[Biojava-dev] Editable sequences

[Schreiber, Mark]

Here is some examples of the use of the biojava Edit object.
 
import org.biojava.bio.seq.*;
import org.biojava.bio.symbol.*;
 
public class EditExamples {

  public static void main(String[] args) throws Exception{

    //you can't actually edit a sequence
    Sequence seq = DNATools.createDNASequence("atggct", "seq");
 
    //so you need to get a copy of the Symbols in it
    //using a "copy constructor"
    SimpleSymbolList syms = new SimpleSymbolList(seq);
 
    //add to the end, while overwriting 0 symbols, "cc"
    Edit e = new Edit(seq.length()+1, 0, DNATools.createDNA("cc"));
    //apply the edit
    syms.edit(e);
    //should now be atggctcc
    System.out.println(syms.seqString());
 
    //insert at the start, while overwriting 0 Symbols "tt"
    e = new Edit(1, 0, DNATools.createDNA("tt"));
    syms.edit(e);
    //should now be ttatggctcc
    System.out.println(syms.seqString());
 
    //insert at position 4, overwriting 0 symbols "aca"
    e = new Edit(4, 0, DNATools.createDNA("aca"));
    syms.edit(e);
    //should now be ttaacatggctcc
    System.out.println(syms.seqString());
 
    //overwrite at position 2, 3 bases with "ggg"
    e = new Edit(2, 3, DNATools.createDNA("ggg"));
    syms.edit(e);
    //should now be tgggcatggctcc
    System.out.println(syms.seqString());
 
    //delete from the start 5 bases (overwrite 5 bases with nothing)
    e = new Edit(1, 5, SymbolList.EMPTY_LIST);
    syms.edit(e);
    //should now be atggctcc
    System.out.println(syms.seqString());
 
    //now a more complex example
    //overwrite positions two and three with aa and then insert tt
    e = new Edit(2, 2, DNATools.createDNA("aatt"));
    syms.edit(e);

    //should now be aaattgctcc
    System.out.println(syms.seqString());
  }
}

	-----Original Message----- 
	From: daviddebeule at pandora.be [mailto:daviddebeule at pandora.be] 
	Sent: Tue 29/07/2003 7:11 p.m. 
	To: biojava-dev at biojava.org 
	Cc: 
	Subject: [Biojava-dev] Editable sequences
	
	

	Hi,
	
	Is there an easy way to make a SimpleSequence 'Editable' ? I want to add/ remove/insert symbols.  I probably need to make something like a SimpleEditableSequence but I am not sure which methods I can to override to accomplish this.
	
	Thanks in advance,
	
	David
	
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