clean up code

rformassspectrometry · Feb 19, 2025 · fdc7973 · fdc7973
1 parent c1b3016
commit fdc7973
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Showing 4 changed files with 3 additions and 55 deletions.
diff --git a/R/MsBackendCached.R b/R/MsBackendCached.R
@@ -328,26 +328,6 @@ setMethod("spectraVariables", "MsBackendCached", function(object) {
         res <- x@localData[, local_cols, drop = FALSE]
     if (length(core_cols)) {
         res <- fillCoreSpectraVariables(res, columns = core_cols)
-        ## mzvals <- NULL
-        ## intvals <- NULL
-        ## lst <- NumericList(numeric(), compress = FALSE)
-        ## if (any(core_cols == "mz")) {
-        ##     core_cols <- core_cols[core_cols != "mz"]
-        ##     mzvals <- lst[rep(1, times = length(x))]
-        ## }
-        ## if (any(core_cols == "intensity")) {
-        ##     core_cols <- core_cols[core_cols != "intensity"]
-        ##     intvals <- lst[rep(1, times = length(x))]
-        ## }
-        ## if (length(core_cols))
-        ##     tmp <- DataFrame(lapply(.SPECTRA_DATA_COLUMNS[core_cols],
-        ##                             function(z, n) rep(as(NA, z), n), length(x)))
-        ## else tmp <- make_zero_col_DFrame(x@nspectra)
-        ## tmp$mz <- mzvals
-        ## tmp$intensity <- intvals
-        ## if (length(res))
-        ##     res <- cbind(res, tmp)
-        ## else res <- tmp
         if (any(core_cols == "dataStorage"))
             res$dataStorage <- dataStorage(x)
     }

diff --git a/R/MsBackendDataFrame.R b/R/MsBackendDataFrame.R
@@ -467,22 +467,8 @@ setMethod("spectraData", "MsBackendDataFrame",
               df_columns <- intersect(columns,colnames(object@spectraData))
               res <- object@spectraData[, df_columns, drop = FALSE]
               other_columns <- setdiff(columns,colnames(object@spectraData))
-              if (length(other_columns)) {
+              if (length(other_columns))
                   res <- fillCoreSpectraVariables(res, columns = other_columns)
-                  ## other_res <- lapply(other_columns, .get_column,
-                  ##                     x = object@spectraData)
-                  ## names(other_res) <- other_columns
-                  ## is_mz_int <- names(other_res) %in% c("mz", "intensity")
-                  ## if (!all(is_mz_int))
-                  ##     res <- cbind(res, as(other_res[!is_mz_int], "DataFrame"))
-                  ## if (any(names(other_res) == "mz"))
-                  ##     res$mz <- if (length(other_res$mz)) other_res$mz
-                  ##               else NumericList(compress = FALSE)
-                  ## if (any(names(other_res) == "intensity"))
-                  ##     res$intensity <- if (length(other_res$intensity))
-                  ##                          other_res$intensity
-                  ##                      else NumericList(compress = FALSE)
-              }
               if (!all(columns %in% colnames(res)))
                   stop("Column(s) ", paste0(columns[!columns %in% names(res)],
                                             collapse = ", "), " not available.",

diff --git a/R/MsBackendMemory-functions.R b/R/MsBackendMemory-functions.R
@@ -49,15 +49,9 @@ MsBackendMemory <- function() {
         sp_vars <- setdiff(columns, p_vars)
         df_columns <- intersect(sp_vars, colnames(object@spectraData))
         res <- object@spectraData[, df_columns, drop = FALSE]
-        ## Get missing core variables.
         other_columns <- setdiff(sp_vars, colnames(object@spectraData))
-        if (length(other_columns)) {
+        if (length(other_columns))
             res <- fillCoreSpectraVariables(res, other_columns)
-            ## other_res <- lapply(other_columns, .get_column,
-            ##                     x = object@spectraData)
-            ## names(other_res) <- other_columns
-            ## res <- cbind(res, as.data.frame(other_res))
-        }
         if (any(columns == "mz"))
             res$mz <- mz(object)
         if (any(columns == "intensity"))

diff --git a/R/MsBackendMzR-functions.R b/R/MsBackendMzR-functions.R
@@ -103,14 +103,6 @@ MsBackendMzR <- function() {
     sp_cols <- columns[columns %in% cn]
     res <- x@spectraData[, sp_cols, drop = FALSE]
     if(!nrow(x@spectraData)) {
-        ## res$mz <- NumericList(compress = FALSE)
-        ## res$intensity <- NumericList(compress = FALSE)
-        ## other_cols <- setdiff(columns, c(sp_cols, "mz", "intensity"))
-        ## if (length(other_cols)) {
-        ##     res_add <- lapply(.SPECTRA_DATA_COLUMNS[other_cols],
-        ##                       do.call, args = list())
-        ##     res <- cbind(res, res_add)
-        ## }
         res <- fillCoreSpectraVariables(res, setdiff(columns, c(sp_cols)))
         return(res[, columns, drop = FALSE])
     }
@@ -125,12 +117,8 @@ MsBackendMzR <- function() {
                                          compress = FALSE)
     }
     other_cols <- setdiff(columns, c(sp_cols, "mz", "intensity"))
-    if (length(other_cols)) {
+    if (length(other_cols))
         res <- fillCoreSpectraVariables(res, other_cols)
-        ## other_res <- lapply(other_cols, .get_column, x = x@spectraData)
-        ## names(other_res) <- other_cols
-        ## res <- cbind(res, as(other_res, "DataFrame"))
-    }
     res[, columns, drop = FALSE]
 }