[Biojava-l] Gapping Sequence problems

[Richard HOLLAND]

I think you could try swapping the use of == for equals() when testing
for equivalence to the gap symbol. It _should_ be the same literal
object, but maybe not. equals() will work in both cases but == will not.

cheers,
Richard

Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: biojava-l-bounces at portal.open-bio.org 
> [mailto:biojava-l-bounces at portal.open-bio.org] On Behalf Of Dan Cardin
> Sent: Wednesday, December 21, 2005 4:16 PM
> To: biojava-l at biojava.org
> Subject: [Biojava-l] Gapping Sequence problems
> 
> 
> Hello all, I am hung up on SimpleGappedSymbolList problem. I 
> want to add
> gaps to DNA sequences that are loaded in from file that 
> contain gaps and
> remove the gaps. I just load the sequences into an instance of type
> Sequence. Here is snippet ,
> 
> private void finalizeAddGapEdit(){
>    SimpleGappedSymbolList list = new
> SimpleGappedSymbolList(node.getSequence());
> 
>    try {
>       list.addGapsInSource(startX+1,counter);
> 
>       Sequence newSequence =
> DNATools.createDNASequence(list.seqString(),node.getSequence()
> .getName());
> 
>       node.setSequence(newSequence);
> 
>       gvc.repaint();
> 
> } catch (IllegalSymbolException e) {
>    // TODO Auto-generated catch block
>    e.printStackTrace();
> }
> 
> }
> 
> My code to draw out the gapped symbols looks like this
> 
> public void paint(Graphics g)
> {
> double leftX;
> Symbol gap;
> double scale_factor;
> boolean inGapState;
> max = 0;
> for(int i=0;i<seq.length;i++){
> 
>   gap = seq[i].getAlphabet().getGapSymbol();
>   leftX = 0;
>   scale_factor = (double) getWidth()/seq[i].length();
>   inGapState = true;
> 
>   for(int j=1;j<=seq[i].length();j++){
> 
>    if(!inGapState && seq[i].symbolAt(j) == gap){
>      g.drawLine((int) (leftX*scale_factor), i*pixels_bw_lines, (int)
>      ((j-1)*scale_factor) , i*pixels_bw_lines);
>      inGapState = true;
>    }
>    else if(inGapState && seq[i].symbolAt(j) != gap){
>    leftX = j-1;
>    inGapState = false;
>    }
>   }
>    //draw the last line
>    g.drawLine((int) (leftX*scale_factor), i*pixels_bw_lines, (int)
>    (seq[i].length()*scale_factor) , i*pixels_bw_lines);
> 
>    if(seq[i].length() > max)
>       max = seq[i].length();
> }
> }
> 
> My sequences load from file and display correctly , but when 
> I add gaps
> they don't show up. I am confused because I believe that the 
> gap symbols
> used in the underlying sequences are the same. The gaps are 
> added and I
> know this from printing out the string of the sequence. Does 
> anyone know
> how to fix this issue or have any suggestions on a better approach?
> 
> -dc
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