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" <[EMAIL PROTECTED]> 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]] > > ______________________________________________ > 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.
