fix for bug report 4525

src/output/masschroqml.cpp

@@ -104,11 +104,9 @@ void MassChroQml::write(ProjectSp sp_project) {
     _output_stream->writeAttribute("type","input");
     _output_stream->writeAttribute("version","2.2");
     //_output_stream->writeAttribute("creationDate", QDateTime::currentDateTime().toString( Qt::ISODate));
-    _output_stream->writeNamespace("http://www.w3.org/2001/XMLSchema-instance","xsi");
     //_output_stream->writeNamespace("http://www.w3.org/2001/XMLSchema-instance","xsi");
-    _output_stream->writeAttribute("xmlns","http://pappso.inra.fr/xsd/masschroqml/2.2");
-    //xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd"
-    _output_stream->writeAttribute("http://www.w3.org/2001/XMLSchema-instance","schemaLocation","http://pappso.inra.fr/xsd/masschroqml/2.2 http://pappso.inra.fr/xsd/masschroq-2.2.xsd");
+    //_output_stream->writeAttribute("xmlns","http://pappso.inra.fr/xsd/masschroqml/2.2");
+    //_output_stream->writeAttribute("http://www.w3.org/2001/XMLSchema-instance","schemaLocation","http://pappso.inra.fr/xsd/masschroqml/2.2 http://pappso.inra.fr/xsd/masschroq-2.2.xsd");
 
     // <rawdata><!-- time_values_dir="directory" to read retention time corrections-->
     _output_stream->writeStartElement("rawdata");
@@ -146,6 +144,9 @@ void MassChroQml::write(ProjectSp sp_project) {
     writeQuantificationTraces();
     writeQuantify();
     _output_stream->writeEndElement();
+    
+    
+    _output_stream->writeEndDocument();
 }
 
 
@@ -215,7 +216,6 @@ void MassChroQml::writeQuantify() {
     _output_stream->writeComment("<mzrt_list>\n				<mzrt mz=\"732.317\" rt=\"230.712\" />\n			<mzrt mz=\"575.256\" rt=\"254.788\" />\n			</mzrt_list>");
 
     //</quantify>
-
     _output_stream->writeEndElement();
 }
 
@@ -231,10 +231,11 @@ void MassChroQml::writeQuantificationMethods() {
     _output_stream->writeComment("max : XIC on BasePeak; sum : XIC on TIC");
     //<ppm_range min="10" max="10"/><!--For XIC extraction on Da use: mz_range-->
 
+    
+    _output_stream->writeComment("For XIC extraction on Da use: mz_range");
     _output_stream->writeStartElement("ppm_range");
     _output_stream->writeAttribute("min","10");
     _output_stream->writeAttribute("max","10");
-    _output_stream->writeComment("For XIC extraction on Da use: mz_range");
     _output_stream->writeEndElement();
     //</xic_extraction>
     _output_stream->writeEndElement();
@@ -330,7 +331,7 @@ void MassChroQml::writeAlignments() {
 
 void MassChroQml::writeIsotopeLabelList() {
     //<isotope_label_list>
-    _output_stream->writeStartElement("isotope_label_list");
+    //_output_stream->writeStartElement("isotope_label_list");
     /*
     	<isotope_label id="iso1">
     		<mod at="Nter" value="28.0" acc="MOD:00429"/>
@@ -341,7 +342,7 @@ void MassChroQml::writeIsotopeLabelList() {
     		<mod at="K" value="32.0" />
     	</isotope_label>*/
     //</isotope_label_list>
-    _output_stream->writeEndElement();
+    //_output_stream->writeEndElement();
 }
 
 void MassChroQml::writePeptideList() {
@@ -352,6 +353,9 @@ void MassChroQml::writePeptideList() {
     for (auto & group_pair :group_store) {
         writePeptideListInGroup(group_pair.second.get());
     }
+    
+    //</peptide_list>
+    _output_stream->writeEndElement();
 } 
     
 void MassChroQml::writePeptideListInGroup(const GroupingGroup * p_group) {
@@ -462,8 +466,6 @@ void MassChroQml::writePeptideListInGroup(const GroupingGroup * p_group) {
         //</peptide>
         _output_stream->writeEndElement();
     }
-    //</peptide_list>
-    _output_stream->writeEndElement();
 }
 
 void MassChroQml::writeGroups() {