Examples of org.rosuda.JRI.Rengine.eval()

org.rosuda.JRI.Rengine.eval()


      // Create an empty xsAnnotate.
      rEngine.eval("an <- xsAnnotate(xs, sample=1)", false);


      // Group by RT.
      rEngine.eval("an <- groupFWHM(an, sigma=" + fwhmSigma
          + ", perfwhm=" + fwhmPercentage + ')', false);
      progress += progressInc;


      // Identify isotopes.
      rEngine.eval(

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      rEngine.eval("an <- groupFWHM(an, sigma=" + fwhmSigma
          + ", perfwhm=" + fwhmPercentage + ')', false);
      progress += progressInc;


      // Identify isotopes.
      rEngine.eval(
          "an <- findIsotopes(an, maxcharge=" + isoMaxCharge
              + ", maxiso=" + isoMaxCount + ", ppm="
              + isoMassTolerance.getPpmTolerance() + ", mzabs="
              + isoMassTolerance.getMzTolerance() + ')', false);
      progress += progressInc;

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              + isoMassTolerance.getMzTolerance() + ')', false);
      progress += progressInc;


      // Split groups by correlating peak shape (need to set xraw to raw
      // data).
      rEngine.eval(
          "an <- groupCorr(an, calcIso=TRUE, xraw=xRaw, cor_eic_th="
              + corrThreshold + ", pval=" + corrPValue + ')',
          false);
      progress += progressInc;

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              + corrThreshold + ", pval=" + corrPValue + ')',
          false);
      progress += progressInc;


      // Get the peak list.
      rEngine.eval("peakList <- getPeaklist(an)", false);


      // Extract the pseudo-spectra and isotope annotations from the peak
      // list.
      final REXP spectraExp = rEngine
          .eval("as.integer(peakList$pcgroup)");

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      // Get the peak list.
      rEngine.eval("peakList <- getPeaklist(an)", false);


      // Extract the pseudo-spectra and isotope annotations from the peak
      // list.
      final REXP spectraExp = rEngine
          .eval("as.integer(peakList$pcgroup)");
      final REXP isotopeExp = rEngine.eval("peakList$isotopes");


      // Add identities.
      if (spectraExp != null) {

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      // Extract the pseudo-spectra and isotope annotations from the peak
      // list.
      final REXP spectraExp = rEngine
          .eval("as.integer(peakList$pcgroup)");
      final REXP isotopeExp = rEngine.eval("peakList$isotopes");


      // Add identities.
      if (spectraExp != null) {


        addPseudoSpectraIdentities(peaks, spectraExp, isotopeExp);

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    final double[][] peaks;
    synchronized (RUtilities.R_SEMAPHORE) {


      // Load XCMS library.
      if (rEngine.eval("require(xcms)").asBool().isFALSE()) {


        throw new IllegalStateException(
            "The \"xcms\" R package couldn't be loaded - is it installed in R?");
      }

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        throw new IllegalStateException(
            "The \"xcms\" R package couldn't be loaded - is it installed in R?");
      }


      // Check version of XCMS.
      if (rEngine
          .eval("packageVersion('xcms') >= '" + XCMS_VERSION + '\'')
          .asBool().isFALSE()) {


        throw new IllegalStateException(
            "An old version of the XCMS package is installed in R - please update XCMS to version "

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      // Set vectors.
      rEngine.assign("scantime", scanTime);
      rEngine.assign("intensity", intensity);


      // Initialize.
      rEngine.eval("mz <- " + mz, false);
      rEngine.eval("numPoints <- length(intensity)", false);


      // Construct xcmsRaw object
      rEngine.eval("xRaw <- new(\"xcmsRaw\")", false);
      rEngine.eval("xRaw@tic <- intensity", false);

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      rEngine.assign("scantime", scanTime);
      rEngine.assign("intensity", intensity);


      // Initialize.
      rEngine.eval("mz <- " + mz, false);
      rEngine.eval("numPoints <- length(intensity)", false);


      // Construct xcmsRaw object
      rEngine.eval("xRaw <- new(\"xcmsRaw\")", false);
      rEngine.eval("xRaw@tic <- intensity", false);
      rEngine.eval("xRaw@scantime <- scantime * " + SECONDS_PER_MINUTE,

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