet = method.getParameters();
-        final var advancedParam = parameterSet
-            .getParameter(IonMobilityTraceBuilderParameters.advancedParameters).getValue();
+        final var advancedParam = parameterSet.getParameter(
+            IonMobilityTraceBuilderParameters.advancedParameters).getValue();
         binWidth = switch (mt) {
           case TIMS ->
               advancedParam.getParameter(AdvancedImsTraceBuilderParameters.timsBinningWidth)
-                  .getValue() ? advancedParam
-                  .getParameter(AdvancedImsTraceBuilderParameters.timsBinningWidth)
-                  .getEmbeddedParameter().getValue()
-                  : getRecommendedBinWidth(
-                      (IMSRawDataFile) flist.getRawDataFile(0));
+                  .getValue() ? advancedParam.getParameter(
+                      AdvancedImsTraceBuilderParameters.timsBinningWidth).getEmbeddedParameter()
+                  .getValue() : getRecommendedBinWidth((IMSRawDataFile) flist.getRawDataFile(0));
           case DRIFT_TUBE ->
               advancedParam.getParameter(AdvancedImsTraceBuilderParameters.dtimsBinningWidth)
-                  .getValue() ? advancedParam
-                  .getParameter(AdvancedImsTraceBuilderParameters.dtimsBinningWidth)
-                  .getEmbeddedParameter().getValue()
-                  : getRecommendedBinWidth(
-                      (IMSRawDataFile) flist.getRawDataFile(0));
+                  .getValue() ? advancedParam.getParameter(
+                      AdvancedImsTraceBuilderParameters.dtimsBinningWidth).getEmbeddedParameter()
+                  .getValue() : getRecommendedBinWidth((IMSRawDataFile) flist.getRawDataFile(0));
           case TRAVELING_WAVE ->
               advancedParam.getParameter(AdvancedImsTraceBuilderParameters.twimsBinningWidth)
-                  .getValue() ? advancedParam
-                  .getParameter(AdvancedImsTraceBuilderParameters.twimsBinningWidth)
-                  .getEmbeddedParameter().getValue()
-                  : getRecommendedBinWidth(
-                      (IMSRawDataFile) flist.getRawDataFile(0));
+                  .getValue() ? advancedParam.getParameter(
+                      AdvancedImsTraceBuilderParameters.twimsBinningWidth).getEmbeddedParameter()
+                  .getValue() : getRecommendedBinWidth((IMSRawDataFile) flist.getRawDataFile(0));
           default -> null;
         };
         break;
@@ -215,30 +210,24 @@ public static Integer getPreviousBinningWith(@NotNull final ModularFeatureList f
       if (method.getModule()
           .equals(MZmineCore.getModuleInstance(RecursiveIMSBuilderModule.class))) {
         final ParameterSet parameterSet = method.getParameters();
-        final var advancedParam = parameterSet
-            .getParameter(RecursiveIMSBuilderParameters.advancedParameters).getValue();
+        final var advancedParam = parameterSet.getParameter(
+            RecursiveIMSBuilderParameters.advancedParameters).getValue();
         binWidth = switch (mt) {
           case TIMS ->
               advancedParam.getParameter(RecursiveIMSBuilderAdvancedParameters.timsBinningWidth)
-                  .getValue() ? advancedParam
-                  .getParameter(RecursiveIMSBuilderAdvancedParameters.timsBinningWidth)
-                  .getEmbeddedParameter().getValue()
-                  : getRecommendedBinWidth(
-                      (IMSRawDataFile) flist.getRawDataFile(0));
+                  .getValue() ? advancedParam.getParameter(
+                      RecursiveIMSBuilderAdvancedParameters.timsBinningWidth).getEmbeddedParameter()
+                  .getValue() : getRecommendedBinWidth((IMSRawDataFile) flist.getRawDataFile(0));
           case DRIFT_TUBE ->
               advancedParam.getParameter(RecursiveIMSBuilderAdvancedParameters.dtimsBinningWidth)
-                  .getValue() ? advancedParam
-                  .getParameter(RecursiveIMSBuilderAdvancedParameters.dtimsBinningWidth)
-                  .getEmbeddedParameter().getValue()
-                  : getRecommendedBinWidth(
-                      (IMSRawDataFile) flist.getRawDataFile(0));
+                  .getValue() ? advancedParam.getParameter(
+                      RecursiveIMSBuilderAdvancedParameters.dtimsBinningWidth).getEmbeddedParameter()
+                  .getValue() : getRecommendedBinWidth((IMSRawDataFile) flist.getRawDataFile(0));
           case TRAVELING_WAVE ->
               advancedParam.getParameter(RecursiveIMSBuilderAdvancedParameters.twimsBinningWidth)
-                  .getValue() ? advancedParam
-                  .getParameter(RecursiveIMSBuilderAdvancedParameters.twimsBinningWidth)
-                  .getEmbeddedParameter().getValue()
-                  : getRecommendedBinWidth(
-                      (IMSRawDataFile) flist.getRawDataFile(0));
+                  .getValue() ? advancedParam.getParameter(
+                      RecursiveIMSBuilderAdvancedParameters.twimsBinningWidth).getEmbeddedParameter()
+                  .getValue() : getRecommendedBinWidth((IMSRawDataFile) flist.getRawDataFile(0));
           default -> null;
         };
         break;
@@ -247,23 +236,23 @@ public static Integer getPreviousBinningWith(@NotNull final ModularFeatureList f
       if (method.getModule().equals(MZmineCore.getModuleInstance(MobilogramBinningModule.class))) {
         final ParameterSet parameterSet = method.getParameters();
         binWidth = switch (mt) {
-          case TIMS -> parameterSet.getParameter(MobilogramBinningParameters.timsBinningWidth)
-              .getValue();
-          case DRIFT_TUBE -> parameterSet
-              .getParameter(MobilogramBinningParameters.dtimsBinningWidth).getValue();
-          case TRAVELING_WAVE -> parameterSet
-              .getParameter(MobilogramBinningParameters.twimsBinningWidth).getValue();
+          case TIMS ->
+              parameterSet.getParameter(MobilogramBinningParameters.timsBinningWidth).getValue();
+          case DRIFT_TUBE ->
+              parameterSet.getParameter(MobilogramBinningParameters.dtimsBinningWidth).getValue();
+          case TRAVELING_WAVE ->
+              parameterSet.getParameter(MobilogramBinningParameters.twimsBinningWidth).getValue();
           default -> null;
         };
         break;
       }
 
