new ODS table sheet to display the number of specific and specific unique peptides by MS samples

src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsComparSpecificUniqueSpectraOutput.java

+/*******************************************************************************
+ * Copyright (c) 2014 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ * 
+ * This file is part of XTandemPipeline.
+ * 
+ *     XTandemPipeline is free software: you can redistribute it and/or modify
+ *     it under the terms of the GNU General Public License as published by
+ *     the Free Software Foundation, either version 3 of the License, or
+ *     (at your option) any later version.
+ * 
+ *     XTandemPipeline is distributed in the hope that it will be useful,
+ *     but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *     GNU General Public License for more details.
+ * 
+ *     You should have received a copy of the GNU General Public License
+ *     along with XTandemPipeline.  If not, see <http://www.gnu.org/licenses/>.
+ * 
+ * Contributors:
+ *     Olivier Langella <Olivier.Langella@moulon.inra.fr>
+ ******************************************************************************/
+
+package fr.inra.pappso.xtandempipeline.output.SpreadSheets;
+
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.TreeMap;
+
+import javax.xml.datatype.DatatypeConfigurationException;
+import javax.xml.stream.XMLStreamException;
+
+import org.apache.log4j.Logger;
+
+import fr.inra.pappso.libodsstream.OdsDocWriter;
+import fr.inra.pappso.xtandempipeline.Utils;
+import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
+import fr.inra.pappso.xtandempipeline.class_msms.Identification;
+import fr.inra.pappso.xtandempipeline.class_msms.MsRun;
+import fr.inra.pappso.xtandempipeline.class_msms.MsRunSet;
+import fr.inra.pappso.xtandempipeline.class_msms.Protein;
+import fr.inra.pappso.xtandempipeline.grouping.Group;
+import fr.inra.pappso.xtandempipeline.grouping.SubGroup;
+
+public class OdsComparSpecificUniqueSpectraOutput {
+	private static final Logger logger = Logger
+			.getLogger(OdsComparSpecificUniqueSpectraOutput.class);
+
+	protected OdsDocWriter odsTable;
+
+	private TreeMap<String, MsRun> msRunOrderedList;
+
+	protected OdsComparSpecificUniqueSpectraOutput() {
+
+	}
+
+	public OdsComparSpecificUniqueSpectraOutput(OutputStream outputStream)
+			throws MSMSException {
+		try {
+			odsTable = new OdsDocWriter(outputStream);
+			odsTable.writeSheet("compar_Specific_Unique");
+		} catch (IOException e) {
+			String message = "IOException " + e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		} catch (XMLStreamException e) {
+			String message = "XMLStreamException " + e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		} catch (DatatypeConfigurationException e) {
+			String message = "DatatypeConfigurationException " + e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		} catch (Exception e) {
+			String message = "Exception " + e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		}
+	}
+
+	public OdsComparSpecificUniqueSpectraOutput(OdsDocWriter odsTable)
+			throws MSMSException {
+		try {
+			this.odsTable = odsTable;
+			odsTable.writeSheet("compar_Specific_Unique");
+		} catch (XMLStreamException e) {
+			String message = "XMLStreamException " + e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		} catch (Exception e) {
+			String message = "Exception " + e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		}
+	}
+
+	public void close() throws MSMSException {
+		try {
+			odsTable.close();
+		} catch (Exception e) {
+			String message = "Exception closing OdsProteinOutput "
+					+ e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		}
+	}
+
+	private void writeHeaders(Identification ident) throws MSMSException {
+		try {
+			// Group Id Sub-group Id Top protein id Top protein Description
+			// Nombre of protein 20121213_Cueff_065_1_C01_Xylo1
+			// 20121213_Cueff_065_1_C02_Xylo2
+
+			odsTable.writeLine();
+			odsTable.writeCell("Group ID");
+			odsTable.writeCell("Sub-group ID");
+			odsTable.writeCell("Top Protein ID");
+			odsTable.writeCell("Top Protein Description");
+			odsTable.writeCell("Number of proteins");
+
+			MsRunSet msSampleList = ident.getMsRunSet();
+			msRunOrderedList = new TreeMap<String, MsRun>();
+			for (MsRun msSample : msSampleList) {
+				msRunOrderedList.put(msSample.getSampleName(), msSample);
+			}
+			for (String msSampleName : msRunOrderedList.keySet()) {
+				odsTable.writeCell(msSampleName);
+			}
+
+		} catch (XMLStreamException e) {
