package au.org.intersect.samifier.parser.mzidentml;

import org.xml.sax.Attributes;
import org.xml.sax.helpers.DefaultHandler;

public class SpectrumIdentificationItemHandler extends DefaultHandler {
    private static final String SPECTRUM_ID_ITEM = "SpectrumIdentificationItem";
    private static final String PEPTIDE_EVIDENCE = "PeptideEvidence";
    private static final String CV_PARAM = "cvParam";
    private static final String MASCOT_SCORE = "mascot:score";
    private static final String ATTR_NAME = "name";
    private static final String ATTR_VALUE = "value";
    private static final String ATTR_ID = "id";
    private static final String ATTR_START = "start";
    private static final String ATTR_END = "end";
    private static final String ATTR_DB_SEQUENCE_REF = "DBSequence_Ref";
    private static final String PEPTIDE_EVIDENCE_REF = "PeptideEvidenceRef";
    private static final String ATTR_PEPTIDE_EVIDENCE_REF = "peptideEvidence_ref";

    private String peptideSequence;
    private String protein;
    private String confidenceScore;
    private String id;
    private String start;
    private String end;
    private String reference;

    private MzidReader reader;

    public SpectrumIdentificationItemHandler(MzidReader mzidReader,
            String peptideSequence) {
        super();
        this.reader = mzidReader;
        this.peptideSequence = peptideSequence;
    }

    public void startElement(String uri, String name, String qName,
            Attributes attrs) {
        if (PEPTIDE_EVIDENCE.equals(qName)) {
            protein = reader.getAccessionFromDbSequenceRef(attrs
                    .getValue(ATTR_DB_SEQUENCE_REF));
            id = attrs.getValue(ATTR_ID);
            start = attrs.getValue(ATTR_START);
            end = attrs.getValue(ATTR_END);
        } else if (CV_PARAM.equals(qName)) {
            if (attrs.getValue(ATTR_NAME).equalsIgnoreCase(MASCOT_SCORE)) {
                confidenceScore = attrs.getValue(ATTR_VALUE);
            }
        } else if (PEPTIDE_EVIDENCE_REF.equals(qName)) {
            reference = attrs.getValue(ATTR_PEPTIDE_EVIDENCE_REF);
        }
    }

    public void endElement(String uri, String name, String qName) {
        if (SPECTRUM_ID_ITEM.equals(qName)) {
            if (id != null) {
                reader.build(id, peptideSequence, protein, start, end,
                        confidenceScore);
            } else if (reference != null) {
                reader.addReference(reference, confidenceScore, peptideSequence);
            }
            reader.removeHandler();
        }
    }
}