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eselmeistereselmeister
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Merge pull request #2688 from Mailaender/amdis-dd
Mark peaks imported from AMDIS as deconvoluted
2 parents fe6f97c + 3bce6a9 commit 3aa8dca

28 files changed

+37
-54
lines changed

‎chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.amdis/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/io/ELUReader.java‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
/*******************************************************************************
2-
* Copyright (c) 2014, 2025 Lablicate GmbH.
2+
* Copyright (c) 2014, 2026 Lablicate GmbH.
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*
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* This program and the accompanying materials are made
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* available under the terms of the Eclipse Public License 2.0
@@ -28,6 +28,7 @@
2828
import org.eclipse.chemclipse.logging.core.Logger;
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import org.eclipse.chemclipse.model.core.IChromatogramOverview;
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import org.eclipse.chemclipse.model.core.IPeakIntensityValues;
31+
import org.eclipse.chemclipse.model.core.PeakType;
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import org.eclipse.chemclipse.model.implementation.PeakIntensityValues;
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import org.eclipse.chemclipse.msd.converter.io.IPeakReader;
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import org.eclipse.chemclipse.msd.converter.supplier.amdis.preferences.PreferenceSupplier;
@@ -268,6 +269,7 @@ private IPeakMSD extractPeak(String peakData, int scanInterval) {
268269
IPeakModelMSD peakModel = new PeakModelMSD(peakMassSpectrum, peakIntensityValues, 0.0f, 0.0f);
269270
extractScanRange(peakModel, peakData);
270271
peak = new PeakMSD(peakModel, "AMDIS (ELU)");
272+
peak.setPeakType(PeakType.DD);
271273
peak.setTemporaryData(header);
272274
} catch(Exception e) {
273275
logger.warn("PeakModel fails for AMDIS (ELU) component: " + header);

‎chemclipse/tests/org.eclipse.chemclipse.msd.converter.supplier.amdis.fragment.test/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/converter/elu/ELUImportConverter_1_ITest.java‎

Lines changed: 3 additions & 1 deletion
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@@ -19,6 +19,7 @@
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import java.io.IOException;
2020
import java.util.List;
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22+
import org.eclipse.chemclipse.model.core.PeakType;
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import org.eclipse.chemclipse.msd.converter.io.IPeakReader;
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import org.eclipse.chemclipse.msd.converter.supplier.amdis.TestPathHelper;
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import org.eclipse.chemclipse.msd.converter.supplier.amdis.io.ELUReader;
@@ -42,7 +43,7 @@ public class ELUImportConverter_1_ITest {
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private File file;
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@BeforeAll
45-
public void setUp() throws IOException {
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public void setUp() {
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reader = new ELUReader();
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file = new File(TestPathHelper.TESTFILE_IMPORT_PEAKS_1_ELU);
@@ -57,6 +58,7 @@ public void testRead_1() throws IOException {
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IProcessingInfo<IPeaksMSD> processingInfo = reader.read(file, new NullProgressMonitor());
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List<IPeakMSD> peaks = processingInfo.getProcessingResult().getPeaks();
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IPeakMSD peak1 = peaks.get(0);
61+
assertEquals(peak1.getPeakType(), PeakType.DD);
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6163
assertEquals(14, peak1.getPeakModel().getTemporarilyInfo(IPeakReader.TEMP_INFO_START_SCAN));
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assertEquals(23, peak1.getPeakModel().getTemporarilyInfo(IPeakReader.TEMP_INFO_STOP_SCAN));

‎chemclipse/tests/org.eclipse.chemclipse.msd.converter.supplier.amdis.fragment.test/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/converter/elu/ELUImportConverter_2_ITest.java‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -19,6 +19,7 @@
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import java.io.IOException;
2020
import java.util.List;
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22+
import org.eclipse.chemclipse.model.core.PeakType;
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import org.eclipse.chemclipse.msd.converter.supplier.amdis.TestPathHelper;
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import org.eclipse.chemclipse.msd.converter.supplier.amdis.io.ELUReader;
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import org.eclipse.chemclipse.msd.converter.supplier.amdis.preferences.PreferenceSupplier;
@@ -41,7 +42,7 @@ public class ELUImportConverter_2_ITest {
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private File file;
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@BeforeAll
44-
public void setUp() throws IOException {
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public void setUp() {
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reader = new ELUReader();
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file = new File(TestPathHelper.TESTFILE_IMPORT_PEAKS_1_ELU);
@@ -57,6 +58,8 @@ public void testRead_1() throws IOException {
5758
List<IPeakMSD> peaks = processingInfo.getProcessingResult().getPeaks();
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IPeakMSD peak1 = peaks.get(0);
61+
assertEquals(peak1.getPeakType(), PeakType.DD);
62+
6063
IPeakMassSpectrum peakMassSpectrum1 = peak1.getPeakModel().getPeakMassSpectrum();
6164
List<IIon> ions1 = peakMassSpectrum1.getIons();
6265

‎chemclipse/tests/org.eclipse.chemclipse.msd.converter.supplier.amdis.fragment.test/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/converter/elu/ELUReader_1_ITest.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -34,7 +34,7 @@ public class ELUReader_1_ITest {
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private File file;
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@BeforeAll
37-
public void setUp() throws IOException {
37+
public void setUp() {
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3939
reader = new ELUReader();
4040
file = new File(TestPathHelper.TESTFILE_IMPORT_PEAKS_1_ELU);

