Merge remote-tracking branch 'mzmine/master'

src/main/java/io/github/mzmine/modules/dataprocessing/filter_rowsfilter/RowsFilterParameters.java

@@ -39,6 +39,7 @@
 import io.github.mzmine.parameters.parametertypes.selectors.FeatureListsParameter;
 import io.github.mzmine.parameters.parametertypes.submodules.OptionalModuleParameter;
 import io.github.mzmine.util.ExitCode;
+import java.text.DecimalFormat;
 
 public class RowsFilterParameters extends SimpleParameterSet {
 
@@ -50,12 +51,14 @@ public class RowsFilterParameters extends SimpleParameterSet {
       "Suffix to be added to feature list name", "filtered");
 
   public static final OptionalParameter<DoubleParameter> MIN_FEATURE_COUNT = new OptionalParameter<>(
-      new DoubleParameter("Minimum features in a row",
-          "Minimum number of feature detections required per row.\nValues <1 will be interpreted as a %-value of the total # samples in the feature list. The value will be rounded down to the nearest whole number."));
+      new DoubleParameter("Minimum features in a row (abs or %)",
+          "Minimum number of feature detections required per row.\nValues <1 will be "
+              + "interpreted as a %-value of the total # samples in the feature list. The value will be rounded down to the nearest whole number.",
+          new DecimalFormat("0.000"), 0.1), false);
 
   public static final OptionalParameter<IntegerParameter> MIN_ISOTOPE_PATTERN_COUNT = new OptionalParameter<>(
       new IntegerParameter("Minimum features in an isotope pattern",
-          "Minimum number of features required in an isotope pattern"));
+          "Minimum number of features required in an isotope pattern", 2), false);
 
   public static final OptionalModuleParameter<Isotope13CFilterParameters> ISOTOPE_FILTER_13C = new OptionalModuleParameter<>(
       "Validate 13C isotope pattern",
@@ -65,40 +68,42 @@ public class RowsFilterParameters extends SimpleParameterSet {
       new Isotope13CFilterParameters(), false);
 
   public static final OptionalParameter<MZRangeParameter> MZ_RANGE = new OptionalParameter<>(
-      new MZRangeParameter());
+      new MZRangeParameter(), false);
 
   public static final OptionalParameter<RTRangeParameter> RT_RANGE = new OptionalParameter<>(
-      new RTRangeParameter());
+      new RTRangeParameter(), false);
 
   public static final OptionalParameter<DoubleRangeParameter> FEATURE_DURATION = new OptionalParameter<>(
       new DoubleRangeParameter("features duration range",
           "Permissible range of (average) feature durations per row",
-          MZmineCore.getConfiguration().getRTFormat(), Range.closed(0.0, 10.0)));
+          MZmineCore.getConfiguration().getRTFormat(), Range.closed(0.0, 3d)), false);
 
   public static final OptionalParameter<DoubleRangeParameter> FWHM = new OptionalParameter<>(
       new DoubleRangeParameter("Chromatographic FWHM",
           "Permissible range of chromatographic FWHM per row",
-          MZmineCore.getConfiguration().getRTFormat(), Range.closed(0.0, 1.0)));
+          MZmineCore.getConfiguration().getRTFormat(), Range.closed(0.0, 1.0)), false);
   public static final OptionalParameter<IntRangeParameter> CHARGE = new OptionalParameter<>(
-      new IntRangeParameter("Charge", "Filter by charge, run isotopic features grouper first"));
+      new IntRangeParameter("Charge", "Filter by charge, run isotopic features grouper first", true,
+          Range.closed(1, 2)), false);
 
   public static final OptionalModuleParameter<KendrickMassDefectFilterParameters> KENDRICK_MASS_DEFECT = new OptionalModuleParameter<>(
       "Kendrick mass defect", "Permissible range of a Kendrick mass defect per row",
-      new KendrickMassDefectFilterParameters());
+      new KendrickMassDefectFilterParameters(), false);
   public static final ComboParameter<Object> GROUPSPARAMETER = new ComboParameter<Object>(
       "Parameter", "Paremeter defining the group of each sample.", new Object[]{defaultGrouping},
       defaultGrouping);
 
   public static final BooleanParameter HAS_IDENTITIES = new BooleanParameter("Only identified?",
-      "Select to filter only identified compounds");
+      "Select to filter only identified compounds", false);
 
   public static final OptionalParameter<StringParameter> IDENTITY_TEXT = new OptionalParameter<>(
       new StringParameter("Text in identity",
-          "Only rows that contain this text in their feature identity field will be retained."));
+          "Only rows that contain this text in their feature identity field will be retained.", ""),
+      false);
 
   public static final OptionalParameter<StringParameter> COMMENT_TEXT = new OptionalParameter<>(
       new StringParameter("Text in comment",
-          "Only rows that contain this text in their comment field will be retained."));
+          "Only rows that contain this text in their comment field will be retained.", ""), false);
 
   public static final ComboParameter<RowsFilterChoices> REMOVE_ROW = new ComboParameter<>(
       "Keep or remove rows", "If selected, rows will be removed based on criteria instead of kept",
@@ -109,15 +114,15 @@ public class RowsFilterParameters extends SimpleParameterSet {
       true);
 
   public static final BooleanParameter MS2_Filter = new BooleanParameter("Feature with MS2 scan",
-      "If checked, the rows that don't contain MS2 scan will be removed.");
+      "If checked, the rows that don't contain MS2 scan will be removed.", false);
   public static final BooleanParameter KEEP_ALL_MS2 = new BooleanParameter(
       "Never remove feature with MS2",
       "If checked, all rows with MS2 are retained without applying any further filters on them.",
-      false);
+      true);
 
   public static final BooleanParameter Reset_ID = new BooleanParameter(
       "Reset the feature number ID",
-      "If checked, the row number of original feature list will be reset.");
+      "If checked, the row number of original feature list will be reset.", false);
 
 
   public static final OptionalParameter<MassDefectParameter> massDefect = new OptionalParameter<>(

src/main/resources/mzmineversion.properties

@@ -1,8 +1,8 @@
 #Generated by the Semver Plugin for Gradle
-#Wed Mar 09 09:21:04 UTC 2022
+#Wed Mar 09 10:16:35 UTC 2022
 version.buildmeta=
 version.major=3
 version.minor=0
-version.patch=8
+version.patch=9
 version.prerelease=
-version.semver=3.0.8
+version.semver=3.0.9