1. Streamer
  2. Commit bd49f347e7d9baa0fe345554984b3db7a07a1ea0
Browse code

remove 'yieldSize' from most functions to simplify interface

- additional misc. tidy


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Streamer@68656 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 21/08/2012 00:42:59
Showing 40 changed files
DESCRIPTION
History View file @ bd49f34
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: Streamer
2 2 
 Type: Package
3 3 
 Title: Enabling stream processing of large files
4 
-Version: 1.3.2
4 
+Version: 1.3.3
5 5 
 Date: 2010-10-13
6 6 
 Author: Martin Morgan, Nishant Gopalakrishnan
7 7 
 Maintainer: Martin Morgan <mtmorgan@fhcrc.org>
R/BufferInterface.R
History View file @ bd49f34
8 8 
deleted file mode 100644
... ... 
@@ -1,41 +0,0 @@
1 
-.BufferInt <- setRefClass("BufferInt",
2 
-    fields=list(
3 
-        length="function",
4 
-        append="function",
5 
-        subset="function"))
6 
-
7 
-.BufferInt$methods(
8 
-    initialize=function(length=.Primitive("length"),
9 
-                        append=.Primitive("c"),
10 
-                        subset=.Primitive("["))
11 
-    {
12 
-        "initialize 'BufferInt'"
13 
-        .self$length <- length
14 
-        .self$append <- append
15 
-        .self$subset <- subset
16 
-        .self
17 
-    })
18 
-
19 
-BufferInt <- function(length=.Primitive("length"), append=.Primitive("c"),
20 
-                     subset=.Primitive("["))
21 
-{
22 
-    .BufferInt$new(length=length, append=append, subset=subset)
23 
-}
24 
-
25 
-
26 
-setGeneric("BufferInterface",
27 
-    function(object) standardGeneric("BufferInterface"))
28 
-
29 
-setMethod("BufferInterface", signature = signature(object = "ANY"),
30 
-    function(object) BufferInt())
31 
-
32 
-setMethod("BufferInterface", signature = signature(object = "data.frame"),
33 
-    function(object)
34 
-{
35 
-    BufferInt(length=nrow, append=rbind, subset=function(x, i) {
36 
-        as.data.frame(sapply(x, .Primitive("["), i))
37 
-    })
38 
-})
39 
-
40 
-
41 
-
R/ConnectionProducer.R
History View file @ bd49f34
... ... 
@@ -10,12 +10,9 @@
10 10 
         parser = rawParserFactory(), ...)
11 11 
     {
12 12 
         "initialize ConnectionProducer"
13 
-        callSuper(...)
14 
-        if (verbose) msg(".ConnectionProducer$initialize")
13 
+        callSuper(..., reader=reader, parser=parser)
15 14 
         if (!missing(con))
16 15 
             .self$con <- con
17 
-        .self$reader <- reader
18 
-        .self$parser <- parser
19 16 
         .self
20 17 
     },
21 18 
     reset = function()
R/Consumer.R
History View file @ bd49f34
... ... 
@@ -1,15 +1,11 @@
1 1 
 .Consumer <- setRefClass("Consumer",
2 2 
     contains="Streamer",
3 
-    fields = list(
4 
-        inputPipe="ANY",
5 
-        .records="ANY",
6 
-        .bufferInt="BufferInt",
7 
-        .bufFun="logical"),
3 
+    fields = list(inputPipe = "ANY"),
8 4 
     methods = list(
9 5 
     initialize = function(..., inputPipe)
10 6 
     {
11 7 
         "initialize 'Consumer'"
12 
-        callSuper(..., .bufferInt=BufferInt(), .bufFun=FALSE)
8 
+        callSuper(...)
13 9 
         if (verbose) msg("Consumer$initialize")
14 10 
         if (!missing(inputPipe))
15 11 
             .self$inputPipe <- inputPipe
... ... 
@@ -40,43 +36,13 @@
40 36 
     {
41 37 
         "delegate yield() to inputPipe"
42 38 
         if (verbose) msg("Consumer$yield()")
43 
-        .fill()
44 
-        idx <- seq_len(min(yieldSize, .self$.bufferInt$length(.records)))
45 
-        records <- .self$.bufferInt$subset(.records,idx)
46 
-        .self$.records <- .self$.bufferInt$subset(.records,-idx)
47 
-        records
39 
+        inputPipe$yield()
48 40 
     },
49 41 
     status = function()
50 42 
     {
51 43 
         "report status of 'Consumer'"
52 44 
         if (verbose) msg("Consumer$status()")
53 
-        c(recLength=.self$.bufferInt$length(.records), inputs=inputs(),
54 
-          callSuper())
55 
-    },
56 
-    .fill = function() {
57 
-        "fill stream with yieldSize records, if available"
58 
-        if(verbose) msg("Consumer$.fill()")
59 
-        if(!.self$.bufFun)
60 
-        {
61 
-            input <- inputPipe$yield()
62 
-            .self$.records <- new(class(input))
63 
-            .self$.bufferInt <- BufferInterface(input)
64 
-            .add(input)
65 
-            .self$.bufFun <- TRUE
66 
-        }
67 
-        while ( .self$.bufferInt$length(.records) < yieldSize &&
68 
-               0 != length(input<- inputPipe$yield()))
69 
-        {
70 
-            .add(input)
71 
-        }
72 
-        .self
73 
-    },
74 
-    .add = function(input)
75 
-    {
76 
-        ".add (incomplete) 'input'"
77 
-        if (verbose) msg("Consumer$.add()")
78 
-        .self$.records <- .self$.bufferInt$append(.records, input)
79 
-        .self
45 
+        c(inputs=inputs(), callSuper())
80 46 
     },
81 47 
     show = function()
82 48 
     {
R/Downsample.R
History View file @ bd49f34
... ... 
@@ -2,16 +2,13 @@
2 2 
     contains = "Consumer",
3 3 
     fields = list(
4 4 
       probability = "numeric",
5 
+      sampledSize = "integer",
5 6 
       .buffer = "ANY"),
6 7 
     methods = list(
7 
-    initialize = function(..., probability)
8 
+    initialize = function(...)
8 9 
     {
9 10 
         "initialize Downsample"
10 
-        callSuper(...)
11 
-        if (verbose) msg("Downsample$initialize")
12 
-        .self$probability <- probability
13 
-        .self$.buffer <- list()
14 
-        .self
11 
+        callSuper(..., .buffer=list())
15 12 
     },
16 13 
     .sample = function(x)
17 14 
     {
... ... 
@@ -22,12 +19,12 @@
22 19 
     },
23 20 
     yield = function()
24 21 
     {
25 
-        "sample records with 'probability' until 'yieldSize' retrieved"
22 
+        "sample records with 'probability' until 'sampledSize' retrieved"
26 23 
         if (verbose) msg("Downsample$yield()")
27 
-        while (length(.buffer) < yieldSize &&
24 
+        while (length(.buffer) < sampledSize &&
28 25 
                0L != length(res <- callSuper()))
29 26 
             .self$.buffer <- c(.buffer, .sample(res))
30 
-        idx <- seq_len(min(length(.buffer), yieldSize))
27 
+        idx <- seq_len(min(length(.buffer), sampledSize))
31 28 
         result <- .buffer[idx]
32 29 
         .self$.buffer <- .buffer[-idx]
33 30 
         result
... ... 
@@ -49,14 +46,15 @@
49 46 
     show = function()
50 47 
     {
51 48 
         callSuper()
52 
-        txt <- sprintf("probability: %.2f; yieldSize: %d",
53 
-                       probability, yieldSize)
49 
+        txt <- sprintf("probability: %.2f; sampledSize: %d",
50 
+                       probability, sampledSize)
54 51 
         cat(txt, "\n")
55 52 
     }))
56 53
57 54 
 Downsample <-
58 
-    function(probability = 0.1, ..., yieldSize = 1e6, verbose=FALSE)
55 
+    function(probability = 0.1, sampledSize = 1e6, ...)
59 56 
 {
60 
-    .Downsample$new(probability=probability, ...,
61 
-                    yieldSize=yieldSize, verbose=verbose)
57 
+    sampledSize <- as.integer(sampledSize)
58 
+    .Downsample$new(probability=probability, sampledSize=sampledSize,
59 
+                    ...)
