[NOP] remove extra print statement

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@273 db641661-14cc-1e01-c2f8-e77ac6f8a696
[INTERNAL] compute trafo filenames in a separate function

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@274 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FEATURE] allow median for peak width computation (set standard)

- add Warning if chromatogram is not available between left/right
  extraction points

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@275 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FEATURE] allow to select output type of the matrix

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@276 db641661-14cc-1e01-c2f8-e77ac6f8a696
[DOC] document options

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@277 db641661-14cc-1e01-c2f8-e77ac6f8a696
[DOC] typos in output

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@278 db641661-14cc-1e01-c2f8-e77ac6f8a696
Deprecation of "cluster" library. Now it is substituted by scikit_learn package.

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@279 db641661-14cc-1e01-c2f8-e77ac6f8a696
requantParallel out_matrix

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@280 db641661-14cc-1e01-c2f8-e77ac6f8a696
new modifications: Oxidation (HW), Deamidation (NQ)

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@281 db641661-14cc-1e01-c2f8-e77ac6f8a696
compute full matrix: excel export

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@282 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FIX] fix if the run id is not an int but a float

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@283 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FIX] replace run id with aligned id

- simply remove reading of the run_id
- replace run_id with aligned run id

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@284 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FEATURE] allow tighter control of verbosity

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@285 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FEATURE] option to remove requantified values

Conflicts:

	analysis/alignment/compute_full_matrix.py

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@286 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FIX] bugfix

- check that chromatogram has at least one peak

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@287 db641661-14cc-1e01-c2f8-e77ac6f8a696
compute full matrix: remove faulty line

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@288 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FEATURE] requant: add more of the original columns

- add more of the original columns to the requant data
- set peak_group_rank to -1 to indicate it is re-quantified

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@289 db641661-14cc-1e01-c2f8-e77ac6f8a696
[DOC] update gui install instructions

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@290 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FIX] Cut down output warnings, just report number of warnings

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@291 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FEATURE] allow for new id format

- support two annotation formats in the id tag of the chromatogram
  (format i and ii)
- skip chromatograms with empty id tag

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@292 db641661-14cc-1e01-c2f8-e77ac6f8a696