---
name: "Bio::Search::HSP::FastaHSP"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Search::HSP::FastaHSP"
---

# Bio::Search::HSP::FastaHSP(3pm)

HSP object for FASTA specific data

## NAME

Bio::Search::HSP::FastaHSP - HSP object for FASTA specific data

## SYNOPSIS

```
  # get a FastaHSP from a SearchIO stream
  my $in = Bio::SearchIO->new(-format => 'fasta', -file => 'filename.fasta');
  while( my $r = $in->next_result) {
      while( my $hit = $r->next_result ) {
           while( my $hsp = $hit->next_hsp ) {
              print "smith-waterman score (if available): ",
                    $hsp->sw_score(),"\n";
           }
      }
  }
```

## DESCRIPTION

Describe the object here

## FEEDBACK

### Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list.  Your participation is much appreciated.

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

### Support

Please direct usage questions or support issues to the mailing list:

*bioperl-l@bioperl.org*

rather than to the module maintainer directly. Many experienced and  reponsive experts will be able look at the problem and quickly  address it. Please include a thorough description of the problem  with code and data examples if at all possible.

### Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

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

## AUTHOR - Jason Stajich

Email jason-at-bioperl.org

## 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::FastaHSP->new();
 Function: Builds a new Bio::Search::HSP::FastaHSP object
 Returns : Bio::Search::HSP::FastaHSP
 Args    : -swscore => smith-waterman score
```

### sw\_score

```
 Title   : sw_score
 Usage   : $obj->sw_score($newval)
 Function: Get/Set Smith-Waterman score
 Returns : value of sw_score
 Args    : newvalue (optional)
```

### evalue2

```
 Title   : evalue2
 Usage   : $obj->evalue2($newval)
 Function: Get/Set E2() expectation value
 Returns : value of evalue2
 Args    : newvalue (optional)
```