[med-svn] [fast5] 01/07: New upstream version 0.6.3
Afif Elghraoui
afif at moszumanska.debian.org
Sat Oct 7 04:08:38 UTC 2017
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository fast5.
commit 6198cc7ff3f6a24876abf4ed7e04a5a539edc6be
Author: Afif Elghraoui <afif at debian.org>
Date: Fri Oct 6 22:48:35 2017 -0400
New upstream version 0.6.3
---
.gitignore | 2 +
.travis.yml | 2 +-
Doxyfile | 2479 ++++++++++++++++++++
README.org | 2 +-
{src => include}/fast5.hpp | 24 +-
{src => include/fast5}/Bit_Packer.hpp | 0
{src => include/fast5}/Huffman_Packer.hpp | 0
{src => include/fast5}/cwmap.fast5_ed_len_1.inl | 0
{src => include/fast5}/cwmap.fast5_ed_skip_1.inl | 0
{src => include/fast5}/cwmap.fast5_ev_move_1.inl | 0
.../fast5}/cwmap.fast5_ev_rel_skip_1.inl | 0
{src => include/fast5}/cwmap.fast5_fq_bp_1.inl | 0
{src => include/fast5}/cwmap.fast5_fq_qv_1.inl | 0
{src => include/fast5}/cwmap.fast5_rw_1.inl | 0
{src => include/fast5}/fast5_version.hpp | 0
{src => include/fast5}/hdf5_tools.hpp | 1449 ++++++++----
{src => include/fast5}/logger.hpp | 1 +
python/bin/f5ls | 4 +-
python/setup.py | 5 +-
src/File_Packer.hpp | 3 +-
src/Makefile | 5 +-
src/f5-mod.cpp | 2 +-
src/f5dump.cpp | 2 +-
src/f5ls-full.cpp | 2 +-
src/f5ls.cpp | 2 +-
src/f5pack.cpp | 3 +-
src/hdf5-mod.cpp | 2 +-
src/huffman-decode.cpp | 4 +-
src/huffman-encode.cpp | 4 +-
29 files changed, 3491 insertions(+), 506 deletions(-)
diff --git a/.gitignore b/.gitignore
index cc2c46e..ac2534a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,5 @@
/build*
/local*
/file.*.fast5
+/doc
+/doxygen.log
diff --git a/.travis.yml b/.travis.yml
index b1bd9f1..0347e18 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,7 +7,7 @@ services:
before_install:
- sudo apt-get update -y
- - sudo apt-get install -y -o Dpkg::Options::="--force-confnew" docker-engine
+ - sudo apt-get install -y -o Dpkg::Options::="--force-confnew" docker-ce
- TZ=$(cat /etc/timezone) USER_ID=$(id -u) USER_NAME=$(id -un) GROUP_ID=$(id -g) GROUP_NAME=$(id -gn) envsubst <.travis.Dockerfile.in | docker build -t fast5 -
install:
diff --git a/Doxyfile b/Doxyfile
new file mode 100644
index 0000000..5fd27cb
--- /dev/null
+++ b/Doxyfile
@@ -0,0 +1,2479 @@
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+HIDE_COMPOUND_REFERENCE= NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
+# the files that are included by a file in the documentation of that file.
+# The default value is: YES.
+
+SHOW_INCLUDE_FILES = YES
+
+# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
+# grouped member an include statement to the documentation, telling the reader
+# which file to include in order to use the member.
+# The default value is: NO.
+
+SHOW_GROUPED_MEMB_INC = NO
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
+# files with double quotes in the documentation rather than with sharp brackets.
+# The default value is: NO.
+
+FORCE_LOCAL_INCLUDES = NO
+
+# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
+# documentation for inline members.
+# The default value is: YES.
+
+INLINE_INFO = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
+# (detailed) documentation of file and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order.
+# The default value is: YES.
+
+SORT_MEMBER_DOCS = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
+# descriptions of file, namespace and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order. Note that
+# this will also influence the order of the classes in the class list.
+# The default value is: NO.
+
+SORT_BRIEF_DOCS = NO
+
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
+# (brief and detailed) documentation of class members so that constructors and
+# destructors are listed first. If set to NO the constructors will appear in the
+# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
+# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
+# member documentation.
+# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
+# detailed member documentation.
+# The default value is: NO.
+
+SORT_MEMBERS_CTORS_1ST = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
+# of group names into alphabetical order. If set to NO the group names will
+# appear in their defined order.
