Examples with CandidateList de.ipbhalle.metfraglib.list.CandidateList used on opensource projects

Example 1 with CandidateList

use of de.ipbhalle.metfraglib.list.CandidateList in project MetFragRelaunched by ipb-halle.

the class DownloadEntriesFromPubChem method downloadFromCandidateFile.

public static void downloadFromCandidateFile(String filenameIn, String filenameOut) {
    MetFragGlobalSettings settingsIn = new MetFragGlobalSettings();
    settingsIn.set(VariableNames.LOCAL_DATABASE_PATH_NAME, filenameIn);
    LocalPSVDatabase dbIn = new LocalPSVDatabase(settingsIn);
    ArrayList<String> identifiers = null;
    try {
        identifiers = dbIn.getCandidateIdentifiers();
    } catch (MultipleHeadersFoundInInputDatabaseException e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    } catch (Exception e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    }
    CandidateList candidates = dbIn.getCandidateByIdentifier(identifiers);
    String[] ids = new String[candidates.getNumberElements()];
    for (int i = 0; i < ids.length; i++) ids[i] = candidates.getElement(i).getIdentifier();
    MetFragGlobalSettings settingsPubChem = new MetFragGlobalSettings();
    settingsPubChem.set(VariableNames.PRECURSOR_DATABASE_IDS_NAME, ids);
    OnlineExtendedPubChemDatabase pubchemDB = new OnlineExtendedPubChemDatabase(settingsPubChem);
    try {
        identifiers = pubchemDB.getCandidateIdentifiers();
    } catch (Exception e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    }
    CandidateList candidatesPubChem = null;
    try {
        candidatesPubChem = pubchemDB.getCandidateByIdentifier(identifiers);
    } catch (Exception e1) {
        e1.printStackTrace();
    }
    for (int i = 0; i < candidatesPubChem.getNumberElements(); i++) {
        String identifier = candidatesPubChem.getElement(i).getIdentifier();
        try {
            ICandidate currentCandidate = dbIn.getCandidateByIdentifier(identifier);
            currentCandidate.setProperty(VariableNames.PUBCHEM_NUMBER_PUBMED_REFERENCES_NAME, candidatesPubChem.getElement(i).getProperty(VariableNames.PUBCHEM_NUMBER_PUBMED_REFERENCES_NAME));
            currentCandidate.setProperty(VariableNames.PUBCHEM_NUMBER_PATENTS_NAME, candidatesPubChem.getElement(i).getProperty(VariableNames.PUBCHEM_NUMBER_PATENTS_NAME));
        } catch (DatabaseIdentifierNotFoundException e) {
            e.printStackTrace();
        }
    }
    CandidateListWriterPSV writer = new CandidateListWriterPSV();
    String filename = filenameOut.replaceAll(".*\\/", "").replaceAll("\\..*$", "");
    String path = filenameOut.replaceAll(filename + "\\..*$", "");
    try {
        writer.write(candidates, filename, path);
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 2 with CandidateList

use of de.ipbhalle.metfraglib.list.CandidateList in project MetFragRelaunched by ipb-halle.

the class DownloadEntriesFromPubChem method downloadFromString.

public static void downloadFromString(String idString) {
    String[] ids = idString.trim().split(",");
    MetFragGlobalSettings settings = new MetFragGlobalSettings();
    settings.set(VariableNames.PRECURSOR_DATABASE_IDS_NAME, ids);
    OnlineExtendedPubChemDatabase db = new OnlineExtendedPubChemDatabase(settings);
    CandidateList candidates = null;
    try {
        candidates = db.getCandidateByIdentifier(db.getCandidateIdentifiers());
    } catch (Exception e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    }
    for (int i = 0; i < candidates.getNumberElements(); i++) {
        ICandidate candidate = candidates.getElement(i);
        try {
            System.out.println(candidate.getIdentifier() + "|" + candidate.getInChI() + "|" + candidate.getMolecularFormula().toString() + "|" + candidate.getMolecularFormula().getMonoisotopicMass() + "|" + candidate.getProperty(VariableNames.PUBCHEM_XLOGP_NAME) + "|" + candidate.getProperty(VariableNames.INCHI_KEY_1_NAME) + "|" + candidate.getProperty(VariableNames.INCHI_KEY_2_NAME) + "|" + candidate.getProperty(VariableNames.PUBCHEM_NUMBER_PATENTS_NAME) + "|" + candidate.getProperty(VariableNames.PUBCHEM_NUMBER_PUBMED_REFERENCES_NAME) + "|" + candidate.getProperty(VariableNames.SMILES_NAME));
        } catch (AtomTypeNotKnownFromInputListException e) {
            e.printStackTrace();
        }
    }
}

