[H5r-commits] r69 - / R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Sep 20 09:16:03 CEST 2011
Author: extemporaneousb
Date: 2011-09-20 09:16:02 +0200 (Tue, 20 Sep 2011)
New Revision: 69
Added:
man/H5Container-class.Rd
man/H5DataFrame-class.Rd
man/envOrNULL-class.Rd
man/hSlab-class.Rd
Removed:
man/H5DataFrame.Rd
Modified:
DESCRIPTION
NEWS
R/h5R.R
man/H5Obj-class.Rd
Log:
Version 1.2 initial checkin. Still needs some finetuning and there are memory issues when doing things with groups and files if you start removing files.
Modified: DESCRIPTION
===================================================================
--- DESCRIPTION 2011-09-20 06:40:42 UTC (rev 68)
+++ DESCRIPTION 2011-09-20 07:16:02 UTC (rev 69)
@@ -1,11 +1,11 @@
Package: h5r
Type: Package
Title: Interface to HDF5 Files
-Version: 1.1
-Date: 2010-01-28
+Version: 1.2
+Date: 2011-09-19
Author: James Bullard
Maintainer: <jbullard at pacificbiosciences.com>
-Depends: R (>= 2.10.0), methods, base
+Depends: R (>= 2.11.0), methods, base
Description: A package for interfacing with HDF5 files.
License: LGPL
Modified: NEWS
===================================================================
--- NEWS 2011-09-20 06:40:42 UTC (rev 68)
+++ NEWS 2011-09-20 07:16:02 UTC (rev 69)
@@ -1,5 +1,25 @@
**************************************************
* *
+ * 1.2 SERIES NEWS *
+ * *
+ **************************************************
+
+
+ CHANGES IN h5r VERSION 1.1
+
+NEW FEATURES
+ o Added 'ls' function
+ o Added 'H5DataFrame' class - this is still a prototype
+
+BUG FIXES
+ o Cleaned up some memory that I was leaving behind. Unfortunately,
+ there are still some small allocations that I probably need to
+ deal with.
+
+
+
+ **************************************************
+ * *
* 1.1 SERIES NEWS *
* *
**************************************************
Modified: R/h5R.R
===================================================================
--- R/h5R.R 2011-09-20 06:40:42 UTC (rev 68)
+++ R/h5R.R 2011-09-20 07:16:02 UTC (rev 69)
@@ -625,13 +625,13 @@
## H5DataFrame interface
##
################################################################
-H5DataFrame <- function(file, nms = NA) {
+H5DataFrame <- function(fileName, nms = NA) {
.getCols <- function(h5) {
nms <- names(listH5Contents(h5))
nms[nms != "."]
}
- h5File <- H5File(file)
+ h5File <- H5File(fileName)
if (is.na(nms)) {
nms <- .getCols(h5File)
}
Added: man/H5Container-class.Rd
===================================================================
--- man/H5Container-class.Rd (rev 0)
+++ man/H5Container-class.Rd 2011-09-20 07:16:02 UTC (rev 69)
@@ -0,0 +1,33 @@
+\name{H5Container-class}
+\Rdversion{1.1}
+\docType{class}
+\alias{H5Container-class}
+\title{Class \code{"H5Container"}}
+\description{
+ This class is the parent class for H5Files and H5Groups.
+}
+\section{Objects from the Class}{
+ These objects are often not directly created by created when
+ instanteating an H5Group or H5File.
+}
+\section{Slots}{
+ \describe{
+ \item{\code{ePtr}:}{Object of class \code{"externalptr"}}
+ }
+}
+\section{Extends}{
+ Class \code{"\linkS4class{H5Obj}"}, directly.