+# The default value is: NO.
+
+SORT_GROUP_NAMES = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
+# fully-qualified names, including namespaces. If set to NO, the class list will
+# be sorted only by class name, not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the alphabetical
+# list.
+# The default value is: NO.
+
+SORT_BY_SCOPE_NAME = NO
+
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
+# type resolution of all parameters of a function it will reject a match between
+# the prototype and the implementation of a member function even if there is
+# only one candidate or it is obvious which candidate to choose by doing a
+# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
+# accept a match between prototype and implementation in such cases.
+# The default value is: NO.
+
+STRICT_PROTO_MATCHING = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
+# list. This list is created by putting \todo commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TODOLIST = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
+# list. This list is created by putting \test commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TESTLIST = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
+# list. This list is created by putting \bug commands in the documentation.
+# The default value is: YES.
+
+GENERATE_BUGLIST = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
+# the deprecated list. This list is created by putting \deprecated commands in
+# the documentation.
+# The default value is: YES.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional documentation
+# sections, marked by \if <section_label> ... \endif and \cond <section_label>
+# ... \endcond blocks.
+
+ENABLED_SECTIONS =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
+# initial value of a variable or macro / define can have for it to appear in the
+# documentation. If the initializer consists of more lines than specified here
+# it will be hidden. Use a value of 0 to hide initializers completely. The
+# appearance of the value of individual variables and macros / defines can be
+# controlled using \showinitializer or \hideinitializer command in the
+# documentation regardless of this setting.
+# Minimum value: 0, maximum value: 10000, default value: 30.
+
+MAX_INITIALIZER_LINES = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
+# the bottom of the documentation of classes and structs. If set to YES, the
+# list will mention the files that were used to generate the documentation.
+# The default value is: YES.
+
+SHOW_USED_FILES = YES
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
+# will remove the Files entry from the Quick Index and from the Folder Tree View
+# (if specified).
+# The default value is: YES.
+
+SHOW_FILES = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
+# page. This will remove the Namespaces entry from the Quick Index and from the
+# Folder Tree View (if specified).
+# The default value is: YES.
+
+SHOW_NAMESPACES = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command command input-file, where command is the value of the
+# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
+# by doxygen. Whatever the program writes to standard output is used as the file
+# version. For an example see the documentation.
+
+FILE_VERSION_FILTER =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. To create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option. You can
+# optionally specify a file name after the option, if omitted DoxygenLayout.xml
+# will be used as the name of the layout file.
+#
+# Note that if you run doxygen from a directory containing a file called
+# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
+# tag is left empty.
+
+LAYOUT_FILE =
+
+# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
+# the reference definitions. This must be a list of .bib files. The .bib
+# extension is automatically appended if omitted. This requires the bibtex tool
+# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info.
+# For LaTeX the style of the bibliography can be controlled using
+# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
+# search path. See also \cite for info how to create references.
+
+CITE_BIB_FILES =
+
+#---------------------------------------------------------------------------
+# Configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated to
+# standard output by doxygen. If QUIET is set to YES this implies that the
+# messages are off.
+# The default value is: NO.
+
+QUIET = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
+# this implies that the warnings are on.
+#
+# Tip: Turn warnings on while writing the documentation.
+# The default value is: YES.
+
+WARNINGS = YES
+
+# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
+# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
+# will automatically be disabled.
+# The default value is: YES.
+
+WARN_IF_UNDOCUMENTED = YES
+
+# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some parameters
+# in a documented function, or documenting parameters that don't exist or using
+# markup commands wrongly.
+# The default value is: YES.
+
+WARN_IF_DOC_ERROR = YES
+
+# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
+# are documented, but have no documentation for their parameters or return
+# value. If set to NO, doxygen will only warn about wrong or incomplete
+# parameter documentation, but not about the absence of documentation.
+# The default value is: NO.
+
+WARN_NO_PARAMDOC = NO
+
+# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
+# a warning is encountered.
+# The default value is: NO.
+
+WARN_AS_ERROR = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that doxygen
+# can produce. The string should contain the $file, $line, and $text tags, which
+# will be replaced by the file and line number from which the warning originated
+# and the warning text. Optionally the format may contain $version, which will
+# be replaced by the version of the file (if it could be obtained via
+# FILE_VERSION_FILTER)
+# The default value is: $file:$line: $text.
+
+WARN_FORMAT = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning and error
+# messages should be written. If left blank the output is written to standard
+# error (stderr).
