Re: [R] xmlEventParse returning trimmed content?

[Duncan Temple Lang]

Hi Johannes

 I would "guess" that the trimming of the text occurs because
you do not specify trim = FALSE in the call to xmlEventParse().
If you specify this, you might well get the results you expect.
If not, can you post the actual file you are reading so we can
reproduce your results.

  D.

Johannes Graumann wrote:

Hello,

I wrote the function below and have the problem, that the "text" bit returns only a trimmed version (686 chars as far as I can see) of the content under the "fetchPeaks" condition.

Any hunches why that might be?

Thanks for pointer, Joh

xmlEventParse(fileName,
    list(
      startElement=function(name, attrs){
        if(name == "scan"){
          if(.GlobalEnv$ms2Scan == TRUE & .GlobalEnv$scanDone == TRUE){
            cat(.GlobalEnv$scanNum,"\n")
            MakeSpektrumEntry()
          }
          .GlobalEnv$scanDone <- FALSE
          .GlobalEnv$fetchPrecMz <- FALSE
          .GlobalEnv$fetchPeaks <- FALSE
          .GlobalEnv$ms2Scan <- FALSE
          if(attrs[["msLevel"]] == "2"){
            .GlobalEnv$ms2Scan <- TRUE
            .GlobalEnv$scanNum <- as.integer(attrs[["num"]])
          }
        } else if(name == "precursorMz" & .GlobalEnv$ms2Scan == TRUE){
          .GlobalEnv$fetchPrecMz <- TRUE
        } else if(name == "peaks" & .GlobalEnv$ms2Scan == TRUE){
          .GlobalEnv$fetchPeaks <- TRUE
        }
      },
      text=function(text){
        if(.GlobalEnv$fetchPrecMz == TRUE){
          .GlobalEnv$precursorMz <- as.numeric(text)
          .GlobalEnv$fetchPrecMz <- FALSE
        }
        if(.GlobalEnv$fetchPeaks == TRUE){
          .GlobalEnv$peaks <- text
          .GlobalEnv$fetchPeaks <- FALSE
          .GlobalEnv$scanDone <- TRUE
        }
      }
    )
  )

sessionInfo()

R version 2.9.0 beta (2009-04-03 r48277) x86_64-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=en_US.UTF-8;LC_ADDRESS=en_US.UTF-8;LC_TELEPHONE=en_US.UTF-8;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=en_US.UTF-8

attached base packages:

[1] splines stats graphics grDevices utils datasets methods [8] base

other attached packages:

[1] caMassClass_1.6 MASS_7.2-46 digest_0.3.1 caTools_1.9 [5] bitops_1.0-4.1 rpart_3.1-43 nnet_7.2-46 e1071_1.5-19 [9] class_7.2-46 PROcess_1.19.1 Icens_1.15.2 survival_2.35-4 [13] RCurl_0.94-1 XML_2.3-0 rkward_0.5.0

loaded via a namespace (and not attached):
[1] tools_2.9.0

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and provide commented, minimal, self-contained, reproducible code.