acnucopen: open and close a remote access to an ACNUC database

In seqinr: Biological Sequences Retrieval and Analysis

open and close a remote access to an ACNUC database

Description

These are low level functions to start and stop a remote access to an ACNUC database.

Usage

acnucopen(db, socket, challenge = NA)
acnucclose(socket)
clientid(id = paste("seqinr_",
 packageDescription("seqinr")$Version, sep = ""),
 socket, verbose = FALSE)
quitacnuc(socket)

Arguments

db	the remote ACNUC database name
socket	an object of class sockconn connecting to an ACNUC server
challenge	unimplemented yet
id	client ID definition defaulting to seqinr + package version number
verbose	logical, if TRUE mode verbose is on

Details

these low level functions are usually not used directly by the user. Use choosebank to open a remote ACNUC database and closebank to close it.

Value

For openacnuc a list with the following components: type : the type of database that was opened. totseqs, totspec, totkey : total number of seqs, species, keywords in opened database. ACC_LENGTH, L_MNEMO, WIDTH_KW, WIDTH_SP, WIDTH_SMJ, WIDTH_AUT, WIDTH_BIB, lrtxt, SUBINLNG: max lengths of record keys in database.

Author(s)

J.R. Lobry

References

citation("seqinr")

See Also

choosebank, closebank

Examples

 ## Not run: # Need internet connection
  mysocket <- socketConnection( host = "pbil.univ-lyon1.fr",
    port = 5558, server = FALSE, blocking = TRUE)
  readLines(mysocket, n = 1) # OK acnuc socket started
  acnucopen("emblTP", socket = mysocket) -> res
  expected <- c("EMBL", "14138095", "236401", "1186228", "8",
    "16", "40", "40", "20", "20", "40", "60", "504")
  stopifnot(all(unlist(res) == expected))
  tryalreadyopen <- try(acnucopen("emblTP", socket = mysocket))
  stopifnot(inherits(tryalreadyopen, "try-error"))
  # Need a fresh socket because acnucopen() close it if error:
  mysocket <- socketConnection( host = "pbil.univ-lyon1.fr",
    port = 5558, server = FALSE, blocking = TRUE)
  tryoff <-  try(acnucopen("off", socket = mysocket))
  stopifnot(inherits(tryoff, "try-error"))

  mysocket <- socketConnection( host = "pbil.univ-lyon1.fr",
    port = 5558, server = FALSE, blocking = TRUE)
  tryinexistent <-  try(acnucopen("tagadatagadatsointsoin", socket = mysocket))
  stopifnot(inherits(tryinexistent, "try-error"))

  mysocket <- socketConnection( host = "pbil.univ-lyon1.fr",
    port = 5558, server = FALSE, blocking = TRUE)
  trycloseunopened <- try(acnucclose(mysocket))
  stopifnot(inherits(trycloseunopened, "try-error"))

 
## End(Not run)

seqinr documentation built on March 31, 2023, 3:05 p.m.