+
+WARN_LOGFILE =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag is used to specify the files and/or directories that contain
+# documented source files. You may enter file names like myfile.cpp or
+# directories like /usr/src/myproject. Separate the files or directories with
+# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
+# Note: If this tag is empty the current directory is searched.
+
+INPUT = src/hdf5_tools.hpp
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
+# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
+# documentation (see: http://www.gnu.org/software/libiconv) for the list of
+# possible encodings.
+# The default value is: UTF-8.
+
+INPUT_ENCODING = UTF-8
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
+# *.h) to filter out the source-files in the directories.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# read by doxygen.
+#
+# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
+# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
+# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
+# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f, *.for, *.tcl,
+# *.vhd, *.vhdl, *.ucf, *.qsf, *.as and *.js.
+
+FILE_PATTERNS = *.c \
+ *.cc \
+ *.cxx \
+ *.cpp \
+ *.c++ \
+ *.java \
+ *.ii \
+ *.ixx \
+ *.ipp \
+ *.i++ \
+ *.inl \
+ *.idl \
+ *.ddl \
+ *.odl \
+ *.h \
+ *.hh \
+ *.hxx \
+ *.hpp \
+ *.h++ \
+ *.cs \
+ *.d \
+ *.php \
+ *.php4 \
+ *.php5 \
+ *.phtml \
+ *.inc \
+ *.m \
+ *.markdown \
+ *.md \
+ *.mm \
+ *.dox \
+ *.py \
+ *.pyw \
+ *.f90 \
+ *.f \
+ *.for \
+ *.tcl \
+ *.vhd \
+ *.vhdl \
+ *.ucf \
+ *.qsf \
+ *.as \
+ *.js
+
+# The RECURSIVE tag can be used to specify whether or not subdirectories should
+# be searched for input files as well.
+# The default value is: NO.
+
+RECURSIVE = NO
+
+# The EXCLUDE tag can be used to specify files and/or directories that should be
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+#
+# Note that relative paths are relative to the directory from which doxygen is
+# run.
+
+EXCLUDE =
+
+# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
+# directories that are symbolic links (a Unix file system feature) are excluded
+# from the input.
+# The default value is: NO.
+
+EXCLUDE_SYMLINKS = NO
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories.
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories for example use the pattern */test/*
+
+EXCLUDE_PATTERNS =
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories use the pattern */test/*
+
+EXCLUDE_SYMBOLS =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or directories
+# that contain example code fragments that are included (see the \include
+# command).
+
+EXAMPLE_PATH =
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
+# *.h) to filter out the source-files in the directories. If left blank all
+# files are included.
+
+EXAMPLE_PATTERNS = *
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude commands
+# irrespective of the value of the RECURSIVE tag.
+# The default value is: NO.
+
+EXAMPLE_RECURSIVE = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or directories
+# that contain images that are to be included in the documentation (see the
+# \image command).
+
+IMAGE_PATH =
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command:
+#
+# <filter> <input-file>
+#
+# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
+# name of an input file. Doxygen will then use the output that the filter
+# program writes to standard output. If FILTER_PATTERNS is specified, this tag
+# will be ignored.
+#
+# Note that the filter must not add or remove lines; it is applied before the
+# code is scanned, but not when the output code is generated. If lines are added
+# or removed, the anchors will not be placed correctly.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
+
+INPUT_FILTER =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis. Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match. The filters are a list of the form: pattern=filter
+# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
+# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
+# patterns match the file name, INPUT_FILTER is applied.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
+
+FILTER_PATTERNS =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will also be used to filter the input files that are used for
+# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
+# The default value is: NO.
+
+FILTER_SOURCE_FILES = NO
+
+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
+# it is also possible to disable source filtering for a specific pattern using
+# *.ext= (so without naming a filter).
+# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
+
+FILTER_SOURCE_PATTERNS =
+
+# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
+# is part of the input, its contents will be placed on the main page
+# (index.html). This can be useful if you have a project on for instance GitHub
+# and want to reuse the introduction page also for the doxygen output.
+
+USE_MDFILE_AS_MAINPAGE =
+
+#---------------------------------------------------------------------------
+# Configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
+# generated. Documented entities will be cross-referenced with these sources.
+#
+# Note: To get rid of all source code in the generated output, make sure that
+# also VERBATIM_HEADERS is set to NO.
+# The default value is: NO.
+
+SOURCE_BROWSER = NO
+
+# Setting the INLINE_SOURCES tag to YES will include the body of functions,
+# classes and enums directly into the documentation.
