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Fixed various minor peak filter related issues #1923

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merged 6 commits into from
Oct 31, 2024
Merged

Fixed various minor peak filter related issues #1923

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7644090
Fix typo.
Mailaender Oct 30, 2024
6d749cc
Use a better description.
Mailaender Oct 30, 2024
eeb2921
Delete descriptions that just repeat the name.
Mailaender Oct 30, 2024
33574e4
Add descriptions.
Mailaender Oct 30, 2024
432f340
Code cleanup.
Mailaender Oct 30, 2024
f0f5db7
Avoid iterations can't be lower than 5 warning by default.
Mailaender Oct 30, 2024
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8 changes: 7 additions & 1 deletion ...rg/eclipse/chemclipse/chromatogram/msd/filter/supplier/xpass/core/HighPassIonsFilter.java
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@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2020, 2023 Lablicate GmbH.
* Copyright (c) 2020, 2024 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand Down Expand Up @@ -35,6 +35,12 @@ public String getName() {
return "High Pass Ions";
}

@Override
public String getDescription() {

return "Remove all but n-highest ions by abundance.";
}

@Override
public Class<HighPassFilterSettings> getConfigClass() {

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8 changes: 7 additions & 1 deletion ...org/eclipse/chemclipse/chromatogram/msd/filter/supplier/xpass/core/LowPassIonsFilter.java
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@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2020, 2023 Lablicate GmbH.
* Copyright (c) 2020, 2024 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand Down Expand Up @@ -35,6 +35,12 @@ public String getName() {
return "Low Pass Ions";
}

@Override
public String getDescription() {

return "Remove all but n-lowest ions by abundance.";
}

@Override
public Class<LowPassFilterSettings> getConfigClass() {

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2 changes: 1 addition & 1 deletion ...s/src/org/eclipse/chemclipse/chromatogram/msd/filter/supplier/xpass/core/XPassFilter.java
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Expand Up @@ -57,7 +57,7 @@ private static void filter(IScanMSD massSpectrum, SortOrder sortOrder, int numbe

List<IIon> ions = new ArrayList<>(massSpectrum.getIons());
Collections.sort(ions, new IonAbundanceComparator(sortOrder));
List<IIon> ionsToRemove = new ArrayList<IIon>();
List<IIon> ionsToRemove = new ArrayList<>();
int counter = 0;
for(IIon ion : ions) {
if(counter >= number) {
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4 changes: 2 additions & 2 deletions ...e/chemclipse/chromatogram/xxd/edit/supplier/snip/settings/MassSpectrumFilterSettings.java
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/*******************************************************************************
* Copyright (c) 2014, 2018 Lablicate GmbH.
* Copyright (c) 2014, 2024 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand All @@ -21,7 +21,7 @@

public class MassSpectrumFilterSettings extends AbstractMassSpectrumFilterSettings {

@JsonProperty(value = "Iterations", defaultValue = "1")
@JsonProperty(value = "Iterations", defaultValue = "100")
@JsonPropertyDescription(value = "The number of iterations to run the filter.")
@IntSettingsProperty(minValue = PreferenceSupplier.MIN_ITERATIONS, maxValue = PreferenceSupplier.MAX_ITERATIONS)
private int iterations = 100;
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4 changes: 2 additions & 2 deletions ...g/eclipse/chemclipse/chromatogram/xxd/edit/supplier/snip/settings/PeakFilterSettings.java
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/*******************************************************************************
* Copyright (c) 2014, 2018 Lablicate GmbH.
* Copyright (c) 2014, 2024 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand All @@ -21,7 +21,7 @@

public class PeakFilterSettings extends AbstractPeakFilterSettings {

@JsonProperty(value = "Iterations", defaultValue = "1")
@JsonProperty(value = "Iterations", defaultValue = "100")
@JsonPropertyDescription(value = "The number of iterations to run the filter.")
@IntSettingsProperty(minValue = PreferenceSupplier.MIN_ITERATIONS, maxValue = PreferenceSupplier.MAX_ITERATIONS)
private int iterations = 100;
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5 changes: 2 additions & 3 deletions ...ipse.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/peaks/DeleteIntegrationsFilter.java
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@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2020, 2022 Lablicate GmbH.
* Copyright (c) 2020, 2024 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand Down Expand Up @@ -35,7 +35,7 @@ public String getName() {
@Override
public String getDescription() {

return "Filter Peak Integrations";
return "Reset calculated area/height.";
}

@Override
Expand All @@ -51,7 +51,6 @@ public void filterPeaks(IChromatogramSelection<?, ?> chromatogramSelection, Dele
if(configuration == null) {
configuration = createConfiguration(peaks);
}
//
if(configuration.isDeleteIntegrations()) {
SubMonitor subMonitor = SubMonitor.convert(context.getProgressMonitor(), peaks.size());
for(IPeak peak : peaks) {
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6 changes: 6 additions & 0 deletions ...ipse.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/peaks/DeletePeaksByModelFilter.java
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Expand Up @@ -34,6 +34,12 @@ public String getName() {
return "Delete Peaks by Model";
}

@Override
public String getDescription() {

return "Filter by internal peak model.";
}

@Override
public Class<DeletePeaksByModelFilterSettings> getConfigClass() {

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8 changes: 7 additions & 1 deletion ...d.filter/src/org/eclipse/chemclipse/xxd/filter/peaks/DeletePeaksByQuantitationFilter.java
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/*******************************************************************************
* Copyright (c) 2019, 2022 Lablicate GmbH.
* Copyright (c) 2019, 2024 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand Down Expand Up @@ -36,6 +36,12 @@ public String getName() {
return "Delete Peaks by Quantitation";
}

