BioJava:CookBook:Count:Frequency

From BioJava

How do I calculate the frequency of a Symbol in a Sequence?

One of the most useful classes in BioJava is the Distribution. A Distribution is a map from a Symbol to a frequency. Distributions are trained with observed Symbols using a DistributionTrainerContext. A DistributionTrainerContext can train several registered Distributions and will handle any Symbol from any Alphabet. Ambiguous Symbols are divided amongst the AtomicSymbols that make up the ambiguous BasisSymbol.

The following program demonstrates the training of three Distributions with Sequences from three different Alphabets.

import org.biojava.bio.seq.*;
import org.biojava.bio.symbol.*;
import org.biojava.bio.dist.*;
import org.biojava.utils.*;
import java.util.*;
 
public class Frequency {
  public static void main(String[] args) {
 
    try {
      //make a DNA SymbolList
      SymbolList dna = DNATools.createDNA("atcgctagcgtyagcntatsggca");
 
      //make a RNA SymbolList
      SymbolList rna = RNATools.createRNA("aucgcuaucccaggga");
 
      //make a protein SymbolList
      SymbolList protein = ProteinTools.createProtein("asrvgchvhilmkapqrt");
 
      SymbolList[] sla = {dna, rna, protein};
 
      //get a DistributionTrainerContext
      DistributionTrainerContext dtc = new SimpleDistributionTrainerContext();
 
      //make three Distributions
      Distribution dnaDist =
          DistributionFactory.DEFAULT.createDistribution(dna.getAlphabet());
      Distribution rnaDist =
          DistributionFactory.DEFAULT.createDistribution(rna.getAlphabet());
      Distribution proteinDist =
          DistributionFactory.DEFAULT.createDistribution(protein.getAlphabet());
 
      Distribution[] da = {dnaDist, rnaDist, proteinDist};
 
      //register the Distributions with the trainer
      dtc.registerDistribution(dnaDist);
      dtc.registerDistribution(rnaDist);
      dtc.registerDistribution(proteinDist);
 
      //for each Sequence
      for (int i = 0; i < sla.length; i++) {
        //count each Symbol to the appropriate Distribution
        for(int j = 1; j <= sla[i].length(); j++){
          dtc.addCount(da[i], sla[i].symbolAt(j), 1.0);
        }
      }
 
      //train the Distributions
      dtc.train();
 
      //print the weights of each Distribution
      for (int i = 0; i < da.length; i++) {
        for (Iterator iter = ((FiniteAlphabet)da[i].getAlphabet()).iterator();
             iter.hasNext(); ) {
 
          Symbol sym = (Symbol)iter.next();
          System.out.println(sym.getName()+" : "+da[i].getWeight(sym));
        }
        System.out.println("\n");
      }
 
    }
    catch (Exception ex) {
      ex.printStackTrace();
    }
  }
}