objects to writer XPIP files

src/fr/inra/pappso/xtandempipeline/output/XpipOutput.java

+package fr.inra.pappso.xtandempipeline.output;
+
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
+import java.util.ArrayList;
+
+import javax.xml.stream.XMLOutputFactory;
+
+//import com.sun.xml.internal.txw2.output.IndentingXMLStreamWriter;
+import javax.xml.stream.XMLStreamWriter;
+
+import org.apache.log4j.Logger;
+
+import fr.inra.moulon.proticport.model.exceptions.ProticPortException;
+import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
+import fr.inra.pappso.xtandempipeline.class_msms.Identification;
+import fr.inra.pappso.xtandempipeline.thread.DataType_Base;
+import fr.inra.pappso.xtandempipeline.thread.process;
+
+public class XpipOutput {
+	private static final Logger logger = Logger.getLogger(XpipOutput.class);
+
+	XMLStreamWriter writer;
+	OutputStream outputStream;
+	XpipWriter xpipWriter;
+
+	public XpipOutput() throws ProticPortException {
+	}
+
+	public void open(OutputStream outputStream) throws MSMSException {
+
+		try {
+
+			this.outputStream = outputStream;
+			XMLOutputFactory factory = XMLOutputFactory.newInstance();
+			// OutputStreamWriter noIndentOutput = new OutputStreamWriter(
+			// outputStream, "UTF8");
+			// XMLStreamWriter writer =
+			// factory.createXMLStreamWriter(noIndentOutput);
+			OutputStreamWriter output = new OutputStreamWriter(outputStream,
+					"UTF8");
+
+			writer = new IndentingXMLStreamWriter(
+					factory.createXMLStreamWriter(output));
+			writer.writeStartDocument("UTF-8", "1.0");
+
+			xpipWriter = new XpipWriter(writer);
+
+			logger.debug("No errors writing XPIP. All seems OK!");
+		} catch (Exception e) {
+			try {
+				outputStream.write(e.getMessage().toString().getBytes());
+			} catch (IOException e1) {
+				logger.debug("ERROR : " + e.getMessage(), e);
+			}
+			// throw new ProticPortException ("ERROR writing mzXml "+
+			// e.getMessage());
+			logger.debug("ERROR writing XPIP : " + e.getMessage(), e);
+		}
+	}
+
+	public void close() {
+		try {
+			xpipWriter.close();
+			outputStream.flush();
+
+			logger.debug("No errors writing XPIP. All seems OK!");
+		} catch (Exception e) {
+			try {
+				outputStream.write(e.getMessage().toString().getBytes());
+			} catch (IOException e1) {
+				logger.debug("ERROR : " + e.getMessage(), e);
+			}
+			// throw new ProticPortException ("ERROR writing mzXml "+
+			// e.getMessage());
+			logger.debug("ERROR writing XPIP : " + e.getMessage(), e);
+		}
+	}
+
+	public void write(ArrayList<Identification> identifications,
+			DataType_Base datatype, process p) throws Exception {
+
+		xpipWriter.write(identifications, datatype, p);
+	}
+}

