Skip to content

Commit

Permalink
Code cleanup.
Browse files Browse the repository at this point in the history
  • Loading branch information
@Mailaender
Mailaender committed Feb 1, 2025
1 parent 69b332e commit a2b13d4
Show file tree
Hide file tree
Showing 7 changed files with 55 additions and 59 deletions.
16 changes: 6 additions & 10 deletions ...c/org/eclipse/chemclipse/chromatogram/xxd/filter/supplier/scan/core/FilterDuplicator.java
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2022, 2024 Lablicate GmbH.
* Copyright (c) 2022, 2025 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand Down Expand Up @@ -81,7 +81,7 @@ private void applyScanDuplicatorFilter(IChromatogramSelection<?, ?> chromatogram
for(IScan scan : chromatogram.getScans()) {
scanMap.put(scan.getRetentionTime(), scan);
}
//

List<IScan> scansToReplace = new ArrayList<>();
for(IScan scan : chromatogram.getScans()) {
/*
Expand All @@ -99,7 +99,7 @@ private void applyScanDuplicatorFilter(IChromatogramSelection<?, ?> chromatogram
IScan scanNext = scanEntryNext.getValue();
int retentionTimeCenter = (int)((scanNext.getRetentionTime() + scan.getRetentionTime()) / 2.0d);
float intensityCenter = (scanNext.getTotalSignal() + scan.getTotalSignal()) / 2.0f;
//

if(scan instanceof IScanCSD) {
/*
* CSD
Expand Down Expand Up @@ -168,13 +168,9 @@ private List<IIon> createTraces(IScanMSD scanMSD) {

List<IIon> traces = new ArrayList<>();
for(IIon trace : scanMSD.getIons()) {
try {
traces.add(new Ion(trace.getIon(), trace.getAbundance()));
} catch(Exception e) {
// logger.warn(e);
}
traces.add(new Ion(trace.getIon(), trace.getAbundance()));
}
//

return traces;
}

Expand All @@ -184,7 +180,7 @@ private Map<Float, Float> getTraces(IScanWSD scanWSD) {
for(IScanSignalWSD trace : scanWSD.getScanSignals()) {
traceMap.put(trace.getWavelength(), trace.getAbsorbance());
}
//

return traceMap;
}
}
12 changes: 7 additions & 5 deletions ...ipse/chemclipse/msd/converter/supplier/mmass/internal/io/MassSpectrumReaderVersion20.java
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2022, 2024 Lablicate GmbH.
* Copyright (c) 2022, 2025 Lablicate GmbH.
*
* All rights reserved.
* This program and the accompanying materials are made available under the
Expand Down Expand Up @@ -68,7 +68,7 @@ public IMassSpectra read(File file, IProgressMonitor monitor) throws IOException
massSpectrum.setFile(file);
massSpectrum.setIdentifier(file.getName());
massSpectrum.setMassSpectrumType(MassSpectrumType.PROFILE);
//

NodeList nodeList = getTopNode(file);
for(int i = 0; i < nodeList.getLength(); i++) {
Node node = nodeList.item(i);
Expand All @@ -85,10 +85,12 @@ public IMassSpectra read(File file, IProgressMonitor monitor) throws IOException
logger.warn(e);
} catch(ParserConfigurationException e) {
logger.warn(e);
} catch(Exception e) {
e.printStackTrace();
} catch(DOMException e) {
logger.warn(e);
} catch(DataFormatException e) {
logger.warn(e);
}
//

IVendorMassSpectra massSpectra = new VendorMassSpectra();
massSpectra.setName(file.getName());
massSpectra.addMassSpectrum(massSpectrum);
Expand Down
8 changes: 5 additions & 3 deletions ...ipse/chemclipse/msd/converter/supplier/mmass/internal/io/MassSpectrumReaderVersion22.java
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2022, 2024 Lablicate GmbH.
* Copyright (c) 2022, 2025 Lablicate GmbH.
*
* All rights reserved.
* This program and the accompanying materials are made available under the
Expand Down Expand Up @@ -85,8 +85,10 @@ public IMassSpectra read(File file, IProgressMonitor monitor) throws IOException
logger.warn(e);
} catch(ParserConfigurationException e) {
logger.warn(e);
} catch(Exception e) {
e.printStackTrace();
} catch(DOMException e) {
logger.warn(e);
} catch(DataFormatException e) {
logger.warn(e);
}
//
IVendorMassSpectra massSpectra = new VendorMassSpectra();
Expand Down
6 changes: 3 additions & 3 deletions ...v/src/org/eclipse/chemclipse/pcr/report/supplier/tabular/csv/core/PCRExportConverter.java
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2022, 2023 Lablicate GmbH.
* Copyright (c) 2022, 2025 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand Down Expand Up @@ -58,9 +58,9 @@
public class PCRExportConverter extends AbstractPlateExportConverter implements IPlateExportConverter {

private static final Logger logger = Logger.getLogger(PCRExportConverter.class);
//

private static final String DESCRIPTION = "PCR CSV Export";
//

private DecimalFormat decimalFormat = new DecimalFormat("00" + PreferenceSupplier.getDecimalSeparator().getCharacter() + "00");

