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Propose new API for instrument type and ionization mode #1568

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Nov 22, 2023
Merged

Propose new API for instrument type and ionization mode #1568

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fd27f5f
Add new API for instrument type.
Mailaender Nov 22, 2023
879ab62
Add a separate field for the ionization mode.
Mailaender Nov 22, 2023
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4 changes: 4 additions & 0 deletions ....supplier.amdis/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/io/MSPReader.java
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Expand Up @@ -71,6 +71,7 @@ public class MSPReader extends AbstractMassSpectraReader implements IMassSpectra
private static final Pattern ionPattern = Pattern.compile("([+]?\\d+\\.?\\d*)([\t ,;:]+)([+-]?\\d+\\.?\\d*([eE][+-]?\\d+)?)");
private static final Pattern precursorTypePattern = Pattern.compile("(Precursor_type:)(.*)", Pattern.CASE_INSENSITIVE);
private static final Pattern precursorMassPattern = Pattern.compile("(PrecursorMZ:)(.*)", Pattern.CASE_INSENSITIVE);
private static final Pattern instrumentTypePattern = Pattern.compile("(Instrument_type:)(.*)", Pattern.CASE_INSENSITIVE);
private static final Pattern instrumentPattern = Pattern.compile("(Instrument:)(.*)", Pattern.CASE_INSENSITIVE);
private static final Pattern collisionEnergyPattern = Pattern.compile("(Collision_energy:)(.*)", Pattern.CASE_INSENSITIVE);
private static final Pattern exactMassPattern = Pattern.compile("(ExactMass:)(.*)", Pattern.CASE_INSENSITIVE);
Expand Down Expand Up @@ -254,6 +255,9 @@ private void addMassSpectrum(IMassSpectra massSpectra, String massSpectrumData,
String instrument = extractContentAsString(massSpectrumData, instrumentPattern, 2);
massSpectrum.putProperty(IRegularLibraryMassSpectrum.PROPERTY_INSTRUMENT_NAME, instrument);
//
String instrumentType = extractContentAsString(massSpectrumData, instrumentTypePattern, 2);
massSpectrum.putProperty(IRegularLibraryMassSpectrum.PROPERTY_INSTRUMENT_TYPE, instrumentType);
//
String ionMode = extractContentAsString(massSpectrumData, ionModePattern, 2);
if(ionMode.equals("POSITIVE")) {
massSpectrum.setPolarity("+");
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2 changes: 2 additions & 0 deletions ...ipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/IRegularLibraryMassSpectrum.java
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Expand Up @@ -18,6 +18,8 @@ public interface IRegularLibraryMassSpectrum extends IRegularMassSpectrum, ILibr
public static final String PROPERTY_PRECURSOR_TYPE = "Precursor Type"; // [M+H]+, [M-H]-, ...
public static final String PROPERTY_COLLISION_ENERGY = "Collision Energy"; // 30
public static final String PROPERTY_INSTRUMENT_NAME = "Instrument Name"; // Agilent QTOF 6530
public static final String PROPERTY_INSTRUMENT_TYPE = "Instrument Type"; // LC-ESI-QTOF
public static final String PROPERTY_IONIZATION_MODE = "Ionization Mode"; // APCI

String getPrecursorType();

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1 change: 1 addition & 0 deletions ...emclipse/msd/converter/supplier/amdis/converter/msp/MassBankMS2ImportConverter_ITest.java
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Expand Up @@ -53,6 +53,7 @@ public void testMassSpectrum() {
assertEquals("30(NCE)", regularLibraryMassSpectrum.getProperty(IRegularLibraryMassSpectrum.PROPERTY_COLLISION_ENERGY));
assertEquals("+", regularLibraryMassSpectrum.getPolarity());
assertEquals("[M+H]+", regularLibraryMassSpectrum.getProperty(IRegularLibraryMassSpectrum.PROPERTY_PRECURSOR_TYPE));
assertEquals("LC-ESI-ITFT", regularLibraryMassSpectrum.getProperty(IRegularLibraryMassSpectrum.PROPERTY_INSTRUMENT_TYPE));
assertEquals("Q-Exactive Orbitrap Thermo Scientific", regularLibraryMassSpectrum.getProperty(IRegularLibraryMassSpectrum.PROPERTY_INSTRUMENT_NAME));
}
}
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