‎chemclipse/tests/org.eclipse.chemclipse.msd.converter.supplier.amdis.fragment.test/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/converter/msl/Encoding_1_ITest.java‎

Lines changed: 1 addition & 2 deletions
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@@ -16,7 +16,6 @@
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import static org.junit.jupiter.api.Assertions.assertNotNull;
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import java.io.File;
19-
import java.io.IOException;
2019

2120
import org.eclipse.chemclipse.msd.converter.supplier.amdis.TestPathHelper;
2221
import org.eclipse.chemclipse.msd.converter.supplier.amdis.io.ImportConverterMslTestCase;
@@ -32,7 +31,7 @@ public class Encoding_1_ITest extends ImportConverterMslTestCase {
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3332
@Override
3433
@BeforeAll
35-
public void setUp() throws IOException {
34+
public void setUp() {
3635

3736
importFile = new File(TestPathHelper.TESTFILE_IMPORT_ENCODING_MSL);
3837
super.setUp();

‎chemclipse/tests/org.eclipse.chemclipse.msd.converter.supplier.amdis.fragment.test/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/converter/msl/MSLExportConverter_1_ITest.java‎

Lines changed: 1 addition & 2 deletions
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@@ -15,7 +15,6 @@
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import java.io.File;
18-
import java.io.IOException;
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2019
import org.eclipse.chemclipse.msd.converter.database.IDatabaseExportConverter;
2120
import org.eclipse.chemclipse.msd.converter.supplier.amdis.TestPathHelper;
@@ -40,7 +39,7 @@ public class MSLExportConverter_1_ITest {
4039
private IMassSpectra massSpectra;
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4241
@BeforeAll
43-
public void setUp() throws IOException {
42+
public void setUp() {
4443

4544
exportConverter = new MSLDatabaseExportConverter();
4645
File exportFolder = new File(TestPathHelper.TESTDIR_EXPORT);

‎chemclipse/tests/org.eclipse.chemclipse.msd.converter.supplier.amdis.fragment.test/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/converter/msl/MSLExportConverter_2_ITest.java‎

Lines changed: 1 addition & 2 deletions
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@@ -17,7 +17,6 @@
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import static org.junit.jupiter.api.Assertions.assertTrue;
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1919
import java.io.File;
20-
import java.io.IOException;
2120
import java.util.List;
2221
import java.util.Set;
2322

@@ -50,7 +49,7 @@ public class MSLExportConverter_2_ITest extends ImportConverterMslTestCase {
5049

5150
@Override
5251
@BeforeAll
53-
public void setUp() throws IOException {
52+
public void setUp() {
5453

5554
/*
5655
* Export

‎chemclipse/tests/org.eclipse.chemclipse.msd.converter.supplier.amdis.fragment.test/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/converter/msl/MSLImportConverter_2_ITest.java‎

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@@ -16,7 +16,6 @@
1616
import static org.junit.jupiter.api.Assertions.assertNotNull;
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import java.io.File;
19-
import java.io.IOException;
2019

2120
import org.eclipse.chemclipse.msd.converter.supplier.amdis.TestPathHelper;
2221
import org.eclipse.chemclipse.msd.converter.supplier.amdis.io.ImportConverterMslTestCase;
@@ -32,7 +31,7 @@ public class MSLImportConverter_2_ITest extends ImportConverterMslTestCase {
3231

3332
@Override
3433
@BeforeAll
35-
public void setUp() throws IOException {
34+
public void setUp() {
3635

3736
importFile = new File(TestPathHelper.TESTFILE_IMPORT_GOLMDB_TEST_MSL);
3837
super.setUp();

‎chemclipse/tests/org.eclipse.chemclipse.msd.converter.supplier.amdis.fragment.test/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/converter/msl/MSLImportConverter_3_ITest.java‎

Lines changed: 1 addition & 2 deletions
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@@ -17,7 +17,6 @@
1717
import static org.junit.jupiter.api.Assertions.assertTrue;
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1919
import java.io.File;
20-
import java.io.IOException;
2120
import java.util.List;
2221
import java.util.Set;
2322

@@ -42,7 +41,7 @@ public class MSLImportConverter_3_ITest extends ImportConverterMslTestCase {
4241

4342
@Override
4443
@BeforeAll
45-
public void setUp() throws IOException {
44+
public void setUp() {
4645

4746
importFile = new File(TestPathHelper.TESTFILE_IMPORT_DB_4);
4847
super.setUp();

‎chemclipse/tests/org.eclipse.chemclipse.msd.converter.supplier.amdis.fragment.test/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/converter/msp/MSPExportConverter_1_ITest.java‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -15,7 +15,6 @@
1515
import static org.junit.jupiter.api.Assertions.assertTrue;
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1717
import java.io.File;
18-
import java.io.IOException;
1918

2019
import org.eclipse.chemclipse.msd.converter.database.IDatabaseExportConverter;
2120
import org.eclipse.chemclipse.msd.converter.supplier.amdis.TestPathHelper;
@@ -40,7 +39,7 @@ public class MSPExportConverter_1_ITest {
4039
private IMassSpectra massSpectra;
4140

4241
@BeforeAll
43-
public void setUp() throws IOException {
42+
public void setUp() {
4443

4544
exportConverter = new MSPDatabaseExportConverter();
4645
File exportFolder = new File(TestPathHelper.TESTDIR_EXPORT);

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