Replace:

    my $parent = $proteinLU{$word};
    my $wIndex = 0;

    while ($wIndex < @words && exists $parent->{$words[$wIndex]}) {
        $parent = $parent->{$words[$wIndex++]}
    }

    print "**$parent->{_name_}** " if exists $parent->{_name_};
    splice @words, 0, $wIndex;

[download]

with:

    my $parent = $proteinLU{$word};
    my $wIndex = 0;
    my @best;

    while ($wIndex < @words && exists $parent->{$words[$wIndex]}) {
        @best = ($parent->{_name_}, $wIndex) if exists $parent->{_name
+_};
        $parent = $parent->{$words[$wIndex++]};
    }

    if (@best) {
        print "**$best[0]** ";
        splice @words, 0, $best[1];
    } else {
        print "$word ";
    }

[download]

There was no fall back to the longest match so far if a longer partial match existed. In the sample case 'MCM2' was being masked by 'MCM2 , FORMERLY'.

There is no need (but no major harm) to provide different case versions of the same match string unless you want to use a case sensitive match with only the given variants allowed (in which case you need to remove lc in the various places it is used).

True laziness is hard work

In reply to Re^6: Tag protein names in sentences by GrandFather
in thread Tag protein names in sentences by sinlam

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