seqinr (version 4.2-36)

acnucopen: 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)

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.

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

Author

J.R. Lobry

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.

References

citation("seqinr")

See Also

choosebank, closebank

Examples

 if (FALSE) # 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"))