better saxbase handler, loading X!Tandem identification with new handler

src/fr/inra/pappso/xtandempipeline/class_msms/IdentificationDataFile/IdentificationXtandemFile.java

@@ -11,10 +11,10 @@ import org.apache.log4j.Logger;
 import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
 import fr.inra.pappso.xtandempipeline.class_msms.Identification;
 import fr.inra.pappso.xtandempipeline.class_msms.MapDb.Peptide;
+import fr.inra.pappso.xtandempipeline.sax_parse.HandlerXtResultFile;
 import fr.inra.pappso.xtandempipeline.sax_parse.HandlerXtResultFile4ProcessingParams;
 import fr.inra.pappso.xtandempipeline.sax_parse.XtandemPhospho;
 import fr.inra.pappso.xtandempipeline.sax_parse.parse_file;
-import fr.inra.pappso.xtandempipeline.sax_parse.xtandem;
 import fr.inra.pappso.xtandempipeline.sax_parse.xtandem_ms2_spectra;
 
 public class IdentificationXtandemFile extends IdentificationDataFile {
@@ -29,7 +29,8 @@ public class IdentificationXtandemFile extends IdentificationDataFile {
 	@Override
 	public Identification loadIdentification(
 			Identification previousIdentification) throws Exception {
-		xtandem tandem = new xtandem(previousIdentification, this);
+		HandlerXtResultFile tandem = new HandlerXtResultFile(
+				previousIdentification, this);
 		new parse_file(tandem, this.file);
 		previousIdentification = tandem.get_identifications();
 		return previousIdentification;

src/fr/inra/pappso/xtandempipeline/sax_parse/SaxBaseHandler.java

@@ -70,10 +70,22 @@ public class SaxBaseHandler extends DefaultHandler {
 		if ("".equals(tag))
 			tag = qName;
 		if ((data != null) && (!data.toString().isEmpty())) {
-			sendData(data.toString());
+			try {
+				sendData(data.toString());
+			} catch (Exception e1) {
+				logger.error("ERROR parsing data in element "
+						+ stack.get(stack.size() - 1) + " at line "
+						+ this.xml_location.getLineNumber() + " and column "
+						+ this.xml_location.getColumnNumber() + "\n"
+						+ e1.getMessage());
+				throw new SAXException("ERROR parsing data in element "
+						+ stack.get(stack.size() - 1) + " element at line "
+						+ this.xml_location.getLineNumber() + " and column "
+						+ this.xml_location.getColumnNumber(), e1);
+			}
 		}
 		stack.push(tag);
-		
+
 		data = new StringBuffer();
 		// String nameSpaceUri, String tag,Attributes attrs
 		@SuppressWarnings("rawtypes")
@@ -165,12 +177,13 @@ public class SaxBaseHandler extends DefaultHandler {
 		}
 	}
 
-	/** send data string in special case
+	/**
+	 * send data string in special case
 	 * 
 	 * @param string
 	 */
 	protected void sendData(String string) {
-		
+
 	}
 
 	/**