[R] Java parser for R data file?

[kchine at ebi.ac.uk]

Dear David,

You may also consider using the biocep project' tools and frameworks. they
provide an advanced  bridge that allow you to exchange between R and Java
any standard R Object and any mapped S4 object.
the object extracted to Java (an RList for you data) can be serialized to
a file (saved as a java object). you can then read the serialized object
very easily from java and this is obviously  much faster than parsing and
more elegant than a "proprietary" serialization/deserialization .

the easiest way to achieve this is to create the Serialized RList via the
Virtual R Workbench (Universal IDE for R).
you can run the R workbench on any kind of OS via the biocep sources:
http://www.ebi.ac.uk/microarray-srv/frontendapp/BIOCEP_README.txt

or just use this link to get the software installed on your machine if you
are using Mac OS or windows
http://www.ebi.ac.uk/microarray-srv/frontendapp/rworkbench.jnlp

create your data via the workbench R Console (you may also use the script
editor or just read your list from a file)
go to the menu "Java", choose "Save R/Java Object to local file"
select the name you've given to your list and choose a file name.

to retrieve your list in java, all you need is to add the RJB.jar to your
class path and use this simple code:

RList l=(RList)new ObjectInputStream(new
FileInputStream("J:/list.ser")).readObject();

and that's it.
this works for much more complex R objects (ExpressionSet..)

best wishes,

Karim


>
> On 12/5/07 12:15 PM, "Prof Brian Ripley" <ripley at stats.ox.ac.uk> wrote:
>
> On Wed, 5 Dec 2007, David Coppit wrote:
>
>> Or, given that I'm dealing with just a single array, would it be better
>> to
>> roll my own I/O using write.table or write.matrix from the MASS package?
>
> It would be much easier.  The save() format is far more complex than you
> need.  However, I would use writeBin() to write a binary file and read
> that in in Java, avoiding the binary -> ASCII -> binary conversion.
>
> Thanks for the suggestion-writeBin works quite well. For posterity, here's
> what I did:
>
> On the R side:
>
> # Assumes that there are no special values in the tofList, such as
> NA_REAL,
> # R_PosInf, R_NegInf, ISNAN, R_FINITE. See the "R Data Import/Export"
> manual.
> saveListAsBinary <- function( tofList, filename )
> {
>   outConn <- file( filename, "wb" );
>
>   for (m in 1:length(tofList)) {
>     writeBin(names(tofList)[[m]], outConn);
>     writeBin(length(tofList[[m]]), outConn, size = 4, endian = "big");
>     writeBin(tofList[[m]], outConn, size = 4, endian = "big");
>   }
>
>   close(outConn);
> }
>
> saveListAsBinary(myList, "outfile.RDat");
>
> On the Java side:
>
>   public static void read_R_Output(String filename, ArrayList<String>
> names,
>       ArrayList<ArrayList<Float>> data)
>   {
>     try {
>       DataInputStream dataInputStream = new DataInputStream(
>         new BufferedInputStream(new FileInputStream(filename)));
>
>       boolean endOfFile = false;
>
>       while (!endOfFile) {
>         try {
>           StringBuffer sb = new StringBuffer();
>
>           byte c;
>           while ((c = dataInputStream.readByte()) != 0)
>             sb.append((char)c);
>
>           names.add(new String(sb));
>
>           int cols = dataInputStream.readInt();
>
>           ArrayList<Float> row = new ArrayList<Float>(cols);
>
>           for (int i = 0; i < cols; i++)
>             row.add(dataInputStream.readFloat());
>
>           data.add(row);
>         } catch (EOFException e) {
>           endOfFile = true;
>         }
>       }
>
>       dataInputStream.close();
>     } catch (Exception e) {
>       e.printStackTrace();
>     }
>   }
>
> Regards,
> David
>
> 	[[alternative HTML version deleted]]
>
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