62 60 
 }
R/ParallelConnector.R
History View file @ bd49f34
... ... 
@@ -3,13 +3,6 @@
3 3 
                 fields=list(.upstream="ANY"))
4 4
5 5 
 .ParallelConnector$methods(
6 
-    initialize = function(...)
7 
-    {
8 
-        "Initialize the fields of the ParallelConnector class"
9 
-        callSuper(...)
10 
-        if (verbose) msg(".ParallelConnector$initialize()")
11 
-        .self
12 
-    },
13 6 
     yield = function()
14 7 
    {
15 8 
         "Read data from childProcess"
... ... 
@@ -27,8 +20,6 @@
27 20 
         }
28 21 
     })
29 22
30 
-ParallelConnector <- function(..., yieldSize=1e6, verbose = FALSE)
31 
-{
32 
-    .ParallelConnector$new(..., yieldSize=yieldSize, verbose = verbose)
33 
-}
23 
+ParallelConnector <- function(...)
24 
+    .ParallelConnector$new(...)
34 25
R/RawInput.R
History View file @ bd49f34
... ... 
@@ -36,18 +36,15 @@ rawParserFactory <-
36 36 
 .RawInput <- setRefClass("RawInput",
37 37 
     contains="ConnectionProducer",
38 38 
     fields = list(
39 
-        .buffer = "raw", .records = "list", .parsedRecords = "integer"
39 
+      yieldSize = "integer",
40 
+      .buffer = "raw", .records = "list", .parsedRecords = "integer"
40 41 
     ))
41 42
42 43 
 .RawInput$methods(
43 44 
     initialize = function(...)
44 45 
     {
45 46 
         "initialize RawInput"
46 
-        callSuper(...)
47 
-        if (verbose) msg(".RawInput$initialize()")
48 
-        .self$.records <- list()
49 
-        .self$.parsedRecords <- 0L
50 
-        .self
47 
+        callSuper(..., .records=list(), .parsedRecords=0L)
51 48 
     },
52 49 
     reset = function()
53 50 
     {
... ... 
@@ -124,14 +121,12 @@ rawParserFactory <-
124 121
125 122
126 123 
 RawInput <-
127 
-    function(con, yieldSize = 1e6,
128 
-             reader=rawReaderFactory(),
129 
-             parser=rawParserFactory(),
130 
-             ..., verbose=FALSE)
124 
+    function(con, yieldSize = 1e6, reader=rawReaderFactory(),
125 
+             parser=rawParserFactory(), ...)
131 126 
 {
132 127 
     if (!is(con, "connection"))
133 128 
         con <- file(con, "rb")
134 
-    .RawInput$new(con=con,
135 
-         reader=reader, parser=parser, ...,
136 
-         yieldSize=yieldSize, verbose=verbose)
129 
+    yieldSize <- as.integer(yieldSize)
130 
+    .RawInput$new(con=con, yieldSize=yieldSize, reader=reader,
131 
+                  parser=parser, ...)
137 132 
 }
R/Seq.R
History View file @ bd49f34
... ... 
@@ -1,19 +1,19 @@
1 1 
 .Seq <- setRefClass("Seq",
2 2 
     fields = list(
3 
-      from="numeric", to="numeric", by="numeric"),
3 
+      from="numeric", to="numeric", by="numeric", length.out="integer"),
4 4 
     contains="Producer",
5 5 
     methods = list(
6 6 
       yield = function() {
7 7 
           if ((from - to) * by > 0)
8 8 
               return(integer())
9 
-          s <- seq(from, by=by, length.out=yieldSize + 1L)
9 
+          s <- seq(from, by=by, length.out=length.out + 1L)
10 10 
           .self$from <- s[length(s)]
11 11 
           s <- s[-length(s)]
12 12 
           s[s <= to]
13 13 
       },
14 14 
       show = function() {
15 15 
           cat("from:", from, "\nto:", to, "\nby:", by,
16 
-              "\nlength.out:", yieldSize, "\n")
16 
+              "\nlength.out:", length.out, "\n")
17 17 
       }))
18 18
19 19 
 Seq <-
... ... 
@@ -31,5 +31,5 @@ Seq <-
31 31 
     if (from > to)
32 32 
         stop("'from' must be less than or equal to 'to'")
33 33 
     length.out <- as.integer(length.out)
34 
-    .Seq$new(from=from, to=to, by=by, yieldSize=length.out, ...)
34 
+    .Seq$new(from=from, to=to, by=by, length.out=length.out, ...)
35 35 
 }
R/Stream.R
History View file @ bd49f34
... ... 
@@ -31,7 +31,7 @@
31 31 
         }
32 32 
         x
33 33 
     }, list(x, ...), right=TRUE)
34 
-    .Stream$new(inputPipe=inputPipe, yieldSize=x$yieldSize, verbose=verbose)
34 
+    .Stream$new(inputPipe=inputPipe, verbose=verbose)
35 35 
 }
36 36
37 37 
 setMethod(length, "Stream",
R/Streamer.R
History View file @ bd49f34
... ... 
@@ -1,16 +1,13 @@
1 1 
 .Streamer <- setRefClass("Streamer",
2 2 
     fields = list(
3 
-      yieldSize="integer",
4 3 
       verbose="logical",
5 4 
       inUse="logical"))
6 5
7 6 
 .Streamer$methods(
8 
-    initialize = function(..., yieldSize=1e6, verbose=FALSE)
7 
+    initialize = function(..., verbose=FALSE)
9 8 
     {
10 9 
         "initialize 'Streamer'"
11 
-        if (verbose) msg("Streamer$initialize")
12 
-        invisible(callSuper(..., yieldSize=as.integer(yieldSize),
13 
-                            verbose=verbose, inUse=FALSE))
10 
+        invisible(callSuper(..., verbose=verbose, inUse=FALSE))
14 11 
     },
15 12 
     msg = function(fmt, ...)
16 13 
     {
... ... 
@@ -34,7 +31,7 @@
34 31 
     {
35 32 
         "report status of Steamer"
36 33 
         if (verbose) msg("Streamer$status()")
37 
-        list(yieldSize=yieldSize, verbose=verbose, inUse=inUse)
34 
+        list(verbose=verbose, inUse=inUse)
38 35 
     },
39 36 
     show = function()
40 37 
     {
R/TConnector.R
History View file @ bd49f34
... ... 
@@ -1,42 +1,28 @@
1 
+## TOut
2 
+
1 3 
 .TOut <- setRefClass("TOut",
2 4 
     contains="Consumer",
3 
-    fields=list(
4 
-        .start="numeric"
5 
-    ))
5 
+    fields=list(.start = "numeric"))
6 6
7 7 
 .TOut$methods(
8 8 
     initialize =function(...)
9 9 
     {
10 10 
        "initialize TOut"
11 
-        callSuper(...)
12 
-        if (verbose) msg(".TOut$initialize()")
13 
-        .self$.start <- 1L
14 
-        .self
11 
+        callSuper(..., .start = 1L)
15 12 
     },
16 13 
     yield = function()
17 
-    {  "Calls yield on the inputPipe"
18 
-       if (verbose) msg(".TOut$yield()")
19 
-       while(length(.self$inputPipe$.records) - .self$.start < yieldSize &&
20 
-              0 != length(input <- .self$inputPipe$.fill()) )
21 
-         .self$inputPipe$.add(input)
22 
-       if( .self$.start + yieldSize  <= length(.self$inputPipe$.records))
23 
-            width <-  .self$.start + yieldSize -1
24 
-       else
25 
-            width <- length(.self$inputPipe$.records) - .self$.start +1
26 
-       if(width>0)
27 
-            idx <- seq(.self$.start, .self$.start + width -1)
28 
-       else  idx <- 0
29 
-       .self$.start <- .self$.start + width
30 
-       dat <- .self$inputPipe$.records[idx]
31 
-       .self$inputPipe$.dump()
32 
-       dat
14 
+    {
15 
+        "Calls yield on the inputPipe"
16 
+        if (verbose) msg(".TOut$yield()")
17 
+        inputPipe$.add(inputPipe$yield())
18 
+        dat <- inputPipe$.records
19 
+        inputPipe$.dump()
20 
+        dat
33 21 
     })
34 22
35 
-TOut <- function( ..., yieldSize=1e6, verbose=FALSE)
36 
-{
37 
-    .TOut$new(..., yieldSize=yieldSize, verbose=verbose)
23 
+TOut <- function(...) .TOut$new(...)
