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

acnucopen {seqinr} | R Documentation

## 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)

[Package seqinr version 3.4-5 Index]