1. 19 Aug, 2020 3 commits
  2. 18 Aug, 2020 4 commits
  3. 12 Aug, 2020 2 commits
    • Todor Kondic's avatar
      Merge branch 'devel' into 'devel' · 16ebf0ae
      Todor Kondic authored
      Devel
      
      See merge request !28
      16ebf0ae
    • Todor Kondic's avatar
      Redo combination and parallelise the rest of wf steps · 963e5822
      Todor Kondic authored
      * run.R(proj_sp_readin): Fixed creation of ws with new ce_index
        column.
      
      (proj_sp_comb): Follow consistent scheme when indexing CEs. Also, keep
      a reference to the original precursor. Will put it in the comment
      later.
      
      (proj_sp_ana2): Load the settings and the compound list in
      futures. This is not consisten in all the steps of the workflow, but
      we should do it.
      
      (step_1_helpr): Load settings.
      
      (proj_mb_rec_entries): Reformat the record so that it passes the
      validator. Move most of the stuff to COMMENT fields.
      963e5822
  4. 11 Aug, 2020 2 commits
    • Todor Kondic's avatar
      Remove the indexing scheme · b8a941be
      Todor Kondic authored
      This is a revert of the previous commit, as it is clear that right
      now, it makes no sense to have built-in index naming schemes. The
      record naming scheme of MassBank is to inflexible for this.
      b8a941be
    • Todor Kondic's avatar
      Add new CE_INDEX_SCHEME · 75c1e8ce
      Todor Kondic authored
      * R/config.R(CE_INDEX_SCHEME): New constant with standard collision
        energy indices, used to derive the MassBank names.
      
      * R/run.R(proj_sp_new): New argument ce_index_scheme which defaults to
        CE_INDEX_SCHEME.
      75c1e8ce
  5. 10 Aug, 2020 5 commits
  6. 08 Aug, 2020 5 commits
    • Todor Kondic's avatar
      Merge branch 'master' into 'master' · 3cb58993
      Todor Kondic authored
      DATASET fix and basic docs.
      
      See merge request !27
      3cb58993
    • Todor Kondic's avatar
      Bump version · ef1c58aa
      Todor Kondic authored
      ef1c58aa
    • Todor Kondic's avatar
      bugfix: Add dataset entry · 32bd77ff
      Todor Kondic authored
      32bd77ff
    • Todor Kondic's avatar
      Merge branch 'master' into 'master' · 3512757c
      Todor Kondic authored
      Fix accesion part of the record name and add some more entries.
      
      See merge request !26
      3512757c
    • Todor Kondic's avatar
      New feature: Fix accession part of the record and add new entries · a4e05d82
      Todor Kondic authored
      * R/run.R(proj_sp_new): New arguments shinyscreen_ver and rmbmix_ver
        give the version numbers of the packages to be written to records.
      
      (proj_sp_comb): Write original acquisition numbers in a data
      table. This is easier for processing.
      
      (proj_mb_info): Copy orig_an column from wsflow to mbflow.
      
      (proj_mb_rec_entries): New function. Run the record workflow until
      step six. Then, add new record entries to MS2 information in
      compiled_ok spectral objects. Afterwards clear up any "OK" spectra
      that turn out not to have MS2 information.
      
      (proj_mb_rec): Some of the stuff done here was eliminated (there was
      an extra workflow re-run which I thought was unnecessary) and some
      moved to proj_mb_rec_entries. Currently, it only executes the final
      step of the workflow.
      
      * man: Updated docs.
      
      * DESCRIPTION: Updated entries.
      
      * NAMESPACE: New exports.
      a4e05d82
  7. 07 Aug, 2020 4 commits
  8. 29 Jul, 2020 6 commits
  9. 28 Jul, 2020 2 commits
  10. 27 Jul, 2020 4 commits
  11. 11 Jul, 2020 2 commits
  12. 08 Jul, 2020 1 commit