Examples with SmallMolecule uk.ac.ebi.pride.jmztab.model.SmallMolecule used on opensource projects

Example 1 with SmallMolecule

use of uk.ac.ebi.pride.jmztab.model.SmallMolecule in project mzmine2 by mzmine.

the class MzTabImportTask method importSmallMolecules.

private void importSmallMolecules(PeakList newPeakList, MZTabFile mzTabFile, Map<Integer, RawDataFile> rawDataFiles) {
    SortedMap<Integer, Assay> assayMap = mzTabFile.getMetadata().getAssayMap();
    Collection<SmallMolecule> smallMolecules = mzTabFile.getSmallMolecules();
    // Loop through SML data
    String formula, description, database, url = "";
    double mzExp = 0, abundance = 0, peak_mz = 0, peak_rt = 0, peak_height = 0, rtValue = 0;
    // int charge = 0;
    int rowCounter = 0;
    for (SmallMolecule smallMolecule : smallMolecules) {
        // Stop the process if cancel() was called
        if (isCanceled())
            return;
        rowCounter++;
        formula = smallMolecule.getChemicalFormula();
        // smile = smallMolecule.getSmiles();
        // inchiKey = smallMolecule.getInchiKey();
        description = smallMolecule.getDescription();
        // species = smallMolecule.getSpecies();
        database = smallMolecule.getDatabase();
        if (smallMolecule.getURI() != null) {
            url = smallMolecule.getURI().toString();
        }
        String identifier = smallMolecule.getIdentifier().toString();
        SplitList<Double> rt = smallMolecule.getRetentionTime();
        if (smallMolecule.getExpMassToCharge() != null) {
            mzExp = smallMolecule.getExpMassToCharge();
        }
        // Calculate average RT if multiple values are available
        if (rt != null && !rt.isEmpty()) {
            rtValue = DoubleMath.mean(rt);
        }
        if ((url != null) && (url.equals("null"))) {
            url = null;
        }
        if (identifier.equals("null")) {
            identifier = null;
        }
        if (description == null && identifier != null) {
            description = identifier;
        }
        // Add shared information to row
        SimplePeakListRow newRow = new SimplePeakListRow(rowCounter);
        newRow.setAverageMZ(mzExp);
        newRow.setAverageRT(rtValue);
        if (description != null) {
            SimplePeakIdentity newIdentity = new SimplePeakIdentity(description, formula, database, identifier, url);
            newRow.addPeakIdentity(newIdentity, false);
        }
        // Add raw data file entries to row
        for (Entry<Integer, RawDataFile> rawDataEntry : rawDataFiles.entrySet()) {
            RawDataFile rawData = rawDataEntry.getValue();
            Assay dataFileAssay = assayMap.get(rawDataEntry.getKey());
            abundance = 0;
            peak_mz = 0;
            peak_rt = 0;
            peak_height = 0;
            if (smallMolecule.getAbundanceColumnValue(dataFileAssay) != null) {
                abundance = smallMolecule.getAbundanceColumnValue(dataFileAssay);
            }
            if (smallMolecule.getOptionColumnValue(dataFileAssay, "peak_mz") != null) {
                peak_mz = Double.parseDouble(smallMolecule.getOptionColumnValue(dataFileAssay, "peak_mz"));
            } else {
                peak_mz = mzExp;
            }
            if (smallMolecule.getOptionColumnValue(dataFileAssay, "peak_rt") != null) {
                peak_rt = Double.parseDouble(smallMolecule.getOptionColumnValue(dataFileAssay, "peak_rt"));
            } else {
                peak_rt = rtValue;
            }
            if (smallMolecule.getOptionColumnValue(dataFileAssay, "peak_height") != null) {
                peak_height = Double.parseDouble(smallMolecule.getOptionColumnValue(dataFileAssay, "peak_height"));
            } else {
                peak_height = 0.0;
            }
            int[] scanNumbers = {};
            DataPoint[] finalDataPoint = new DataPoint[1];
            finalDataPoint[0] = new SimpleDataPoint(peak_mz, peak_height);
            int representativeScan = 0;
            int fragmentScan = 0;
            int[] allFragmentScans = new int[] { 0 };
            Range<Double> finalRTRange = Range.singleton(peak_rt);
            Range<Double> finalMZRange = Range.singleton(peak_mz);
            Range<Double> finalIntensityRange = Range.singleton(peak_height);
            FeatureStatus status = FeatureStatus.DETECTED;
            Feature peak = new SimpleFeature(rawData, peak_mz, peak_rt, peak_height, abundance, scanNumbers, finalDataPoint, status, representativeScan, fragmentScan, allFragmentScans, finalRTRange, finalMZRange, finalIntensityRange);
            if (abundance > 0) {
                newRow.addPeak(rawData, peak);
            }
        }
        // Add row to feature list
        newPeakList.addRow(newRow);
    }
}