+# The default value is: NO.
+
+INLINE_SOURCES = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
+# special comment blocks from generated source code fragments. Normal C, C++ and
+# Fortran comments will always remain visible.
+# The default value is: YES.
+
+STRIP_CODE_COMMENTS = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
+# function all documented functions referencing it will be listed.
+# The default value is: NO.
+
+REFERENCED_BY_RELATION = NO
+
+# If the REFERENCES_RELATION tag is set to YES then for each documented function
+# all documented entities called/used by that function will be listed.
+# The default value is: NO.
+
+REFERENCES_RELATION = NO
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
+# to YES then the hyperlinks from functions in REFERENCES_RELATION and
+# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
+# link to the documentation.
+# The default value is: YES.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
+# source code will show a tooltip with additional information such as prototype,
+# brief description and links to the definition and documentation. Since this
+# will make the HTML file larger and loading of large files a bit slower, you
+# can opt to disable this feature.
+# The default value is: YES.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+SOURCE_TOOLTIPS = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code will
+# point to the HTML generated by the htags(1) tool instead of doxygen built-in
+# source browser. The htags tool is part of GNU's global source tagging system
+# (see http://www.gnu.org/software/global/global.html). You will need version
+# 4.8.6 or higher.
+#
+# To use it do the following:
+# - Install the latest version of global
+# - Enable SOURCE_BROWSER and USE_HTAGS in the config file
+# - Make sure the INPUT points to the root of the source tree
+# - Run doxygen as normal
+#
+# Doxygen will invoke htags (and that will in turn invoke gtags), so these
+# tools must be available from the command line (i.e. in the search path).
+#
+# The result: instead of the source browser generated by doxygen, the links to
+# source code will now point to the output of htags.
+# The default value is: NO.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+USE_HTAGS = NO
+
+# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
+# verbatim copy of the header file for each class for which an include is
+# specified. Set to NO to disable this.
+# See also: Section \class.
+# The default value is: YES.
+
+VERBATIM_HEADERS = YES
+
+# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the
+# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the
+# cost of reduced performance. This can be particularly helpful with template
+# rich C++ code for which doxygen's built-in parser lacks the necessary type
+# information.
+# Note: The availability of this option depends on whether or not doxygen was
+# generated with the -Duse-libclang=ON option for CMake.
+# The default value is: NO.
+
+CLANG_ASSISTED_PARSING = NO
+
+# If clang assisted parsing is enabled you can provide the compiler with command
+# line options that you would normally use when invoking the compiler. Note that
+# the include paths will already be set by doxygen for the files and directories
+# specified with INPUT and INCLUDE_PATH.
+# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
+
+CLANG_OPTIONS =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
+# compounds will be generated. Enable this if the project contains a lot of
+# classes, structs, unions or interfaces.
+# The default value is: YES.
+
+ALPHABETICAL_INDEX = YES
+
+# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
+# which the alphabetical index list will be split.
+# Minimum value: 1, maximum value: 20, default value: 5.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+COLS_IN_ALPHA_INDEX = 5
+
+# In case all classes in a project start with a common prefix, all classes will
+# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
+# can be used to specify a prefix (or a list of prefixes) that should be ignored
+# while generating the index headers.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+IGNORE_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
+# The default value is: YES.
+
+GENERATE_HTML = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_OUTPUT = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
+# generated HTML page (for example: .htm, .php, .asp).
+# The default value is: .html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FILE_EXTENSION = .html
+
+# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
+# each generated HTML page. If the tag is left blank doxygen will generate a
+# standard header.
+#
+# To get valid HTML the header file that includes any scripts and style sheets
+# that doxygen needs, which is dependent on the configuration options used (e.g.
+# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
+# default header using
+# doxygen -w html new_header.html new_footer.html new_stylesheet.css
+# YourConfigFile
+# and then modify the file new_header.html. See also section "Doxygen usage"
+# for information on how to generate the default header that doxygen normally
+# uses.
+# Note: The header is subject to change so you typically have to regenerate the
+# default header when upgrading to a newer version of doxygen. For a description
+# of the possible markers and block names see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_HEADER =
+
+# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
+# generated HTML page. If the tag is left blank doxygen will generate a standard
+# footer. See HTML_HEADER for more information on how to generate a default
+# footer and what special commands can be used inside the footer. See also
+# section "Doxygen usage" for information on how to generate the default footer
+# that doxygen normally uses.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FOOTER =
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
+# sheet that is used by each HTML page. It can be used to fine-tune the look of
+# the HTML output. If left blank doxygen will generate a default style sheet.
