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Changed polarity from String to Enum #1567

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Nov 22, 2023
Merged

Changed polarity from String to Enum #1567

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5 changes: 3 additions & 2 deletions ....supplier.amdis/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/io/MSPReader.java
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Expand Up @@ -40,6 +40,7 @@
import org.eclipse.chemclipse.msd.model.core.IIon;
import org.eclipse.chemclipse.msd.model.core.IMassSpectra;
import org.eclipse.chemclipse.msd.model.core.IRegularLibraryMassSpectrum;
import org.eclipse.chemclipse.msd.model.core.Polarity;
import org.eclipse.chemclipse.msd.model.exceptions.IonLimitExceededException;
import org.eclipse.chemclipse.msd.model.implementation.Ion;
import org.eclipse.chemclipse.msd.model.implementation.MassSpectra;
Expand Down Expand Up @@ -256,9 +257,9 @@ private void addMassSpectrum(IMassSpectra massSpectra, String massSpectrumData,
//
String ionMode = extractContentAsString(massSpectrumData, ionModePattern, 2);
if(ionMode.equals("POSITIVE")) {
massSpectrum.setPolarity("+");
massSpectrum.setPolarity(Polarity.POSITIVE);
} else if(ionMode.equals("NEGATIVE")) {
massSpectrum.setPolarity("-");
massSpectrum.setPolarity(Polarity.NEGATIVE);
}
/*
* MS/MS
Expand Down
13 changes: 6 additions & 7 deletions ...d.model/src/org/eclipse/chemclipse/msd/model/core/AbstractRegularLibraryMassSpectrum.java
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Expand Up @@ -32,7 +32,7 @@ public abstract class AbstractRegularLibraryMassSpectrum extends AbstractRegular
//
private ILibraryInformation libraryInformation;
private String precursorType;
private String polarity; // TODO enum?
private Polarity polarity;
private double neutralMass = 0.0d;
private Map<String, String> properties = null; // Initialization on demand

Expand Down Expand Up @@ -87,25 +87,24 @@ public void setNeutralMass(double neutralMass) {
}

@Override
public String getPolarity() {
public Polarity getPolarity() {

if(polarity != null) {
return polarity;
}
if(properties != null) {
String precursorType = getProperty(PROPERTY_PRECURSOR_TYPE);
if(precursorType.contains("]+")) {
return "+";
return Polarity.POSITIVE;
} else if(precursorType.contains("]-")) {
return "-";
return Polarity.NEGATIVE;
}
}
//
return "";
return Polarity.NONE;
}

@Override
public void setPolarity(String polarity) {
public void setPolarity(Polarity polarity) {

this.polarity = polarity;
}
Expand Down
16 changes: 3 additions & 13 deletions ...ipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/IRegularLibraryMassSpectrum.java
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Expand Up @@ -27,19 +27,9 @@ public interface IRegularLibraryMassSpectrum extends IRegularMassSpectrum, ILibr

void setNeutralMass(double neutralMass);

/**
* Returns the polarity if set.
*
* Otherwise returns the polarity (+) or (-)
* if the precursor type is set.
*
* If none is available "" will be returned.
*
* @return String
*/
String getPolarity();

void setPolarity(String polarity);
Polarity getPolarity();

void setPolarity(Polarity polarity);

Set<String> getPropertyKeySet();

Expand Down
39 changes: 39 additions & 0 deletions .../org.eclipse.chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/Polarity.java
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@@ -0,0 +1,39 @@
/*******************************************************************************
* Copyright (c) 2023 Lablicate GmbH.
*
* All rights reserved.
* This program and the accompanying materials are made available under the
* terms of the Eclipse Public License v1.0 which accompanies this distribution,
* and is available at http://www.eclipse.org/legal/epl-v10.html
*
* Contributors:
* Matthias Mailänder - initial API and implementation
*******************************************************************************/
package org.eclipse.chemclipse.msd.model.core;

import org.eclipse.chemclipse.support.text.ILabel;

public enum Polarity implements ILabel {

POSITIVE("+"), //
NEGATIVE("-"), //
NONE("");

private String label;

private Polarity(String label) {

this.label = label;
}

@Override
public String label() {

return label;
}

public static String[][] getOptions() {

return ILabel.getOptions(values());
}
}
3 changes: 2 additions & 1 deletion ...emclipse/msd/converter/supplier/amdis/converter/msp/MassBankMS2ImportConverter_ITest.java
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Expand Up @@ -17,6 +17,7 @@
import org.eclipse.chemclipse.msd.converter.supplier.amdis.io.ImportConverterMspTestCase;
import org.eclipse.chemclipse.msd.model.core.IRegularLibraryMassSpectrum;
import org.eclipse.chemclipse.msd.model.core.IScanMSD;
import org.eclipse.chemclipse.msd.model.core.Polarity;
import org.junit.Test;

