Mike

[StPeter] - Implemented the changes David requested, rolling back the code to the last stable version and creating the new features from scratch. Use the -r option to enable separate by run analysis.

[StPeter] - rolling back David's changes because it destroyed the correct implementation for many existing datasets. Rather than parameterize the changes necessary to analyze David's one dataset, the entire functionality of StPeter was changed so that all datasets must be analyzed as if they were acquired identical to that one dataset. This broke the fundamental functionality of StPeter, and produces incorrect analyses for thousands of other datasets, including the entirety of the LC data col...

[StPeter] - bugfix when processing n-terminal modifications.

[mzParser] - remove scan reading interrupt when reading scan headers.

[mzParser] : silence error message when precursor scans can not be found in the index because they've been excised from the file.

[mzParser] fix spectrum flags to know the difference between having an ion mobility associated with the spectrum and having an actual ion mobility data array.

[mzParser] - more restoring of code lost in the previous merge. NOTE: there is additional code that has still not been restored: this is deliberate to remove cruft.

[mzParser] - sorry everyone, lost a few lines in a bad merge on my part. Restoring them here.