Example 3 with CandidateList

use of de.ipbhalle.metfraglib.list.CandidateList in project MetFragRelaunched by ipb-halle.

the class CandidateListWriterXLS method writeFile.

public boolean writeFile(File xlsFile, IList list, Settings settings) throws Exception {
    CandidateList candidateList = null;
    int numberOfPeaksUsed = 0;
    if (list instanceof ScoredCandidateList || list instanceof SortedScoredCandidateList) {
        candidateList = (ScoredCandidateList) list;
        numberOfPeaksUsed = ((ScoredCandidateList) list).getNumberPeaksUsed();
    }
    if (list instanceof CandidateList) {
        candidateList = (CandidateList) list;
    }
    if (candidateList == null)
        return false;
    java.util.ArrayList<Integer> correctIndeces = new java.util.ArrayList<Integer>();
    for (int i = 0; i < candidateList.getNumberElements(); i++) {
        int countExplainedPeaks = 0;
        ICandidate scoredCandidate = candidateList.getElement(i);
        if (settings != null)
            scoredCandidate.setUseSmiles((Boolean) settings.get(VariableNames.USE_SMILES_NAME));
        try {
            scoredCandidate.initialisePrecursorCandidate();
        } catch (Exception e) {
            continue;
        }
        if (scoredCandidate.getMatchList() != null) {
            MatchList matchList = scoredCandidate.getMatchList();
            for (int l = 0; l < matchList.getNumberElements(); l++) {
                try {
                    matchList.getElement(l).getMatchedPeak().getIntensity();
                } catch (RelativeIntensityNotDefinedException e1) {
                    continue;
                }
                countExplainedPeaks++;
            }
        }
        String peaksExplained = "";
        String sumFormulasOfFragmentsExplainedPeaks = "";
        if (scoredCandidate.getMatchList() != null) {
            for (int ii = 0; ii < scoredCandidate.getMatchList().getNumberElements(); ii++) {
                try {
                    double intensity = scoredCandidate.getMatchList().getElement(ii).getMatchedPeak().getIntensity();
                    peaksExplained += scoredCandidate.getMatchList().getElement(ii).getMatchedPeak().getMass() + "_" + intensity + ";";
                } catch (RelativeIntensityNotDefinedException e1) {
                    continue;
                }
                String formula = scoredCandidate.getMatchList().getElement(ii).getModifiedFormulaStringOfBestMatchedFragment(scoredCandidate.getPrecursorMolecule());
                sumFormulasOfFragmentsExplainedPeaks += scoredCandidate.getMatchList().getElement(ii).getMatchedPeak().getMass() + ":" + formula + ";";
            }
            if (sumFormulasOfFragmentsExplainedPeaks.length() != 0)
                sumFormulasOfFragmentsExplainedPeaks = sumFormulasOfFragmentsExplainedPeaks.substring(0, sumFormulasOfFragmentsExplainedPeaks.length() - 1);
            if (peaksExplained.length() != 0)
                peaksExplained = peaksExplained.substring(0, peaksExplained.length() - 1);
            if (peaksExplained.length() == 0)
                peaksExplained = "NA";
            if (sumFormulasOfFragmentsExplainedPeaks.length() == 0)
                sumFormulasOfFragmentsExplainedPeaks = "NA";
            scoredCandidate.setProperty("ExplPeaks", peaksExplained);
