---
name: "Bio::Search::HSP::WABAHSP"
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::WABAHSP"
---

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

HSP object suitable for describing WABA alignments

## NAME

Bio::Search::HSP::WABAHSP - HSP object suitable for describing WABA alignments

## SYNOPSIS

\# use this object as you would a GenericHSP # a few other methods have been added including state

## DESCRIPTION

This object implements a few of the extra methods such as hmmstate\_string which returns the HMM state representation for the WABA alignment.  We also must implement a method to calculate homology\_string since it is not returned by the algorithm in the machine readable format.

## 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@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::WABAHSP->new();
 Function: Builds a new Bio::Search::HSP::WABAHSP object
 Returns : Bio::Search::HSP::WABAHSP
 Args    : -hmmstate_seq => the string representing the state output from WABA
```

### hmmstate\_string

```
 Title   : hmmstate_string
 Usage   : my $hmmseq = $wabahsp->hmmstate_string();
 Function: Get/Set the WABA HMM stateseq
 Returns : string
 Args    : [optional] string
```

### homology\_string

```
 Title   : homolgy_string
 Usage   : my $homology_str = $hsp->homology_string();
 Function: Homology string must be calculated for a WABA HSP so we can do
           so here and cache the result so it is only done once
 Returns : string
 Args    : none
```