[Bioperl-l] proposed change -- symbols SimpleAlign

[Albert Vilella]

Hi,

Am I right in thinking that the '_symbols' hash in SimpleAlign is only
used if one calls the symbol_chars method?

When I comment out this line:

map { $self->{'_symbols'}->{$_} = 1; } split(//,$seq->seq) if
$seq->seq; # line 257

I get a nice speed boost on loading alignments.

Can I comment this line out in the CVS HEAD?

Cheers,

    Albert.

[init] 5.96046447753906e-06 secs...
[loading aln /home/avilella/ensembl/exoseq/test/ENSG00000162399.chr1.fasta]
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[loading aln /home/avilella/ensembl/exoseq/test/ENSG00000121957.chr1.fasta]
15.8402290344238 secs...

avilella at magneto:~$ perl
/home/avilella/src/ensembl_main/ensembl-personal/avilella/exoseq/ancestral_alleles.pl
-dir /home/avilella/ensembl/exoseq/test -verbose
[init] 1.21593475341797e-05 secs...
[loading aln /home/avilella/ensembl/exoseq/test/ENSG00000162399.chr1.fasta]
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