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extend tooltips of some ims parameters #2148

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Merged
robinschmid merged 1 commit into from
Oct 23, 2024
Merged

extend tooltips of some ims parameters #2148

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15 changes: 9 additions & 6 deletions ...modules/dataprocessing/id_ccscalibration/reference/ReferenceCCSCalibrationParameters.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2004-2022 The MZmine Development Team
* Copyright (c) 2004-2024 The mzmine Development Team
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
Expand Down Expand Up @@ -54,15 +54,17 @@ public class ReferenceCCSCalibrationParameters extends SimpleParameterSet {
public static final FeatureListsParameter flists = new FeatureListsParameter(
"Feature list (with reference compounds)", 1, Integer.MAX_VALUE);

public static final FileNameParameter referenceList = new FileNameParameter("Reference list",
"The file containing the reference compounds for m/z and mobility.", FileSelectionType.OPEN,
false);
public static final FileNameParameter referenceList = new FileNameParameter("Reference list", """
The file containing the reference compounds for m/z and mobility.
Must contain the columns "mz", "mobility", "ccs", "charge". Columns must be separated by ";".""",
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@robinschmid robinschmid Oct 18, 2024

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example export could maybe help:
FileNameWithExampleExportParameter
Is this file usually provided by the instrument or manually created?

FileSelectionType.OPEN, false);

public static final MZToleranceParameter mzTolerance = new MZToleranceParameter("m/z tolerance",
"Tolerance for the given reference compound list", 0.005, 5);

public static final MobilityToleranceParameter mobTolerance = new MobilityToleranceParameter(
"Mobility tolerance", "Tolerance for the given reference compound list",
"Mobility tolerance",
"Tolerance for the given reference compound list in the unit of the respective mobility separation device.",
new MobilityTolerance(0.1f));

public static final RTRangeParameter rtRange = new RTRangeParameter(
Expand All @@ -75,7 +77,8 @@ public class ReferenceCCSCalibrationParameters extends SimpleParameterSet {

public ReferenceCCSCalibrationParameters() {
super(new Parameter[]{files, flists, referenceList, mzTolerance, mobTolerance, rtRange,
minHeight}, "https://mzmine.github.io/mzmine_documentation/module_docs/id_ccs_calibration/ccs_calibration.html#reference-css-calibration");
minHeight},
"https://mzmine.github.io/mzmine_documentation/module_docs/id_ccs_calibration/ccs_calibration.html#reference-css-calibration");
}

@Override
Expand Down
11 changes: 6 additions & 5 deletions ...io/github/mzmine/modules/tools/batchwizard/subparameters/IonMobilityWizardParameters.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2004-2022 The MZmine Development Team
* Copyright (c) 2004-2024 The mzmine Development Team
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
Expand Down Expand Up @@ -38,14 +38,15 @@
public final class IonMobilityWizardParameters extends WizardStepParameters {

public static final DoubleParameter approximateImsFWHM = new DoubleParameter(
"Approximate feature FWHM",
"The approximate feature width (IMS peak width) in ion mobility (full-width-at-half-maximum, FWHM).",
"Approximate feature FWHM", """
The approximate feature width (IMS peak width) in ion mobility dimension (full-width-at-half-maximum, FWHM).
The value is interpreted in the unit of the mobility analyzer. E.g., ms for DTIMS and TWIMS and Vs/cm2 for TIMS.""",
new DecimalFormat("0.0000"), 0.04d);

public static final IntegerParameter minNumberOfDataPoints = new IntegerParameter(
"Minimum consecutive scans",
"Minimum number of consecutive scans with detected data points as used in ion mobility feature resolving.", 5, 1,
Integer.MAX_VALUE);
"Minimum number of consecutive scans with detected data points as used in ion mobility feature resolving.",
5, 1, Integer.MAX_VALUE);

public static final HiddenParameter<Boolean> imsActive = new HiddenParameter<>(
new BooleanParameter("IMS active", "Flag if IMS is active", false));
Expand Down
9 changes: 8 additions & 1 deletion ...rc/main/java/io/github/mzmine/modules/visualization/frames/FrameVisualizerParameters.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2004-2022 The MZmine Development Team
* Copyright (c) 2004-2024 The mzmine Development Team
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
Expand All @@ -26,8 +26,10 @@
package io.github.mzmine.modules.visualization.frames;

import io.github.mzmine.parameters.Parameter;
import io.github.mzmine.parameters.impl.IonMobilitySupport;
import io.github.mzmine.parameters.impl.SimpleParameterSet;
import io.github.mzmine.parameters.parametertypes.selectors.RawDataFilesParameter;
import org.jetbrains.annotations.NotNull;

public class FrameVisualizerParameters extends SimpleParameterSet {

Expand All @@ -36,4 +38,9 @@ public class FrameVisualizerParameters extends SimpleParameterSet {
public FrameVisualizerParameters() {
super(new Parameter[]{files});
}

@Override
public @NotNull IonMobilitySupport getIonMobilitySupport() {
return IonMobilitySupport.ONLY;
}
}