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

org.rosuda.JRI.Rengine.assign()

          System.out.println("");
      }
      
      // push a boolean array
      boolean by[] = { true, false, false };
      re.assign("bool", by);
      System.out.println(x=re.eval("bool"));
      // asBool returns the first element of the array as RBool
      // (mostly useful for boolean arrays of the length 1). is should return true
      System.out.println("isTRUE? "+x.asBool().isTRUE());

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          System.out.println("");
      }
      
      // push a boolean array
      boolean by[] = { true, false, false };
      re.assign("bool", by);
      System.out.println(x=re.eval("bool"));
      // asBool returns the first element of the array as RBool
      // (mostly useful for boolean arrays of the length 1). is should return true
      System.out.println("isTRUE? "+x.asBool().isTRUE());

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      }


      try {


        // Set chromatogram.
        rEngine.assign("chromatogram", chromatogram);


        // Calculate baseline.
        baseline = rEngine.eval(
            "asysm(chromatogram," + smoothing + ',' + asymmetry
                + ')').asDoubleArray();

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          pointIndex++;
        }
      }


      // Set vectors.
      rEngine.assign("scantime", scanTimes);
      rEngine.assign("scanindex", scanIndices);
      rEngine.assign("mass", masses);
      rEngine.assign("intensity", intensities);


      // Construct xcmsRaw object

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        }
      }


      // Set vectors.
      rEngine.assign("scantime", scanTimes);
      rEngine.assign("scanindex", scanIndices);
      rEngine.assign("mass", masses);
      rEngine.assign("intensity", intensities);


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

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      }


      // Set vectors.
      rEngine.assign("scantime", scanTimes);
      rEngine.assign("scanindex", scanIndices);
      rEngine.assign("mass", masses);
      rEngine.assign("intensity", intensities);


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

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      // Set vectors.
      rEngine.assign("scantime", scanTimes);
      rEngine.assign("scanindex", scanIndices);
      rEngine.assign("mass", masses);
      rEngine.assign("intensity", intensities);


      // 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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      // Set file (dummy) file path.
      rEngine.eval("xs@filepaths  <- ''", false);


      // Set sample name.
      rEngine.assign("sampleName", peakList.getName());
      rEngine.eval("sampnames(xs) <- sampleName", false);


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

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            "An old version of the XCMS package is installed in R - please update XCMS to version "
                + XCMS_VERSION + " or later");
      }


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


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

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                + XCMS_VERSION + " or later");
      }


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


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

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