Added mode to RmbSpectraSet

R/RmbWorkspaceUpdate.R

@@ -252,6 +252,7 @@
 							},
 							set@children, analyzedSpec$msmsdata)
 							set@children <- as(children, "SimpleList")
+							set@mode <- analyzedSpec$mode
 							return(set)
 				},
 				spectra, analyzedSpecs)

R/SpectrumClasses.R

@@ -9,7 +9,8 @@
 				dbe = "numeric",
 				formulaCount = "integer",
 				dppm = "numeric",
-				dppmBest = "numeric"
+				dppmBest = "numeric",
+				ok = "logical"
 		),
 		contains=c("Spectrum2"),
 		prototype = prototype(
@@ -23,6 +24,7 @@
 				formulaCount = integer(),
 				dppm = numeric(),
 				dppmBest = numeric(),
+				ok = logical(),
 				new("Versioned", versions=c(classVersion("Spectrum2"), RmbSpectrum2 = "0.1.0"))
 		),
 )
@@ -71,5 +73,5 @@
 
 
 setGeneric("getData",	function(s) standardGeneric("getData"))
-setGeneric("setData",	function(s, df) standardGeneric("setData"))
+setGeneric("setData",	function(s, df, ...) standardGeneric("setData"))
 

R/SpectrumMethods.R

@@ -20,7 +20,7 @@ setMethod("setData", c("RmbSpectrum2", "data.frame"), function(s, df, clean = TR
 			cols <- c("mz", "intensity", "satellite", "low", "rawOK", "good", "mzCalc", "formula", "dppm")
 			types <- c("mz" = "numeric", "intensity" = "numeric", "satellite" = "logical", "low" = "logical",
 					"rawOK" = "logical", "good" = "logical", "mzCalc" = "numeric", "formula" = "character", 
-					"dppm" = "numeric"
+					"dppm" = "numeric", "ok" = "numeric"
 					)
 			s@peaksCount <- as.integer(nrow(df))
 			cols.inDf <- which(cols %in% colnames(df))
@@ -33,7 +33,7 @@ setMethod("setData", c("RmbSpectrum2", "data.frame"), function(s, df, clean = TR
 			cols.no <- cols[cols.notinDf]
 			if(clean)
 			{
-				for(col in cols.df)
+				for(col in cols.no)
 				{
 					slot(s, col) <- c()
 				}