R/acnucopen.R

In seqinr: Biological Sequences Retrieval and Analysis

acnucopen <- function(db, socket, challenge = NA){
    #
    # Check arguments:
    #
    if(!is.na(challenge) ) stop("password protection not implemented yet")
    #
    # Build request:
    #
    request <- paste("acnucopen&db=", db, sep = "")
    writeLines(request, socket, sep = "\n")
    answerFromServer <- readLines(socket, n = 1)
    #
    # Check that there is an answer from server:
    #
    if(length(answerFromServer) == 0){
        close(socket)
        stop("Empty answer from server")
    }
    res <- parser.socket(answerFromServer)
    #
    # Check that no error is returned:
    #
    if(res[1] != "0"){
        close(socket)
        if( res[1] == "1" ){
            stop("unrecognized command") # should not happen
        }
        if( res[1] == "2" ){
            stop("missing db= argument") # should not happen
        }
        if( res[1] == "3" ){
            stop(paste("Database with name -->", db, "<-- is not known by server.\n", sep = ""))
        }
        if( res[1] == "4" ){
            stop(paste("Database with name -->", db, "<-- is currently off for maintenance, please try again later.\n", sep = ""))
        }
        if( res[1] == "5" ){
            stop("A database is currently opened and has not been closed.\n")
        }
        if( res[1] == "6" ){
            stop(paste("Database with name -->", db, "<-- is protected by a password (unimplemented).\n", sep = ""))
        }
        stop(paste("I don't know what this error code means for acnucopen:", res[1]))
    }
    return(list(type = res[2], totseqs = as.numeric(res[3]), totspecs = as.numeric(res[4]),
                totkeys = as.numeric(res[5]), ACC_LENGTH = as.numeric(res[6]),
                L_MNEMO = as.numeric(res[7]), WIDTH_KW = as.numeric(res[8]),
                WIDTH_SP = as.numeric(res[9]), WIDTH_SMJ = as.numeric(res[10]),
                WIDTH_AUT = as.numeric(res[11]), WIDTH_BIB = as.numeric(res[12]),
                lrtxt = as.numeric(res[13]), SUBINLNG = as.numeric(res[14])))
}