headerCache fix 3 and "partially matched" fix

R/leMsMs.r

@@ -1375,9 +1375,9 @@ recalibrateSpectra <- function(mode, rawspec = NULL, rc = NULL, rc.ms1=NULL, w =
 						  colnames(p) <- c("mzFound", "int")
 						  drecal <- predict(rc.ms1, newdata= p)
 						  if(recalibrateBy == "dppm")
-							  p$mzRecal <- p$mz / ( 1 + drecal/1e6 )
+							  p$mzRecal <- p$mzFound / ( 1 + drecal/1e6 )
 						  else
-							  p$mzRecal <- p$mz - drecal
+							  p$mzRecal <- p$mzFound - drecal
 						  colnames(p) <- c("mz", "int", "mzRecal")
 					  }
 					  p <- as.matrix(p)
@@ -1404,9 +1404,9 @@ recalibrateSingleSpec <- function(spectrum, rc,
 		colnames(p) <- c("mzFound", "int")
 		drecal <- predict(rc, newdata= p)
 		if(recalibrateBy == "dppm")
-			p$mzRecal <- p$mz / ( 1 + drecal/1e6 )
+			p$mzRecal <- p$mzFound / ( 1 + drecal/1e6 )
 		else
-			p$mzRecal <- p$mz - drecal
+			p$mzRecal <- p$mzFound - drecal
 		# And rename them back so our "mz" column is
 		# called "mz" again
 		colnames(p) <- c("mz", "int", "mzRecal")

R/leMsmsRaw.R

@@ -249,17 +249,17 @@ findMsMsHR.direct <- function(msRaw, cpdID, mode = "pH", confirmMode = 0, useRtL
 			,fillPrecursorScan, deprofile)
 	# check whether a) spectrum was found and b) enough spectra were found
 	if(length(spectra) < (confirmMode + 1))
-		sp <- new("RmbSpectraSet", found=FALSE)
+		sp <- list(foundOK = FALSE)
 	else
 		sp <- spectra[[confirmMode + 1]]
 	
-	#sp@mz <- mzLimits
-	sp@id <- as.integer(cpdID)
-	sp@name <- findName(cpdID)
-	sp@formula <- findFormula(cpdID)
+	sp$mz <- mzLimits
+	sp$id <- cpdID
+	sp$formula <- findFormula(cpdID)
 	return(sp)
 }
 
+
 #' Read in mz-files using XCMS
 #' 
 #' Picks peaks from mz-files and returns the pseudospectra that CAMERA creates with the help of XCMS