featurealigner: transform.tr to inputname.tr

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@265 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FEATURE] compute_full_matrix preserves original filename

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@266 db641661-14cc-1e01-c2f8-e77ac6f8a696
requantParallel

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@267 db641661-14cc-1e01-c2f8-e77ac6f8a696
requantParallel with --thread option

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@268 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FIX] amend to r266 (fix if filename is NA)

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@269 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FIX] fix bug introduced in r265

- the path would be appended two times but we only wanted to take the
  name of the csv file
- fix by using basename() and removing the path from the "fn" variable

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@270 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FIX] fix extra two columns appended to each outfile

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@271 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FIX] write per-transition information into outfile

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@272 db641661-14cc-1e01-c2f8-e77ac6f8a696