diff --git a/src/main/java/io/github/mzmine/modules/dataprocessing/filter_rowsfilter/RowsFilterParameters.java b/src/main/java/io/github/mzmine/modules/dataprocessing/filter_rowsfilter/RowsFilterParameters.java index 10ff39e0cb..5734ac0229 100644 --- a/src/main/java/io/github/mzmine/modules/dataprocessing/filter_rowsfilter/RowsFilterParameters.java +++ b/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 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 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 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 MZ_RANGE = new OptionalParameter<>( - new MZRangeParameter()); + new MZRangeParameter(), false); public static final OptionalParameter RT_RANGE = new OptionalParameter<>( - new RTRangeParameter()); + new RTRangeParameter(), false); public static final OptionalParameter 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 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 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 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 GROUPSPARAMETER = new ComboParameter( "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 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 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 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 massDefect = new OptionalParameter<>( diff --git a/src/main/resources/mzmineversion.properties b/src/main/resources/mzmineversion.properties index a31e0950e9..67e38dd7cb 100644 --- a/src/main/resources/mzmineversion.properties +++ b/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