            scoredCandidate.setProperty("FormulasOfExplPeaks", sumFormulasOfFragmentsExplainedPeaks);
            scoredCandidate.setProperty("NumberPeaksUsed", numberOfPeaksUsed);
            scoredCandidate.setProperty("NoExplPeaks", countExplainedPeaks);
        }
        scoredCandidate.resetPrecursorMolecule();
        correctIndeces.add(i);
    }
    boolean withImages = false;
    xlsFile.createNewFile();
    WritableWorkbook workbook = Workbook.createWorkbook(xlsFile);
    WritableSheet sheet = workbook.createSheet("MetFrag result list", 0);
    WritableFont arial10font = new WritableFont(WritableFont.ARIAL, 10);
    WritableCellFormat arial10format = new WritableCellFormat(arial10font);
    try {
        arial10font.setBoldStyle(WritableFont.BOLD);
    } catch (WriteException e1) {
        System.out.println("Warning: Could not set WritableFont");
    }
    int numberCells = 0;
    java.util.Map<String, Integer> labels = new java.util.HashMap<String, Integer>();
    int columnWidthAdd = withImages ? 3 : 0;
    int rowHeightAdd = withImages ? 9 : 1;
    List<RenderedImage> molImages = null;
    if (withImages) {
        molImages = convertMoleculesToImages(candidateList);
        for (int i = 0; i < molImages.size(); i++) {
            // File imageFile = new File(resultspath + fileSep + fileName+
            // "_" +i+".png");
            File imageFile = File.createTempFile("file" + i, ".png", new File(Constants.OS_TEMP_DIR));
            imageFile.deleteOnExit();
            if (ImageIO.write(molImages.get(i), "png", imageFile)) {
                WritableImage wi = new WritableImage(0, (i * rowHeightAdd) + 1, columnWidthAdd, rowHeightAdd, imageFile);
                sheet.addImage(wi);
            }
        }
    }
    for (int i = 0; i < correctIndeces.size(); i++) {
        java.util.Hashtable<String, Object> properties = candidateList.getElement(correctIndeces.get(i)).getProperties();
        Iterator<String> propNames = properties.keySet().iterator();
        while (propNames.hasNext()) {
            String propName = (String) propNames.next();
            if (!labels.containsKey(propName)) {
                labels.put(propName, Integer.valueOf(numberCells));
                try {
                    sheet.addCell(new Label(labels.get(propName) + columnWidthAdd, 0, propName, arial10format));
                } catch (RowsExceededException e) {
                    e.printStackTrace();
                } catch (WriteException e) {
                    e.printStackTrace();
                }
                numberCells++;
            }
            try {
                String prop = String.valueOf(properties.get(propName));
                if (prop.trim().length() == 0)
                    prop = "NA";
                if (propName.equals(VariableNames.IDENTIFIER_NAME))
                    prop = prop.replaceAll("\\|[0-9]+", "");
                sheet.addCell(new Label(labels.get(propName) + columnWidthAdd, (i * rowHeightAdd) + 1, prop));
            } catch (RowsExceededException e) {
                e.printStackTrace();
            } catch (WriteException e) {
                e.printStackTrace();
            }
        }
    }
    workbook.write();
    workbook.close();
    return true;
}