38 24
39 
-}
25 
+## TConnector
40 26
41 27 
 .TConnector <- setRefClass("TConnector",
42 28 
     contains = "Consumer",
... ... 
@@ -49,16 +35,8 @@ TOut <- function( ..., yieldSize=1e6, verbose=FALSE)
49 35 
     initialize = function(...)
50 36 
     {
51 37 
         "initialize TConnector"
52 
-        callSuper(...)
53 
-        if (verbose) msg("TConnector$initialize()")
54 
-        .self$.tOuts <- list()
55 
-        .self
38 
+        callSuper(..., .tOuts = list())
56 39 
     },
57 
-    .fill = function()
58 
-    {   "Fills the stream with yieldSize records"
59 
-        if (verbose) msg("TConnector$.fill")
60 
-        .self$inputPipe$yield()
61 
-    },
62 40 
     .add = function(input)
63 41 
     {
64 42 
         ".add (incomplete) 'input'"
... ... 
@@ -70,25 +48,15 @@ TOut <- function( ..., yieldSize=1e6, verbose=FALSE)
70 48 
     {
71 49 
         "Clear .records that are used"
72 50 
         if (verbose) msg("TConnector$.dump()")
73 
-        mn <- min(sapply(.self$.tOuts, function(x) {
74 
-                    x$.start
75 
-               }))
76 
-        if(mn !=1) {
77 
-            len <- length(.self$.tOuts)
78 
-            for(i in 1:len)
79 
-            {
80 
-              .self$.tOuts[[i]]$.start <-  .self$.tOuts[[i]]$.start - mn +1
81 
-
82 
-            }
83 
-            .self$.records[seq_len(mn-1)] <- NULL
51 
+        mn <- min(sapply(.tOuts, function(x) x$.start))
52 
+        if (mn != 1L) {
53 
+            for(i in seq_along(.tOuts))
54 
+                .self$.tOuts[[i]]$.start <- .tOuts[[i]]$.start - mn +1L
55 
+            .self$.records[seq_len(mn - 1L)] <- NULL
84 56 
         }
85 57 
         .self
86 58 
    })
87 59
88 
-
89 
-
90 
-TConnector <- function(..., yieldSize=1e6, verbose=FALSE) {
91 
-    .TConnector$new(..., yieldSize=yieldSize, verbose=verbose)
92 
-}
60 
+TConnector <- function(...) .TConnector$new(...)
93 61
94 62
R/UserFunction-class.R
History View file @ bd49f34
... ... 
@@ -1,28 +1,23 @@
1 1 
 .UserFunction <-
2 2 
     setRefClass("UserFunction",
3 3 
         contains = "Consumer",
4 
-        fields = list(
5 
-            .fun= "function"))
4 
+        fields = list(FUN = "function"))
6 5
7 6 
 .UserFunction$methods(
8 
-    initialize = function(..., fun)
7 
+    initialize = function(..., FUN)
9 8 
     {
10 9 
         "initialize myCons"
11 
-        callSuper(...)
12 
-        if (.self$verbose)
13 
-            .self$msg("myCons$initialize")
14 
-        .self$.fun <- fun
15 
-        .self
10 
+        callSuper(..., FUN=FUN)
16 11 
     },
17 12 
     yield = function()
18 13 
     {
19 14 
         "yield data from UserFunction"
20 15 
         if (verbose) msg("UserFunction$yield")
21 
-        .self$.fun(callSuper())
16 
+        FUN(callSuper())
22 17 
     })
23 18
24 
-UserFunction <- function(fun, ..., yieldSize = 1e6, verbose = FALSE)
19 
+UserFunction <- function(FUN, ...)
25 20 
 {
26 
-    .UserFunction$new(fun=fun,..., yieldSize=yieldSize, verbose=verbose)
21 
+    .UserFunction$new(FUN=FUN,...)
27 22 
 }
28 23
R/Utility.R
History View file @ bd49f34
... ... 
@@ -15,11 +15,8 @@
15 15 
          sapply(callSuper(), rawToChar)
16 16 
     }))
17 17
18 
-RawToChar <-
19 
-    function(yieldSize=1e6, verbose=FALSE)
20 
-{
21 
-    .RawToChar$new(yieldSize=yieldSize, verbose=verbose)
22 
-}
18 
+RawToChar <- function(...)
19 
+    .RawToChar$new(...)
23 20
24 21 
 ## Rev
25 22
... ... 
@@ -32,62 +29,64 @@ RawToChar <-
32 29 
         sapply(callSuper(), rev)
33 30 
     }))
34 31
35 
-Rev <-
36 
-    function(yieldSize=1e6,verbose=FALSE)
37 
-{
38 
-    .Rev$new(yieldSize=yieldSize, verbose=verbose)
39 
-}
32 
+Rev <- function(...)
33 
+    .Rev$new(...)
40 34
35 
+## connect
41 36
42 
-connect <- function(blocks, df)
37 
+connect <-
38 
+    function(blocks, df)
43 39 
 {
44 
-    use <- sapply(blocks, function(x) {
45 
-        all(x$inUse)
46 
-    })
40 
+    inUse <- sapply(blocks, function(x) all(x$inUse))
47 41 
     cls <- sapply(blocks, class)
48 
-    if(any(use)) {
49 
-        msg <- sprintf("%s : already in use in another stream",
50 
-                       paste(cls[which(use)], sep = " ", collapse = ", "))
42 
+    if (any(inUse)) {
43 
+        msg <- sprintf("%s: already in use in another stream",
44 
+                       paste(cls[which(inUse)], collapse = ", "))
51 45 
         stop(msg)
52 46 
     }
47 
+
53 48 
     len <- length(blocks)
54 49 
     n <- nrow(df)
55 
-    df <- cbind(df, "weight" =rep(1L, n))
56 
-    g <- graphBAM(df,edgemode="directed")
57 
-    outDeg <- degree(g)$outDegree
58 
-    nms <- names(outDeg[outDeg==0])
59 
-    for(i in 1:n)
50 
+    df$weight <- 1L
51 
+
52 
+    for (i in seq_len(n))
60 53 
     {
61 
-        left <- blocks[[as.character(df$from[i])]]
62 
-        right <- blocks[[as.character(df$to[i])]]
63 
-        if(is(right, "YConnector")) {
64 
-            right$.upstream[[as.character(df$from[i])]] <- left
65 
-        }
66 
-        if(is(left, "TConnector"))
54 
+        fromi <- as.character(df$from[i])
55 
+        toi <- as.character(df$to[i])
56 
+        left <- blocks[[fromi]]
57 
+        right <- blocks[[toi]]
58 
+        if (is(right, "YConnector"))
59 
+            right$.upstream[[fromi]] <- left
60 
+
61 
+        if (is(left, "TConnector"))
67 62 
         {
68 63 
             orig <- left$.tOuts
69 
-            temp <- TOut(yieldSize = left$yieldSize)
64 
+            temp <- TOut()
70 65 
             temp$inputPipe <- left
71 66 
             right$inputPipe <- temp
72 67 
             left$.tOuts <- c(left$.tOuts, temp)
73 68 
         } else {
74 69 
             right$inputPipe <- left
75 
-
76 70 
         }
77 
-        if ( is(right, "ParallelConnector")) {
71 
+
72 
+        if (is(right, "ParallelConnector")) {
78 73 
             right$.upstream <- mcparallel(quote({
79 74 
                 while(TRUE) {
80 75 
                     prime <- yield(left)
81 
-                    sendMaster(prime)
82 
-        }}))
76 
+                    parallel:::sendMaster(prime)
77 
+                }}))
83 78
84 79 
         }
85 80 
     }
81 
+
82 
+    nms <- local({
83 
+        g <- graphBAM(df, edgemode="directed")
84 
+        outDeg <- degree(g)$outDegree
85 
+        names(outDeg[outDeg==0])
86 
+    })
86 87 
     s <- lapply(blocks[nms], stream)
87 
-    for(i in 1:len)
88 
-    {
88 
+    for (i in seq_len(len))
89 89 
         blocks[[i]]$inUse <- TRUE
90 
-    }
91 90 
     s
92 91 
 }
93 92
R/ValueInput.R
History View file @ bd49f34
... ... 
