Bio::S...PSLHSP(3pm)

💖 NAME 💖

Bio::Search::HSP::PSLHSP — bestie, it's an HSP but for PSL output 🦋

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✨ SYNOPSIS ✨

  # get a PSLHSP somehow (SearchIO::psl)

That's it, that's the whole vibe. You don't build it by hand, you just... get one. iykyk 💅

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🌸 DESCRIPTION 🌸

okay so this is an HSP specifically for PSL output, which means we get to handle seq_inds differently than the regular ones do. That's literally the whole point. no cap. ✨

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🫶 FEEDBACK 🫶

💌 Mailing Lists

ngl, user feedback is an integral part of the evolution of this module and every other Bioperl module. So if you've got comments or suggestions, pls pls pls send them to the Bioperl mailing list — your participation is much appreciated, fr fr 🥹

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🌈 Support

bestie, listen: send your usage questions and support issues to the mailing list 👑

  bioperl-l@bioperl.org

...and not to the module maintainer directly, okay? 😭 Like, there are so many experienced and responsive experts on there who will look at your problem and address it fast. If it's at all possible, include a thorough description of the problem with code and data examples. the more deets the better, periodt 💯

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution. Bug reports can be submitted via the web 🕸️✨

  https://github.com/bioperl/bioperl-live/issues

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👑 AUTHOR - Jason Stajich 👑

Email: jason-at-bioperl-dot-org 💌

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ 🔍

🎀 new

  Title   : new
  Usage   : my $obj = Bio::Search::HSP::PSLHSP->new();
  Function: Builds a new Bio::Search::HSP::PSLHSP object
  Returns : an instance of Bio::Search::HSP::PSLHSP
  Args    : -gapblocks => arrayref of gap locations which are [start,length]
                              of gaps

Builds a brand new Bio::Search::HSP::PSLHSP object for you 🫶 The -gapblocks arg takes an arrayref of gap locations, and each one is [start,length] of gaps. iconic.

🧚 gap_blocks

  Title   : gap_blocks
  Usage   : $obj->gap_blocks($seqtype,$blocks)
  Function: Get/Set the gap blocks
  Returns : value of gap_blocks (a scalar)
  Args    : sequence type - 'query' or 'hit'
            blocks - arrayref of block start,length

Get/set the gap blocks ✨ It returns the value of gap_blocks (a scalar, bestie). When you're setting, the args are the sequence type — either 'query' or 'hit' — and the blocks, which is an arrayref of block start,length. 💅

💀 mismatches

  Title   : mismatches
  Usage   : $obj->mismatches($newval)
  Function: Get/Set the number of mismatches
  Returns : value of mismatches (a scalar)
  Args    : on set, new value (a scalar or undef, optional)

Get/set the number of mismatches 🌸 Returns the value of mismatches (a scalar). On set, the new value is a scalar or undef, and it's optional. lowkey the chillest method here 🍓

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perl v5.32.1 · 2021-08-15 — and that's the whole page, bestie!! go forth and handle those seq_inds differently, you absolute main character 👑💖✨