@Override
public String getDescription() {

return "Filter by name or concentration.";
}

@Override
public Class<DeletePeaksByQuantitationFilterSettings> getConfigClass() {

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8 changes: 7 additions & 1 deletion ...pse.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/peaks/DeletePeaksByTargetFilter.java
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/*******************************************************************************
* Copyright (c) 2019, 2022 Lablicate GmbH.
* Copyright (c) 2019, 2024 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand Down Expand Up @@ -37,6 +37,12 @@ public String getName() {
return "Delete Peaks by Target";
}

@Override
public String getDescription() {

return "Filter by identification results.";
}

@Override
public Class<DeletePeaksByTargetFilterSettings> getConfigClass() {

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8 changes: 7 additions & 1 deletion ...ipse.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/peaks/DeletePeaksByTraceFilter.java
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@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2023 Lablicate GmbH.
* Copyright (c) 2023, 2024 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand Down Expand Up @@ -39,6 +39,12 @@ public String getName() {
return "Delete Peaks by Trace";
}

@Override
public String getDescription() {

return "Filter by mass traces.";
}

@Override
public Class<DeletePeaksByTraceFilterSettings> getConfigClass() {

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8 changes: 1 addition & 7 deletions ...ilter/src/org/eclipse/chemclipse/xxd/filter/peaks/DeleteQuantitationReferencesFilter.java
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@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2022 Lablicate GmbH.
* Copyright (c) 2022, 2024 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand Down Expand Up @@ -32,12 +32,6 @@ public String getName() {
return "Delete Quantitation References";
}

@Override
public String getDescription() {

return "Delete the peak quantitation references.";
}

@Override
public Class<DeleteQuantitationReferencesFilterSettings> getConfigClass() {

Expand Down
8 changes: 1 addition & 7 deletions ...pse.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/peaks/DeleteQuantitationsFilter.java
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/*******************************************************************************
* Copyright (c) 2020, 2022 Lablicate GmbH.
* Copyright (c) 2020, 2024 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand Down Expand Up @@ -32,12 +32,6 @@ public String getName() {
return "Delete Quantitations";
}

@Override
public String getDescription() {

return "Filter Peak Quantitations";
}

@Override
public Class<DeleteQuantitationsFilterSettings> getConfigClass() {

Expand Down
4 changes: 2 additions & 2 deletions ...mclipse.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/peaks/DeleteStandardsFilter.java
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/*******************************************************************************
* Copyright (c) 2020, 2022 Lablicate GmbH.
* Copyright (c) 2020, 2024 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand Down Expand Up @@ -35,7 +35,7 @@ public String getName() {
@Override
public String getDescription() {

return "Filter Peak Standards";
return "Remove internal standard information.";
}

@Override
Expand Down
4 changes: 2 additions & 2 deletions ...hemclipse.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/peaks/DeleteTargetsFilter.java
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@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2020, 2022 Lablicate GmbH.
* Copyright (c) 2020, 2024 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand Down Expand Up @@ -36,7 +36,7 @@ public String getName() {
@Override
public String getDescription() {

return "Filter Peak Targets";
return "Remove all identification results.";
}

@Override
Expand Down
9 changes: 7 additions & 2 deletions ...e.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/peaks/PeakActiveForAnalysisFilter.java
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@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2022 Lablicate GmbH.
* Copyright (c) 2022, 2024 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand Down Expand Up @@ -32,6 +32,12 @@ public String getName() {
return "Activate/Deactivate for Analysis";
}

@Override
public String getDescription() {

return "Sets the active for analysis status for all peaks.";
}

@Override
public Class<PeakActiveForAnalysisSettings> getConfigClass() {

Expand All @@ -45,7 +51,6 @@ public void filterPeaks(IChromatogramSelection<?, ?> chromatogramSelection, Peak
if(configuration == null) {
configuration = createConfiguration(peaks);
}
//
SubMonitor subMonitor = SubMonitor.convert(context.getProgressMonitor(), peaks.size());
boolean activeForAnalysis = configuration.isActiveForAnalysis();
for(IPeak peak : peaks) {
Expand Down
8 changes: 7 additions & 1 deletion ...lipse.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/peaks/SignalToNoisePeakFilter.java
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@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2020, 2023 Lablicate GmbH.
* Copyright (c) 2020, 2024 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand Down Expand Up @@ -36,6 +36,12 @@ public String getName() {
return "Signal to Noise";
}

@Override
public String getDescription() {

return "Filter by s/n ratio.";
}

@Override
public Class<SignalToNoisePeakFilterSettings> getConfigClass() {

Expand Down
4 changes: 2 additions & 2 deletions ...ipse/chemclipse/xxd/filter/peaks/settings/DeleteQuantitationReferencesFilterSettings.java
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/*******************************************************************************
* Copyright (c) 2022 Lablicate GmbH.
* Copyright (c) 2022, 2024 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand All @@ -17,7 +17,7 @@
public class DeleteQuantitationReferencesFilterSettings {

@JsonProperty(value = "Delete Quantitation References", defaultValue = "")
@JsonPropertyDescription(value = "If empty, all references are deleted. Otherwise the speficied reference if available.")
@JsonPropertyDescription(value = "If empty, all references are deleted. Otherwise the specified reference if available.")
private String quantitationReference = "";

public String getQuantitationReference() {
Expand Down