@@ -41,21 +41,15 @@ scanParserFactory <- concatenationParserFactory
41 41 
 .ReadLinesInput <- setRefClass("ReadLinesInput",
42 42 
     contains = "ConnectionProducer",
43 43 
     fields = list(
44 
+      yieldSize = "integer",
44 45 
       .records = "character"))
45 46
46 47 
 .ReadLinesInput$methods(
47 
-    initialize = function(...)
48 
-    {
49 
-        "initialize 'ReadLinesInput'"
50 
-        callSuper(...)
51 
-        if (verbose) msg("ReadLinesInput$initialize()")
52 
-        .self
53 
-    },
54 48 
     reset = function()
55 49 
     {
56 50 
         "reset ReadLinesInput"
57 
-        callSuper()
58 51 
         if (verbose) msg("ReadLinesInput$reset()")
52 
+        callSuper()
59 53 
         .self$.records <- character()
60 54 
         .self$.parsedRecords <- 0L
61 55 
         .self
... ... 
@@ -93,15 +87,15 @@ scanParserFactory <- concatenationParserFactory
93 87
94 88 
 ReadLinesInput <-
95 89 
     function(con, reader=readLinesReaderFactory(),
96 
-             parser=readLinesParserFactory(), ...,
97 
-             yieldSize=1e6, verbose=FALSE)
98 
-    {
99 
-        if (!is(con, "connection"))
100 
-            con <- file(con, "r")
101 
-        .ReadLinesInput$new(con=con,
102 
-                      reader=reader, parser=parser, ...,
103 
-                      yieldSize=yieldSize, verbose=verbose)
104 
-    }
90 
+             parser=readLinesParserFactory(),
91 
+             yieldSize=1e6, ...)
92 
+{
93 
+    if (!is(con, "connection"))
94 
+        con <- file(con, "r")
95 
+    yieldSize <- as.integer(yieldSize)
96 
+    .ReadLinesInput$new(con=con, reader=reader, parser=parser,
97 
+                        yieldSize=yieldSize, ...)
98 
+}
105 99
106 100
107 101
R/YConnector.R
History View file @ bd49f34
... ... 
@@ -5,14 +5,11 @@
5 5
6 6 
 .YConnector$methods(
7 7 
     initialize = function(..., fun)
8 
-    {   "initialize YConnector"
9 
-        callSuper(...)
10 
-        if(verbose) msg(".YConnector$initialize")
11 
-        .self$.upstream <- list()
8 
+    {
9 
+        "initialize YConnector"
12 10 
         if(missing(fun))
13 
-            .self$.fun <- function(){}
14 
-        else .self$.fun <- fun
15 
-        .self
11 
+            fun <- function(...) as.list(...)
12 
+        callSuper(..., .upstream=list(), .fun=fun)
16 13 
     },
17 14 
     yield = function()
18 15 
     {
... ... 
@@ -25,13 +22,11 @@
25 22 
     show = function()
26 23 
     {
27 24 
         callSuper()
28 
-        upstream <- paste(lapply(.upstream, "class"), collapse = " ,")
25 
+        upstream <- paste(sapply(.upstream, "class"), collapse = " ,")
29 26 
         upstream[!nzchar(upstream)] <- "uninitialized field"
30 27 
         txt <- sprintf("upstream: %s", upstream)
31 28 
         cat(strwrap(txt, exdent=2), sep="\n")
32 29 
     })
33 30
34 
-YConnector <- function(fun, ...,  yieldSize =1e6, verbose = FALSE)
35 
-{
36 
-    .YConnector$new(fun=fun, ..., yieldSize=yieldSize, verbose=verbose)
37 
-}
31 
+YConnector <- function(fun, ...)
32 
+    .YConnector$new(fun=fun, ...)
R/generics.R
History View file @ bd49f34
... ... 
@@ -7,9 +7,3 @@ setGeneric("reset", function(x, ...) standardGeneric("reset"))
7 7 
 setGeneric("yield", function(x, ...) standardGeneric("yield"))
8 8
9 9 
 setGeneric("status", function(x, ...) standardGeneric("status"))
10 
-
11 
-## Generic Functions for NetCDFFile class
12 
-
13 
-setGeneric("precision", function(x, ...) standardGeneric("precision"))
14 
-
15 
-setGeneric("dimensions", function(x, ...) standardGeneric("dimensions"))
inst/doc/Streamer.Rnw
History View file @ bd49f34
16 10 
Binary files a/inst/doc/Streamer.Rnw and b/inst/doc/Streamer.Rnw differ
inst/unitTests/test_BinaryInput.R
History View file @ bd49f34
17 11 
similarity index 84%
18 12 
rename from inst/unitTests/test_BinaryInput.R
19 13 
rename to inst/unitTests/test_RawInput.R
... ... 
@@ -1,11 +1,7 @@
1 
-test_recordReader <- function()
2 
-{
3 
-}
4 
-
5 
-test_binary_parse_count_records <- function()
1 
+test_raw_parse_count_records <- function()
6 2 
 {
7 3 
     f <- function(...)
8 
-        .Call(Streamer:::.binary_parse_count_records, ...)
4 
+        .Call(Streamer:::.raw_parse_count_records, ...)
9 5
10 6 
     sep <- charToRaw("\n")
11 7
... ... 
@@ -32,9 +28,9 @@ test_binary_parse_count_records <- function()
32 28 
     checkIdentical(1L, f(charToRaw("foo\nfoo\n"), sep))
33 29 
 }
34 30
35 
-test_binary_parse <- function()
31 
+test_raw_parse <- function()
36 32 
 {
37 
-    f <- function(...) .Call(Streamer:::.binary_parse, ...)
33 
+    f <- function(...) .Call(Streamer:::.raw_parse, ...)
38 34
39 35 
     sep <- charToRaw("\n")
40 36 
     trim <- sep
... ... 
@@ -75,25 +71,25 @@ test_binary_parse <- function()
75 71 
                    f(charToRaw("@foo\n@bar\n@"), sep, trim))
76 72 
 }
77 73
78 
-test_binaryParserFactory <- function()
74 
+test_rawParserFactory <- function()
79 75 
 {
80 
-    checkException(binaryParserFactory("\n"),
76 
+    checkException(rawParserFactory("\n"),
81 77 
                    "'separator' must be 'raw()'", TRUE)
82 
-    checkException(binaryParserFactory(trim="\n"),
78 
+    checkException(rawParserFactory(trim="\n"),
83 79 
                    "'trim' must be 'raw()'", TRUE)
84 
-    checkException(binaryParserFactory(charToRaw("\n@"),
80 
+    checkException(rawParserFactory(charToRaw("\n@"),
85 81 
                                        charToRaw("@")),
86 82 
                    "'trim' must equal separator[seq_along(trim)]",
87 83 
                    TRUE)
88 
-    checkException(binaryParserFactory(charToRaw("\n@"),
84 
+    checkException(rawParserFactory(charToRaw("\n@"),
89 85 
                                        charToRaw("\n@x")),
90 86 
                    "'length(separator)' must be >= length(trim)",
91 87 
                    TRUE)
92 88 
 }
93 89
94 
-test_binaryParser <- function()
90 
+test_rawParser <- function()
95 91 
 {
96 
-    p <- binaryParserFactory()
92 
+    p <- rawParserFactory()
97 93 
     checkIdentical(list(), p(raw(), raw()))
98 94
99 95 
     foo <- charToRaw("foo")
... ... 
