# topdownr 1.5
- New version for Bioc 3.9 (devel)

Changes in version 1.5.6
- Revert changes for NULL indices of `DataFrame` introduced in 1.5.4
  (a419f59, c4bfc1c) because they are fixed upstream in `S4Vectors`.
  Keep unit tests in place. [2019-03-27]

Changes in version 1.5.5
- Depends on R >= 3.5.0 now, because the seralization format changed in R.

Changes in version 1.5.4
- Fix for internal `.makeRowNames`/`.colsToLogical`/`.colsToRle`
  on `DataFrame` without any `numeric`/`character` columns.
- Fix unit test that uses `set.seed` (order changed during R-devel upgrade).

Changes in version 1.5.3
- biocViews: ImmunoOncology added by
  Kayla-Morrell <kayla.morrell@roswellpark.org> [2019-01-04].

Changes in version 1.5.2
- Add `expandMs1Conditions`, `expandTms2Conditions`,
  `createExperimentsFragmentOptimisation` functions to allow more flexibility
  in method creation; see also #77 [2018-12-07].
- Modify interface/arguments of `writeMethodXmls` to adapt to new method
  creation workflow (the old interface will be defunct in Bioconductor 3.10 and
  removed in 3.11) [2018-12-07].
- Adapt the `data-generation` vignette to the new workflow [2018-12-07].
- Deprecated `defaultMs1Settings` and `defaultMs2Settings`. They will be
  defunct in Bioconductor 3.10 and removed in 3.11 [2018-12-07].

Changes in version 1.5.1
- `readTopDownFiles` gains the argument `conditions` to control wheter
  "FilterStrings" or a given number of conditions is used to create condition
  IDs; see #77 [2018-11-07].

# topdownr 1.4
- New version for Bioc 3.8 (release)

# topdownr 1.3

Changes in version 1.3.6
- Add Pavel's and Ole's ORCID to DESCRIPTION [2018-10-23].

Changes in version 1.3.5
- Fix format of roxygen links to foreign packages to avoid link warning in
  `R CMD check` [2018-10-10].

Changes in version 1.3.4
- Add inst/CITATION file [2018-09-26].

Changes in version 1.3.3
- Revert commit c6e8dfd: "Adapt to `MSnbase 2.7.2` with internal fragments; see
    #82 [2018-06-03]."

Changes in version 1.3.2
- Use `BiocManager::install` [2018-07-16].

Changes in version 1.3.1
- Adapt to `MSnbase 2.7.2` with internal fragments; see
    #82 [2018-06-03].
- Fix `FragmentViews` start/end/width and labels for internal fragments
    [2018-06-03].
- Fix `as(tds, "MSnSet")` unit test [2018-07-06].
- Use `elementMetadata(..., use.names=FALSE)` in
  `combine,FragmentViews,FragmentViews-method` to avoid duplicated rownames in
  elementMetadata slot [2018-07-06].

Changes in version 1.3.0
- New version for Bioc 3.8 (devel)

# topdownr 1.2

Changes in version 1.2.0
- New version for Bioc 3.7 (release)

# topdownr 1.1

Changes in version 1.1.7
- Add `mz,FragmentViews-method` [2018-02-01].
- Remove internal `fragmentMass` and `fragmentNames` functions [2018-02-22].
- Parse "spectrumId" column of the mzML header to find the scan number (instead
  of the "acquisitionNum") because ProteomDiscover generates non-standard
  "spectrumId" and proteowizard fails to translated it into a valid
  "acquisitionNum". See #73 for details [2018-02-22].
- Recalculate TotIonCurrent in the main loop of `.readMzMl` [2018-02-22].
- Add `FragmentCoverage` and `BondCoverage` columns to
  `bestConditions,NCBSet-method` [2018-02-23].
- Use retention times to test for correct matching between ScanHeadsman .txt
  output and mzML files; closes #74; [2018-02-23].