+# See also section "Doxygen usage" for information on how to generate the style
+# sheet that doxygen normally uses.
+# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
+# it is more robust and this tag (HTML_STYLESHEET) will in the future become
+# obsolete.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_STYLESHEET =
+
+# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# cascading style sheets that are included after the standard style sheets
+# created by doxygen. Using this option one can overrule certain style aspects.
+# This is preferred over using HTML_STYLESHEET since it does not replace the
+# standard style sheet and is therefore more robust against future updates.
+# Doxygen will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list). For an example see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_STYLESHEET =
+
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
+# files will be copied as-is; there are no commands or markers available.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_FILES =
+
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
+# will adjust the colors in the style sheet and background images according to
+# this color. Hue is specified as an angle on a colorwheel, see
+# http://en.wikipedia.org/wiki/Hue for more information. For instance the value
+# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
+# purple, and 360 is red again.
+# Minimum value: 0, maximum value: 359, default value: 220.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_HUE = 220
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
+# in the HTML output. For a value of 0 the output will use grayscales only. A
+# value of 255 will produce the most vivid colors.
+# Minimum value: 0, maximum value: 255, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_SAT = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
+# luminance component of the colors in the HTML output. Values below 100
+# gradually make the output lighter, whereas values above 100 make the output
+# darker. The value divided by 100 is the actual gamma applied, so 80 represents
+# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
+# change the gamma.
+# Minimum value: 40, maximum value: 240, default value: 80.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_GAMMA = 80
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting this
+# to YES can help to show when doxygen was last run and thus if the
+# documentation is up to date.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_TIMESTAMP = NO
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_DYNAMIC_SECTIONS = NO
+
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
+# shown in the various tree structured indices initially; the user can expand
+# and collapse entries dynamically later on. Doxygen will expand the tree to
+# such a level that at most the specified number of entries are visible (unless
+# a fully collapsed tree already exceeds this amount). So setting the number of
+# entries 1 will produce a full collapsed tree by default. 0 is a special value
+# representing an infinite number of entries and will result in a full expanded
+# tree by default.
+# Minimum value: 0, maximum value: 9999, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files will be
+# generated that can be used as input for Apple's Xcode 3 integrated development
+# environment (see: http://developer.apple.com/tools/xcode/), introduced with
+# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a
+# Makefile in the HTML output directory. Running make will produce the docset in
+# that directory and running make install will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
+# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
+# for more information.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_DOCSET = NO
+
+# This tag determines the name of the docset feed. A documentation feed provides
+# an umbrella under which multiple documentation sets from a single provider
+# (such as a company or product suite) can be grouped.
+# The default value is: Doxygen generated docs.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_FEEDNAME = "Doxygen generated docs"
+
+# This tag specifies a string that should uniquely identify the documentation
+# set bundle. This should be a reverse domain-name style string, e.g.
+# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_BUNDLE_ID = org.doxygen.Project
+
+# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
+# the documentation publisher. This should be a reverse domain-name style
+# string, e.g. com.mycompany.MyDocSet.documentation.
+# The default value is: org.doxygen.Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_ID = org.doxygen.Publisher
+
+# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
+# The default value is: Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_NAME = Publisher
+
+# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
+# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
+# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
+# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on
+# Windows.
+#
+# The HTML Help Workshop contains a compiler that can convert all HTML output
+# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
+# files are now used as the Windows 98 help format, and will replace the old
+# Windows help format (.hlp) on all Windows platforms in the future. Compressed
+# HTML files also contain an index, a table of contents, and you can search for
+# words in the documentation. The HTML workshop also contains a viewer for
+# compressed HTML files.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_HTMLHELP = NO
+
+# The CHM_FILE tag can be used to specify the file name of the resulting .chm
+# file. You can add a path in front of the file if the result should not be
+# written to the html output directory.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_FILE =
+
+# The HHC_LOCATION tag can be used to specify the location (absolute path
+# including file name) of the HTML help compiler (hhc.exe). If non-empty,
+# doxygen will try to run the HTML help compiler on the generated index.hhp.
+# The file has to be specified with full path.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+HHC_LOCATION =
+
+# The GENERATE_CHI flag controls if a separate .chi index file is generated
+# (YES) or that it should be included in the master .chm file (NO).