@@ -108,12 +104,12 @@ test_binaryParser <- function()
108 104 
     checkIdentical(list(foo, foo), p(foo_n, foo))
109 105 
 }
110 106
111 
-test_BinaryInput <- function()
107 
+test_RawInput <- function()
112 108 
 {
113 109 
     fl <- system.file("extdata", "s_1_sequence.txt", package="Streamer")
114 110
115 111 
     ## default yield
116 
-    s <- BinaryInput(fl)
112 
+    s <- RawInput(fl)
117 113 
     y <- yield(s)
118 114 
     checkIdentical(1024L,length(y))
119 115 
     checkIdentical(list(), yield(s))    # no more records
... ... 
@@ -126,8 +122,8 @@ test_BinaryInput <- function()
126 122 
     checkIdentical(list(), yield(s))
127 123
128 124 
     ## yield w/ sep & trim arguments -- fastq records
129 
-    parser <- binaryParserFactory(charToRaw("\n@"), charToRaw("\n"))
130 
-    s <- BinaryInput(fl, parser=parser)
125 
+    parser <- rawParserFactory(charToRaw("\n@"), charToRaw("\n"))
126 
+    s <- RawInput(fl, parser=parser)
131 127 
     y2 <- yield(s)
132 128 
     checkIdentical(256L, length(y2))
133 129 
     checkIdentical(sapply(y1, rawToChar),
inst/unitTests/test_RevStream.R
History View file @ bd49f34
... ... 
@@ -1,9 +1,9 @@
1 
-test_RevStream <-
1 
+test_Rev <-
2 2 
     function()
3 3 
 {
4 
-    checkTrue(validObject(RevStream()))
4 
+    checkTrue(validObject(Rev()))
5 5
6 6 
     fl <- system.file("extdata", "s_1_sequence.txt", package="Streamer")
7 
-    s <- stream(RevStream(), BinaryInput(fl))
7 
+    s <- stream(Rev(), RawInput(fl))
8 8 
     res <- yield(s)
9 9 
 }
inst/unitTests/test_ncdf.R
History View file @ bd49f34
10 10 
deleted file mode 100644
... ... 
@@ -1,76 +0,0 @@
1 
-test_2D_Data_read <- function() {
2 
-    file <- system.file("extdata", "NetCDFData.nc", package = "Streamer")
3 
-    ncFile <- NetCDFFile(file)
4 
-
5 
-    vars <- names(dimensions(ncFile))
6 
-    checkIdentical(vars, c( "2dIntData", "2dFloatData"))
7 
-
8 
-    current <- dimensions(ncFile)
9 
-    target <- list(`2dIntData` = c(sampleDim=5L, snpDim=10L),
10 
-                   `2dFloatData` = c(sampleDim=5L, snpDim=10L ))
11 
-    checkIdentical(current, target)
12 
-
13 
-    ncprod <- NetCDFInput(ncFile, "2dIntData")
14 
-    current <- names(dimensions(ncprod))
15 
-    checkIdentical(current, "2dIntData")
16 
-
17 
-    slice <- c(sampleDim = 5, snpDim = 5)
18 
-    ncprod <- NetCDFInput(ncFile, "2dIntData", slice)
19 
-    current <- ncprod$slice
20 
-    nms <-  c("sampleDim", "snpDim")
21 
-    target <-  structure( c(5L, 5L), names = nms)
22 
-    checkIdentical(current, target)
23 
-
24 
-    dat <- yield(ncprod)
25 
-    current <- status(ncprod)
26 
-    target <- structure(c(1L, 6L), names = c("sampleDim", "snpDim"))
27 
-    checkEquals(target, current)
28 
-
29 
-    reset(ncprod)
30 
-    current <- status(ncprod)
31 
-    target <- structure(c(1L, 1L), names = c("sampleDim", "snpDim"))
32 
-    checkEquals(target, current)
33 
-
34 
-    current <- yield(ncprod)
35 
-    target <- matrix(1:25, ncol = 5)
36 
-    checkEquals(target ,current)
37 
-
38 
-    current <- yield(ncprod)
39 
-    target <- matrix(26:50, ncol = 5)
40 
-    checkEquals(target ,current)
41 
-
42 
-    current <- yield(ncprod)
43 
-    target <- matrix(numeric(0), 0, 0)
44 
-    checkEquals(target ,current)
45 
-
46 
-    slice <- c(sampleDim = 4, snpDim = 4)
47 
-    ncprod <- NetCDFInput(ncFile, "2dIntData", slice)
48 
-
49 
-    current <- yield(ncprod)
50 
-    target <- matrix(c(1:4, 6:9, 11:14, 16:19), ncol = 4)
51 
-    checkEquals(target ,current)
52 
-
53 
-    current <- yield(ncprod)
54 
-    target <-  c(5,10, 15, 20)
55 
-    checkEquals(target , as.numeric(current))
56 
-
57 
-    current <- yield(ncprod)
58 
-    target <- c(21:24, 26:29, 31:34, 36:39)
59 
-    checkEquals(target , as.numeric(current))
60 
-    current <- yield(ncprod)
61 
-    target <-  c(25, 30, 35, 40)
62 
-    checkEquals(target , as.numeric(current))
63 
-
64 
-    current <- yield(ncprod)
65 
-    target <- matrix(c(41: 44, 46:49), ncol =2)
66 
-    checkEquals(target ,current)
67 
-
68 
-    current <- yield(ncprod)
69 
-    target <- c(45, 50)
70 
-    checkEquals(target , as.numeric(current))
71 
-
72 
-    current <- yield(ncprod)
73 
-    target <- matrix(numeric(0), 0, 0)
74 
-    checkEquals(target ,current)
75 
-}
76 
-
man/BufferInt-class.Rd
History View file @ bd49f34
77 0 
deleted file mode 100644
... ... 
@@ -1,68 +0,0 @@
1 
-\name{BufferInt-class}
2 
-\Rdversion{1.1}
3 
-\docType{class}
4 
-\alias{BufferInt-class}
5 
-\alias{BufferInt}
6 
-\alias{BufferInterface}
7 
-\alias{BufferInterface,ANY-method}
8 
-\alias{BufferInterface,data.frame-method}
9 
-\alias{show,BufferInt-method}
10 
-
11 
-\title{Class "BufferInt"}
12 
-
13 
-\description{
14 
-
15 
- An internal reference class container used by the \code{Consumer}-class to
16 
- store functions that operate on the records stored in the \code{.records} field
17 
- of the \code{Consumer}-class.  Operations performed on
18 
- the \code{.records} field by the \code{Consumer}-class include \code{length},
19 
- \code{append}, \code{subset}.
20 
-
21 
- Users have the options of modifying the behaviour of the above mentioned
22 
- operations for records of different data types by declaring an S4
23 
- method \code{BufferInterface} that returns an object of \code{BufferInt}-class.
24 
-}
25 
-
26 
-\section{Constructors}{
27 
-  Instances from this class are constructed with calls to \code{BufferInt}
28 
-  constructor.
29 
-}
30 
-
31 
-
32 
-\section{Fields}{
33 
-  \describe{
34 
-    \item{\code{length}:}{Object of class \code{function} that returns the length
35 
-        of the records.}
36 
-    \item{\code{append}:}{Object of class \code{function} that appends records
37 
-        together. This function is called when a new records is read and is to
38 
-        be added to the existing buffer. }
39 
-    \item{\code{subset}:}{Object of class \code{function} that subsets records.
40 
-    This function is called when records have been yielded and are to be removed
41 
-    from the buffer}
42 
-  }
43 
-}
44 
-
45 
-\section{Methods}{
46 
-  Users have the option of controlling the beaviour of the functions
47 
-  \code{length}, \code{append} and \code{subset} used to manipulate the
48 
-  \code{.records} field of the \code{Consumer}-class by declaring a function
49 
-  \code{BufferInterface}.
50 
-  \describe{BufferInterface}{Returns an object of class \code{BufferInt} that
51 
-      holds functions for manipulating the record of the \code{Consumer} class.
52 
-  }
53 
-}
54 
-
55 
-\author{Nishant Gopalakrishnan \url{ngopalak@fhcrc.org}}
56 
-
57 
-\seealso{
58 
-
59 
-  \code{\link{Streamer-package}}, \code{\linkS4class{Consumer}-class}.
60 
-
61 
-}
62 
-
63 
-\examples{
64 
-showClass("BufferInt")
65 
-selectMethod("BufferInterface", "data.frame")
66 
-}
67 
-
68 
-\keyword{classes}
man/ConnectionProducer-class.Rd
History View file @ bd49f34
... ... 
