[R] xmlEventParse returning trimmed content?

[Johannes Graumann]

Hi Duncan,

Thanks for your thoughts. "trim=FALSE" does not fix my issues, so I attach 
pared down versions of my script and data file. Thanks for any further hint.

Joh

Duncan Temple Lang wrote:

> 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
>> 
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html and provide commented,
>> minimal, self-contained, reproducible code.
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html and provide commented,
> minimal, self-contained, reproducible code.