Example 4 with CandidateList

use of de.ipbhalle.metfraglib.list.CandidateList in project MetFragRelaunched by ipb-halle.

the class CandidateListWriterZippedPSV method writeFile.

public boolean writeFile(File file, IList list, Settings settings) throws Exception {
    CandidateList candidateList = null;
    int numberOfPeaksUsed = 0;
    if (list instanceof ScoredCandidateList || list instanceof SortedScoredCandidateList) {
        candidateList = (ScoredCandidateList) list;
        numberOfPeaksUsed = ((ScoredCandidateList) list).getNumberPeaksUsed();
    }
    if (list instanceof CandidateList) {
        candidateList = (CandidateList) list;
    }
    if (candidateList == null)
        return false;
    if (candidateList == null || candidateList.getNumberElements() == 0) {
        writeDefaultHeader(file);
        return false;
    }
    String[] lines = new String[candidateList.getNumberElements()];
    String heading = "";
    for (int i = 0; i < candidateList.getNumberElements(); i++) {
        int countExplainedPeaks = 0;
        ICandidate scoredCandidate = candidateList.getElement(i);
        if (settings != null)
            scoredCandidate.setUseSmiles((Boolean) settings.get(VariableNames.USE_SMILES_NAME));
        scoredCandidate.initialisePrecursorCandidate();
        if (scoredCandidate.getMatchList() != null) {
            MatchList matchList = scoredCandidate.getMatchList();
            for (int l = 0; l < matchList.getNumberElements(); l++) {
                try {
                    matchList.getElement(l).getMatchedPeak().getIntensity();
                } catch (RelativeIntensityNotDefinedException e1) {
                    continue;
                }
                countExplainedPeaks++;
            }
        }
        String peaksExplained = "";
        String sumFormulasOfFragmentsExplainedPeaks = "";
        if (scoredCandidate.getMatchList() != null) {
            for (int ii = 0; ii < scoredCandidate.getMatchList().getNumberElements(); ii++) {
                try {
                    double intensity = scoredCandidate.getMatchList().getElement(ii).getMatchedPeak().getIntensity();
                    peaksExplained += scoredCandidate.getMatchList().getElement(ii).getMatchedPeak().getMass() + "_" + intensity + ";";
                } catch (RelativeIntensityNotDefinedException e1) {
                    continue;
                }
                String formula = scoredCandidate.getMatchList().getElement(ii).getModifiedFormulaStringOfBestMatchedFragment(scoredCandidate.getPrecursorMolecule());
                sumFormulasOfFragmentsExplainedPeaks += scoredCandidate.getMatchList().getElement(ii).getMatchedPeak().getMass() + ":" + formula + ";";
            }
            if (sumFormulasOfFragmentsExplainedPeaks.length() != 0)
                sumFormulasOfFragmentsExplainedPeaks = sumFormulasOfFragmentsExplainedPeaks.substring(0, sumFormulasOfFragmentsExplainedPeaks.length() - 1);
            if (peaksExplained.length() != 0)
                peaksExplained = peaksExplained.substring(0, peaksExplained.length() - 1);
            if (peaksExplained.length() == 0)
                peaksExplained = "NA";
            if (sumFormulasOfFragmentsExplainedPeaks.length() == 0)
                sumFormulasOfFragmentsExplainedPeaks = "NA";
            scoredCandidate.setProperty(VariableNames.EXPLAINED_PEAKS_COLUMN, peaksExplained);
            scoredCandidate.setProperty(VariableNames.FORMULAS_OF_PEAKS_EXPLAINED_COLUMN, sumFormulasOfFragmentsExplainedPeaks);
            scoredCandidate.setProperty(VariableNames.NUMBER_PEAKS_USED_COLUMN, numberOfPeaksUsed);
            scoredCandidate.setProperty(VariableNames.NUMBER_EXPLAINED_PEAKS_COLUMN, countExplainedPeaks);
        }
        java.util.Enumeration<String> keys = scoredCandidate.getProperties().keys();
        if (keys.hasMoreElements()) {
            String key = keys.nextElement();
            if (i == 0)
                heading += key;
            lines[i] = "" + checkEmptyProperty(scoredCandidate.getProperty(key));
        }
        while (keys.hasMoreElements()) {
            String key = keys.nextElement();
            if (i == 0)
                heading += "|" + key;
            lines[i] += "|" + checkEmptyProperty(scoredCandidate.getProperty(key));
        }
    }
    java.io.BufferedWriter bwriter;
    bwriter = new java.io.BufferedWriter(new FileWriter(file));
    bwriter.write(heading);
    bwriter.newLine();
    for (int i = 0; i < lines.length; i++) {
        bwriter.write(lines[i]);
        bwriter.newLine();
    }
    bwriter.close();
    this.zipFile(file);
    file.delete();
    return true;
}

Example 5 with CandidateList

use of de.ipbhalle.metfraglib.list.CandidateList in project MetFragRelaunched by ipb-halle.

the class CandidateWriterXLS method writeFile.