@@ -7,20 +7,24 @@
7 7
8 8 
 \description{
9 9
10 
-  A virtual class containing components that are required to create a custom
11 
-  \code{Producer}-class to read data from file connections. Users can inherit from
12 
-  the \code{ConnectionProducer}-class to create their own \code{Producer}
13 
-  classes that interact with files. Users are expected to pass in appropriate
14 
-  \code{reader} and \code{parser} functions for files when creating instances of
15 
-  classes that inherit from \code{ConnectionProducer}-class.
10 
+  A virtual class containing components that are required to create a
11 
+  custom \code{Producer}-class to read data from file connections. Users
12 
+  can inherit from the \code{ConnectionProducer}-class to create their
13 
+  own \code{Producer} classes that interact with files. Users are
14 
+  expected to pass in appropriate \code{reader} and \code{parser}
15 
+  functions for files when creating instances of classes that inherit
16 
+  from \code{ConnectionProducer}-class.
16 17
17 18 
 }
18 19
19 20 
 \section{Fields}{
20 21 
   \describe{
21 
-    The \code{ConnectionProducer} class inherits the fields \code{verbose}, \code{inUse}
22 
-    and \code{yieldSize} fields from the \code{Streamer} class. Please refer to
23 
-    the \code{\link{Streamer}} class for more details.
22 
+
23 
+    The \code{ConnectionProducer} class inherits the fields
24 
+    \code{verbose} and \code{inUse} fields from the \code{Streamer}
25 
+    class. Please refer to the \code{\link{Streamer}} class for more
26 
+    details.
27 
+
24 28 
     \item{\code{con}:}{An object of class \code{connection}.}
25 29 
     \item{\code{reader}:}{A function that reads data from a file
26 30 
         connection}
... ... 
@@ -30,14 +34,16 @@
30 34
31 35 
 \section{Class-Based Methods}{
32 36 
   \describe{
33 
-    The \code{ConnectionProducer} class inherits the methods \code{initialize}, \code{msg},
34 
-    \code{reset}, \code{status} and \code{yield} from the \code{Streamer}
35 
-    virtual class. Please refer to the \code{\link{Streamer}} class for more
36 
-    details.
37 
+
38 
+    The \code{ConnectionProducer} class inherits the methods
39 
+    \code{initialize}, \code{msg}, \code{reset}, \code{status} and
40 
+    \code{yield} from the \code{Streamer} virtual class. Please refer to
41 
+    the \code{\link{Streamer}} class for more details.
37 42
38 
-    Derived classes should implement an appropriate  \code{yield} method to
39 
-    return the contents of the current stream. The default method for the base
40 
-    virtual \code{Streamer} class returns a \code{list()}
43 
+    Derived classes should implement an appropriate \code{yield} method
44 
+    to return the contents of the current stream. The default method for
45 
+    the base virtual \code{Streamer} class returns a \code{list()}
46 
+
41 47 
   }
42 48 
 }
43 49
man/Consumer-class.Rd
History View file @ bd49f34
... ... 
@@ -29,15 +29,15 @@
29 29
30 30 
 \section{Fields}{
31 31 
   \describe{
32 
+
32 33 
     \item{\code{inputPipe}:}{Object of class \code{Streamer},
33 
-      representing the \code{Producer} or \code{Consumer} connected up-stream to
34 
-      it and from which records are yielded.}
35 
-    \item{\code{.records}:}{Object of class\code{list} which is used as a
36 
-        temporary buffer for storing records.}
34 
+      representing the \code{Producer} or \code{Consumer} connected
35 
+      up-stream to it and from which records are yielded.}
37 36
38 
-    The \code{Consumer} class inherits the fields \code{yieldSize},
39 
-    \code{verbose} and \code{inUse} from the virtual \code{Streamer} class.
40 
-    Please refer to the \code{\link{Streamer}} class for more details.
37 
+    The \code{Consumer} class inherits the fields \code{verbose} and
38 
+    \code{inUse} from the virtual \code{Streamer} class.  Please refer
39 
+    to the \code{\link{Streamer}} class for more details.
40 
+
41 41 
   }
42 42 
 }
43 43
... ... 
@@ -46,38 +46,37 @@
46 46 
     \item{\code{initialize(..., inputPipe)}:}{A method to
47 47 
       initialize the fields of the \code{Consumer} class.
48 48 
       \describe{
49 
-	\item{\code{inputPipe}:}{An object of class \code{Streamer} connected
50 
-        up-stream to it. The class could be a  \code{Consumer} or \code{Producer}
51 
-	  which yields data to the \code{Consumer} class.}
52 
-	\item{\code{...}:}{Additonal arguments, currently unused.}
53 
-	\item{\code{verbose}:}{A \code{logical(1)} instance indicating
54 
-	  whether methods invoked on the class should be reported to the
55 
-	  user.}
49 
+	\item{\code{inputPipe}:}{An object of class \code{Streamer}
50 
+          connected up-stream to it. The class could be a
51 
+          \code{Consumer} or \code{Producer} which yields data to the
52 
+          \code{Consumer} class.}
56 53 
       }
57 54 
     }
55 
+
58 56 
     \item{\code{reset()}:}{Return the result of delegating
59 57 
       \code{reset()} to the object in the field \code{inputPipe}.}
58 
+
60 59 
     \item{\code{yield()}:}{Return the result of delegating
61 60 
       \code{yield()} to the object in the field \code{inputPipe}.}
61 
+
62 62 
     \item{\code{inputs()}:}{Return a \code{character} vector
63 63 
       representing up-stream components.}
64 
-    \item{\code{status{}}:}{Reports the status of the \code{Consumer} class. A
65 
-        \code{list} of the status of the length of the object in the \code{.records}
66 
-        field, the classes connected to the \code{inputPipe} field and the status of the fields
67 
-        of the virtual class \code{Streamer} are returned.}
68 
-    \item{\code{.fill()}:}{An internal method that fills the \code{.records}
69 
-        field with \code{yieldSize} records if available.}
70 
-    \item{\code{.add(input)}:}{An internal method that appends the value passed to the argument
71 
-    \code{input} to the \code{.records} field.}
72 
-    }
64 
+
65 
+    \item{\code{status{}}:}{Reports the status of the \code{Consumer}
66 
+      class. A \code{list} of the status of the length of the object in
67 
+      the \code{.records} field, the classes connected to the
68 
+      \code{inputPipe} field and the status of the fields of the virtual
69 
+      class \code{Streamer} are returned.}
70 
+
71 
+  }
73 72 
 }
74 73
75 74 
 \author{Martin Morgan \url{mtmorgan@fhcrc.org}}
76 75
77 
-
78 76 
 \seealso{
79 77
80 
-  \code{\link{Streamer-package}}, \code{\linkS4class{Streamer}-class}, \code{\linkS4class{Producer}-class},
78 
+  \code{\link{Streamer-package}}, \code{\linkS4class{Streamer}-class},
79 
+  \code{\linkS4class{Producer}-class},
81 80 
   \code{\linkS4class{Stream}-class}.
82 81
83 82 
 }
man/Downsample-class.Rd
History View file @ bd49f34
... ... 
@@ -18,7 +18,7 @@
18 18 
 }
19 19
20 20 
 \usage{
21 
-Downsample(probability=0.1, ..., yieldSize=1e6, verbose=FALSE)
21 
+Downsample(probability=0.1, sampledSize=1e6, ...)
22 22 
 }
23 23
24 24 
 \arguments{
... ... 
