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

Example 1 with MatchList

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

the class SimulateSpectrumHDX method generateDeuteratedSpectrumNegative.

/**
 * @param candidate
 * @return
 * @throws AtomTypeNotKnownFromInputListException
 * @throws Exception
 */
public static double[][] generateDeuteratedSpectrumNegative(ICandidate candidate, int method) throws AtomTypeNotKnownFromInputListException, Exception {
    int numberPositions = searchForDeuteriumExchangeablePositions((TopDownBitArrayPrecursor) candidate.getPrecursorMolecule()).length;
    HDTopDownBitArrayPrecursor preHDX = new HDTopDownBitArrayPrecursor(candidate.getImplicitHydrogenAtomContainer(), (byte) numberPositions);
    preHDX.preprocessPrecursor();
    MatchList matchList = candidate.getMatchList();
    double[][] spectrumHDX = null;
    if (method == 3)
        spectrumHDX = new double[matchList.getNumberElements() * 2][2];
    else
        spectrumHDX = new double[matchList.getNumberElements()][2];
    for (int i = 0; i < matchList.getNumberElements(); i++) {
        IFragment frag = matchList.getElement(i).getBestMatchedFragment();
        IPeak peak = matchList.getElement(i).getMatchedPeak();
        int[] setAtoms = ((DefaultBitArrayFragment) frag).getAtomsFastBitArray().getSetIndeces();
        int numberDeuteriums = 0;
        for (int k = 0; k < setAtoms.length; k++) {
            numberDeuteriums += preHDX.getNumberDeuteriumsConnectedToAtomIndex(0, setAtoms[k]);
        }
        spectrumHDX[i][1] = peak.getAbsoluteIntensity();
        // [M-D]-
        if (method == 1) {
            spectrumHDX[i][0] = peak.getMass() - (numberDeuteriums) * Constants.HYDROGEN_MASS + (numberDeuteriums) * Constants.getMonoisotopicMassOfAtom("D");
            spectrumHDX[i][0] += Constants.HYDROGEN_MASS - Constants.getMonoisotopicMassOfAtom("D");
        } else // [M]-
        if (method == 2) {
            spectrumHDX[i][0] = peak.getMass() - (numberDeuteriums) * Constants.HYDROGEN_MASS + (numberDeuteriums) * Constants.getMonoisotopicMassOfAtom("D");
        // nothing to do
        } else // [M]- [M-D]-
        if (method == 3) {
            spectrumHDX[i * 2][0] = peak.getMass() - (numberDeuteriums) * Constants.HYDROGEN_MASS + (numberDeuteriums) * Constants.getMonoisotopicMassOfAtom("D");
            spectrumHDX[(i * 2) + 1][0] = peak.getMass() - (numberDeuteriums) * Constants.HYDROGEN_MASS + (numberDeuteriums) * Constants.getMonoisotopicMassOfAtom("D");
            spectrumHDX[(i * 2) + 1][0] += Constants.HYDROGEN_MASS - Constants.getMonoisotopicMassOfAtom("D");
        } else // predict based on deuteriums
        if (method == 4) {
            spectrumHDX[i][0] = peak.getMass() - (numberDeuteriums) * Constants.HYDROGEN_MASS + (numberDeuteriums) * Constants.getMonoisotopicMassOfAtom("D");
            if (numberDeuteriums != 0)
                spectrumHDX[i][0] += Constants.HYDROGEN_MASS - Constants.getMonoisotopicMassOfAtom("D");
        } else // predict based on adduct
        if (method == 5) {
            byte adductTypeIndex = ((DefaultFragmentToPeakMatch) matchList.getElement(i)).getBestMatchedFragmentAdductTypeIndex();
            spectrumHDX[i][0] = peak.getMass() - (numberDeuteriums) * Constants.HYDROGEN_MASS + (numberDeuteriums) * Constants.getMonoisotopicMassOfAtom("D");
            if (adductTypeIndex == 1)
                spectrumHDX[i][0] += Constants.getMonoisotopicMassOfAtom("D") - Constants.HYDROGEN_MASS;
        }
    }
    return spectrumHDX;
}

Example 2 with MatchList

use of de.ipbhalle.metfraglib.list.MatchList 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 3 with MatchList

use of de.ipbhalle.metfraglib.list.MatchList 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 4 with MatchList

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

the class CandidateWriterXLS method convertMoleculeFragmentsToImages.

