Merge branch 'april2013hackfest' of https://github.com/meowcat/RMassBank into april2013hackfest

NAMESPACE

@@ -36,6 +36,7 @@ export(findMsMsHRperxcms.direct)
 export(findMz)
 export(findMz.formula)
 export(findName)
+export(findProgress)
 export(findRt)
 export(findSmiles)
 export(flatten)
@@ -69,6 +70,7 @@ export(plotRecalibration)
 export(plotRecalibration.direct)
 export(ppm)
 export(problematicPeaks)
+export(progressBarHook)
 export(readMbdata)
 export(reanalyzeFailpeak)
 export(reanalyzeFailpeaks)

R/leMsMs.r

@@ -42,7 +42,8 @@ archiveResults <- function(w, fileName, settings = getOption("RMassBank"))
 #' @usage msmsWorkflow(w, mode="pH", steps=c(1:8), confirmMode = FALSE, newRecalibration = TRUE, 
 #' 		useRtLimit = TRUE, archivename=NA, readMethod = "mzR", findPeaksArgs = NA, plots = FALSE,
 #' 		precursorscan.cf = FALSE,
-#' 		settings = getOption("RMassBank"), analyzeMethod = "formula")
+#' 		settings = getOption("RMassBank"), analyzeMethod = "formula",
+#' 		progressbar = "progressBarHook")
 #' @param w A \code{msmsWorkspace} to work with.
 #' @param mode \code{"pH", "pNa", "pM", "mH", "mM", "mFA"} for different ions 
 #' 			([M+H]+, [M+Na]+, [M]+, [M-H]-, [M]-, [M+FA]-).
@@ -69,6 +70,8 @@ archiveResults <- function(w, fileName, settings = getOption("RMassBank"))
 #' @param settings Options to be used for processing. Defaults to the options loaded via
 #' 			\code{\link{loadRmbSettings}} et al. Refer to there for specific settings.
 #' @param analyzeMethod The "method" parameter to pass to \code{\link{analyzeMsMs}}.
+#' @param progressbar The progress bar callback to use. Only needed for specialized applications.
+#' 			Cf. the documentation of \code{\link{progressBarHook}} for usage.
 #' @return The processed \code{msmsWorkspace}.
 #' @seealso \code{\link{msmsWorkspace-class}}
 #' @author Michael Stravs, Eawag <michael.stravs@@eawag.ch>
@@ -1477,7 +1480,7 @@ filterPeakSatellites <- function(peaks, filterSettings = getOption("RMassBank")$
 #' 
 #' @aliases reanalyzeFailpeaks reanalyzeFailpeak
 #' @usage reanalyzeFailpeaks(specs, custom_additions, mode, filterSettings =
-#' 				getOption("RMassBank")$filterSettings)
+#' 				getOption("RMassBank")$filterSettings, progressbar = "progressBarHook")
 #' reanalyzeFailpeak(custom_additions, mass, cpdID, counter, pb = NULL, mode,
 #' 				filterSettings = getOption("RMassBank")$filterSettings)
 #' @param specs An \code{aggregatedRcSpecs} object (after the electronic noise
@@ -1488,7 +1491,11 @@ filterPeakSatellites <- function(peaks, filterSettings = getOption("RMassBank")$
 #' @param cpdID Compound ID of this spectrum.
 #' @param counter Current peak index (used exclusively for the progress
 #' indicator)
-#' @param pb A txtProgressBar object to display progress on. No progress is displayed if NULL.
+#' @param pb A progressbar object to display progress on, as passed by
+#'  \code{reanalyzeFailpeaks} to \code{reanalyzeFailpeak}. No progress 
+#' is displayed if NULL.
+#' @param progressbar The progress bar callback to use. Only needed for specialized
+#'  applications.	Cf. the documentation of \code{\link{progressBarHook}} for usage.
 #' @param filterSettings Settings for filtering data. Refer to\code{\link{analyzeMsMs}} for settings.
 #' @return The returning list contains two tables: 
 #' \item{peaksReanalyzed}{All reanalyzed peaks with or without matching formula.}
@@ -2116,7 +2123,37 @@ recalibrate.identity <- function(rcdata)
 	return(lm(recalfield ~ 0, data=rcdata))
 }
 
-
+#' Standard progress bar hook.
+#' 
+#' This function provides a standard implementation for the progress bar in RMassBank.
+#' 
+#' RMassBank calls the progress bar function in the following three ways:
+#' \code{pb <- progressBarHook(object=NULL, value=0, min=0, max=LEN)}
+#' to create a new progress bar.
+#' \code{pb <- progressBarHook(object=pb, value= VAL)}
+#' to set the progress bar to a new value (between the set \code{min} and \code{max})
+#' \code{progressBarHook(object=pb, close=TRUE)}
+#' to close the progress bar. (The actual calls are performed with \code{do.call}, 
+#' e.g. 
+#' \code{progressbar <- "progressBarHook"
+#' pb <- do.call(progressbar, list(object=pb, value= nProg))
+#' }. See the source code for details.)
+#' 
+#' To substitute the standard progress bar for an alternative implementation (e.g. for
+#' use in a GUI), the developer can write his own function which behaves in the same way
+#' as \code{progressBarHook}, i.e. takes the same parameters and can be called in the 
+#' same way. 
+#'  
+#' @param object An identifier representing an instance of a progress bar. 
+#' @param value The new value to assign to the progress indicator
+#' @param min The minimal value of the progress indicator
+#' @param max The maximal value of the progress indicator
+#' @param close If \code{TRUE}, the progress bar is closed.
+#' @return Returns a progress bar instance identifier (i.e. an identifier
+#' 		which can be used as \code{object} in subsequent calls.) 
+#' 
+#' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
+#' @export
 progressBarHook <- function(object = NULL, value = 0, min = 0, max = 100, close = FALSE)
 {
 	if(is.null(object))