@@ -26,48 +26,25 @@ Downsample(probability=0.1, ..., yieldSize=1e6, verbose=FALSE)
26 26 
     probability with which a record should be retained.}
27 27 
   \item{...}{Additional arguments, passed to the \code{$new} method of
28 28 
     the underlying reference class. Currently unused.}
29 
-  \item{yieldSize}{A \code{integer(1)} indicating the number of
30 
-    records to yield.}
31 
-  \item{verbose}{\code{logical(1)} indicating whether class methods
32 
-    should report to the user.}
29 
+  \item{sampledSize}{A \code{integer(1)} indicating the number of
30 
+    records to return.}
33 31 
 }
34 32
35 33 
 \section{Fields}{
36 34 
   \describe{
37 
-    \item{\code{inputPipe}:}{Object of class \code{ANY}. The component
38 
-      from which input is retrieved.}
39 35 
     \item{\code{probability}:}{Object of class \code{numeric}. The
40 36 
       probability of including a record in the \code{yield}.}
41 
-    \item{\code{yieldSize}:}{Object of class \code{integer}
37 
+    \item{\code{sampledSize}:}{Object of class \code{integer}
42 38 
       storing the number of records to produced each time \code{yield}
43 39 
       is invoked.}
44 40 
     \item{\code{.buffer}:}{Object of class \code{ANY}, used internally
45 41 
       to store read but not yet parsed records.}
46 
-    \item{\code{verbose}:}{Object of class \code{logical}. Display
47 
-      method invokation messages to the user.}
48 42 
   }
49 43 
 }
50 44
51 45 
 \section{Class-Based Methods}{
52 46 
   \describe{
53 
-    \item{\code{initialize(..., probability, yieldSize,
54 
-	verbose)}:}{Initialize the instance.
55 
-      \describe{
56 
-	\item{\code{probability}:}{The probability with which a record
57 
-	  is included in the sample.}
58 
-	\item{\code{yieldSize}:}{The number of records to return when
59 
-	  \code{yield} is invoked.}
60 
-	\item{\code{...}:}{Additional arguments, currently ignored.}
61 
-	\item{\code{verbose}:}{Display method invokation messages to the
62 
-	  user.}
63 
-      }}
64 
-    \item{\code{reset()}:}{Reset sample buffer and delegate \code{reset}
65 
-      to \code{inputPipe}.}
66 
-    \item{\code{yield()}:}{Continually invoke \code{yield} on
67 
-      \code{inputPipe}, accumulating a random sample of
68 
-      \code{yieldSize} records until the \code{yield} of
69 
-      \code{inputPipe} has length 0. The result is a \code{list} of
70 
-      length \code{yieldSize}.}
47 
+    \item{\code{.sample(x)}:}{Sample from amongst the incoming records.}
71 48 
   }
72 49 
 }
73 50
man/ParallelConnector-class.Rd
History View file @ bd49f34
... ... 
@@ -7,21 +7,20 @@
7 7
8 8 
 \description{
9 9
10 
-  The \code{ParallelConnector} \code{\linkS4class{Consumer}}-class can be used
11 
-  to parallelize the computations done by blocks directly connected to the
12 
-  \code{ParallelConnector} and all blocks down-stream to the
13 
-  \code{ParallelConnector}. i.e Computations performed by the block directly
14 
-  connected  up-stream to the \code{ParallelConnector} and all blocks connected
15 
-  down-stream to the \code{ParallelConnector} in a stream happen simultaneously.
10 
+  The \code{ParallelConnector} \code{\linkS4class{Consumer}}-class can
11 
+  be used to parallelize the computations done by blocks directly
12 
+  connected to the \code{ParallelConnector} and all blocks down-stream
13 
+  to the \code{ParallelConnector}. i.e Computations performed by the
14 
+  block directly connected up-stream to the \code{ParallelConnector} and
15 
+  all blocks connected down-stream to the \code{ParallelConnector} in a
16 
+  stream happen simultaneously.
17 
+
16 18 
 }
17 19
18 
-\usage{ParallelConnector(..., yieldSize=1e6, verbose=FALSE)}
20 
+\usage{ParallelConnector(...)}
19 21
20 22 
 \arguments{
21 23 
   \item{...}{Additional arguments to be passed to the constructor.}
22 
-  \item{yieldSize}{The number of records the input parser is to yield.}
23 
-  \item{verbose}{\code{logical(1)} indicating whether class methods
24 
-    should report to the user.}
25 24 
 }
26 25
27 26 
 \section{Constructors}{
... ... 
@@ -57,4 +56,3 @@
57 56 
 \examples{showClass("ParallelConnector")}
58 57
59 58 
 \keyword{classes}
60 
-
man/Producer-class.Rd
History View file @ bd49f34
... ... 
@@ -30,9 +30,11 @@
30 30
31 31 
 \section{Fields}{
32 32 
   \describe{
33 
-    The \code{Producer} class inherits the fields \code{verbose}, \code{inUse}
34 
-    and \code{yieldSize} fields from the \code{Streamer} class. Please refer to
33 
+
34 
+    The \code{Producer} class inherits the fields \code{verbose} and
35 
+    \code{inUse} fields from the \code{Streamer} class. Please refer to
35 36 
     the \code{\link{Streamer}} class for more details.
37 
+
36 38 
   }
37 39 
 }
38 40
man/RawInput-class.Rd
History View file @ bd49f34
... ... 
@@ -34,7 +34,7 @@
34 34
35 35 
 \usage{
36 36 
 RawInput(con, yieldSize = 1e+06, reader = rawReaderFactory(),
37 
-    parser = rawParserFactory(), ..., verbose = FALSE)
37 
+    parser = rawParserFactory(), ...)
38 38 
 rawReaderFactory(blockSize = 1e+06, what)
39 39 
 rawParserFactory(separator = charToRaw("\n"), trim = separator)
40 40 
 }
... ... 
@@ -51,12 +51,12 @@ rawParserFactory(separator = charToRaw("\n"), trim = separator)
51 51 
     parsing the \code{raw} vector \code{c(buf, bin)} into records.}
52 52 
   \item{...}{Additional arguments, passed to the \code{$new} method of
53 53 
     this class. Currently ignored.}
54 
-  \item{verbose}{\code{logical(1)} indicating whether class methods
55 
-    should report to the user.}
54 
+
56 55 
   % rawReaderFactory
57 56 
   \item{blockSize}{The number of bytes to read at one time.}
58 57 
   \item{what}{The type of data to read, as the argument to
59 58 
     \code{\link{readBin}}.}
59 
+
60 60 
   % rawParserFactory
61 61 
   \item{separator}{A \code{raw} vector indicating the unique sequence of
62 62 
     bytes by which record starts are to be recognized. The parser
... ... 
@@ -68,41 +68,40 @@ rawParserFactory(separator = charToRaw("\n"), trim = separator)
68 68
69 69 
 \section{Fields}{
70 70 
   \describe{
71 
+
71 72 
     \item{\code{con}:}{Object of class \code{connection}. An R
72 73 
       \code{\link{connection}} opened in \dQuote{rb} mode from which
73 74 
       data will be read.}
75 
+
74 76 
     \item{\code{blockSize}:}{Object of class \code{integer}. Size
75 77 
       (e.g., number of raw bytes) input during each
76 78 
       \code{\link{yield}}.}
79 
+
77 80 
     \item{\code{reader}:}{Object of class \code{function}. A function
78 81 
       used to input \code{blockSize} elements. See
79 82 
       \code{\link{rawReaderFactory}}.}
83 
+
80 84 
     \item{\code{parser}:}{Object of class \code{function}. A function
81 85 
       used to parse raw input into records, e.g., breaking a
82 86 
       \code{raw} vector on new lines \sQuote{\\n}. See
83 87 
       \code{\link{rawParserFactory}}}
88 
+
84 89 
     \item{\code{.buffer}:}{Object of class \code{raw}. Contains read but
85 90 
       not parsed raw stream data.}
91 
+
86 92 
     \item{\code{.records}:}{Object of class \code{list}. Parsed but not
87 93 
       yet yield-ed records.}
94 
+
88 95 
     \item{\code{.parsedRecords}:}{Object of class \code{integer}. Total
89 96 
       number of records parsed by the Producer.}
90 
-    \item{\code{verbose}:}{Object of class \code{logical}. Should
91 
-      progress be reported?}
97 
+
92 98 
   }
93 99 
 }
94 100
95 101 
 \section{Class-Based Methods}{
96 102 
   \describe{
97 
-    \item{\code{initialize(con, blockSize, reader, parser,
98 
-	verbose)}:}{Called during object creation with values to
99 
-      initialize fields.}
100 103 
     \item{\code{reset()}:}{Remove buffer and current records, reset
101 104 
       record counter, re-open \code{con}.}
102 
-    \item{\code{status()}:}{Summarize status of stream.}
103 
-    \item{\code{yield()}:}{Process stream to yield as many complete
104 
-      records as are represented in the current \code{blockSize}
105 
-      elements.}
106 105 
   }
107 106 
 }
108 107
man/RawToChar-class.Rd
History View file @ bd49f34
... ... 
