[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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