man/findProgress.Rd

+\name{findProgress}
+\alias{findProgress}
+\title{Determine processed steps}
+\usage{
+  findProgress(workspace)
+}
+\arguments{
+  \item{workspace}{A \code{msmsWorkspace} object.}
+}
+\value{
+  An array containing all \code{msmsWorkflow} steps which
+  have likely been processed.
+}
+\description{
+  This function reads out the content of different slots of
+  the \code{workspace} object and finds out which steps
+  have already been processed on it.
+}
+\author{
+  Stravs MA, Eawag <michael.stravs@eawag.ch>
+}
+

man/msmsWorkflow.Rd

@@ -6,7 +6,8 @@
     FALSE, newRecalibration = TRUE, useRtLimit = TRUE,
     archivename=NA, readMethod = "mzR", findPeaksArgs = NA,
     plots = FALSE, precursorscan.cf = FALSE, settings =
-    getOption("RMassBank"), analyzeMethod = "formula")
+    getOption("RMassBank"), analyzeMethod = "formula",
+    progressbar = "progressBarHook")
 }
 \arguments{
   \item{w}{A \code{msmsWorkspace} to work with.}
@@ -61,6 +62,11 @@
 
   \item{analyzeMethod}{The "method" parameter to pass to
   \code{\link{analyzeMsMs}}.}
+
+  \item{progressbar}{The progress bar callback to use. Only
+  needed for specialized applications.  Cf. the
+  documentation of \code{\link{progressBarHook}} for
+  usage.}
 }
 \value{
   The processed \code{msmsWorkspace}.

man/progressBarHook.Rd

+\name{progressBarHook}
+\alias{progressBarHook}
+\title{Standard progress bar hook.}
+\usage{
+  progressBarHook(object = NULL, value = 0, min = 0,
+    max = 100, close = FALSE)
+}
+\arguments{
+  \item{object}{An identifier representing an instance of a
+  progress bar.}
+
+  \item{value}{The new value to assign to the progress
+  indicator}
+
+  \item{min}{The minimal value of the progress indicator}
+
+  \item{max}{The maximal value of the progress indicator}
+
+  \item{close}{If \code{TRUE}, the progress bar is closed.}
+}
+\value{
+  Returns a progress bar instance identifier (i.e. an
+  identifier which can be used as \code{object} in
+  subsequent calls.)
+}
+\description{
+  This function provides a standard implementation for the
+  progress bar in RMassBank.
+}
+\details{
+  RMassBank calls the progress bar function in the
+  following three ways: \code{pb <-
+  progressBarHook(object=NULL, value=0, min=0, max=LEN)} to
+  create a new progress bar. \code{pb <-
+  progressBarHook(object=pb, value= VAL)} to set the
+  progress bar to a new value (between the set \code{min}
+  and \code{max}) \code{progressBarHook(object=pb,
+  close=TRUE)} to close the progress bar. (The actual calls
+  are performed with \code{do.call}, e.g. \code{progressbar
+  <- "progressBarHook" pb <- do.call(progressbar,
+  list(object=pb, value= nProg)) }. See the source code for
+  details.)
+
+  To substitute the standard progress bar for an
+  alternative implementation (e.g. for use in a GUI), the
+  developer can write his own function which behaves in the
+  same way as \code{progressBarHook}, i.e. takes the same
+  parameters and can be called in the same way.
+}
+\author{
+  Michele Stravs, Eawag <stravsmi@eawag.ch>
+}
+

man/reanalyzeFailpeaks.Rd

@@ -4,7 +4,8 @@
 \title{Reanalyze unmatched peaks}
 \usage{
   reanalyzeFailpeaks(specs, custom_additions, mode,
-    filterSettings = getOption("RMassBank")$filterSettings)
+    filterSettings = getOption("RMassBank")$filterSettings,
+    progressbar = "progressBarHook")
     reanalyzeFailpeak(custom_additions, mass, cpdID,
     counter, pb = NULL, mode, filterSettings =
     getOption("RMassBank")$filterSettings)
@@ -28,8 +29,15 @@
   \item{counter}{Current peak index (used exclusively for
   the progress indicator)}
 
-  \item{pb}{A txtProgressBar object to display progress on.
-  No progress is displayed if NULL.}
+  \item{pb}{A progressbar object to display progress on, as
+  passed by \code{reanalyzeFailpeaks} to
+  \code{reanalyzeFailpeak}. No progress is displayed if
+  NULL.}
+
+  \item{progressbar}{The progress bar callback to use. Only
+  needed for specialized applications. Cf. the
+  documentation of \code{\link{progressBarHook}} for
+  usage.}
 
   \item{filterSettings}{Settings for filtering data. Refer
   to\code{\link{analyzeMsMs}} for settings.}