Example 2 with SmallMolecule

use of uk.ac.ebi.pride.jmztab.model.SmallMolecule in project mzmine2 by mzmine.

the class MzTabExportTask method run.

public void run() {
    setStatus(TaskStatus.PROCESSING);
    // Shall export several files?
    boolean substitute = fileName.getPath().contains(plNamePattern);
    // Total number of rows
    for (PeakList peakList : peakLists) {
        totalRows += peakList.getNumberOfRows();
    }
    // Process feature lists
    for (PeakList peakList : peakLists) {
        File curFile = fileName;
        try {
            // Filename
            if (substitute) {
                // Cleanup from illegal filename characters
                String cleanPlName = peakList.getName().replaceAll("[^a-zA-Z0-9.-]", "_");
                // Substitute
                String newFilename = fileName.getPath().replaceAll(Pattern.quote(plNamePattern), cleanPlName);
                curFile = new File(newFilename);
            }
            // Open file
            FileWriter writer;
            try {
                writer = new FileWriter(curFile);
            } catch (Exception e) {
                setStatus(TaskStatus.ERROR);
                setErrorMessage("Could not open file " + curFile + " for writing.");
                return;
            }
            // Metadata
            Metadata mtd = new Metadata();
            mtd.setMZTabMode(MZTabDescription.Mode.Summary);
            mtd.setMZTabType(MZTabDescription.Type.Quantification);
            mtd.setDescription(peakList.getName());
            mtd.addSoftwareParam(1, new CVParam("MS", "MS:1002342", "MZmine", MZmineCore.getMZmineVersion()));
            mtd.setSmallMoleculeQuantificationUnit(new CVParam("PRIDE", "PRIDE:0000330", "Arbitrary quantification unit", null));
            mtd.addSmallMoleculeSearchEngineScoreParam(1, new CVParam("MS", "MS:1001153", "search engine specific score", null));
            mtd.addFixedModParam(1, new CVParam("MS", "MS:1002453", "No fixed modifications searched", null));
            mtd.addVariableModParam(1, new CVParam("MS", "MS:1002454", "No variable modifications searched", null));
            // Create stable columns
            MZTabColumnFactory factory = MZTabColumnFactory.getInstance(Section.Small_Molecule);
            factory.addDefaultStableColumns();
            // Add optional columns which have stable order
            factory.addURIOptionalColumn();
            factory.addBestSearchEngineScoreOptionalColumn(SmallMoleculeColumn.BEST_SEARCH_ENGINE_SCORE, 1);
            final RawDataFile[] rawDataFiles = peakList.getRawDataFiles();
            int fileCounter = 0;
            for (RawDataFile file : rawDataFiles) {
                fileCounter++;
                /**
                 * TO DO: Add path to original imported raw file to MZmine and write it out here instead
                 */
                // MS run location
                MsRun msRun = new MsRun(fileCounter);
                msRun.setLocation(new URL("file:///" + file.getName()));
                mtd.addMsRun(msRun);
                mtd.addAssayMsRun(fileCounter, msRun);
                // Add samples to study variable assay
                for (UserParameter<?, ?> p : project.getParameters()) {
                    Assay assay = mtd.getAssayMap().get(fileCounter);
                    for (StudyVariable studyVariable : mtd.getStudyVariableMap().values()) {
                        if (studyVariable.getDescription().equals(String.valueOf(p) + ": " + String.valueOf(project.getParameterValue(p, file)))) {
                            mtd.addStudyVariableAssay(studyVariable.getId(), assay);
                        }
                    }
                }
                // Additional columns
                factory.addAbundanceOptionalColumn(new Assay(fileCounter));
                factory.addOptionalColumn(new Assay(fileCounter), "peak_mz", String.class);
                factory.addOptionalColumn(new Assay(fileCounter), "peak_rt", String.class);
                factory.addOptionalColumn(new Assay(fileCounter), "peak_height", String.class);
            }
            // Variable descriptions
            int parameterCounter = 0;
            for (UserParameter<?, ?> p : project.getParameters()) {
                for (Object e : ((ComboParameter<?>) p).getChoices()) {