@Override
Expand Down
18 changes: 9 additions & 9 deletions ...r.csv/src/org/eclipse/chemclipse/xxd/converter/supplier/csv/io/core/CSVPeakConverter.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -107,19 +107,19 @@ public IProcessingInfo<File> convert(File file, IPeaksMSD peaks, boolean append,

private static StringBuilder writeIntensities(IPeakModelMSD peakModel) {

StringBuilder sb = new StringBuilder();
StringBuilder stringBuilder = new StringBuilder();
if(peakModel != null) {
List<Integer> retentionTimes = peakModel.getRetentionTimes();
for(Integer rt : retentionTimes) {
if(sb.length() > 0) {
sb.append(SEPERATOR_RECORD);
if(stringBuilder.length() > 0) {
stringBuilder.append(SEPERATOR_RECORD);
}
sb.append(rt);
sb.append(SEPERATOR_VALUE);
sb.append(peakModel.getPeakAbundance(rt));
stringBuilder.append(rt);
stringBuilder.append(SEPERATOR_VALUE);
stringBuilder.append(peakModel.getPeakAbundance(rt));
}
}
return sb;
return stringBuilder;
}

private static StringBuilder writeMassSpectrum(IIonProvider provider) {
Expand Down Expand Up @@ -217,7 +217,7 @@ public static IPeaksMSD readPeaks(Reader reader) throws IOException, ParseExcept
synchronized(NUMBER_FORMAT) {
nf = (NumberFormat)NUMBER_FORMAT.clone();
}
//

for(CSVRecord csvRecord : parser) {
PeakModelMSD peakModel = new PeakModelMSD(parseMassSpectrum(csvRecord.get(HEADER_MZ)), parseIntensityValues(csvRecord.get(HEADER_INTENSITIES)));
IScan maximum = peakModel.getPeakMaximum();
Expand Down Expand Up @@ -279,7 +279,7 @@ public static String getName(IPeak peak) {
if(libraryInformation != null) {
return libraryInformation.getName();
}
//

return "";
}
}
26 changes: 11 additions & 15 deletions ...csv/src/org/eclipse/chemclipse/xxd/converter/supplier/csv/io/core/ChromatogramReader.java
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2011, 2024 Lablicate GmbH.
* Copyright (c) 2011, 2025 Lablicate GmbH.
*
* All rights reserved.
* This program and the accompanying materials are made available under the
Expand Down Expand Up @@ -38,7 +38,7 @@
public class ChromatogramReader extends AbstractChromatogramMSDReader implements IChromatogramMSDReader {

private static final Logger logger = Logger.getLogger(ChromatogramReader.class);
//

private static final String ZERO_VALUE = "0.0";
private static final int ION_COLUMN_START = 3;

Expand Down Expand Up @@ -69,15 +69,15 @@ public static boolean isValidFileFormat(File file) throws IOException {
char[] chars = new char[ChromatogramWriter.RT_MILLISECONDS_COLUMN.length()];
reader.read(chars);
reader.close();
//

String firstColumn = new String(chars);
return firstColumn.equals(ChromatogramWriter.RT_MILLISECONDS_COLUMN);
}

private IChromatogramMSD readChromatogram(File file, boolean overview) throws IOException {

IChromatogramMSD chromatogram = null;
//

try (FileReader fileReader = new FileReader(file)) {
String zeroMarker = PreferenceSupplier.getImportZeroMarker();
zeroMarker = zeroMarker.startsWith(ZERO_VALUE) ? zeroMarker : ZERO_VALUE;
Expand All @@ -99,7 +99,7 @@ private IChromatogramMSD readChromatogram(File file, boolean overview) throws IO
IRegularMassSpectrum supplierMassSpectrum = getScan(csvRecord, ionsMap, zeroMarker, overview);
chromatogram.addScan(supplierMassSpectrum);
}
//

int scanDelay = chromatogram.getScan(1).getRetentionTime();
chromatogram.setScanDelay(scanDelay);
csvParser.close();
Expand Down Expand Up @@ -136,23 +136,19 @@ private IRegularMassSpectrum getScan(CSVRecord csvRecord, Map<Integer, Float> io
float retentionIndex = Float.parseFloat(retentionIndexValue);
massSpectrum.setRetentionIndex(retentionIndex);
if(overview) {
try {
IIon ion = getIonsOverview(csvRecord, zeroMarker);
massSpectrum.addIon(ion);
} catch(Exception e) {
// logger.warn(e); - Don't log this.
}
IIon ion = getIonsOverview(csvRecord, zeroMarker);
massSpectrum.addIon(ion);
} else {
List<IIon> ions = getIons(csvRecord, ionsMap, zeroMarker);
for(IIon ion : ions) {
massSpectrum.addIon(ion);
}
}
//

