OpenMS/OpenMS — pull request #892 by hendrikweisser (2014-07-15 13:35:11+00:00)
Title: Enable loading of some pepXML files that used to cause crashes

I recently had to deal with pepXML files that were apparently exported from Thermo's ProteomeDiscoverer (e.g. http://www.ebi.ac.uk/pride/archive/files/29050146). While valid pepXML, slight differences in the format compared to "usual" pepXMLs would cause IDFileConverter to crash (segfault) when trying to convert them to idXML. The differences:
1. There's an "analysis_summary" section containing a "search_summary" element, which our parser confused with the "search_summary" element in "msms_run_summary".
2. Multiple searches are numbered (in the "search_id" attribute of "search_summary") consecutively across "msms_run_summary" sections - e.g. "1" in the first "msms_run_summary", "2" in the second, etc. We expected the numbering to start at "1" each time.

The changes here account for these differences and enable the pepXML parser to handle the respective files.