diff MsFileDb.R @ 6:b8f70d8216b3 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty

--- a/MsFileDb.R	Thu Mar 16 08:15:11 2017 -0400
+++ b/MsFileDb.R	Mon Mar 27 06:27:29 2017 -0400
@@ -82,7 +82,7 @@
 		if (is.null(.self$.db)) {
 
 			# Load database
-			.db <<- read.table(.self$.file, sep = "\t", quote = "\"", header = TRUE, stringsAsFactors = FALSE, row.names = NULL)
+			.db <<- read.table(.self$.file, sep = "\t", quote = "\"", header = TRUE, stringsAsFactors = FALSE, row.names = NULL, check.names = FALSE, comment.char = '')
 
 			# Check that colnames are unique
 			dupcol <- duplicated(colnames(.self$.db))
@@ -396,8 +396,8 @@
 
 		# Filter on retention time
 		if ( ! is.null(rt.low) && ! is.na(rt.low) && ! is.null(rt.high) && ! is.na(rt.high)) {
-			scale <- if (.self$.rt.unit == MSDB.RTUNIT.MIN) 60 else 1
-			db <- db[db[[MSDB.TAG.COLRT]] * scale >= rt.low & db[[MSDB.TAG.COLRT]] <= rt.high, ]
+			scale <- if (.self$getRtUnit() == MSDB.RTUNIT.MIN) 60 else 1
+			db <- db[db[[MSDB.TAG.COLRT]] * scale >= rt.low & db[[MSDB.TAG.COLRT]] * scale <= rt.high, ]
 		}
 
 		# Remove retention times and column information
@@ -411,19 +411,6 @@
 		# Filter on mz
 		db <- db[db[[MSDB.TAG.MZTHEO]] >= mz.low & db[[MSDB.TAG.MZTHEO]] <= mz.high, ]
 
-		# Rename database fields
-#		conv <- c( mz = 'mztheo', rt = 'colrt') # solving mismatch of field names between database and output
-#		cols <- colnames(db)
-#		for (db.field in names(.self$.fields)) {
-#			output.field <- if (db.field %in% names(conv)) conv[[db.field]] else db.field
-#			if (.self$.fields[[db.field]] %in% cols && output.field %in% names(.self$.output.fields))
-#				cols[cols %in% .self$.fields[[db.field]]] <- .self$.output.fields[[output.field]]
-#		}
-#		colnames(db) <- cols
-
-		# Remove unwanted columns
-#		db <- db[, colnames(db) %in% .self$.output.fields]
-
 		return(db)
 	})
 	
@@ -489,7 +476,7 @@
 			rt[col] <- list(colrts)
 		}
 
-		if (.self$.rt.unit == MSDB.RTUNIT.MIN)
+		if (.self$getRtUnit() == MSDB.RTUNIT.MIN)
 			rt <- 60 * rt
 
 		return(rt)