com.compomics.colims.distributed.io.maxquant.parsers.MaxQuantQuantificationSettingsParser.java Source code

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Here is the source code for com.compomics.colims.distributed.io.maxquant.parsers.MaxQuantQuantificationSettingsParser.java

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package com.compomics.colims.distributed.io.maxquant.parsers;

import com.compomics.colims.core.ontology.OntologyMapper;
import com.compomics.colims.core.ontology.OntologyTerm;
import com.compomics.colims.core.service.QuantificationReagentService;
import com.compomics.colims.core.service.QuantificationSettingsService;
import com.compomics.colims.model.*;
import com.compomics.colims.model.enums.QuantificationEngineType;
import org.apache.log4j.Logger;
import org.springframework.stereotype.Component;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

/**
 * @author demet
 */
@Component("maxQuantQuantificationSettingsParser")
public class MaxQuantQuantificationSettingsParser {

    /**
     * Logger instance.
     */
    private static Logger LOGGER = Logger.getLogger(MaxQuantSearchSettingsParser.class);

    private static final String SILAC_LABEL = "SILAC";

    /**
     * The quantification settings indexed by analytical run (key: AnalyticalRun ; value: QuantificationSettings)
     */
    private final Map<AnalyticalRun, QuantificationSettings> runsAndQuantificationSettings = new HashMap<>();

    private final OntologyMapper ontologyMapper;
    private final QuantificationSettingsService quantificationSettingsService;
    private final QuantificationReagentService quantificationReagentService;
    private final MaxQuantSearchSettingsParser maxQuantSearchSettingsParser;

    public MaxQuantQuantificationSettingsParser(QuantificationSettingsService quantificationSettingsService,
            OntologyMapper ontologyMapper, QuantificationReagentService quantificationReagentService,
            MaxQuantSearchSettingsParser maxQuantSearchSettingsParser) {
        this.quantificationSettingsService = quantificationSettingsService;
        this.ontologyMapper = ontologyMapper;
        this.quantificationReagentService = quantificationReagentService;
        this.maxQuantSearchSettingsParser = maxQuantSearchSettingsParser;
    }

    /**
     * Get map of analytical run and quantification settings
     *
     * @return runsAndQuantificationSettings
     */
    public Map<AnalyticalRun, QuantificationSettings> getRunsAndQuantificationSettings() {
        return runsAndQuantificationSettings;
    }

    /**
     * Clear resources.
     */
    public void clear() {
        runsAndQuantificationSettings.clear();
    }

    /**
     * Parse the quantification parameters for a MaxQuant experiment.
     *
     * @param analyticalRuns
     * @param quantificationLabel
     * @param reagents
     */
    public void parse(List<AnalyticalRun> analyticalRuns, String quantificationLabel, List<String> reagents) {

        OntologyTerm ontologyTerm = ontologyMapper.getColimsMapping().getQuantificationMethods()
                .get(quantificationLabel);

        // create quantificationCvParam
        QuantificationMethod quantificationMethod = new QuantificationMethod(ontologyTerm.getOntologyPrefix(),
                ontologyTerm.getOboId(), ontologyTerm.getLabel());
        quantificationMethod.getQuantificationMethodHasReagents()
                .addAll(createQuantificationReagent(quantificationMethod, quantificationLabel, reagents));
        // check if quantificationMethodCvParam is in the db
        quantificationMethod = quantificationSettingsService.getQuantificationMethodCvParams(quantificationMethod);
        // create quantificationSettings
        QuantificationSettings quantificationSettings = new QuantificationSettings();
        quantificationSettings.setQuantificationMethod(quantificationMethod);
        quantificationSettings.setQuantificationEngine(quantificationSettingsService.getQuantificationEngine(
                QuantificationEngineType.MAXQUANT, maxQuantSearchSettingsParser.getVersion()));
        analyticalRuns.forEach(analyticalRun -> {
            QuantificationSettings quantSettings = new QuantificationSettings();
            quantSettings.setAnalyticalRun(analyticalRun);
            quantSettings.setQuantificationMethod(quantificationSettings.getQuantificationMethod());
            quantSettings.setQuantificationEngine(quantificationSettings.getQuantificationEngine());
            runsAndQuantificationSettings.put(analyticalRun, quantSettings);

        });
    }

    /**
     * This method is to create QuantificationReagent and its link to QuantificationMethodCvParam.
     *
     * @param quantificationMethod
     * @param quantificationLabel
     * @param reagents
     * @return QuantificationMethodHasReagents list
     */
    public List<QuantificationMethodHasReagent> createQuantificationReagent(
            QuantificationMethod quantificationMethod, String quantificationLabel, List<String> reagents) {
        List<QuantificationMethodHasReagent> quantificationMethodHasReagents = new ArrayList<>();

        reagents.forEach(reagent -> {
            OntologyTerm ontologyTerm = null;
            if (quantificationLabel.equals(SILAC_LABEL)) {
                ontologyTerm = ontologyMapper.getColimsMapping().getQuantificationReagents().get(reagent);
            } else {
                ontologyTerm = ontologyMapper.getMaxQuantMapping().getQuantificationReagents().get(reagent);
            }

            QuantificationMethodHasReagent quantificationMethodHasReagent = new QuantificationMethodHasReagent();
            if (ontologyTerm != null) {
                QuantificationReagent quantificationReagent = new QuantificationReagent(
                        ontologyTerm.getOntologyPrefix(), ontologyTerm.getOboId(), ontologyTerm.getLabel());

                // check if quantificationReagent is in the db
                quantificationReagent = quantificationReagentService
                        .getQuantificationReagent(quantificationReagent);

                quantificationMethodHasReagent.setQuantificationReagent(quantificationReagent);
                quantificationMethodHasReagent.setQuantificationMethod(quantificationMethod);
                quantificationMethodHasReagents.add(quantificationMethodHasReagent);
            }
        });

        return quantificationMethodHasReagents;
    }

}