/**
 * @param candidateList
 * @return
 * @throws Exception
 */
private java.util.List<RenderedImage> convertMoleculeFragmentsToImages(ICandidate candidate) throws Exception {
    java.util.List<RenderedImage> molImages = new java.util.ArrayList<RenderedImage>();
    de.ipbhalle.metfraglib.imagegenerator.HighlightSubStructureImageGenerator imageGenerator = new de.ipbhalle.metfraglib.imagegenerator.HighlightSubStructureImageGenerator();
    imageGenerator.setBackgroundColor(new Color(1f, 1f, 1f, 1f));
    imageGenerator.setImageHeight(200);
    imageGenerator.setImageWidth(200);
    MatchList matchList = candidate.getMatchList();
    for (int i = 0; i < matchList.getNumberElements(); i++) {
        RenderedImage renderedImage = imageGenerator.generateImage(candidate.getPrecursorMolecule(), matchList.getElement(i).getBestMatchedFragment());
        molImages.add(renderedImage);
    }
    return molImages;
}

Example 5 with MatchList

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

the class HDCandidateListWriterPSV 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;
    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.Hashtable<String, java.util.ArrayList<ICandidate>> hdGroupedCandidates = new java.util.Hashtable<String, java.util.ArrayList<ICandidate>>();
    String[] lines = new String[candidateList.getNumberElements()];
    String heading = "";
    for (int i = 0; i < candidateList.getNumberElements(); i++) {
        ICandidate candidate = candidateList.getElement(i);
        if (hdGroupedCandidates.containsKey((String) candidate.getProperty(VariableNames.HD_GROUP_FLAG_NAME)))
            ((java.util.ArrayList<ICandidate>) hdGroupedCandidates.get((String) candidate.getProperty(VariableNames.HD_GROUP_FLAG_NAME))).add(candidate);
        else {
            java.util.ArrayList<ICandidate> vec = new java.util.ArrayList<ICandidate>();
            vec.add(candidate);
            hdGroupedCandidates.put((String) candidate.getProperty(VariableNames.HD_GROUP_FLAG_NAME), vec);
        }
        candidate.getProperties().remove(VariableNames.HD_GROUP_FLAG_NAME);
    }
    java.util.ArrayList<String> propertyNames = new java.util.ArrayList<String>();
    java.util.Iterator<?> it = (java.util.Iterator<?>) hdGroupedCandidates.keys();
    while (it.hasNext()) {
        String currentGroup = (String) it.next();
        java.util.ArrayList<ICandidate> vec = hdGroupedCandidates.get(currentGroup);
        int originalCandidate = -1;
        int maxPropertySize = 0;
        // find original candidate properties
        for (int i = 0; i < vec.size(); i++) {
            if (vec.get(i).getProperties().size() > maxPropertySize) {
                originalCandidate = i;
                maxPropertySize = vec.get(i).getProperties().size();
            }
        }
        // fill in missing properties
        java.util.Hashtable<String, Object> properties = vec.get(originalCandidate).getProperties();
        for (int i = 0; i < vec.size(); i++) {
            ICandidate currentCandidate = vec.get(i);
            java.util.Iterator<?> prop_it = (java.util.Iterator<?>) properties.keys();
            while (prop_it.hasNext()) {
                String key = (String) prop_it.next();
                if (!propertyNames.contains(key))
                    propertyNames.add(key);
                if (currentCandidate.getProperty(key) == null)
                    currentCandidate.setProperty(key, properties.get(key));
            }
        }
    }
    for (int i = 0; i < candidateList.getNumberElements(); i++) {
        ICandidate scoredCandidate = candidateList.getElement(i);
        if (propertyNames.size() >= 1) {
            String key = propertyNames.get(0);
            if (i == 0)
                heading += key;
            lines[i] = "" + checkEmptyProperty(scoredCandidate.getProperty(key), key);
        }
        for (int k = 1; k < propertyNames.size(); k++) {
            String key = propertyNames.get(k);
            if (i == 0)
                heading += "|" + key;
            String prop = checkEmptyProperty(scoredCandidate.getProperty(key), key).toString();
            lines[i] += "|" + prop;
        }
    }
    java.io.BufferedWriter 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();
    return true;
}