[FIX] pepXML writing format.
[FIX] Distinguish PeptideProphet_pepXMl and raw_pepXMl.

[FIX] RT_index information from XTandem is added to spectrum id and scan_id in stored pepXML file.

[FIX] change parameter name and uncrustify.
[FIX] add test data for PepXMLFile and XTandemAdapter.
[FIX] Fix the spectrum_query in test data for PepXMLFile().store.
[FIX] pepXML: replace spaces by tabs; adapt the raw_data type; edit documentation.
Merge branch 'develop' into pepXMl
[FEATURE] add conversion of tandem.xml output into idXML.
          add test files for tandem.xml conversion.
[FIX] small edit of last commit.
[INTERNAL] check for peak not found in filter 2
[INTERNAL] check for peak not found in filter 3
[FIX] Enable multiple identification runs result, multiple protein hits and FDR/q-value analysed results.
add peptideHit metaValue nextscore in XTandemFile() and remove scan_index
[TEST] add test files.
Merge branch 'develop' into pepXMl
[INTERNAL] check for -1 indices and NaN intensities added
[INTERNAL] check for -1 indices and NaN intensities added
[INTERNAL] debug output fixed
[DOC] debug removed
[INTERNAL] minor fix
[INTERNAL] fix for evaluation at last node
[TEST] now non-zero intensity at right boundary of test interval