       if (method.getModule().equals(MZmineCore.getModuleInstance(ImsExpanderModule.class))) {
         final ParameterSet parameterSet = method.getParameters();
-        binWidth = parameterSet.getParameter(ImsExpanderParameters.mobilogramBinWidth)
-            .getValue() ? parameterSet.getParameter(ImsExpanderParameters.mobilogramBinWidth)
-            .getEmbeddedParameter().getValue() : getRecommendedBinWidth(
-            (IMSRawDataFile) flist.getRawDataFile(0));
+        binWidth = parameterSet.getParameter(ImsExpanderParameters.mobilogramBinWidth).getValue()
+            ? parameterSet.getParameter(ImsExpanderParameters.mobilogramBinWidth)
+            .getEmbeddedParameter().getValue()
+            : getRecommendedBinWidth((IMSRawDataFile) flist.getRawDataFile(0));
         break;
       }
     }
@@ -281,8 +270,8 @@ private void clearIntensities() {
 
   /**
    * Re-bins an already summed mobilogram. Note that re-binning an already binned mobilogram with a
-   * lower binnign width than before will lead to 0-intensity values. Consider using {@link
-   * #setMobilogram(List)} instead.
+   * lower binnign width than before will lead to 0-intensity values. Consider using
+   * {@link #setMobilogram(List)} instead.
    *
    * @param summedMobilogram
    */

diff --git a/src/main/java/io/github/mzmine/datamodel/features/ModularFeatureList.java b/src/main/java/io/github/mzmine/datamodel/features/ModularFeatureList.java
@@ -37,6 +37,7 @@
 import io.github.mzmine.project.impl.ProjectChangeEvent;
 import io.github.mzmine.util.CorrelationGroupingUtils;
 import io.github.mzmine.util.DataTypeUtils;
+import io.github.mzmine.util.FeatureListRowSorter;
 import io.github.mzmine.util.MemoryMapStorage;
 import io.github.mzmine.util.files.FileAndPathUtil;
 import java.text.DateFormat;
@@ -490,10 +491,16 @@ public List<FeatureListRow> getRowsInsideScanRange(Range<Float> rtRange) {
   @Override
   public List<FeatureListRow> getRowsInsideScanAndMZRange(Range<Float> rtRange,
       Range<Double> mzRange) {
-    // TODO handle if mz or rt is not present
-    return modularStream().filter(
-            row -> rtRange.contains(row.getAverageRT()) && mzRange.contains(row.getAverageMZ()))
-        .collect(Collectors.toCollection(FXCollections::observableArrayList));
+    List<FeatureListRow> rows = new ArrayList<>();
+    for(var row : getRows()) {
+      Float rt = row.getAverageRT();
+      if(rt==null || (rtRange.contains(rt) && mzRange.contains(row.getAverageMZ()))) {
+        rows.add(row);
+      } else if(rt>rtRange.upperEndpoint()) {
+        break;
+      }
+    }
+    return rows;
   }
 
