Examples with Advocate com.compomics.util.experiment.identification.Advocate used on opensource projects

Example 1 with Advocate

use of com.compomics.util.experiment.identification.Advocate in project peptide-shaker by compomics.

the class PeptideShakerMethods method getSearchEnginesText.

/**
 * Returns the search engines usage details.
 *
 * @param projectDetails the PeptideShaker project details
 *
 * @return the search engines usage details
 */
public static String getSearchEnginesText(ProjectDetails projectDetails) {
    StringBuilder text = new StringBuilder();
    text.append("Peak lists obtained from MS/MS spectra were identified using ");
    ArrayList<Integer> searchEngines = projectDetails.getIdentificationAlgorithms();
    Collections.sort(searchEngines);
    HashMap<String, ArrayList<String>> algorithmToVersionMap = projectDetails.getAlgorithmNameToVersionsMap();
    for (int i = 0; i < searchEngines.size(); i++) {
        if (i > 0) {
            if (i == searchEngines.size() - 1) {
                text.append(" and ");
            } else {
                text.append(", ");
            }
        }
        Advocate advocate = Advocate.getAdvocate(searchEngines.get(i));
        String ref = advocate.getPmid();
        if (ref == null) {
            ref = "add reference here";
        }
        text.append(advocate.getName()).append(" ");
        ArrayList<String> versions = algorithmToVersionMap.get(advocate.getName());
        if (versions == null || versions.isEmpty()) {
            text.append("version [add version here]");
        } else if (versions.size() == 1) {
            if (versions.get(0) != null) {
                text.append("version ").append(versions.get(0));
            } else {
                text.append("version unknown");
            }
        } else {
            text.append("versions ");
            Collections.sort(versions);
            for (int j = 0; j < versions.size(); j++) {
                if (j > 0) {
                    if (j == versions.size() - 1) {
                        text.append(" and ");
                    } else {
                        text.append(", ");
                    }
                }
                if (versions.get(0) != null) {
                    text.append(versions.get(j));
                } else {
                    text.append("unknown");
                }
            }
        }
        text.append(" [PMID ").append(ref).append("]");
    }
    text.append(".");
    return text.toString();
}

Example 2 with Advocate

use of com.compomics.util.experiment.identification.Advocate in project peptide-shaker by compomics.

the class PepXmlExport method writeSearchHit.

