Re: Help tightening up a subroutine please

I am willing to bet your grep is the slowest bit, but have you profiled the code? Anyhow, assuming the grep bit is your bottleneck:

## your original code
@{$sets{$fasta_id}[$setscounter]{$sitekey}} = grep {
     $_ >= $lowerlimit and $_ <= $upperlimit
}  @{$matches{$fasta_id}{$sitekey}};
[download]

Depending on your data, you may gain some performance by using a sorted array instead:

@{$sets{$fasta_id}[$setscounter]{$sitekey}} = ();
foreach ( sort @{$matches{$fasta_id}{$sitekey}} ) {
    last if $_ > $upperlimit;
    next if $_ < $lowerlimit;
    push @{$sets{$fasta_id}[$setscounter]{$sitekey}}, $_;
}
[download]

This will only have an advantage if sort is sufficiently fast and there are many elements above $upperlimit, so this suggestion comes with an extreme case of "know thy data".

<–radiant.matrix–>
Ramblings and references
The Code that can be seen is not the true Code
I haven't found a problem yet that can't be solved by a well-placed trebuchet

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Re^2: Help tightening up a subroutine please by mdunnbass (Monk) on Jan 23, 2007 at 20:32 UTC
Your code here: `@{$sets{$fasta_id}[$setscounter]{$sitekey}} = (); foreach ( sort @{$matches{$fasta_id}{$sitekey}} ) { last if $_ > $upperlimit; next if $_ < $lowerlimit; push @{$sets{$fasta_id}[$setscounter]{$sitekey}}, $_;` [download] Looks a lot like my original code, in the first bit, here: `for my $hit (@{$matches{$fasta_id}{$sitekey}}) { next unless ($hit >= $lowerlimit); last unless ($hit <= $upperlimit); my $ggg = $hit + 0; push (@arrayA, $ggg);` [download] And indeed, it does have a speed advantage. I don't need the sort, as the elements are already sorted in numerical order, so I can (and do) leave that out. As for knowing thy data, this here's the tricky part. I am going through the numbers in the arrays, and basically setting aside clusters of EVERY group of numbers `$span` distance apart. Starting from the lowest element, and proceeding all the way to the highest. So, how many elements there are above `$upperlimit` is as variable as possible. It goes from all to none. Thanks for the input, though. Matt	[reply] [d/l] [select]
Re^3: Help tightening up a subroutine please by radiantmatrix (Parson) on Jan 24, 2007 at 22:16 UTC
Hm, somehow I missed that. Given the extra bit of data you supplied, I might recommend the use of List::MoreUtil's `firstidx` and `lastidx` functions. The fact that it's XS ought to help with the speed. `# for clarity... my $result; my $src = $matches{$fasta_id}{$sitekey}; # Use a slice and firstidx/lastidx to copy the range of values @newArray = @$src[ (firstidx {$_ >= $lowerlimit} @$src )..(lastidx {$_ <= $upperlimit} + @$src) ]; $result = \@newArray;` [download] <–radiant.matrix–> Ramblings and references The Code that can be seen is not the true Code I haven't found a problem yet that can't be solved by a well-placed trebuchet	[reply] [d/l] [select]