                    parameterCounter++;
                    mtd.addStudyVariableDescription(parameterCounter, String.valueOf(p) + ": " + String.valueOf(e));
                    StudyVariable studyVariable = new StudyVariable(parameterCounter);
                    factory.addAbundanceOptionalColumn(studyVariable);
                }
            }
            // Write to file
            BufferedWriter out = new BufferedWriter(writer);
            out.write(mtd.toString());
            out.write(newLine);
            out.write(factory.toString());
            out.write(newLine);
            // Write data rows
            for (PeakListRow peakListRow : peakList.getRows()) {
                // Cancel?
                if (isCanceled()) {
                    return;
                }
                PeakIdentity peakIdentity = peakListRow.getPreferredPeakIdentity();
                if (exportall || peakIdentity != null) {
                    SmallMolecule sm = new SmallMolecule(factory, mtd);
                    if (peakIdentity != null) {
                        // Identity information
                        String identifier = escapeString(peakIdentity.getPropertyValue("ID"));
                        String database = peakIdentity.getPropertyValue("Identification method");
                        String formula = peakIdentity.getPropertyValue("Molecular formula");
                        String description = escapeString(peakIdentity.getPropertyValue("Name"));
                        String url = peakIdentity.getPropertyValue("URL");
                        if (identifier != null) {
                            sm.setIdentifier(identifier);
                        }
                        if (database != null) {
                            sm.setDatabase(database);
                        }
                        if (formula != null) {
                            sm.setChemicalFormula(formula);
                        }
                        if (description != null) {
                            sm.setDescription(description);
                        }
                        if (url != null) {
                            sm.setURI(url);
                        }
                    }
                    Double rowMZ = peakListRow.getAverageMZ();
                    int rowCharge = peakListRow.getRowCharge();
                    String rowRT = String.valueOf(peakListRow.getAverageRT());
                    if (rowMZ != null) {
                        sm.setExpMassToCharge(rowMZ);
                    }
                    if (rowCharge > 0) {
                        sm.setCharge(rowCharge);
                    }
                    if (rowRT != null) {
                        sm.setRetentionTime(rowRT);
                    }
                    int dataFileCount = 0;
                    for (RawDataFile dataFile : rawDataFiles) {
                        dataFileCount++;
                        Feature peak = peakListRow.getPeak(dataFile);
                        if (peak != null) {
                            String peakMZ = String.valueOf(peak.getMZ());
                            String peakRT = String.valueOf(String.valueOf(peak.getRT()));
                            String peakHeight = String.valueOf(peak.getHeight());
                            Double peakArea = peak.getArea();
                            sm.setOptionColumnValue(new Assay(dataFileCount), "peak_mz", peakMZ);
                            sm.setOptionColumnValue(new Assay(dataFileCount), "peak_rt", peakRT);
                            sm.setOptionColumnValue(new Assay(dataFileCount), "peak_height", peakHeight);
                            sm.setAbundanceColumnValue(new Assay(dataFileCount), peakArea);
                        }
                    }
                    out.write(sm.toString());
                    out.write(newLine);
                }
            }
            out.flush();
            out.close();
            writer.close();
        } catch (Exception e) {
            e.printStackTrace();
            setStatus(TaskStatus.ERROR);
            setErrorMessage("Could not export feature list to file " + curFile + ": " + e.getMessage());
            return;
        }
    }
    if (getStatus() == TaskStatus.PROCESSING)
        setStatus(TaskStatus.FINISHED);
}