/**
 * Writes a search hit section.
 *
 * @param sw the XML file writer
 * @param identification the identification object containing the
 * identification results
 * @param identificationParameters the identification parameters
 * @param waitingHandler a waiting handler to display progress and allow
 * interrupting the process
 *
 * @throws IOException exception thrown whenever an error is encountered
 * while reading or writing a file
 */
private void writeSearchHit(SimpleXmlWriter sw, IdentificationParameters identificationParameters, PeptideAssumption peptideAssumption, double precursorMz, PSParameter psParameter, boolean mainHit) throws IOException {
    Peptide peptide = peptideAssumption.getPeptide();
    StringBuilder searchHitStart = new StringBuilder();
    searchHitStart.append("<search_hit hit_rank=\"").append(peptideAssumption.getRank()).append("\" ").append("peptide=\"").append(peptide.getSequence()).append("\" ");
    TreeMap<String, int[]> proteinMapping = peptide.getProteinMapping();
    String proteins = proteinMapping.navigableKeySet().stream().collect(Collectors.joining(","));
    searchHitStart.append("protein=\"").append(proteins).append("\" ").append("num_tot_proteins=\"").append(proteinMapping.size()).append("\" ").append("calc_neutral_pep_mass=\"").append(peptideAssumption.getTheoreticMass()).append("\" ").append("massdiff=\"").append(peptideAssumption.getDeltaMz(precursorMz, false, identificationParameters.getSearchParameters().getMinIsotopicCorrection(), identificationParameters.getSearchParameters().getMaxIsotopicCorrection())).append("\">");
    sw.writeLine(searchHitStart.toString());
    sw.increaseIndent();
    if (proteinMapping.size() > 1) {
        for (String accession : proteinMapping.navigableKeySet()) {
            StringBuilder proteinLine = new StringBuilder();
            proteinLine.append("<alternative_protein protein=\"").append(accession).append("\"/>");
            sw.writeLine(proteinLine.toString());
        }
    }
    ModificationMatch[] modificationMatches = peptide.getVariableModifications();
    if (modificationMatches.length > 0) {
        HashMap<Integer, Double> modifiedAminoAcids = new HashMap<>(modificationMatches.length);
        Double nTermMass = null;
        Double cTermMass = null;
        for (ModificationMatch modificationMatch : modificationMatches) {
            Modification modification = modificationFactory.getModification(modificationMatch.getModification());
            ModificationType modificationType = modification.getModificationType();
            if (modificationType == ModificationType.modn_protein || modificationType == ModificationType.modn_peptide) {
                if (nTermMass == null) {
                    nTermMass = Atom.H.getMonoisotopicMass();
                }
                nTermMass += modification.getMass();
            } else if (modificationType == ModificationType.modc_protein || modificationType == ModificationType.modc_peptide) {
                if (cTermMass == null) {
                    cTermMass = Atom.H.getMonoisotopicMass() + Atom.O.getMonoisotopicMass();
                }
                cTermMass += modification.getMass();
            } else {
                int site = modificationMatch.getSite();
                Double modMass = modifiedAminoAcids.get(site);
                if (modMass == null) {
                    modMass = 0.0;
                }
                modMass += modification.getMass();
                modifiedAminoAcids.put(site, modMass);
            }
        }
        StringBuilder modificationStart = new StringBuilder();
        modificationStart.append("<modification_info");
        if (nTermMass != null) {
            modificationStart.append(" mod_nterm_mass=\"").append(nTermMass).append("\"");
        }
        if (cTermMass != null) {
            modificationStart.append(" mod_cterm_mass=\"").append(nTermMass).append("\"");
        }
        modificationStart.append(">");
        sw.writeLine(modificationStart.toString());
        if (!modifiedAminoAcids.isEmpty()) {
            sw.increaseIndent();
            for (Integer site : modifiedAminoAcids.keySet()) {
                double modifiedMass = modifiedAminoAcids.get(site);
                StringBuilder modificationSite = new StringBuilder();
                modificationSite.append("<mod_aminoacid_mass position=\"").append(site).append("\" mass=\"").append(modifiedMass).append("\"/>");
                sw.writeLine(modificationSite.toString());
            }
            sw.decreaseIndent();
        }
        sw.writeLine("</modification_info>");
    }
    if (mainHit) {
        StringBuilder searchScore = new StringBuilder();
        searchScore.append("<search_score name=\"PSM raw score\" value=\"").append(psParameter.getTransformedScore()).append("\"/>");
        sw.writeLine(searchScore.toString());
        searchScore = new StringBuilder();
        searchScore.append("<search_score name=\"PSM score\" value=\"").append(psParameter.getTransformedScore()).append("\"/>");
        sw.writeLine(searchScore.toString());
        searchScore = new StringBuilder();
        searchScore.append("<search_score name=\"PSM PEP\" value=\"").append(psParameter.getProbability()).append("\"/>");
        sw.writeLine(searchScore.toString());
        searchScore = new StringBuilder();
        searchScore.append("<search_score name=\"PSM confidence\" value=\"").append(psParameter.getConfidence()).append("\"/>");
        sw.writeLine(searchScore.toString());
    } else {
        StringBuilder searchScore = new StringBuilder();
        searchScore.append("<search_score name=\"Identification algorithm raw score\" value=\"").append(peptideAssumption.getRawScore()).append("\"/>");
        sw.writeLine(searchScore.toString());
        searchScore = new StringBuilder();
        searchScore.append("<search_score name=\"Identification algorithm score\" value=\"").append(peptideAssumption.getScore()).append("\"/>");
        sw.writeLine(searchScore.toString());
        searchScore = new StringBuilder();
        searchScore.append("<search_score name=\"Identification algorithm PEP\" value=\"").append(psParameter.getProbability()).append("\"/>");
        sw.writeLine(searchScore.toString());
        searchScore = new StringBuilder();
        searchScore.append("<search_score name=\"Identification algorithm confidence\" value=\"").append(psParameter.getConfidence()).append("\"/>");
        sw.writeLine(searchScore.toString());
    }
    sw.writeLine("<analysis_result>");
    int advocateId = peptideAssumption.getAdvocate();
    Advocate advocate = Advocate.getAdvocate(advocateId);
    StringBuilder parameterLine = new StringBuilder();
    parameterLine.append("<parameter name=\"algorithm\" value=\"").append(advocate.getName()).append("\"/>");
    sw.writeLineIncreasedIndent(parameterLine.toString());
    for (ModificationMatch modificationMatch : modificationMatches) {
        parameterLine = new StringBuilder();
        parameterLine.append("<parameter name=\"ptm\" value=\"").append(modificationMatch.getModification()).append(" (").append(modificationMatch.getSite()).append(")").append("\"/>");
        sw.writeLine(parameterLine.toString());
    }
    parameterLine = new StringBuilder();
    parameterLine.append("<parameter name=\"charge\" value=\"").append(Integer.toString(peptideAssumption.getIdentificationCharge())).append("\"/>");
    sw.writeLine(parameterLine.toString());
    parameterLine = new StringBuilder();
    parameterLine.append("<parameter name=\"isotope\" value=\"").append(peptideAssumption.getIsotopeNumber(precursorMz, identificationParameters.getSearchParameters().getMinIsotopicCorrection(), identificationParameters.getSearchParameters().getMaxIsotopicCorrection())).append("\"/>");
    sw.writeLine(parameterLine.toString());
    sw.writeLineDecreasedIndent("</analysis_result>");
    sw.writeLineDecreasedIndent("</search_hit>");
}

Example 3 with Advocate

use of com.compomics.util.experiment.identification.Advocate in project peptide-shaker by compomics.

the class PsProjectSection method writeSection.