+}
+\section{Methods}{
+ \describe{
+ \item{createH5Dataset}{\code{signature(h5Obj = "H5Container", datasetName = "character")}: ... }
+ \item{createH5Group}{\code{signature(h5Obj = "H5Container", groupName = "character")}: ... }
+ \item{deleteH5Obj}{\code{signature(h5Obj = "H5Container")}: ... }
+ \item{getH5Dataset}{\code{signature(h5Obj = "H5Container", datasetName = "character")}: ... }
+ \item{getH5Group}{\code{signature(h5Obj = "H5Container", groupName = "character")}: ... }
+ }
+}
+\examples{
+ showClass("H5Container")
+}
+\keyword{classes}
Added: man/H5DataFrame-class.Rd
===================================================================
--- man/H5DataFrame-class.Rd (rev 0)
+++ man/H5DataFrame-class.Rd 2011-09-20 07:16:02 UTC (rev 69)
@@ -0,0 +1,74 @@
+\name{H5DataFrame-class}
+\Rdversion{1.1}
+\docType{class}
+\alias{H5DataFrame-class}
+\alias{H5DataFrame}
+\alias{writeH5DataFrame}
+\alias{[,H5DataFrame,ANY,ANY,ANY-method}
+\alias{[[,H5DataFrame-method}
+\alias{$,H5DataFrame-method}
+\alias{as.data.frame,H5DataFrame-method}
+\alias{colnames,H5DataFrame-method}
+\alias{dim,H5DataFrame-method}
+\alias{ncol,H5DataFrame-method}
+\alias{nrow,H5DataFrame-method}
+
+\title{Class \code{"H5DataFrame"}}
+\description{
+ Presents a data.frame style interface to an HDF5 file. The data for
+ each column is stored in a separate H5Dataset.
+}
+\usage{
+ H5DataFrame(fileName, nms = NA)
+ writeH5DataFrame(df, fileName, overwrite = T)
+}
+\arguments{
+ \item{nms}{
+ File names.
+ }
+ \item{df}{
+ The input data.frame from which to construct an H5DataFrame
+ }
+ \item{fileName}{
+ The fileName to either store or load the H5DataFrame from.
+ }
+ \item{overwrite}{
+ Flag as to whether to overwrite the file.
+ }
+}
+\section{Objects from the Class}{
+ Objects can be created by calls of the form \code{H5DataFrame()}.
+}
+\section{Slots}{
+ \describe{
+ \item{\code{.Data}:}{Object of class \code{"list"}}
+ \item{\code{h5File}:}{Object of class \code{"H5File"}}
+ \item{\code{h5Datasets}:}{Object of class \code{"list"}}
+ \item{\code{names}:}{Object of class \code{"character"}}
+ \item{\code{row.names}:}{Object of class \code{"data.frameRowLabels"}}
+ \item{\code{.S3Class}:}{Object of class \code{"character"}}
+ }
+}
+\section{Extends}{
+ Class \code{"\linkS4class{data.frame}"}, directly.
+ Class \code{"\linkS4class{list}"}, by class "data.frame", distance 2.
+ Class \code{"\linkS4class{oldClass}"}, by class "data.frame", distance 2.
+ Class \code{"\linkS4class{vector}"}, by class "data.frame", distance 3.
+}
+\section{Methods}{
+ \describe{
+ \item{[}{\code{signature(x = "H5DataFrame", i = "ANY", j = "ANY", drop = "ANY")}: ... }
+ \item{[[}{\code{signature(x = "H5DataFrame")}: ... }
+ \item{$}{\code{signature(x = "H5DataFrame")}: ... }
+ \item{as.data.frame}{\code{signature(x = "H5DataFrame")}: ... }
+ \item{colnames}{\code{signature(x = "H5DataFrame")}: ... }
+ \item{dim}{\code{signature(x = "H5DataFrame")}: ... }
+ \item{ncol}{\code{signature(x = "H5DataFrame")}: ... }
+ \item{nrow}{\code{signature(x = "H5DataFrame")}: ... }
+ }
+}
+\examples{
+ require(h5r)
+ showClass("H5DataFrame")
+}
+\keyword{classes}
Deleted: man/H5DataFrame.Rd
===================================================================
--- man/H5DataFrame.Rd 2011-09-20 06:40:42 UTC (rev 68)
+++ man/H5DataFrame.Rd 2011-09-20 07:16:02 UTC (rev 69)
@@ -1,27 +0,0 @@
-\name{H5DataFrame}
-\alias{H5DataFrame}
-\alias{writeH5DataFrame}
-\title{
- Create an H5 Data Frame
-}
-\description{
- 'H5DataFrame' is a function that creates a list of equal-length
- vectors.
-}
-\usage{
-H5DataFrame(file, nms = NA)
-}
-\arguments{
- \item{file}{
- H5 file.
- }
- \item{nms}{
- File names.
