Query-class: Class '"Query"'

In gschofl/blastr: A wrapper for NCBI Blast

Description

An S4 class that holds data parsed from an NCBI BLAST XML ‘iteration’ element. Each "Query" instance contains data from one query.

Usage

## S4 method for signature 'Query'
nhsps(x)

## S4 method for signature 'Query'
getHit(x, i, drop = TRUE, ...)

## S4 method for signature 'Query'
nhits(x)

## S4 method for signature 'Query'
getQueryNum(x)

## S4 method for signature 'Query'
getQueryID(x)

## S4 method for signature 'Query'
getQueryDef(x)

## S4 method for signature 'Query'
getQueryLen(x)

Methods (by generic)

• nhsps: Returns the number of HSPs for each hit; <integer>.

• getHit: Return a Hit or HitList

• nhits: Returns the number of hits; <numeric>.

• getQueryNum: Returns the query (iteration) number; <integer>.

• getQueryID: Returns the query ID; <character>.

• getQueryDef: Returns the query definition; <character>.

• getQueryLen: Returns the query length; <integer>.

Slots

iter_num

The number of the queries (iterations); <integer>.

query_id

Query identifier; "character".

query_def

Query definition; "character".

query_len

Query length; "integer".

hits

List of hits; "HitList".

query_env

Shared container for query_id, query_def, query_len, and hit_len; "environment".

Examples

showClass("Query")

gschofl/blastr documentation built on May 17, 2019, 8:52 a.m.