Can you give an example where it's not doing what you want? Specifically can you include info like this:
print STDERR "\$hystackPatt[$j] = $haystackPatt[$j]\n";
print STDERR "\$rxHaystack[$j] = $rxHaystack[$j]\n";
print STDERR "BEFORE: \$text_seqs[$i] = $text_seqs[$i]\n";
$text_seqs[$i] =~ s{$rxHaystack[$j]}{<span class=$class[$a]>$1</span>}
+gmx;
print STDERR "AFTER: \$text_seqs[$i] = $text_seqs[$i]\n";

[download]
I had to delete the "e" from the "gemx" on the end of your substitution.

In reply to Re: s/// only replacing most of the time... by Thelonius
in thread s/// only replacing most of the time... by mdunnbass

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.