## ----include=FALSE------------------------------------------------------------
knitr::opts_chunk$set(
  comment = "NA",
  collapse = TRUE
)

run <- if (ssw::is_installed_ssw_py()) TRUE else FALSE
knitr::opts_chunk$set(eval = run)

## -----------------------------------------------------------------------------
#  library("ssw")

## -----------------------------------------------------------------------------
#  read <- "ACGT"

## -----------------------------------------------------------------------------
#  read |> align("TTTTACGTCCCCC")

## -----------------------------------------------------------------------------
#  a <- read |> align("TTTTACGTCCCCC")

## -----------------------------------------------------------------------------
#  a$alignment$optimal_score

## -----------------------------------------------------------------------------
#  a$alignment$sub_optimal_score

## -----------------------------------------------------------------------------
#  read |> align("TTTTACAGTCCCCC")

## -----------------------------------------------------------------------------
#  read |> align("TTTTACTCCCCC", gap_open = 3)

## -----------------------------------------------------------------------------
#  read |> align("TTTTACTCCCCC", gap_open = 0)

## -----------------------------------------------------------------------------
#  a <- align("ACTG", "ACTCACTG", start_idx = 4)
#  a

## -----------------------------------------------------------------------------
#  a |> print(start_idx = 4)

## -----------------------------------------------------------------------------
#  a <- force_align("ACTG", "TTTTCTGCCCCCACG")
#  a

## -----------------------------------------------------------------------------
#  b <- a |> formatter()
#  b

## -----------------------------------------------------------------------------
#  a |> formatter(print = TRUE)