/** * Helper to handle metadata in the document * * @throws CheckedIOException */ private void writeMetaData(PeakList peaklist) { // skip if previously done if (hasWrittenMetaData) { return; } // flag meta-data as writter hasWrittenMetaData = true; // try to get meta-data if it is available if (peaklist instanceof MzXMLPeakList) { MzXMLPeakList mzxml = (MzXMLPeakList) peaklist; msRun = mzxml.getMsRun(); } else { msRun = new MsRun(); } try { // write out all the parent files for (ParentFile pf : msRun.getParentFiles()) { xmlw.writeEmptyElement("parentFile"); writeNonNull(xmlw, "fileName", pf.getFileName()); writeNonNull(xmlw, "fileType", pf.getFileType()); writeNonNull(xmlw, "fileSha1", pf.getFileSHA()); } // write out all the msInstrument information MsInstrument msInstrument = msRun.getMsInstrument(); if (msInstrument != null) { xmlw.writeStartElement("msInstrument"); // write out msManufacture if (msInstrument.getMsManufacturer() != null) { xmlw.writeEmptyElement("msManufacturer"); writeNonNull(xmlw, "category", msInstrument.getMsManufacturer().getCategory()); if (msInstrument.getMsManufacturer().getValue() != null) writeNonNull(xmlw, "value", msInstrument.getMsManufacturer().getValue()); } // write out msModel if (msInstrument.getMsModel() != null) { xmlw.writeEmptyElement("msModel"); writeNonNull(xmlw, "category", msInstrument.getMsModel().getCategory()); writeNonNull(xmlw, "value", msInstrument.getMsModel().getValue()); } // write out msManufacture if (msInstrument.getMsIonisation() != null) { xmlw.writeEmptyElement("msIonisation"); writeNonNull(xmlw, "category", msInstrument.getMsIonisation().getCategory()); writeNonNull(xmlw, "value", msInstrument.getMsIonisation().getValue()); } // write out msManufacture if (msInstrument.getMsMassAnalyzer() != null) { xmlw.writeEmptyElement("msMassAnalyzer"); writeNonNull(xmlw, "category", msInstrument.getMsMassAnalyzer().getCategory()); writeNonNull(xmlw, "value", msInstrument.getMsMassAnalyzer().getValue()); } // write out msManufacture if (msInstrument.getMsDetector() != null) { xmlw.writeEmptyElement("msDetector"); writeNonNull(xmlw, "category", msInstrument.getMsDetector().getCategory()); writeNonNull(xmlw, "value", msInstrument.getMsDetector().getValue()); } // write out software if (msInstrument.getSoftware() != null) { xmlw.writeEmptyElement("software"); writeNonNull(xmlw, "type", msInstrument.getSoftware().getType()); writeNonNull(xmlw, "name", msInstrument.getSoftware().getName()); writeNonNull(xmlw, "version", msInstrument.getSoftware().getVersion()); writeNonNull(xmlw, "completionTime", msInstrument.getSoftware().getCompletionTime()); } // write out msResolution if (msInstrument.getMsResolution() != null) { xmlw.writeEmptyElement("msResolution"); writeNonNull(xmlw, "category", msInstrument.getMsResolution().getCategory()); writeNonNull(xmlw, "value", msInstrument.getMsResolution().getValue()); } // write out operator if (msInstrument.getOperator() != null) { xmlw.writeEmptyElement("operator"); writeNonNull(xmlw, "first", msInstrument.getOperator().getFirst()); writeNonNull(xmlw, "last", msInstrument.getOperator().getLast()); writeNonNull(xmlw, "email", msInstrument.getOperator().getEmail()); writeNonNull(xmlw, "phone", msInstrument.getOperator().getPhone()); writeNonNull(xmlw, "URI", msInstrument.getOperator().getURI()); } xmlw.writeEndElement(); } // write out all the dataProcessing information for (DataProcessing dp : msRun.getDataProcessings()) { xmlw.writeStartElement("dataProcessing"); writeNonNull(xmlw, "intensityCutoff", dp.getIntensityCutoff()); writeNonNull(xmlw, "centroided", dp.getCentroided()); writeNonNull(xmlw, "deisotoped", dp.getDeisotoped()); writeNonNull(xmlw, "chargeDeconvoluted", dp.getChargeDeconvoluted()); writeNonNull(xmlw, "spotIntegration", dp.getSpotIntegration()); // get all software Software software = dp.getSoftware(); // write out software if (software != null) { xmlw.writeEmptyElement("software"); writeNonNull(xmlw, "type", software.getType()); writeNonNull(xmlw, "name", software.getName()); writeNonNull(xmlw, "version", software.getVersion()); writeNonNull(xmlw, "completionTime", software.getCompletionTime()); } xmlw.writeEndElement(); } } catch (XMLStreamException e) { throw new RuntimeException("Can't write mzXML meta-data!", e); } }
public static void main(String[] args) { // # INPUT # DataProcessing data = new DataProcessing(); data.GetDataParameters(); data.GetDataFromFile(); // # DATA PROCESSING # // - Energy int windowLength = 30; for (int i = 0; i < data.GetDataCounter(); i++) { data.modifiedData[i] = 0; for (int k = 0; k < windowLength * data.GetSamplingRate(); k++) { if ((i - k) >= 0) { data.modifiedData[i] += Math.pow(data.originalData[i - k], 2); } } } // # OUTPUT # data.modifiedData = data.NormalizeData(data.modifiedData, data.modifiedData); data.PutDataFile(data.modifiedData, "normalizedModifiedData.txt"); data.originalData = data.NormalizeData(data.originalData, data.originalData); data.PutDataFile(data.originalData, "normalizedOriginalData.txt"); }