BioJava:Cookbook:Locations:Point

From BioJava

How do I specify a PointLocation?

In BioJava locations in a Sequence are specified by simple objects that implement the interface Location.

A point location is the inclusive location of a single symbol in a SymbolList or Sequence. PointLocations have public constructors and are easy to instantiate. The following example demonstrates the creation of a PointLocation and it's specification of a single Symbol in a SymbolList.

Remember that BioJava uses the biological coordinate system thus the first PointLocation in a Sequence will be 1 not 0.

As of BioJava 1.8, you may want to consider using RichLocation from the BioJavax extension.

import org.biojava.bio.symbol.*;
import org.biojava.bio.seq.*;
 
public class SpecifyPoint {
  public static void main(String[] args) {
    try {
      //make a PointLocation specifying the third residue
      PointLocation point = new PointLocation(3);
      //print the location
      System.out.println("Location: "+point.toString());
 
      //make a SymbolList
      SymbolList sl = RNATools.createRNA("gcagcuaggcggaaggagc");
      System.out.println("SymbolList: "+sl.seqString());
 
      //get the SymbolList specified by the Location
      SymbolList sym = point.symbols(sl);
      //in this case the SymbolList will only have one base
      System.out.println("Symbol specified by Location: "+sym.seqString());
    }
    catch (IllegalSymbolException ex) {
      //illegal symbol used to make sl
      ex.printStackTrace();
    }
  }
}