Package org.rosuda.JRI

Examples of org.rosuda.JRI.REXP


        }
      }

      // Do peak picking.
      final REXP centWave = roi <= 1
          ? null
          : rEngine
              .eval("findPeaks.centWave(xRaw, ppm=0, mzdiff=0, verbose=TRUE"
                  + ", peakwidth=c("
                  + peakWidth.getMin()
                  * SECONDS_PER_MINUTE
                  + ", "
                  + peakWidth.getMax()
                  * SECONDS_PER_MINUTE
                  + ')'
                  + ", snthresh="
                  + snrThreshold
                  + ", integrate="
                  + integrationMethod.getIndex()
                  + ", ROI.list=ROIs)");
      peaks = centWave == null ? null : centWave.asMatrix();
    }
    return peaks;
  }
View Full Code Here


        RVector vetor = rexp.asVector();
        if (vetor == null) {
            return null;
        }
        REXP r = (REXP) vetor.get(0);
        double[][] ret = new double[vetor.size()][((double[]) r.getContent()).length];


        for (int col = 0; col < ret.length; col++) {
            REXP coluna = (REXP) vetor.get(col);
            for (int lin = 0; lin < ret[col].length; lin++) {
                ret[col][lin] = ((double[]) coluna.getContent())[lin];
            }
        }
        return ret;
    }
View Full Code Here

        }

    /* High-level API - do not use RNI methods unless there is no other way
      to accomplish what you want */
    try {
      REXP x;
      re.eval("data(iris)",false);
      System.out.println(x=re.eval("iris"));
      // generic vectors are RVector to accomodate names
      RVector v = x.asVector();
      if (v.getNames()!=null) {
        System.out.println("has names:");
        for (Enumeration e = v.getNames().elements() ; e.hasMoreElements() ;) {
          System.out.println(e.nextElement());
        }
      }
      // for compatibility with Rserve we allow casting of vectors to lists
      RList vl = x.asList();
      String[] k = vl.keys();
      if (k!=null) {
        System.out.println("and once again from the list:");
        int i=0; while (i<k.length) System.out.println(k[i++]);
      }     

      // get boolean array
      System.out.println(x=re.eval("iris[[1]]>mean(iris[[1]])"));
      // R knows about TRUE/FALSE/NA, so we cannot use boolean[] this way
      // instead, we use int[] which is more convenient (and what R uses internally anyway)
      int[] bi = x.asIntArray();
      {
          int i = 0; while (i<bi.length) { System.out.print(bi[i]==0?"F ":(bi[i]==1?"T ":"NA ")); i++; }
          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());

      // now for a real dotted-pair list:
      System.out.println(x=re.eval("pairlist(a=1,b='foo',c=1:5)"));
      RList l = x.asList();
      if (l!=null) {
        int i=0;
        String [] a = l.keys();
        System.out.println("Keys:");
        while (i<a.length) System.out.println(a[i++]);
        System.out.println("Contents:");
        i=0;
        while (i<a.length) System.out.println(l.at(i++));
      }
      System.out.println(re.eval("sqrt(36)"));
    } catch (Exception e) {
      System.out.println("EX:"+e);
      e.printStackTrace();
    }
   
    // Part 2 - low-level API - for illustration purposes only!
    //System.exit(0);
   
        // simple assignment like a<-"hello" (env=0 means use R_GlobalEnv)
        long xp1 = re.rniPutString("hello");
        re.rniAssign("a", xp1, 0);

        // Example: how to create a named list or data.frame
        double da[] = {1.2, 2.3, 4.5};
        double db[] = {1.4, 2.6, 4.2};
        long xp3 = re.rniPutDoubleArray(da);
        long xp4 = re.rniPutDoubleArray(db);
       
        // now build a list (generic vector is how that's called in R)
        long la[] = {xp3, xp4};
        long xp5 = re.rniPutVector(la);

        // now let's add names
        String sa[] = {"a","b"};
        long xp2 = re.rniPutStringArray(sa);
        re.rniSetAttr(xp5, "names", xp2);

        // ok, we have a proper list now
        // we could use assign and then eval "b<-data.frame(b)", but for now let's build it by hand:      
        String rn[] = {"1", "2", "3"};
        long xp7 = re.rniPutStringArray(rn);
        re.rniSetAttr(xp5, "row.names", xp7);
       
        long xp6 = re.rniPutString("data.frame");
        re.rniSetAttr(xp5, "class", xp6);
       
        // assign the whole thing to the "b" variable
        re.rniAssign("b", xp5, 0);
       
        {
            System.out.println("Parsing");
            long e=re.rniParse("data(iris)", 1);
            System.out.println("Result = "+e+", running eval");
            long r=re.rniEval(e, 0);
            System.out.println("Result = "+r+", building REXP");
            REXP x=new REXP(re, r);
            System.out.println("REXP result = "+x);
        }
        {
            System.out.println("Parsing");
            long e=re.rniParse("iris", 1);
            System.out.println("Result = "+e+", running eval");
            long r=re.rniEval(e, 0);
            System.out.println("Result = "+r+", building REXP");
            REXP x=new REXP(re, r);
            System.out.println("REXP result = "+x);
        }
        {
            System.out.println("Parsing");
            long e=re.rniParse("names(iris)", 1);
            System.out.println("Result = "+e+", running eval");
            long r=re.rniEval(e, 0);
            System.out.println("Result = "+r+", building REXP");
            REXP x=new REXP(re, r);
            System.out.println("REXP result = "+x);
            String s[]=x.asStringArray();
            if (s!=null) {
                int i=0; while (i<s.length) { System.out.println("["+i+"] \""+s[i]+"\""); i++; }
            }
        }
        {
            System.out.println("Parsing");
            long e=re.rniParse("rnorm(10)", 1);
            System.out.println("Result = "+e+", running eval");
            long r=re.rniEval(e, 0);
            System.out.println("Result = "+r+", building REXP");
            REXP x=new REXP(re, r);
            System.out.println("REXP result = "+x);
            double d[]=x.asDoubleArray();
            if (d!=null) {
                int i=0; while (i<d.length) { System.out.print(((i==0)?"":", ")+d[i]); i++; }
                System.out.println("");
            }
            System.out.println("");
        }
        {
            REXP x=re.eval("1:10");
            System.out.println("REXP result = "+x);
            int d[]=x.asIntArray();
            if (d!=null) {
                int i=0; while (i<d.length) { System.out.print(((i==0)?"":", ")+d[i]); i++; }
                System.out.println("");
            }
        }
View Full Code Here

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