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@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@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.
______________________________________________
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