+			String message = "XMLStreamException in writeHeaders() "
+					+ e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		} catch (Exception e) {
+			String message = "Exception in writeHeaders() " + e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		}
+
+	}
+
+	public void write(Identification ident) throws MSMSException {
+		try {
+
+			this.writeHeaders(ident);
+			for (Group group : ident.getGrouping().getGroupList()) {
+				for (SubGroup sg : group.getSubGroupSet().getSubGroupList()) {
+					this.writeOneSubGroup(ident, group, sg);
+				}
+
+			}
+			odsTable.writeLine();
+			odsTable.writeLine();
+
+		} catch (XMLStreamException e) {
+			String message = "XMLStreamException in write(Identification ident) "
+					+ e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		} catch (Exception e) {
+			String message = "Exception in write(Identification ident) "
+					+ e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		}
+	}
+
+	private void writeOneSubGroup(Identification ident, Group group, SubGroup sg)
+			throws MSMSException {
+		try {
+			logger.debug("writeOneSubGroup begin " + group);
+			odsTable.writeLine();
+
+			// odsTable.writeCell("Group ID");
+			odsTable.writeCell(Utils.getPappsoGroupId(group));
+
+			// odsTable.writeCell("Sub-group ID");
+			odsTable.writeCell(Utils.getPappsoSubGroupId(group, sg));
+			Protein topProt = (Protein) sg.getHashSampleScanSetProtList()
+					.get(0).getGrpProtMatch().getGrpProtein();
+			// odsTable.writeCell("Top Protein ID");
+			odsTable.writeCell(Utils.getPappsoGroupingNumber(group, sg, 1));
+			// odsTable.writeCell("Top Protein Description");
+			odsTable.writeCell(topProt.get_description());
+
+			// odsTable.writeCell("Number of proteins");
+			odsTable.writeCell(sg.getHashSampleScanSetProtList().size());
+
+			for (String msSampleName : msRunOrderedList.keySet()) {
+				odsTable.writeCell(group
+						.getNumberOfSpecificUniquePeptideInSubGroupGrpMsSample(
+								sg.getHashSampleScanSetProtList().get(0),
+								this.msRunOrderedList.get(msSampleName)));
+			}
+
+			logger.debug("writeOneSubGroup end");
+		} catch (XMLStreamException e) {
+			String message = "XMLStreamException in writeOneSubGroup "
+					+ e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		} catch (Exception e) {
+			String message = "Exception in writeOneSubGroup " + e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		}
+	}
+}

src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsComparUniqueSpectraOutput.java

+/*******************************************************************************
+ * Copyright (c) 2014 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ * 
+ * This file is part of XTandemPipeline.
+ * 
+ *     XTandemPipeline is free software: you can redistribute it and/or modify
+ *     it under the terms of the GNU General Public License as published by
+ *     the Free Software Foundation, either version 3 of the License, or
+ *     (at your option) any later version.
+ * 
+ *     XTandemPipeline is distributed in the hope that it will be useful,
+ *     but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *     GNU General Public License for more details.
+ * 
+ *     You should have received a copy of the GNU General Public License
+ *     along with XTandemPipeline.  If not, see <http://www.gnu.org/licenses/>.
+ * 
+ * Contributors:
+ *     Olivier Langella <Olivier.Langella@moulon.inra.fr>
+ ******************************************************************************/
+
+package fr.inra.pappso.xtandempipeline.output.SpreadSheets;
+
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.TreeMap;
+
+import javax.xml.datatype.DatatypeConfigurationException;
+import javax.xml.stream.XMLStreamException;
+
+import org.apache.log4j.Logger;
+
+import fr.inra.pappso.libodsstream.OdsDocWriter;
+import fr.inra.pappso.xtandempipeline.Utils;
+import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
+import fr.inra.pappso.xtandempipeline.class_msms.Identification;
+import fr.inra.pappso.xtandempipeline.class_msms.MsRun;
+import fr.inra.pappso.xtandempipeline.class_msms.MsRunSet;
+import fr.inra.pappso.xtandempipeline.class_msms.Protein;
+import fr.inra.pappso.xtandempipeline.grouping.Group;
+import fr.inra.pappso.xtandempipeline.grouping.SubGroup;
+
+public class OdsComparUniqueSpectraOutput {
+	private static final Logger logger = Logger
+			.getLogger(OdsComparUniqueSpectraOutput.class);
+
+	protected OdsDocWriter odsTable;
+
+	private TreeMap<String, MsRun> msRunOrderedList;
+
+	protected OdsComparUniqueSpectraOutput() {
+
+	}
+
