From a2b13d4e6ddff04a4010ec0f8262cef20d397e6f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20Mail=C3=A4nder?= Date: Sat, 1 Feb 2025 15:40:35 +0100 Subject: [PATCH] Code cleanup. --- .../supplier/scan/core/FilterDuplicator.java | 16 ++++------- .../io/MassSpectrumReaderVersion20.java | 12 ++++---- .../io/MassSpectrumReaderVersion22.java | 8 ++++-- .../tabular/csv/core/PCRExportConverter.java | 6 ++-- .../csv/io/core/CSVPeakConverter.java | 18 ++++++------ .../csv/io/core/ChromatogramReader.java | 26 ++++++++--------- .../pca/core/PcaExtractionFileText.java | 28 +++++++++---------- 7 files changed, 55 insertions(+), 59 deletions(-) diff --git a/chemclipse/plugins/org.eclipse.chemclipse.chromatogram.xxd.filter.supplier.scan/src/org/eclipse/chemclipse/chromatogram/xxd/filter/supplier/scan/core/FilterDuplicator.java b/chemclipse/plugins/org.eclipse.chemclipse.chromatogram.xxd.filter.supplier.scan/src/org/eclipse/chemclipse/chromatogram/xxd/filter/supplier/scan/core/FilterDuplicator.java index 0c46cfda65..16529154ad 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.chromatogram.xxd.filter.supplier.scan/src/org/eclipse/chemclipse/chromatogram/xxd/filter/supplier/scan/core/FilterDuplicator.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.chromatogram.xxd.filter.supplier.scan/src/org/eclipse/chemclipse/chromatogram/xxd/filter/supplier/scan/core/FilterDuplicator.java @@ -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 @@ -81,7 +81,7 @@ private void applyScanDuplicatorFilter(IChromatogramSelection chromatogram for(IScan scan : chromatogram.getScans()) { scanMap.put(scan.getRetentionTime(), scan); } - // + List scansToReplace = new ArrayList<>(); for(IScan scan : chromatogram.getScans()) { /* @@ -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 @@ -168,13 +168,9 @@ private List createTraces(IScanMSD scanMSD) { List 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; } @@ -184,7 +180,7 @@ private Map getTraces(IScanWSD scanWSD) { for(IScanSignalWSD trace : scanWSD.getScanSignals()) { traceMap.put(trace.getWavelength(), trace.getAbsorbance()); } - // + return traceMap; } } diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/src/org/eclipse/chemclipse/msd/converter/supplier/mmass/internal/io/MassSpectrumReaderVersion20.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/src/org/eclipse/chemclipse/msd/converter/supplier/mmass/internal/io/MassSpectrumReaderVersion20.java index 09d2519cde..3bbdf1d3c0 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/src/org/eclipse/chemclipse/msd/converter/supplier/mmass/internal/io/MassSpectrumReaderVersion20.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/src/org/eclipse/chemclipse/msd/converter/supplier/mmass/internal/io/MassSpectrumReaderVersion20.java @@ -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 @@ -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); @@ -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); diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/src/org/eclipse/chemclipse/msd/converter/supplier/mmass/internal/io/MassSpectrumReaderVersion22.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/src/org/eclipse/chemclipse/msd/converter/supplier/mmass/internal/io/MassSpectrumReaderVersion22.java index 77fd805e81..85b8388aa3 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/src/org/eclipse/chemclipse/msd/converter/supplier/mmass/internal/io/MassSpectrumReaderVersion22.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/src/org/eclipse/chemclipse/msd/converter/supplier/mmass/internal/io/MassSpectrumReaderVersion22.java @@ -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 @@ -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(); diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.report.supplier.tabular.csv/src/org/eclipse/chemclipse/pcr/report/supplier/tabular/csv/core/PCRExportConverter.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.report.supplier.tabular.csv/src/org/eclipse/chemclipse/pcr/report/supplier/tabular/csv/core/PCRExportConverter.java index 76cd1cf405..92c1793019 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.pcr.report.supplier.tabular.csv/src/org/eclipse/chemclipse/pcr/report/supplier/tabular/csv/core/PCRExportConverter.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.report.supplier.tabular.csv/src/org/eclipse/chemclipse/pcr/report/supplier/tabular/csv/core/PCRExportConverter.java @@ -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 @@ -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 diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.csv/src/org/eclipse/chemclipse/xxd/converter/supplier/csv/io/core/CSVPeakConverter.