[Biojava-l] Issues with FlexibleAlignment

[Matthew Pocock]

Hi,

This should be returning the symbol AlphabetManager.getGap(), which should be 
the same as EMPTY_ALPHABET.getGap(). Could somebody fix this?

Matthew

On Thursday 24 November 2005 14:54, Russ Kepler wrote:
> In working with FlexibleAlignment I've found a problem.  When an overlap is
> empty the underlying code in AbstractULAlignment will return nulls for
> positions not containing symbols, and this confuses things later on.  An
> example program below will demonstrate a simple case of the problem (code
> stolen from TestSimpleAlignment.java and modified).
>
> Is there a symbol that should be returned for this case?  It should be
> distinct from the gap symbol as areas outside the aligning sequence isn't
> gap space, it just doesn't exist. Some comments in the list archive suggest
> that a space was going to be returned, but I can't see an attempt to
> implement that (it's not added to the alphabet, as an example) and right
> now a null is returned.
>
>
> package symbol;
>
> import java.util.ArrayList;
> import java.util.Iterator;
>
> import org.biojava.bio.alignment.FlexibleAlignment;
> import org.biojava.bio.alignment.SimpleAlignmentElement;
> import org.biojava.bio.symbol.RangeLocation;
> import org.biojava.bio.symbol.SymbolList;
>
> public class TestFlexibleAlignment {
>     public static void main(String[] args) {
>         try {
>           // make three random sequences
>           SymbolList res1 = Tools.createSymbolList(10);
>           SymbolList res2 = Tools.createSymbolList(10);
>           SymbolList res3 = Tools.createSymbolList(10);
>
>           // think of three names
>           String name1 = "pigs";
>           String name2 = "dogs";
>           String name3 = "cats";
>
>           // create list with reference sequence
>           ArrayList list = new ArrayList(1);
>           SymbolList refSeq = Tools.createSymbolList(30);
>           list.add(new SimpleAlignmentElement("reference", refSeq, new
> RangeLocation(1, 30))); // create the alignment with the reference sequence
>           FlexibleAlignment ali = new FlexibleAlignment(list);
>
>           // add the sequences as alignments
>           ali.addSequence(new SimpleAlignmentElement(name1, res1, new
> RangeLocation(1, 10))); ali.addSequence(new SimpleAlignmentElement(name2,
> res2, new RangeLocation(11, 20))); ali.addSequence(new
> SimpleAlignmentElement(name3, res3, new RangeLocation(21, 30)));
>
>           // print out each row in the alignment
>           System.out.println("Sequences in alignment");
>           for(Iterator i = ali.getLabels().iterator(); i.hasNext(); ) {
>             String label = (String) i.next();
>             SymbolList rl = ali.symbolListForLabel(label);
>             System.out.println(label + ":\t" + rl.seqString());
>           }
>           System.out.flush();
>
>           // print out each column
>           System.out.println("Columns");
>           for(int i = 1; i <= ali.length(); i++) {
>             System.out.println(i + ":\t" + ali.symbolAt(i).getName());
>           }
>         } catch (Exception ex) {
>           ex.printStackTrace(System.err);
>           System.exit(1);
>         }
>     }
> }
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