- }
-}
-\examples{
- require(h5r)
- h5 <- H5File("test.h5", 'w')
-}
-\keyword{datagen}
-
Modified: man/H5Obj-class.Rd
===================================================================
--- man/H5Obj-class.Rd 2011-09-20 06:40:42 UTC (rev 68)
+++ man/H5Obj-class.Rd 2011-09-20 07:16:02 UTC (rev 69)
@@ -7,11 +7,11 @@
\alias{H5Dataset-class}
\alias{H5DataContainer-class}
\alias{H5Attribute-class}
-\alias{getH5Group,H5Obj,character-method}
+\alias{getH5Group,H5Container,character-method}
\alias{getH5Group}
\alias{getH5Attribute,H5Obj,character-method}
\alias{getH5Attribute}
-\alias{getH5Dataset,H5Obj,character-method}
+\alias{getH5Dataset,H5Container,character-method}
\alias{getH5Dataset}
\alias{getH5Dim,H5DataContainer-method}
\alias{getH5Dim}
@@ -27,22 +27,16 @@
\alias{listH5Contents}
\alias{print.H5ContentList}
\alias{h5Exists}
-\alias{hSlab}
\alias{start}
\alias{width}
\alias{[,H5DataContainer,ANY,ANY,ANY-method}
\alias{[,H5Dataset,ANY,ANY,ANY-method}
-\alias{[,H5Dataset,hSlab,missing,missing-method}
-\alias{length,hSlab-method}
\alias{show,H5DataContainer-method}
\alias{show,H5File-method}
\alias{show,H5Group-method}
\alias{show,H5Obj-method}
-\alias{start,hSlab-method}
-\alias{width,hSlab-method}
+\alias{ls,H5Obj-method}
-
-
\title{Class "H5Obj"}
\description{Classes for objects originating from HDF5 files.}
\section{Objects from the Class}{
Added: man/envOrNULL-class.Rd
===================================================================
--- man/envOrNULL-class.Rd (rev 0)
+++ man/envOrNULL-class.Rd 2011-09-20 07:16:02 UTC (rev 69)
@@ -0,0 +1,17 @@
+\name{envOrNULL-class}
+\Rdversion{1.1}
+\docType{class}
+\alias{envOrNULL-class}
+
+\title{Class \code{"envOrNULL"}}
+\description{
+ A union class used to abstract whether data is in memory or out.
+}
+\section{Objects from the Class}{A virtual Class: No objects may be created from it.}
+\section{Methods}{
+No methods defined with class "envOrNULL" in the signature.
+}
+\examples{
+showClass("envOrNULL")
+}
+\keyword{classes}
Added: man/hSlab-class.Rd
===================================================================
--- man/hSlab-class.Rd (rev 0)
+++ man/hSlab-class.Rd 2011-09-20 07:16:02 UTC (rev 69)
@@ -0,0 +1,39 @@
+\name{hSlab-class}
+\Rdversion{1.1}
+\docType{class}
+\alias{hSlab-class}
+\alias{[,H5Dataset,hSlab,missing,missing-method}
+\alias{hSlab}
+\alias{[,H5Dataset,hSlab,missing,missing-method}
+\alias{start,hSlab-method}
+\alias{width,hSlab-method}
+\alias{length,hSlab-method}
+
+\title{Class \code{"hSlab"}}
+\description{
+ A class used to represent hyper slabs. This class is often not as
+ useful as directly using integers due to the performance cost of S4
+ class construction.
+}
+\section{Objects from the Class}{
+Objects can be created by calls of the form \code{new("hSlab", ...)}.
+}
+\section{Slots}{
+ \describe{
+ \item{\code{s}:}{Object of class \code{"integer"} representing the
+ start of the extents. There will be exactly n points where n
+ represents the number of dimensions of the selection.}
+ \item{\code{w}:}{Object of class \code{"integer"} representing the
+ extent of the selection. This will be the same length as 's'}
+ }
+}
+\section{Methods}{
+ \describe{
+ \item{[}{\code{signature(x = "H5Dataset", i = "hSlab", j = "missing", drop = "missing")}: ... }
+ \item{length}{\code{signature(x = "hSlab")}: ... }
+ }
+}
+\examples{
+ showClass("hSlab")
+}
+\keyword{classes}
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