public class MassBankMS2ImportConverter_ITest extends ImportConverterMspTestCase {
Expand Down Expand Up @@ -51,7 +52,7 @@ public void testMassSpectrum() {
assertEquals(288.1225d, regularLibraryMassSpectrum.getPrecursorIon());
assertEquals(287.11575d, regularLibraryMassSpectrum.getNeutralMass());
assertEquals("30(NCE)", regularLibraryMassSpectrum.getProperty(IRegularLibraryMassSpectrum.PROPERTY_COLLISION_ENERGY));
assertEquals("+", regularLibraryMassSpectrum.getPolarity());
assertEquals(Polarity.POSITIVE, regularLibraryMassSpectrum.getPolarity());
assertEquals("[M+H]+", regularLibraryMassSpectrum.getProperty(IRegularLibraryMassSpectrum.PROPERTY_PRECURSOR_TYPE));
assertEquals("Q-Exactive Orbitrap Thermo Scientific", regularLibraryMassSpectrum.getProperty(IRegularLibraryMassSpectrum.PROPERTY_INSTRUMENT_NAME));
}
Expand Down
3 changes: 2 additions & 1 deletion ...rc/org/eclipse/chemclipse/msd/model/implementation/RegularLibraryMassSpectrum_4_Test.java
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Expand Up @@ -12,6 +12,7 @@
package org.eclipse.chemclipse.msd.model.implementation;

import org.eclipse.chemclipse.msd.model.core.IRegularLibraryMassSpectrum;
import org.eclipse.chemclipse.msd.model.core.Polarity;

import junit.framework.TestCase;

Expand Down Expand Up @@ -52,7 +53,7 @@ public void test3() {

public void test4() {

assertEquals("", massSpectrum.getPolarity());
assertEquals(Polarity.NONE, massSpectrum.getPolarity());
}

public void test5() {
Expand Down
3 changes: 2 additions & 1 deletion ...rc/org/eclipse/chemclipse/msd/model/implementation/RegularLibraryMassSpectrum_5_Test.java
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Expand Up @@ -12,6 +12,7 @@
package org.eclipse.chemclipse.msd.model.implementation;

import org.eclipse.chemclipse.msd.model.core.IRegularLibraryMassSpectrum;
import org.eclipse.chemclipse.msd.model.core.Polarity;

import junit.framework.TestCase;

Expand Down Expand Up @@ -55,7 +56,7 @@ public void test3() {

public void test4() {

assertEquals("+", massSpectrum.getPolarity());
assertEquals(Polarity.POSITIVE, massSpectrum.getPolarity());
}

public void test5() {
Expand Down
3 changes: 2 additions & 1 deletion ...rc/org/eclipse/chemclipse/msd/model/implementation/RegularLibraryMassSpectrum_6_Test.java
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Expand Up @@ -12,6 +12,7 @@
package org.eclipse.chemclipse.msd.model.implementation;

import org.eclipse.chemclipse.msd.model.core.IRegularLibraryMassSpectrum;
import org.eclipse.chemclipse.msd.model.core.Polarity;

import junit.framework.TestCase;

Expand Down Expand Up @@ -55,7 +56,7 @@ public void test3() {

public void test4() {

assertEquals("-", massSpectrum.getPolarity());
assertEquals(Polarity.NEGATIVE, massSpectrum.getPolarity());
}

public void test5() {
Expand Down
3 changes: 2 additions & 1 deletion ...rc/org/eclipse/chemclipse/msd/model/implementation/RegularLibraryMassSpectrum_7_Test.java
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Expand Up @@ -12,6 +12,7 @@
package org.eclipse.chemclipse.msd.model.implementation;

import org.eclipse.chemclipse.msd.model.core.IRegularLibraryMassSpectrum;
import org.eclipse.chemclipse.msd.model.core.Polarity;

import junit.framework.TestCase;

Expand Down Expand Up @@ -55,7 +56,7 @@ public void test3() {

public void test4() {

assertEquals("+", massSpectrum.getPolarity());
assertEquals(Polarity.POSITIVE, massSpectrum.getPolarity());
}

public void test5() {
Expand Down
3 changes: 2 additions & 1 deletion ...rc/org/eclipse/chemclipse/msd/model/implementation/RegularLibraryMassSpectrum_8_Test.java
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Expand Up @@ -12,6 +12,7 @@
package org.eclipse.chemclipse.msd.model.implementation;

import org.eclipse.chemclipse.msd.model.core.IRegularLibraryMassSpectrum;
import org.eclipse.chemclipse.msd.model.core.Polarity;

import junit.framework.TestCase;

Expand Down Expand Up @@ -55,7 +56,7 @@ public void test3() {

public void test4() {

assertEquals("+", massSpectrum.getPolarity());
assertEquals(Polarity.POSITIVE, massSpectrum.getPolarity());
}

public void test5() {
Expand Down