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.csv/src/org/eclipse/chemclipse/xxd/converter/supplier/csv/io/core/CSVPeakConverter.java index 56c92778aa..ef120fd438 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.csv/src/org/eclipse/chemclipse/xxd/converter/supplier/csv/io/core/CSVPeakConverter.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.csv/src/org/eclipse/chemclipse/xxd/converter/supplier/csv/io/core/CSVPeakConverter.java @@ -107,19 +107,19 @@ public IProcessingInfo 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 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) { @@ -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(); @@ -279,7 +279,7 @@ public static String getName(IPeak peak) { if(libraryInformation != null) { return libraryInformation.getName(); } - // + return ""; } } diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.csv/src/org/eclipse/chemclipse/xxd/converter/supplier/csv/io/core/ChromatogramReader.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.csv/src/org/eclipse/chemclipse/xxd/converter/supplier/csv/io/core/ChromatogramReader.java index f665934f84..28eafb27bc 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.csv/src/org/eclipse/chemclipse/xxd/converter/supplier/csv/io/core/ChromatogramReader.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.csv/src/org/eclipse/chemclipse/xxd/converter/supplier/csv/io/core/ChromatogramReader.java @@ -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 @@ -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; @@ -69,7 +69,7 @@ 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); } @@ -77,7 +77,7 @@ public static boolean isValidFileFormat(File file) throws IOException { 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; @@ -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(); @@ -136,23 +136,19 @@ private IRegularMassSpectrum getScan(CSVRecord csvRecord, Map 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 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++) { @@ -162,7 +158,7 @@ private IIon getIonsOverview(CSVRecord csvRecord, String zeroMarker) { abundanceTotalSignal += abundance; } } - // + return new VendorIon(IIon.TIC_ION, abundanceTotalSignal); } @@ -182,7 +178,7 @@ private List getIons(CSVRecord csvRecord, Map ionsMap, Str } } } - // + return ions; } } \ No newline at end of file diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.process.supplier.pca/src/org/eclipse/chemclipse/xxd/process/supplier/pca/core/PcaExtractionFileText.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.process.supplier.pca/src/org/eclipse/chemclipse/xxd/process/supplier/pca/core/PcaExtractionFileText.java index 4aba72eca9..53ec6c3b8f 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.process.supplier.pca/src/org/eclipse/chemclipse/xxd/process/supplier/pca/core/PcaExtractionFileText.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.process.supplier.pca/src/org/eclipse/chemclipse/xxd/process/supplier/pca/core/PcaExtractionFileText.java @@ -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 @@ -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 dataInputEntries; @@ -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"); @@ -109,7 +109,7 @@ private Samples extract() { Map sampleMap = new HashMap<>(); Map> samplesVariablesMap = new HashMap<>(); - // + for(IDataInputEntry dataInputEntry : dataInputEntries) { String inputFile = dataInputEntry.getInputFile(); File file = new File(inputFile); @@ -190,7 +190,7 @@ private Samples extract() { List variables = extractVariables(samplesVariablesMap); samples.getVariables().addAll(variables); setExtractData(samplesVariablesMap, samples); - // + return samples; } @@ -218,23 +218,23 @@ private List extractVariables(Map variables = new ArrayList<>(targets.values()); - Collections.sort(variables, (v1, v2) -> v1.compareTo(v2)); + Collections.sort(variables, Comparable::compareTo); return variables; } private void setExtractData(Map> samplesVariablesMap, Samples samples) { List variables = samples.getVariables(); - // + for(Sample sample : samples.getSamples()) { Iterator iterator = variables.iterator(); Map 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 { @@ -246,7 +246,7 @@ private void setExtractData(Map> samplesVariablesMap logger.warn(e); } } - // + if(addEmpty) { PeakSampleData sampleData = new PeakSampleData(); sample.getSampleData().add(sampleData); @@ -259,11 +259,11 @@ private Map extractIndexMap(CSVParser parser) { Map indexMap = new HashMap<>(); Map headerMap = parser.getHeaderMap(); - // + for(Map.Entry entry : headerMap.entrySet()) { indexMap.put(entry.getValue(), entry.getKey()); } - // + return indexMap; } } \ No newline at end of file