src/fr/inra/pappso/xtandempipeline/output/XpipWriter.java

+package fr.inra.pappso.xtandempipeline.output;
+
+import java.util.ArrayList;
+
+import javax.xml.stream.XMLStreamException;
+//import com.sun.xml.internal.txw2.output.IndentingXMLStreamWriter;
+import javax.xml.stream.XMLStreamWriter;
+
+import org.apache.log4j.Logger;
+
+import fr.inra.moulon.proticport.model.Controller;
+import fr.inra.pappso.xtandempipeline.XtandemPipelineMain;
+import fr.inra.pappso.xtandempipeline.XtandemPipelineSession;
+import fr.inra.pappso.xtandempipeline.class_msms.Identification;
+import fr.inra.pappso.xtandempipeline.class_msms.Match;
+import fr.inra.pappso.xtandempipeline.class_msms.Modifs;
+import fr.inra.pappso.xtandempipeline.class_msms.MsRun;
+import fr.inra.pappso.xtandempipeline.class_msms.MapDb.Peptide;
+import fr.inra.pappso.xtandempipeline.thread.DataType_Base;
+import fr.inra.pappso.xtandempipeline.thread.process;
+
+public class XpipWriter {
+	private static final Logger logger = Logger.getLogger(XpipWriter.class);
+
+	private ArrayList<Identification> idents;
+
+	private XMLStreamWriter writer;
+
+	private process pro;
+
+	protected XpipWriter(XMLStreamWriter writer) throws Exception {
+		logger.info("Save project ...");
+
+		this.writer = writer;
+
+		writer.writeStartElement("xtandem_pipeline");
+		writer.writeAttribute("version", XtandemPipelineMain.version);
+	}
+
+	private void write_result_to(Identification ident) throws Exception {
+		writer.writeStartElement("identification");
+
+		writer.writeStartElement("modifs_list_mass");
+		for (Modifs mod : ident.get_modifs_liste().get_modifs_order()) {
+			writer.writeEmptyElement("modifs_mass");
+			writer.writeAttribute("modvalue", "" + mod.get_modvalue());
+		}
+		writer.writeEndElement();
+
+		writer.writeStartElement("samples");
+		for (MsRun samp : ident.getMsRunSet()) {
+			writer.writeEmptyElement("sample");
+			writer.writeAttribute("value", samp.getSampleName());
+		}
+
+		writer.writeEndElement();
+		writer.writeStartElement("match_list");
+		for (Match m : ident.get_protein_liste().getMatchOrder())
+			this.write_match_to(m, ident);
+		writer.writeEndElement();
+		// on ferme l'ident
+		writer.writeEndElement();
+		// writer.flush();
+	}
+
+	private void write_match_to(Match m, Identification ident) throws Exception {
+		writer.writeStartElement("match");
+
+		writer.writeAttribute("validate", "" + m.isIsvalidate());
+
+		writer.writeAttribute("PAI", "" + m.getPAI());
+		writer.writeAttribute("emPAI", "" + m.getEmPAI());
+
+		writer.writeStartElement("protein");
+		writer.writeAttribute("peptide_number", ""
+				+ m.get_protein_match().get_peptides_numbers());
+		writer.writeAttribute("evalue", "" + m.get_protein_match().get_evalue());
+		writer.writeAttribute("URL", m.get_protein_match().getDatabase()
+				.getDatabasePath());
+		writer.writeAttribute("description", m.get_protein_match()
+				.get_description());
+		// sample evalue
+		for (MsRun sample : m.get_protein_match().get_hash_sample_evalue()
+				.keySet()) {
+			writer.writeEmptyElement("protein_evalue");
+			writer.writeAttribute("evalue", ""
+					+ m.get_protein_match().get_hash_sample_evalue()
+							.get(sample));
+			writer.writeAttribute("sample", sample.getSampleName());
+			// writer.writeCharacters(endline);
+		}
+
+		writer.writeStartElement("sequence");
+		writer.writeCharacters(m.get_protein_match().get_sequence());
+		writer.writeEndElement();
+		writer.writeEndElement();
+
+		writer.writeStartElement("peptide_list");
+		for (Peptide pep : m.get_all_peptides())
+			this.write_peptide_to(pep);
+		writer.writeEndElement();
+		// on ferme le match
+		writer.writeEndElement();
+		// on compte les match
+		pro.add_current_progress();
+	}
+
+	private void write_peptide_to(Peptide pep) throws Exception {
+		writer.writeStartElement("peptide");
+		writer.writeAttribute("sample", pep.get_sample());
+		pep.getIdentificationDataSource().writeXpipPeptideSourceAttribute(
+				writer);
+		writer.writeAttribute("scan", "" + pep.get_scan());
+		writer.writeAttribute("scan_in_xtandem", "" + pep.get_scan());
+		writer.writeAttribute("RT", "" + pep.get_RT_in_sec());
+		writer.writeAttribute("mhplus_obser", "" + pep.get_mhplus_obser());
+		writer.writeAttribute("mhplus_theo", "" + pep.get_mhplus_theo());
+		writer.writeAttribute("deltamass", "" + pep.get_deltamass());
+		writer.writeAttribute("sequence", pep.getSequence());
+		writer.writeAttribute("pre", pep.get_pre());
+		writer.writeAttribute("post", pep.get_post());
+		writer.writeAttribute("start", "" + pep.get_start());
+		writer.writeAttribute("stop", "" + pep.get_stop());
+		writer.writeAttribute("charge", "" + pep.get_charge());
+		writer.writeAttribute("evalue", "" + pep.get_evalue());
+		writer.writeAttribute("hypercorr", "" + pep.get_hypercorr());
+		writer.writeAttribute("validate", "" + pep.isValidate());
+		writer.writeStartElement("modifs");
+		for (Modifs mod : pep.get_Modifs()) {
+			writer.writeEmptyElement("modif");
+			writer.writeAttribute("aa", "" + mod.get_AA());
+			writer.writeAttribute("modvalue", "" + mod.get_modvalue());
+			writer.writeAttribute("posi", "" + mod.get_posi());
+			writer.writeAttribute("posi_in_prot", "" + mod.getPosi_in_prot());
+		}
+		writer.writeEndElement();
+		// on ferme le peptide
+		writer.writeEndElement();
+	}
+
+	protected void close() throws XMLStreamException {
+		writer.writeEndDocument();
+	}
+
+	protected void write(ArrayList<Identification> identifications,
+			DataType_Base datatype, process p) throws Exception {
+		this.idents = identifications;
+		this.pro = p;
+
+		// <DataSource>
+		// <PROTICport
+		// url="http://uln.moulon.inra.fr/~langella/proticdev/web_view/proticport/"
+		// user="langella" />
+		// </DataSource>
+		if (XtandemPipelineSession.getInstance().isPROTICportDataSource()) {
+			writer.writeStartElement("DataSource");
+			writer.writeEmptyElement("PROTICport");
+			Controller ppc = XtandemPipelineSession.getInstance()
+					.getPROTICportController();
+			writer.writeAttribute("url", ppc.getProticPortUrl().toString());
+			writer.writeAttribute("user", ppc.getUser().getLogin());
+			writer.writeEndElement();
+		}
+		writer.writeEmptyElement("information");
+		writer.writeAttribute("Data_Type", datatype.getType());
+		int count = 0;
+		for (Identification ident : idents)
+			count += ident.get_protein_liste().size();
+		writer.writeAttribute("match_number", "" + count);
+
+		writer.writeEmptyElement("filter_params");
+		writer.writeAttribute("pep_evalue", ""
+				+ datatype.getConf().get_peptide_evalue());
+		writer.writeAttribute("prot_evalue", ""
+				+ datatype.getConf().get_protein_evalue());
+		writer.writeAttribute("pep_number", ""
+				+ datatype.getConf().get_peptide_number());
+		writer.writeAttribute("filter_to_all", ""
+				+ datatype.getConf().get_protein_filter_to_complete());
+		writer.writeAttribute("database_filter", datatype.getConf()
+				.get_database_filter().getPath());
+
+		writer.writeStartElement("identifications");
+		for (Identification ident : idents)
+			this.write_result_to(ident);
+		writer.writeEndElement();
+		// on ferme le root
+		writer.writeEndElement();
+		writer.writeEndDocument();
+		writer.flush();
+		writer.close();
+
+		logger.info("Save project finish");
+	}
+
+}