+	public OdsComparUniqueSpectraOutput(OutputStream outputStream)
+			throws MSMSException {
+		try {
+			odsTable = new OdsDocWriter(outputStream);
+			odsTable.writeSheet("compar_Unique");
+		} catch (IOException e) {
+			String message = "IOException " + e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		} catch (XMLStreamException e) {
+			String message = "XMLStreamException " + e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		} catch (DatatypeConfigurationException e) {
+			String message = "DatatypeConfigurationException " + e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		} catch (Exception e) {
+			String message = "Exception " + e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		}
+	}
+
+	public OdsComparUniqueSpectraOutput(OdsDocWriter odsTable)
+			throws MSMSException {
+		try {
+			this.odsTable = odsTable;
+			odsTable.writeSheet("compar_Unique");
+		} catch (XMLStreamException e) {
+			String message = "XMLStreamException " + e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		} catch (Exception e) {
+			String message = "Exception " + e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		}
+	}
+
+	public void close() throws MSMSException {
+		try {
+			odsTable.close();
+		} catch (Exception e) {
+			String message = "Exception closing OdsProteinOutput "
+					+ e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		}
+	}
+
+	private void writeHeaders(Identification ident) throws MSMSException {
+		try {
+			// Group Id Sub-group Id Top protein id Top protein Description
+			// Nombre of protein 20121213_Cueff_065_1_C01_Xylo1
+			// 20121213_Cueff_065_1_C02_Xylo2
+
+			odsTable.writeLine();
+			odsTable.writeCell("Group ID");
+			odsTable.writeCell("Sub-group ID");
+			odsTable.writeCell("Top Protein ID");
+			odsTable.writeCell("Top Protein Description");
+			odsTable.writeCell("Number of proteins");
+
+			MsRunSet msSampleList = ident.getMsRunSet();
+			msRunOrderedList = new TreeMap<String, MsRun>();
+			for (MsRun msSample : msSampleList) {
+				msRunOrderedList.put(msSample.getSampleName(), msSample);
+			}
+			for (String msSampleName : msRunOrderedList.keySet()) {
+				odsTable.writeCell(msSampleName);
+			}
+
+		} catch (XMLStreamException e) {
+			String message = "XMLStreamException in writeHeaders() "
+					+ e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		} catch (Exception e) {
+			String message = "Exception in writeHeaders() " + e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		}
+
+	}
+
+	public void write(Identification ident) throws MSMSException {
+		try {
+
+			this.writeHeaders(ident);
+			for (Group group : ident.getGrouping().getGroupList()) {
+				for (SubGroup sg : group.getSubGroupSet().getSubGroupList()) {
+					this.writeOneSubGroup(ident, group, sg);
+				}
+
+			}
+			odsTable.writeLine();
+			odsTable.writeLine();
+
+		} catch (XMLStreamException e) {
+			String message = "XMLStreamException in write(Identification ident) "
+					+ e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		} catch (Exception e) {
+			String message = "Exception in write(Identification ident) "
+					+ e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		}
+	}
+
+	private void writeOneSubGroup(Identification ident, Group group, SubGroup sg)
+			throws MSMSException {
+		try {
+			logger.debug("writeOneSubGroup begin " + group);
+			odsTable.writeLine();
+
+			// odsTable.writeCell("Group ID");
+			odsTable.writeCell(Utils.getPappsoGroupId(group));
+
+			// odsTable.writeCell("Sub-group ID");
+			odsTable.writeCell(Utils.getPappsoSubGroupId(group, sg));
+			Protein topProt = (Protein) sg.getHashSampleScanSetProtList()
+					.get(0).getGrpProtMatch().getGrpProtein();
+			// odsTable.writeCell("Top Protein ID");
+			odsTable.writeCell(Utils.getPappsoGroupingNumber(group, sg, 1));
+			// odsTable.writeCell("Top Protein Description");
+			odsTable.writeCell(topProt.get_description());
+
+			// odsTable.writeCell("Number of proteins");
+			odsTable.writeCell(sg.getHashSampleScanSetProtList().size());
+
+			for (String msSampleName : msRunOrderedList.keySet()) {
+				odsTable.writeCell(sg
+						.getNumberOfUniquePeptideByGrpMsSample(this.msRunOrderedList
+								.get(msSampleName)));
+			}
+
+			logger.debug("writeOneSubGroup end");
+		} catch (XMLStreamException e) {
+			String message = "XMLStreamException in writeOneSubGroup "
+					+ e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		} catch (Exception e) {
+			String message = "Exception in writeOneSubGroup " + e.getMessage();
+			logger.error(message);
+			throw new MSMSException(message);
+		}
+	}
+}