return massSpectrum;
}

private IIon getIonsOverview(CSVRecord csvRecord, String zeroMarker) {
private IIon getIonsOverview(CSVRecord csvRecord, String zeroMarker) {

float abundanceTotalSignal = 0.0f;
for(int index = ION_COLUMN_START; index < csvRecord.size(); index++) {
Expand All @@ -162,7 +158,7 @@ private IIon getIonsOverview(CSVRecord csvRecord, String zeroMarker) {
abundanceTotalSignal += abundance;
}
}
//

return new VendorIon(IIon.TIC_ION, abundanceTotalSignal);
}

Expand All @@ -182,7 +178,7 @@ private List<IIon> getIons(CSVRecord csvRecord, Map<Integer, Float> ionsMap, Str
}
}
}
//

return ions;
}
}
28 changes: 14 additions & 14 deletions ...r.pca/src/org/eclipse/chemclipse/xxd/process/supplier/pca/core/PcaExtractionFileText.java
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2020, 2024 Lablicate GmbH.
* Copyright (c) 2020, 2025 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand Down Expand Up @@ -38,13 +38,13 @@
public class PcaExtractionFileText implements IExtractionData {

private static final Logger logger = Logger.getLogger(PcaExtractionFileText.class);
//

public static final String DESCRIPTION = "PCA Data Matrix";
public static final String FILE_EXTENSION = ".pdm";
public static final String FILE_NAME = DESCRIPTION.replaceAll("\\s", "") + FILE_EXTENSION;
public static final String FILTER_EXTENSION = "*" + FILE_EXTENSION;
public static final String FILTER_NAME = DESCRIPTION + " (*" + FILE_EXTENSION + ")";
//

private static final String DELIMITER = "\t";
private final List<IDataInputEntry> dataInputEntries;

Expand Down Expand Up @@ -76,10 +76,10 @@ public static void exportDemoContent(PrintWriter printWriter) {
* Data
*/
for(int j = 0; j < 20; j++) {
//

int sampleNumber = j + 1;
double type = Math.random();
//

printWriter.print("Sample ");
if(sampleNumber < 10) {
printWriter.print("0");
Expand Down Expand Up @@ -109,7 +109,7 @@ private Samples extract() {

Map<String, Sample> sampleMap = new HashMap<>();
Map<String, Map<String, Target>> samplesVariablesMap = new HashMap<>();
//

for(IDataInputEntry dataInputEntry : dataInputEntries) {
String inputFile = dataInputEntry.getInputFile();
File file = new File(inputFile);
Expand Down Expand Up @@ -190,7 +190,7 @@ private Samples extract() {
List<? extends IVariable> variables = extractVariables(samplesVariablesMap);
samples.getVariables().addAll(variables);
setExtractData(samplesVariablesMap, samples);
//

return samples;
}

Expand Down Expand Up @@ -218,23 +218,23 @@ private List<? extends IVariable> extractVariables(Map<String, Map<String, Targe
}
}
}
//

List<? extends IVariable> variables = new ArrayList<>(targets.values());
Collections.sort(variables, (v1, v2) -> v1.compareTo(v2));
Collections.sort(variables, Comparable::compareTo);
return variables;
}

private void setExtractData(Map<String, Map<String, Target>> samplesVariablesMap, Samples samples) {

List<IVariable> variables = samples.getVariables();
//

for(Sample sample : samples.getSamples()) {
Iterator<IVariable> iterator = variables.iterator();
Map<String, Target> extractPeak = samplesVariablesMap.get(sample.getSampleName());
while(iterator.hasNext()) {
String variable = iterator.next().getValue();
Target target = extractPeak.get(variable);
//

boolean addEmpty = true;
if(target != null) {
try {
Expand All @@ -246,7 +246,7 @@ private void setExtractData(Map<String, Map<String, Target>> samplesVariablesMap
logger.warn(e);
}
}
//

if(addEmpty) {
PeakSampleData sampleData = new PeakSampleData();
sample.getSampleData().add(sampleData);
Expand All @@ -259,11 +259,11 @@ private Map<Integer, String> extractIndexMap(CSVParser parser) {

Map<Integer, String> indexMap = new HashMap<>();
Map<String, Integer> headerMap = parser.getHeaderMap();
//

for(Map.Entry<String, Integer> entry : headerMap.entrySet()) {
indexMap.put(entry.getValue(), entry.getKey());
}
//

return indexMap;
}
}

0 comments on commit a2b13d4

Please sign in to comment.