Adapt to MSnbase 2.7.2 with internal fragments; see lgatto/MSnbase#82

Author: sgibb

DESCRIPTION

@@ -27,7 +27,7 @@ Imports:
     utils,
     Biobase,
     Matrix (>= 1.2.10),
-    MSnbase (>= 2.3.10),
+    MSnbase (>= 2.7.2),
     ggplot2 (>= 2.2.1),
     mzR (>= 2.11.4)
 Suggests:

R/fragments.R

@@ -38,7 +38,8 @@
 #' @param verbose `logical`, verbose output?
 #' @return `FragmentViews`
 #' @noRd
-.calculateFragments <- function(sequence, type=c("a", "b", "c", "x", "y", "z"),
+.calculateFragments <- function(sequence, type=c("a", "b", "c", "x", "y", "z",
+                                                 "aIx", "bIy", "cIz"),
                                 modifications=c(
                                     "Carbamidomethyl", "Acetyl",
                                     "Met-loss"

R/functions-TopDownSet.R

@@ -35,10 +35,8 @@
 #' @param pattern `character`,
 #' a filename pattern, the default `.*` means all files.
 #' @param type `character`,
-#' type of fragments, currently *a-c* and *x-z* are
-#' supported, see
-#' [MSnbase::calculateFragments()]
-#' for details.
+#' type of fragments, currently *a*, *b* *c*, *x*, *y*, *z*, *aIx*, *bIy* and
+#' *cIz* are supported, see [MSnbase::calculateFragments()] for details.
 #' @param modifications `character`,
 #' unimod names of modifications that should be applied.
 #' Currenlty just *Acetyl* (Unimod:1 but just protein N-term),