/**
 * Writes the desired section.
 *
 * @param experiment the experiment name
 * @param projectDetails the details of this project
 * @param waitingHandler the waiting handler
 *
 * @throws IOException exception thrown whenever an error occurred while
 * writing the file
 */
public void writeSection(String experiment, ProjectDetails projectDetails, WaitingHandler waitingHandler) throws IOException {
    if (waitingHandler != null) {
        waitingHandler.setSecondaryProgressCounterIndeterminate(true);
    }
    if (header) {
        if (indexes) {
            writer.writeHeaderText("");
            writer.addSeparator();
        }
        writer.writeHeaderText("Parameter");
        writer.addSeparator();
        writer.writeHeaderText("Value");
        writer.newLine();
    }
    int line = 1;
    for (PsProjectFeature projectFeature : projectFeatures) {
        if (indexes) {
            writer.write(Integer.toString(line));
            writer.addSeparator();
        }
        writer.write(projectFeature.getTitle());
        writer.addSeparator();
        switch(projectFeature) {
            case date:
                writer.write(projectDetails.getCreationDate() + "");
                break;
            case experiment:
                writer.write(experiment);
                break;
            case peptide_shaker:
                writer.write(projectDetails.getPeptideShakerVersion());
                break;
            case identification_algorithms:
                ArrayList<Integer> advocatesIds = projectDetails.getIdentificationAlgorithms();
                Collections.sort(advocatesIds);
                for (int i = 0; i < advocatesIds.size(); i++) {
                    if (i > 0) {
                        if (i == advocatesIds.size() - 1) {
                            writer.write(" and ");
                        } else {
                            writer.write(", ");
                        }
                    }
                    Integer advocateId = advocatesIds.get(i);
                    Advocate advocate = Advocate.getAdvocate(advocateId);
                    writer.write(advocate.getName());
                }
                break;
            case algorithms_versions:
                advocatesIds = projectDetails.getIdentificationAlgorithms();
                HashMap<String, ArrayList<String>> versions = projectDetails.getAlgorithmNameToVersionsMap();
                Collections.sort(advocatesIds);
                for (int i = 0; i < advocatesIds.size(); i++) {
                    if (i > 0) {
                        if (i == advocatesIds.size() - 1) {
                            writer.write(" and ");
                        } else {
                            writer.write(", ");
                        }
                    }
                    Integer advocateId = advocatesIds.get(i);
                    Advocate advocate = Advocate.getAdvocate(advocateId);
                    String advocateName = advocate.getName();
                    writer.write(advocateName + " (");
                    ArrayList<String> algorithmVersions = versions.get(advocateName);
                    if (algorithmVersions == null || algorithmVersions.isEmpty()) {
                        writer.write("unknown version)");
                    } else {
                        if (algorithmVersions.size() == 1) {
                            writer.write("version " + algorithmVersions.get(0) + ")");
                        } else {
                            writer.write("versions ");
                            for (int j = 0; j < algorithmVersions.size(); j++) {
                                if (j > 0) {
                                    if (j == algorithmVersions.size() - 1) {
                                        writer.write(" and ");
                                    } else {
                                        writer.write(", ");
                                    }
                                }
                                writer.write(algorithmVersions.get(j));
                            }
                            writer.write(")");
                        }
                    }
                }
                break;
            default:
                writer.write("Not implemented");
        }
        writer.newLine();
        line++;
    }
}

Example 4 with Advocate

use of com.compomics.util.experiment.identification.Advocate in project peptide-shaker by compomics.

the class ProjectDetails method getIdentificationAlgorithms.

/**
 * Returns a list of identification algorithms used based on the
 * identification files of the project.
 *
 * @return a list of identification algorithms indexed by the static field
 * of the Advocate class
 */
public ArrayList<Integer> getIdentificationAlgorithms() {
    ArrayList<Integer> result = new ArrayList<>();
    for (HashMap<String, ArrayList<String>> advocateVersions : identificationAlgorithms.values()) {
        for (String advocateName : advocateVersions.keySet()) {
            Advocate advocate = Advocate.getAdvocate(advocateName);
            if (advocate == null) {
                throw new IllegalArgumentException("Identification algorithm " + advocateName + " not recognized.");
            }
            int advocateId = advocate.getIndex();
            if (!result.contains(advocateId)) {
                result.add(advocateId);
            }
        }
    }
    return result;
}