refactor: merge calculateFragments and calculateFragments2 (#19)

* Create fragments-calculate2.R

feat: calculateFragments2 
Provides modifications to the generated theoretical fragments

* Create test_fragments2.R

feat: tests for calculateFragments2

* Update fragments-calculate2.R

* Update fragments-calculate2.R

* Update fragments-calculate2.R

* Update documentation

* Update documentation

* Delete PSMatch.Rproj

* Update NEWS.md

* Update DESCRIPTION

* Update fragments-calculate2.R

Updates based on reviewed PR

* Update test_fragments2.R

Updates according to reviewed PR

* Update R/fragments-calculate2.R

Co-authored-by: Sebastian Gibb <[email protected]>

* Update fragments-calculate2.R

* Update fragments-calculate2.R

Corrected .cumsumFragmentMasses

* Update DESCRIPTION

* git ignore Rproj file

* update .cumsumFragmentMasses

* update: testthat .cumsumFragmentMasses

* update variable_modifications default to empty numeric

* Update fragments-calculate2.R

Change modified peptide layout into AGC[57.02]AK instead of AG[C]AK to specify the modified mass

* Add warning for modifications parameter

* Remove redundancy in strplit(sequence)

* Update documentation

* update documentation

* Merge calculateFragments and calculateFragments2 into one true calculateFragments

* Remove redundancies and update calculateFragments based on PR

* Updated failed unit test

* Update comments in addFragments

---------

Co-authored-by: Sebastian Gibb <[email protected]>

NAMESPACE

@@ -4,7 +4,6 @@ export("reduced<-")
 export(ConnectedComponents)
 export(PSM)
 export(addFragments)
-export(calculateFragments2)
 export(ccMatrix)
 export(connectedComponents)
 export(defaultNeutralLoss)

R/fragments-add.R

@@ -80,6 +80,12 @@ addFragments <- function(x,
     x_data <- Spectra::peaksData(x)[[1L]]
     y_data <- calculateFragments(y, verbose = FALSE, ...)
     y_data <- y_data[order(y_data$mz), ]
+
+    ## stop if variable modifications used
+    ## Temporary check to allow plotSpectra to work fine
+    ## Will need to be removed once plotSpectra accepts variable modifications
+    ## See issue: https://github.com/rformassspectrometry/Spectra/issues/346
+    stopifnot(length(unique(y_data[["peptide"]])) == 1)
 
     ## Find common peaks and prepare annotations
     idx <- which(MsCoreUtils::common(x_data[, "mz"], y_data[, "mz"],