Archie Cobbs
992971e53f
One package less failing in science. OBS-URL: https://build.opensuse.org/request/show/726471 OBS-URL: https://build.opensuse.org/package/show/science/xtandem?expand=0&rev=18
86 lines
3.2 KiB
Diff
86 lines
3.2 KiB
Diff
diff --git a/src/saxmzmlhandler.cpp b/src/saxmzmlhandler.cpp
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index 9348b62..88dd906 100644
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--- a/src/saxmzmlhandler.cpp
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+++ b/src/saxmzmlhandler.cpp
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@@ -93,6 +93,7 @@ void SAXMzmlHandler::startElement(const XML_Char *el, const XML_Char **attr)
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const char* name = getAttrValue("name", attr);
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cout.flush();
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const char* accession = getAttrValue("accession", attr);
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+ const char* unitAccession = getAttrValue("unitAccession", attr);
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const char* value = getAttrValue("value", attr);
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if (m_bInRefGroup)
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{
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@@ -100,12 +101,13 @@ void SAXMzmlHandler::startElement(const XML_Char *el, const XML_Char **attr)
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m_cvParam.refGroupName = string(m_ccurrentRefGroupName);
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m_cvParam.name = string(name);
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m_cvParam.accession = string(accession);
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+ m_cvParam.unitAccession = string(unitAccession);
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m_cvParam.value = string(value);
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m_refGroupCvParams.push_back(m_cvParam);
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}
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else
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{
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- processCVParam(name,accession,value);
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+ processCVParam(name,accession,unitAccession,value);
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}
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}
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else if (isElement("referenceableParamGroupRef", el))
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@@ -115,7 +117,7 @@ void SAXMzmlHandler::startElement(const XML_Char *el, const XML_Char **attr)
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{
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if(!strcmp(groupName,m_refGroupCvParams[i].refGroupName.c_str()))
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{
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- processCVParam(m_refGroupCvParams[i].name.c_str(), m_refGroupCvParams[i].accession.c_str(), m_refGroupCvParams[i].value.c_str());
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+ processCVParam(m_refGroupCvParams[i].name.c_str(), m_refGroupCvParams[i].accession.c_str(), m_refGroupCvParams[i].unitAccession.c_str(), m_refGroupCvParams[i].value.c_str());
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}
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}
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}
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@@ -165,7 +167,7 @@ void SAXMzmlHandler::characters(const XML_Char *s, int len)
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}
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}
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-void SAXMzmlHandler::processCVParam(const char* name, const char* accession, const char* value)
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+void SAXMzmlHandler::processCVParam(const char* name, const char* accession, const char* unitAccession, const char* value)
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{
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if ((!strcmp(name, "ms level") || !strcmp(accession,"MS:1000511")) && !strcmp(value,"2")){
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m_bInMsLevel2 = true;
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@@ -178,9 +180,16 @@ void SAXMzmlHandler::processCVParam(const char* name, const char* accession, con
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// m_strDesc = value;
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}
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else if(!strcmp(name, "scan start time") || !strcmp(accession,"MS:1000016")) {
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- if(atof(value) > 0.0) {
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+ float fvalue = atof(value);
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+ if (!strcmp(unitAccession, "UO:0000010")) // seconds
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+ fvalue *= 1.0;
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+ else if (!strcmp(unitAccession, "UO:0000031")) // minutes
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+ fvalue *= 60.0;
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+ else
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+ fvalue *= 60.0; // backward compat
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+ if(fvalue > 0.0) {
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char pLine[256];
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- sprintf(pLine,"PT%.3lfS",60.0*atof(value));
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+ sprintf(pLine,"PT%.3lfS",fvalue);
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m_strRt = pLine;
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}
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else {
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diff --git a/src/saxmzmlhandler.h b/src/saxmzmlhandler.h
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index c11eae9..3a4a387 100644
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--- a/src/saxmzmlhandler.h
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+++ b/src/saxmzmlhandler.h
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@@ -63,7 +63,7 @@ private:
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/**
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* Process cv params
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*/
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- void processCVParam(const char* name, const char* accession, const char* value);
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+ void processCVParam(const char* name, const char* accession, const char* unitAccession, const char* value);
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private:
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// Flags indicating parser is inside a particular tag.
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@@ -81,6 +81,7 @@ private:
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string name;
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string accession;
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string value;
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+ string unitAccession;
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};
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vector <cvParam> m_refGroupCvParams;
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