   @Override

diff --git a/src/main/java/io/github/mzmine/datamodel/impl/SimpleFrame.java b/src/main/java/io/github/mzmine/datamodel/impl/SimpleFrame.java
@@ -37,6 +37,7 @@
 import java.util.Objects;
 import java.util.Optional;
 import java.util.Set;
+import java.util.logging.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 
@@ -46,6 +47,8 @@
  */
 public class SimpleFrame extends SimpleScan implements Frame {
 
+  private static Logger logger = Logger.getLogger(SimpleFrame.class.getName());
+
   private final MobilityType mobilityType;
 
   @NotNull
@@ -177,9 +180,17 @@ public List<MobilityScan> getSortedMobilityScans() {
   }
 
   public int setMobilities(double[] mobilities) {
+    if (mobilities.length == 0) {
+      logger.info(
+          () -> String.format("No mobilities detected in frame #%d of file %s.", getFrameId(),
+              getDataFile().getName()));
+      mobilities = new double[]{1d};
+      mobilityRange = Range.openClosed(1d, 1d); // empty range
+    } else {
+      mobilityRange = Range.singleton(mobilities[0]);
+      mobilityRange = mobilityRange.span(Range.singleton(mobilities[mobilities.length - 1]));
+    }
     mobilitySegment = ((IMSRawDataFile) getDataFile()).addMobilityValues(mobilities);
-    mobilityRange = Range.singleton(mobilities[0]);
-    mobilityRange = mobilityRange.span(Range.singleton(mobilities[mobilities.length - 1]));
     return mobilitySegment;
   }
 

diff --git a/...ain/java/io/github/mzmine/modules/dataprocessing/adap_hierarchicalclustering/EICPlot.java b/...ain/java/io/github/mzmine/modules/dataprocessing/adap_hierarchicalclustering/EICPlot.java
@@ -23,6 +23,9 @@
 import java.util.List;
 import java.util.Map.Entry;
 import java.util.NavigableMap;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
 import org.jfree.chart.JFreeChart;
 import org.jfree.chart.axis.NumberAxis;
 import org.jfree.chart.labels.XYToolTipGenerator;
@@ -41,6 +44,7 @@
  */
 
 public class EICPlot extends EChartViewer {
+  private static java.util.logging.Logger logger = Logger.getLogger(EICPlot.class.getName());
   private final XYSeriesCollection xyDataset;
   private final List<Double> colorDataset;
   private final List<String> toolTips;
@@ -149,7 +153,7 @@ public void updateData(List<List<NavigableMap<Double, Double>>> clusters, List<D
           xyDataset.addSeries(series);
         }
         catch(Exception e) {
-          System.out.println(e.getMessage());
+          logger.log(Level.WARNING, e.getMessage(), e);
         }
         finally {
           colorDataset.add(color);

diff --git a/...ava/io/github/mzmine/modules/dataprocessing/adap_mcr/ADAP3DecompositionV2SetupDialog.java b/...ava/io/github/mzmine/modules/dataprocessing/adap_mcr/ADAP3DecompositionV2SetupDialog.java
@@ -49,12 +49,9 @@
 import javafx.scene.control.Label;
 import javafx.scene.control.Separator;
 
-import javax.swing.*;
-
 /**
  * @author Du-Lab Team <dulab.binf@gmail.com>
  */
-
 public class ADAP3DecompositionV2SetupDialog extends ParameterSetupDialog {
   /**
    * Minimum dimensions of plots

diff --git a/...main/java/io/github/mzmine/modules/dataprocessing/align_adap3/ADAP3AlignerParameters.java b/...main/java/io/github/mzmine/modules/dataprocessing/align_adap3/ADAP3AlignerParameters.java
@@ -45,7 +45,7 @@ public class ADAP3AlignerParameters extends SimpleParameterSet {
   public static final DoubleParameter SAMPLE_COUNT_RATIO = new DoubleParameter(
       "Min confidence (between 0 and 1)",
       "A fraction of the total number of samples. An aligned feature must be detected at "
-          + "least in several samples. This parameter determines the minimum number of samples where a "
+          + "least in several samples.\nThis parameter determines the minimum number of samples where a "
           + "feature must be detected.",
       NumberFormat.getInstance(), 0.7, 0.0, 1.0);
 
@@ -71,6 +71,7 @@ public class ADAP3AlignerParameters extends SimpleParameterSet {
 
   public ADAP3AlignerParameters() {
     super(new Parameter[] {PEAK_LISTS, SAMPLE_COUNT_RATIO, RET_TIME_RANGE, MZ_RANGE,
-        SCORE_TOLERANCE, SCORE_WEIGHT, EIC_SCORE, NEW_PEAK_LIST_NAME});
+        SCORE_TOLERANCE, SCORE_WEIGHT, EIC_SCORE, NEW_PEAK_LIST_NAME},
+        "https://mzmine.github.io/mzmine_documentation/module_docs/align_adap/align_adap_gc.html");
   }
 }