@@ -13,37 +13,20 @@
13 13
14 14 
 }
15 15
16 
-\usage{RawToChar(yieldSize = 1e6,verbose = FALSE)}
16 
+\usage{RawToChar(...)}
17 17
18 18 
 \arguments{
19 
-  \item{yieldSize}{A \code{integer(1)} indicating the number of
20 
-      records to yield.}
21 
-  \item{verbose}{\code{logical(1)} indicating whether class methods
22 
-    should report to the user.}
19 
+  \item{...}{Arguments passed to the \code{\linkS4class{Consumer}}-class
20 
+    constructors.}
23 21 
 }
24 22
25 23 
 \section{Constructors}{
26 24 
   Use \code{RawToChar} to construct instances of this class.
27 25 
 }
28 26
29 
-\section{Fields}{
30 
-  \describe{
31 
-    \item{\code{inputPipe}:}{Object of class \code{ANY}. The component
32 
-      from which input is retrieved.}
33 
-    \item{\code{yieldSize}:}{A \code{integer(1)} indicating the number of
34 
-      records to yield.}
35 
-     \item{\code{verbose}:}{Object of class \code{logical}. Display
36 
-      method invokation messages to the user.}
37 
-  }
38 
-}
27 
+\section{Fields}{There are no fields unique to this class.}
39 28
40 
-\section{Methods}{
41 
-  \describe{
42 
-    \item{\code{yield()}:}{Convert the result of applying \code{yield}
43 
-      to \code{inputPipe} (which must be a list of \code{raw}) into a
44 
-      vector of \code{character}.}
45 
-  }
46 
-}
29 
+\section{Methods}{There are no methods unique to this class.}
47 30
48 31 
 \author{Martin Morgan \url{mtmorgan@fhcrc.org}}
49 32
man/ReadLinesInput-class.Rd
History View file @ bd49f34
... ... 
@@ -15,24 +15,24 @@
15 15
16 16 
 \description{
17 17
18 
-  A \code{\linkS4class{Producer}}-class to interpret text files. Users interact
19 
-  with this class through the constructor \code{ReadLinesInput} and methods
20 
-  \code{\link{yield}}, \code{\link{reset}}, and \code{\link{stream}}.
18 
+  A \code{\linkS4class{Producer}}-class to interpret text files. Users
19 
+  interact with this class through the constructor \code{ReadLinesInput}
20 
+  and methods \code{\link{yield}}, \code{\link{reset}}, and
21 
+  \code{\link{stream}}.
21 22
22 23 
   This class requires two helper functions; the \sQuote{factory} methods
23 24 
   defined on this page can be used to supply these.
24 25 
   \code{readLinesReaderFactory} creates a \sQuote{reader}, whose
25 
-  responsibility it is to accept a connection and return a  \code{character}
26 
-  vector.  \code{readLinesParserFactory} creates  a \sQuote{parser},
27 
-  responsible for parsing a buffer and vector of the
28 
-  same type as produced by the reader into records.
26 
+  responsibility it is to accept a connection and return a
27 
+  \code{character} vector.  \code{readLinesParserFactory} creates a
28 
+  \sQuote{parser}, responsible for parsing a buffer and vector of the
29 
+  same type as produced by the reader into records.
29 30
30 31 
 }
31 32
32 33 
 \usage{
33 34 
 ReadLinesInput(con, reader = readLinesReaderFactory(),
34 
-    parser = readLinesParserFactory(), ..., yieldSize = 1e+06,
35 
-    verbose = FALSE)
35 
+    parser = readLinesParserFactory(), yieldSize = 1e+06, ...)
36 36 
 readLinesReaderFactory(blockSize=1e+06, ...)
37 37 
 scanReaderFactory(blockSize=1e06, ...)
38 38 
 }
... ... 
@@ -47,10 +47,10 @@ scanReaderFactory(blockSize=1e06, ...)
47 47 
     reader function) that returns a vector of type \code{character}.}
48 48 
   \item{parser}{A function of two arguments (\code{buf}, \code{bin}),
49 49 
     parsing the \code{raw} vector \code{c(buf, bin)} into records.}
50 
-  \item{verbose}{\code{logical(1)} indicating whether class methods
51 
-    should report to the user.}
50 
+
52 51 
   % readLinesReaderFactory
53 52 
   \item{blockSize}{The number of characters to read at one time.}
53 
+
54 54 
   \item{...}{Additional arugments.}
55 55 
  }
56 56
man/Rev-class.Rd
History View file @ bd49f34
... ... 
@@ -14,36 +14,18 @@
14 14
15 15 
 }
16 16
17 
-\usage{Rev(yieldSize = 1e6, verbose=FALSE)}
17 
+\usage{Rev(...)}
18 18
19 19 
 \arguments{
20 
-   \item{yieldSize}{A \code{integer(1)} indicating the number of
21 
-      records to yield.}
22 
-   \item{verbose}{\code{logical(1)} indicating whether class methods
23 
-    should report to the user.}
20 
+  \item{...}{Arguments passed to the \code{\linkS4class{Consumer}}-class
21 
+    constructors.}
24 22 
 }
25 23
26 
-\section{Constructors}{
27 
-  Use \code{Rev} to construct instances of this class.
28 
-}
24 
+\section{Constructors}{Use \code{Rev} to construct instances of this class.}
29 25
30 
-\section{Fields}{
31 
-  \describe{
32 
-    \item{\code{inputPipe}:}{Object of class \code{ANY}. The component
33 
-      from which input is retrieved.}
34 
-    \item{\code{yieldSize}:}{A \code{integer(1)} indicating the number of
35 
-      records to yield.}
36 
-    \item{\code{verbose}:}{Object of class \code{logical}. Display
37 
-      method invokation messages to the user.}
38 
-  }
39 
-}
26 
+\section{Fields}{There are no fields unique to this class.}
40 27
41 
-\section{Methods}{
42 
-  \describe{
43 
-    \item{\code{yield()}:}{Reverse the result of applyng \code{yield} to
44 
-      \code{inputPipe}.}
45 
-  }
46 
-}
28 
+\section{Methods}{There are no methods unique to this class.}
47 29
48 30 
 \author{Martin Morgan \url{mtmorgan@fhcrc.org}}
49 31
man/Streamer-class.Rd
History View file @ bd49f34
... ... 
@@ -20,8 +20,6 @@
20 20
21 21 
 \section{Fields}{
22 22 
   \describe{
23 
-      \item{\code{yieldSize}:}{ An \code{integer} for the number of records
24 
-          to be returned.}
25 23 
       \item{\code{verbose}:}{A \code{logical(1)} instance indicating
26 24 
       whether methods invoked on the class should be reported to the
27 25 
       user.}
... ... 
@@ -32,17 +30,23 @@
32 30
33 31 
 \section{Class-Based Methods}{
34 32 
   \describe{
33 
+
35 34 
     \item{\code{initialize(..., verbose = FALSE)}:}{Initialize
36 
-      \code{Streamer}, setting \code{verbose}, \code{yieldSize} and \code{inUse}
37 
-      fields, returning \code{.self} invisibly.}
35 
+      \code{Streamer}, setting \code{verbose} and \code{inUse} fields,
36 
+      returning \code{.self} invisibly.}
37 
+
38 38 
     \item{\code{msg(fmt, ...)}:}{Use \code{msg} to print
39 39 
       \code{sprintf(fmt, ...)} messages to user.}
40 
+
40 41 
     \item{\code{reset()}:}{Reset \code{Streamer}; this default method is
41 42 
       a no-op.}
43 
+
42 44 
     \item{\code{yield()}:}{Yield default value \code{list()}.}
43 
-    \item{\code{status()}:}{Reports the status of the \code{Streamer} class.
44 
-       A \code{list} of the status of \code{yieldSize}, \code{verbose} and
45 
+