Changes in version 1.1.6
- Rotate fragment labels (vertical orientation) in `plot` [2018-01-17].
- Replace signature for `updateMedianInjectionTime,TopDownSet-method` to
  `updateMedianInjectionTime,AbstractTopDownSet-method`; closes #69; see
  also #71 [2018-01-27].
- Fix `.matchFragments` for `length(fmass) == 0` [2018-01-27].
- Just plot fragments that are present in current `TopDownSet` see #70
  [2018-01-27].
- Add `combine,FragmentViews,FragmentViews-method` [2018-01-27].
- Allow to `combine` `TopDownSet` objects with different fragment types;
  closes #71 [2018-01-27].
- Add `all.equal` for `AbstractTopDownSet` objects [2018-01-27].
- Allow the user to decide how to handle redundant fragment matching. Current
  default is `redundantFragmentMatch="remove"` and
  `redundantIonMatch="remove"`. This will reduce the number of fragment
  matches. Choose `"closest"` for both to get the old behaviour.
  See also #72 [2018-01-29].
- `TopDownSet` object store the matching `tolerance` and strategies
  (`redundantIonMatch`, `redundantFragmentMatch`). `AbstractTopDownSet` and
  `NCBSet` lost their `tolerance` slot. Saved objects need to be recreated
  [2018-01-30].
- `bestConditions,NCBSet-method` returns a 5-column matrix now.
  Colums are: Index, FragmentsAddedToCombination, BondsAddedToCombination,
  FragmentsInCondition, BondsInCondition; see #52 [2018-01-30].

Changes in version 1.1.5
- Keep full filename (before `basename` was used) in `AbstractTopDownSet`
  objects [2017-12-28].
- Add `plot,TopDownSet-method` [2017-12-29].
- `bestConditions,NCBSet-method` gains a new argument `maximise` that allows to
  optimise for number of fragments or bonds covered (default: `"fragments"`);
  see #52 [2018-01-15].

Changes in version 1.1.4
- Add missing export of `combine` and documentation [2017-12-28].
- Resave `tds` example data set to reflect changes in `colData` introduced in
  version 1.1.2 [2017-12-28].

Changes in version 1.1.3
- Add `conditionNames,AbstractTopDownSet-method` to access
  `rownames(colData(tds))` [2017-12-23].
- Add `updateConditionNames,AbstractTopDownSet-method`
  (closes #60) [2017-12-23].
- Turn `updateMedianInjectionTime,TopDownSet-method` into
  `updateMedianInjectionTime,AbstractTopDownSet-method` to work with
  `TopDownSet` and `NCBSet` objects [2017-12-27].
- Add `combine,AbstractTopDownSet-method` to combine multiple
  `TopDownSet`/`NCBSet` objects (closes #69) [2017-12-28].

Changes in version 1.1.2
- Add `.rbind` to combine scan and method information with different number of
  colums (could happen when CID/HCD and UVPD scans are taken independently with
  different software versions) [2017-12-22].
- Don't replace NA values with zeros in the `colData` [2017-12-22].
- Convert On/Off `character` columns in scan and method information to
  `logical` [2017-12-22].
- Fix `.camelCase` to avoid "TIC" to "TIc" and "UseCalibratedUVPDTimeMs2" to
  "UseCalibrateduvpdTimems2" conversion (now: "Tic" and
  "UseCalibratedUvpdTimeMs2") [2017-12-22].

Changes in version 1.1.1
- Respect assigned intensity in conditions for `bestConditions,NCBSet-method`
  and `fragmentationMap`
  (closes #62) [2017-12-02].
- Fix explanation of random forest barchart in analysis vignette [2017-12-02].
- Create all fragmentation methods in `.readScanHeadsTable` to avoid error if
  any is missing (fixes #68) [2017-12-20].
- Never remove Activation column in `colData` (even not if
  `readTopDownFiles(..., dropNonInformativeColumns=TRUE)`) [2017-12-20].
- Allow UVPD in `fragmentationMap,NCBSet-method` [2017-12-20].
- Add new method: `updateMedianInjectionTime,TopDownSet-method`
  (closes #66) [2017-12-20].

Changes in version 1.1.0
- New version for Bioc 3.7 (devel)

# topdownr 1.0

Changes in version 1.0.0
- New version for Bioc 3.6 (release)

# topdownr 0.9

Changes in version 0.99.0
- First public release.
