From 56cfb56b1294b42a85a4d545759db6443bb1d4d9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20Mail=C3=A4nder?= Date: Fri, 14 Feb 2025 16:56:06 +0100 Subject: [PATCH] Cite the AMDIS paper. --- .../settings/10.1016S1044-03059900047-1.ris | 19 ++++++++++ .../settings/AbstractProcessSettings.java | 35 ++++++++++++++++++- 2 files changed, 53 insertions(+), 1 deletion(-) create mode 100644 openchrom/plugins/net.openchrom.chromatogram.msd.peak.detector.supplier.amdis/src/net/openchrom/chromatogram/msd/peak/detector/supplier/amdis/settings/10.1016S1044-03059900047-1.ris diff --git a/openchrom/plugins/net.openchrom.chromatogram.msd.peak.detector.supplier.amdis/src/net/openchrom/chromatogram/msd/peak/detector/supplier/amdis/settings/10.1016S1044-03059900047-1.ris b/openchrom/plugins/net.openchrom.chromatogram.msd.peak.detector.supplier.amdis/src/net/openchrom/chromatogram/msd/peak/detector/supplier/amdis/settings/10.1016S1044-03059900047-1.ris new file mode 100644 index 000000000..46cff08ae --- /dev/null +++ b/openchrom/plugins/net.openchrom.chromatogram.msd.peak.detector.supplier.amdis/src/net/openchrom/chromatogram/msd/peak/detector/supplier/amdis/settings/10.1016S1044-03059900047-1.ris @@ -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 - diff --git a/openchrom/plugins/net.openchrom.chromatogram.msd.peak.detector.supplier.amdis/src/net/openchrom/chromatogram/msd/peak/detector/supplier/amdis/settings/AbstractProcessSettings.java b/openchrom/plugins/net.openchrom.chromatogram.msd.peak.detector.supplier.amdis/src/net/openchrom/chromatogram/msd/peak/detector/supplier/amdis/settings/AbstractProcessSettings.java index 35309b1f7..0301ce466 100644 --- a/openchrom/plugins/net.openchrom.chromatogram.msd.peak.detector.supplier.amdis/src/net/openchrom/chromatogram/msd/peak/detector/supplier/amdis/settings/AbstractProcessSettings.java +++ b/openchrom/plugins/net.openchrom.chromatogram.msd.peak.detector.supplier.amdis/src/net/openchrom/chromatogram/msd/peak/detector/supplier/amdis/settings/AbstractProcessSettings.java @@ -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 @@ -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; @@ -101,4 +114,24 @@ public void setModelPeakOption(ModelPeakOption modelPeakOption) { this.modelPeakOption = modelPeakOption; } + + @Override + public List getLiteratureReferences() { + + List 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); + } }