@Override
public boolean writeFile(File xlsFile, IList list, Settings settings) throws Exception {
    CandidateList candidateList = null;
    boolean isScoredCandidate = false;
    if (list instanceof ScoredCandidateList || list instanceof SortedScoredCandidateList) {
        candidateList = (ScoredCandidateList) list;
        isScoredCandidate = true;
    }
    if (list instanceof CandidateList) {
        candidateList = (CandidateList) list;
    }
    if (candidateList == null || candidateList.getNumberElements() == 0)
        return false;
    ICandidate candidate = candidateList.getElement(0);
    if (settings != null)
        candidate.setUseSmiles((Boolean) settings.get(VariableNames.USE_SMILES_NAME));
    candidate.initialisePrecursorCandidate();
    xlsFile.createNewFile();
    WritableWorkbook workbook = Workbook.createWorkbook(xlsFile);
    WritableSheet sheet1 = workbook.createSheet("MetFrag Candidate Result", 0);
    WritableFont arial10fontBold = new WritableFont(WritableFont.ARIAL, 10);
    arial10fontBold.setBoldStyle(WritableFont.BOLD);
    WritableCellFormat arial10formatBold = new WritableCellFormat(arial10fontBold);
    WritableFont arial10font = new WritableFont(WritableFont.ARIAL, 10);
    arial10font.setBoldStyle(WritableFont.NO_BOLD);
    WritableCellFormat arial10format = new WritableCellFormat(arial10font);
    sheet1.addCell(new Label(0, 0, VariableNames.IDENTIFIER_NAME, arial10formatBold));
    sheet1.addCell(new Label(1, 0, candidate.getIdentifier().replaceAll("\\|[0-9]+", ""), arial10format));
    java.util.Hashtable<String, Object> properties = candidate.getProperties();
    java.util.Enumeration<?> keys = properties.keys();
    int propertyRow = 1;
    while (keys.hasMoreElements()) {
        String currentKey = (String) keys.nextElement();
        sheet1.addCell(new Label(0, propertyRow, currentKey, arial10formatBold));
        String value = "";
        Object obj = properties.get(currentKey);
        if (obj instanceof java.lang.Double)
            value = String.valueOf((Double) obj);
        else if (obj instanceof java.lang.Integer)
            value = String.valueOf((Integer) obj);
        else if (obj instanceof java.lang.String)
            value = (String) obj;
        sheet1.addCell(new Label(1, propertyRow, value, arial10format));
        propertyRow++;
    }
    java.util.List<RenderedImage> molFragmentImages = null;
    RenderedImage molImage = this.convertMoleculeToImages(candidate);
    File imageFile = File.createTempFile("file", ".png", new File(Constants.OS_TEMP_DIR));
    imageFile.deleteOnExit();
    int rowHeightImage = 10;
    int colWidthImage = 3;
    int fragmentColumns = 1;
    sheet1.addCell(new Label(0, propertyRow + 1, "Precursor", arial10formatBold));
    if (ImageIO.write(molImage, "png", imageFile)) {
        WritableImage wi = new WritableImage(0, propertyRow + 2, colWidthImage, rowHeightImage, imageFile);
        sheet1.addImage(wi);
    }
    if (isScoredCandidate) {
        molFragmentImages = this.convertMoleculeFragmentsToImages(candidate);
        if (molFragmentImages.size() > 0) {
            sheet1.addCell(new Label(0, (propertyRow + 4) + rowHeightImage, "Fragments", arial10formatBold));
        }
        int imagesWritten = 1;
        int fragmentRow = 0;
        for (int i = 0; i < molFragmentImages.size(); i++) {
            File imageFileFragment = File.createTempFile("file" + i, ".png", new File(Constants.OS_TEMP_DIR));
            imageFileFragment.deleteOnExit();
            if (ImageIO.write(molFragmentImages.get(i), "png", imageFileFragment)) {
                int column = (((imagesWritten - 1) % fragmentColumns)) * (colWidthImage + 3);
                if ((imagesWritten - 1) % fragmentColumns == 0)
                    fragmentRow++;
                WritableImage wi = new WritableImage(column, (propertyRow + 5) + (rowHeightImage * fragmentRow), colWidthImage, rowHeightImage, imageFileFragment);
                sheet1.addImage(wi);
                FragmentMassToPeakMatch match = (FragmentMassToPeakMatch) candidate.getMatchList().getElement(imagesWritten - 1);
                sheet1.addCell(new Label(column + colWidthImage, (propertyRow + 5) + (rowHeightImage * fragmentRow), "Fragment " + imagesWritten, arial10formatBold));
                sheet1.addCell(new Label(column + colWidthImage, (propertyRow + 5) + (rowHeightImage * fragmentRow) + 2, "Formula", arial10formatBold));
                sheet1.addCell(new Label(column + colWidthImage + 1, (propertyRow + 5) + (rowHeightImage * fragmentRow) + 2, match.getModifiedFormulaStringOfBestMatchedFragment(candidate.getPrecursorMolecule()), arial10format));
                sheet1.addCell(new Label(column + colWidthImage, (propertyRow + 5) + (rowHeightImage * fragmentRow) + 3, "Mass", arial10formatBold));
                sheet1.addCell(new Label(column + colWidthImage + 1, (propertyRow + 5) + (rowHeightImage * fragmentRow) + 3, String.valueOf(MathTools.round(match.getBestMatchFragmentMass())), arial10format));
                sheet1.addCell(new Label(column + colWidthImage, (propertyRow + 5) + (rowHeightImage * fragmentRow) + 4, "Peak m/z", arial10formatBold));
                sheet1.addCell(new Label(column + colWidthImage + 1, (propertyRow + 5) + (rowHeightImage * fragmentRow) + 4, String.valueOf(match.getMatchedPeak().getMass()), arial10format));
                imagesWritten++;
            }
        }
    }
    workbook.write();
    workbook.close();
    return true;
}