Mercurial > repos > prog > lcmsmatching
diff MsDbInputDataFrameStream.R @ 5:fb9c0409d85c draft
planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 608d9e59a0d2dcf85a037968ddb2c61137fb9bce
| author | prog |
|---|---|
| date | Wed, 19 Apr 2017 10:00:05 -0400 |
| parents | 20d69a062da3 |
| children |
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--- a/MsDbInputDataFrameStream.R Tue Mar 14 12:40:22 2017 -0400 +++ b/MsDbInputDataFrameStream.R Wed Apr 19 10:00:05 2017 -0400 @@ -7,18 +7,19 @@ # CLASS DECLARATION # ##################### - MsDbInputDataFrameStream <- setRefClass("MsDbInputDataFrameStream", contains = 'MsDbInputStream', fields = list( .df = "ANY", .i = "integer")) + MsDbInputDataFrameStream <- setRefClass("MsDbInputDataFrameStream", contains = 'MsDbInputStream', fields = list( .df = "ANY", .i = "integer", .rtunit = 'character')) ############### # CONSTRUCTOR # ############### - MsDbInputDataFrameStream$methods( initialize = function(df = data.frame(), input.fields = msdb.get.dft.input.fields(), ...) { + MsDbInputDataFrameStream$methods( initialize = function(df = data.frame(), input.fields = msdb.get.dft.input.fields(), rtunit = MSDB.RTUNIT.SEC, ...) { + + callSuper(input.fields = input.fields, ...) .df <<- df .i <<- 0L - - callSuper(input.fields = input.fields, ...) + .rtunit <<- rtunit }) ########## @@ -39,10 +40,15 @@ MsDbInputDataFrameStream$methods( getRt = function() { - if (.self$.i > 0 && .self$.i <= nrow(.self$.df) && ! is.null(.self$.input.fields[[MSDB.TAG.RT]])) - return(.self$.df[.self$.i, .self$.input.fields[[MSDB.TAG.RT]]]) + rt <- NULL - return(NULL) + if (.self$.i > 0 && .self$.i <= nrow(.self$.df) && ! is.null(.self$.input.fields[[MSDB.TAG.RT]])) { + rt <- .self$.df[.self$.i, .self$.input.fields[[MSDB.TAG.RT]]] + if (.self$.rtunit == MSDB.RTUNIT.MIN) + rt <- rt * 60 + } + + return(rt) }) ###########