"subscript cannot contain duplicates and must preserve the "
## return a matrix where each row indicates a hit (query and subject index)
"'optional' and arguments in '...' are ignored"
### Returns a list, with an element for each query, containing the subject hits
### FIXME: this needs a new name given the switch to Vector
"'x' and 'table' are incompatible by subject and query length"
### About 10x faster and uses 4x less memory than my first attempt in pure
"'group.sizes' must be an integer vector"
## First Element In group i.e. first elt associated with each group.
# length of original vector (i.e. before grouping)
## Original Group Size Assignment i.e. group size associated with each
## Hit Group Assignment i.e. group associated with each hit.
## Hit Group Size Assignment i.e. group size associated with each hit.
### Remap the query and/or subject hits.
### Returns 'arg' as a NULL, an integer vector, or a factor.
".map' is specified and is not a factor"
"'query.map' cannot contain NAs, or values that "
"'subject.map' cannot contain NAs, or values that "

queryHits="integer",     # integer vector of length N
subjectHits="integer",   # integer vector of length N
stop("subscript cannot contain duplicates and must preserve the ",
"order of elements when subsetting a ", class(x), " object")
else new("DataFrame", nrows = length(from)))
as.data.frame.Hits <- function(x, row.names=NULL, optional=FALSE, ...)
if (!identical(optional, FALSE) || length(list(...)))
warning("'optional' and arguments in '...' are ignored")
as.data.frame(as(x, "DataFrame"), row.names = row.names)
as.list.Hits <- function(x, ...) .as.list.Hits(x, ...)
setMethod("as.table", "Hits", function(x, ...) {
subjectLength(x) == subjectLength(y) && queryLength(x) == queryLength(y)
stop("'x' and 'table' are incompatible by subject and query length")
stop("\"match\" method for Hits objects ",
function (x, method = c("auto", "quick", "hash")) {
selfmatchIntegerPairs(queryHits(x), subjectHits(x), method = method)
stop("'group.sizes' must be an integer vector")
stop("'hit.type' must be a single integer")
N <- sum(GS)  # length of original vector (i.e. before grouping)
NH <- length(query_hits)  # same as sum(GS2)
subject_hits <- (0:(NH-1L) - CGSr2[HGA]) %% GS[HGA] + FEIG[HGA]
cat("Hits of length ", length(object), "\n", sep = "")
cat("queryLength: ", queryLength(object), "\n", sep = "")
cat("subjectLength: ", subjectLength(object), "\n", sep = "")
.normargMap <- function(arg, sidename, old.length)
stop("'" , sidename, ".map' must be a vector of integers")
stop("'" , sidename, ".map' must have the length of the ", sidename)
.normargNewLength <- function(arg, sidename, map)
stop("'new.", sidename, "Length' must be a single number or NA")
stop("'new.", sidename, "Length' must be NA ",
stop("supplied 'new.", sidename, "Length' must ",
stop("'new.", sidename, "Length' must be specified when ",
"'" , sidename, ".map' is specified and is not a factor")
remapHits <- function(x, query.map=NULL, new.queryLength=NA,
query.map <- .normargMap(query.map, "query", queryLength(x))
subject.map <- .normargMap(subject.map, "subject", subjectLength(x))
stop("'query.map' cannot contain NAs, or values that ",
stop("'subject.map' cannot contain NAs, or values that ",