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Cite the AMDIS paper #603

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Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
TY - JOUR
T1 - An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data
AU - Stein, S. E.
Y1 - 1999/08/01
PY - 1999
DA - 1999/08/01
N1 - doi: 10.1016/S1044-0305(99)00047-1
DO - 10.1016/S1044-0305(99)00047-1
T2 - Journal of the American Society for Mass Spectrometry
JF - Journal of the American Society for Mass Spectrometry
JO - J. Am. Soc. Mass Spectrom.
SP - 770
EP - 781
VL - 10
IS - 8
PB - American Society for Mass Spectrometry. Published by the American Chemical Society. All rights reserved.
M3 - doi: 10.1016/S1044-0305(99)00047-1
UR - https://doi.org/10.1016/S1044-0305(99)00047-1
ER -
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2008, 2024 Lablicate GmbH.
* Copyright (c) 2008, 2025 Lablicate GmbH.
*
* All rights reserved.
* This program and the accompanying materials are made available under the
Expand All @@ -11,22 +11,35 @@
*******************************************************************************/
package net.openchrom.chromatogram.msd.peak.detector.supplier.amdis.settings;

import java.io.IOException;
import java.util.ArrayList;
import java.util.List;

import org.eclipse.chemclipse.chromatogram.msd.peak.detector.settings.AbstractPeakDetectorSettingsMSD;
import org.eclipse.chemclipse.logging.core.Logger;
import org.eclipse.chemclipse.support.literature.LiteratureReference;

import com.fasterxml.jackson.annotation.JsonProperty;

public class AbstractProcessSettings extends AbstractPeakDetectorSettingsMSD implements IProcessSettings {

private static final Logger logger = Logger.getLogger(AbstractProcessSettings.class);

@JsonProperty(value = "Min S/N Ratio", defaultValue = "0.0")
private float minSignalToNoiseRatio = 0.0f;

@JsonProperty(value = "Min Leading", defaultValue = "0.1")
private float minLeading = 0.1f;

@JsonProperty(value = "Max Leading", defaultValue = "2.0")
private float maxLeading = 2.0f;

@JsonProperty(value = "Min Tailing", defaultValue = "0.1")
private float minTailing = 0.1f;

@JsonProperty(value = "Max Tailing", defaultValue = "2.0")
private float maxTailing = 2.0f;

@JsonProperty(value = "Filter Model Peaks", defaultValue = "MP1")
private ModelPeakOption modelPeakOption = ModelPeakOption.MP1;

Expand Down Expand Up @@ -101,4 +114,24 @@ public void setModelPeakOption(ModelPeakOption modelPeakOption) {

this.modelPeakOption = modelPeakOption;
}

@Override
public List<LiteratureReference> getLiteratureReferences() {

List<LiteratureReference> literatureReferences = new ArrayList<>();
literatureReferences.add(createLiteratureReference("10.1016S1044-0305(99)00047-1.ris", "10.1016/S1044-0305(99)00047-1"));
return literatureReferences;
}

private static LiteratureReference createLiteratureReference(String file, String doi) {

String content;
try {
content = new String(AbstractProcessSettings.class.getResourceAsStream(file).readAllBytes());
} catch(IOException | NullPointerException e) {
content = doi;
logger.warn(e);
}
return new LiteratureReference(content);
}
}