Add basic metadata for MALDI-TOF MS spectra

eclipse · Feb 21, 2022 · 3a653b0 · 3a653b0
1 parent 82a5d7f
commit 3a653b0
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Showing 4 changed files with 79 additions and 11 deletions.
diff --git a/...ipse/chemclipse/msd/converter/supplier/mmass/internal/io/MassSpectrumReaderVersion22.java b/...ipse/chemclipse/msd/converter/supplier/mmass/internal/io/MassSpectrumReaderVersion22.java
@@ -16,6 +16,9 @@
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 import java.nio.FloatBuffer;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.Locale;
 import java.util.zip.DataFormatException;
 import java.util.zip.Inflater;
 
@@ -103,13 +106,19 @@ private void readDescription(Element element, IVendorMassSpectrum massSpectrum)
 			Node node = descriptionList.item(i);
 			Element description = (Element)node;
 			massSpectrum.setIdentifier(description.getElementsByTagName("title").item(0).getTextContent());
-			// TODO store and display
-			description.getElementsByTagName("date").item(0).getAttributes().getNamedItem("value").getTextContent();
-			description.getElementsByTagName("operator").item(0).getAttributes().getNamedItem("value").getTextContent();
-			description.getElementsByTagName("contact").item(0).getAttributes().getNamedItem("value").getTextContent();
-			description.getElementsByTagName("institution").item(0).getAttributes().getNamedItem("value").getTextContent();
-			description.getElementsByTagName("instrument").item(0).getAttributes().getNamedItem("value").getTextContent();
-			description.getElementsByTagName("notes").item(0).getTextContent();
+			try {
+				String date = description.getElementsByTagName("date").item(0).getAttributes().getNamedItem("value").getTextContent();
+				SimpleDateFormat dateFormat = new SimpleDateFormat("EEE MMM dd HH:mm:ss yyyy", Locale.ENGLISH);
+				massSpectrum.setAcquisitionDate(dateFormat.parse(date));
+			} catch(ParseException e) {
+				logger.warn(e);
+			}
+			String operator = description.getElementsByTagName("operator").item(0).getAttributes().getNamedItem("value").getTextContent();
+			String contact = description.getElementsByTagName("contact").item(0).getAttributes().getNamedItem("value").getTextContent();
+			String institution = description.getElementsByTagName("institution").item(0).getAttributes().getNamedItem("value").getTextContent();
+			massSpectrum.setOperator(operator + " " + contact + " " + institution);
+			massSpectrum.setInstrument(description.getElementsByTagName("instrument").item(0).getAttributes().getNamedItem("value").getTextContent());
+			description.getElementsByTagName("notes").item(0).getTextContent(); // TODO
 		}
 	}
 

diff --git a/...lipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/AbstractVendorMassSpectrum.java b/...lipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/AbstractVendorMassSpectrum.java
@@ -13,16 +13,20 @@
 package org.eclipse.chemclipse.msd.model.core;
 
 import java.io.File;
+import java.util.Date;
 
 public abstract class AbstractVendorMassSpectrum extends AbstractRegularMassSpectrum implements IVendorMassSpectrum {
 
 	/**
 	 * Renew the serialVersionUID any time you have changed some fields or
 	 * methods.
 	 */
-	private static final long serialVersionUID = 5013842421250687341L;
+	private static final long serialVersionUID = 5013842421250687342L;
 	//
 	private File file;
+	private String operator;
+	private Date acquisitionDate;
+	private String instrument;
 
 	@Override
 	public File getFile() {
@@ -68,4 +72,40 @@ public void setRetentionTime(int retentionTime) {
 			super.setRetentionTime(retentionTime);
 		}
 	}
+
+	@Override
+	public String getOperator() {
+
+		return operator;
+	}
+
+	@Override
+	public void setOperator(String operator) {
+
+		this.operator = operator;
+	}
+
+	@Override
+	public Date getAcquisitionDate() {
+
+		return acquisitionDate;
+	}
+
+	@Override
+	public void setAcquisitionDate(Date acquisitionDate) {
+
+		this.acquisitionDate = acquisitionDate;
+	}
+
+	@Override
+	public String getInstrument() {
+
+		return instrument;
+	}
+
+	@Override
+	public void setInstrument(String instrument) {
+
+		this.instrument = instrument;
+	}
 }
diff --git a/...e.chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/IVendorMassSpectrum.java b/...e.chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/IVendorMassSpectrum.java
@@ -12,6 +12,7 @@
 package org.eclipse.chemclipse.msd.model.core;
 
 import java.io.File;
+import java.util.Date;
 
 /**
  * More informations about the class structure of mass spectra are stored in {@link IScanMSD}.
@@ -74,4 +75,16 @@ public interface IVendorMassSpectrum extends IRegularMassSpectrum {
 	 * @return int
 	 */
 	int getMaxPossibleRetentionTime();
+
+	String getOperator();
+
+	void setOperator(String operator);
+
+	Date getAcquisitionDate();
+
+	void setAcquisitionDate(Date acquisitionDate);
+
+	String getInstrument();
+
+	void setInstrument(String instrument);
 }
diff --git a/...n.xxd.ui/src/org/eclipse/chemclipse/ux/extension/xxd/ui/ExtendedMassSpectrumHeaderUI.java b/...n.xxd.ui/src/org/eclipse/chemclipse/ux/extension/xxd/ui/ExtendedMassSpectrumHeaderUI.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2020, 2021 Lablicate GmbH.
+ * Copyright (c) 2020, 2022 Lablicate GmbH.
  *
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -12,6 +12,7 @@
 package org.eclipse.chemclipse.ux.extension.xxd.ui;
 
 import org.eclipse.chemclipse.msd.model.core.IVendorMassSpectrum;
+import org.eclipse.chemclipse.support.text.ValueFormat;
 import org.eclipse.swt.SWT;
 import org.eclipse.swt.layout.FillLayout;
 import org.eclipse.swt.widgets.Composite;
@@ -32,10 +33,15 @@ public void updateMassSpectrum(IVendorMassSpectrum massSpectrum) {
 		StringBuilder builder = new StringBuilder();
 		if(massSpectrum != null) {
 			addHeaderLine(builder, "Name", massSpectrum.getName());
-			addHeaderLine(builder, "Type Description", massSpectrum.getMassSpectrumTypeDescription());
+			addHeaderLine(builder, "Data", massSpectrum.getMassSpectrumTypeDescription());
 			addHeaderLine(builder, "File", massSpectrum.getFile().getName());
-			addHeaderLine(builder, "Mass Spectrometer", "MS" + massSpectrum.getMassSpectrometer());
+			addHeaderLine(builder, "Technique", "MS" + massSpectrum.getMassSpectrometer());
+			addHeaderLine(builder, "Instrument", massSpectrum.getInstrument());
 			addHeaderLine(builder, "Ions", Integer.toString(massSpectrum.getNumberOfIons()));
+			addHeaderLine(builder, "Operator", massSpectrum.getOperator());
+			if(massSpectrum.getAcquisitionDate() != null) {
+				addHeaderLine(builder, "Date", ValueFormat.getDateFormatEnglish().format(massSpectrum.getAcquisitionDate()));
+			}
 		}
 		//
 		text.setText(builder.toString());