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+GENERATE_CHI = NO
+
+# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
+# and project file content.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_INDEX_ENCODING =
+
+# The BINARY_TOC flag controls whether a binary table of contents is generated
+# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
+# enables the Previous and Next buttons.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+BINARY_TOC = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members to
+# the table of contents of the HTML help documentation and to the tree view.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+TOC_EXPAND = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
+# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
+# (.qch) of the generated HTML documentation.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_QHP = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
+# the file name of the resulting .qch file. The path specified is relative to
+# the HTML output folder.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QCH_FILE =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
+# Project output. For more information please see Qt Help Project / Namespace
+# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace).
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_NAMESPACE = org.doxygen.Project
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
+# Help Project output. For more information please see Qt Help Project / Virtual
+# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual-
+# folders).
+# The default value is: doc.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_VIRTUAL_FOLDER = doc
+
+# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
+# filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_NAME =
+
+# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_ATTRS =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's filter section matches. Qt Help Project / Filter Attributes (see:
+# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_SECT_FILTER_ATTRS =
+
+# The QHG_LOCATION tag can be used to specify the location of Qt's
+# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
+# generated .qhp file.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHG_LOCATION =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
+# generated, together with the HTML files, they form an Eclipse help plugin. To
+# install this plugin and make it available under the help contents menu in
+# Eclipse, the contents of the directory containing the HTML and XML files needs
+# to be copied into the plugins directory of eclipse. The name of the directory
+# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
+# After copying Eclipse needs to be restarted before the help appears.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_ECLIPSEHELP = NO
+
+# A unique identifier for the Eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have this
+# name. Each documentation set should have its own identifier.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
+
+ECLIPSE_DOC_ID = org.doxygen.Project
+
+# If you want full control over the layout of the generated HTML pages it might
+# be necessary to disable the index and replace it with your own. The
+# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
+# of each HTML page. A value of NO enables the index and the value YES disables
+# it. Since the tabs in the index contain the same information as the navigation
+# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+DISABLE_INDEX = NO
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information. If the tag
+# value is set to YES, a side panel will be generated containing a tree-like
+# index structure (just like the one that is generated for HTML Help). For this
+# to work a browser that supports JavaScript, DHTML, CSS and frames is required
+# (i.e. any modern browser). Windows users are probably better off using the
+# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
+# further fine-tune the look of the index. As an example, the default style
+# sheet generated by doxygen has an example that shows how to put an image at
+# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
+# the same information as the tab index, you could consider setting
+# DISABLE_INDEX to YES when enabling this option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_TREEVIEW = NO
+
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
+# doxygen will group on one line in the generated HTML documentation.
+#
+# Note that a value of 0 will completely suppress the enum values from appearing
+# in the overview section.
+# Minimum value: 0, maximum value: 20, default value: 4.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+ENUM_VALUES_PER_LINE = 4
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
+# to set the initial width (in pixels) of the frame in which the tree is shown.
+# Minimum value: 0, maximum value: 1500, default value: 250.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+TREEVIEW_WIDTH = 250
+
+# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to
+# external symbols imported via tag files in a separate window.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+EXT_LINKS_IN_WINDOW = NO
+
+# Use this tag to change the font size of LaTeX formulas included as images in
+# the HTML documentation. When you change the font size after a successful
+# doxygen run you need to manually remove any form_*.png images from the HTML
+# output directory to force them to be regenerated.
+# Minimum value: 8, maximum value: 50, default value: 10.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_FONTSIZE = 10
+
+# Use the FORMULA_TRANPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are not
+# supported properly for IE 6.0, but are supported on all modern browsers.
+#
+# Note that when changing this option you need to delete any form_*.png files in
+# the HTML output directory before the changes have effect.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_TRANSPARENT = YES
+
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
+# http://www.mathjax.org) which uses client side Javascript for the rendering
+# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX
+# installed or if you want to formulas look prettier in the HTML output. When
+# enabled you may also need to install MathJax separately and configure the path
+# to it using the MATHJAX_RELPATH option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+USE_MATHJAX = NO
+
+# When MathJax is enabled you can set the default output format to be used for
+# the MathJax output. See the MathJax site (see:
+# http://docs.mathjax.org/en/latest/output.html) for more details.
+# Possible values are: HTML-CSS (which is slower, but has the best
+# compatibility), NativeMML (i.e. MathML) and SVG.
+# The default value is: HTML-CSS.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_FORMAT = HTML-CSS
+
+# When MathJax is enabled you need to specify the location relative to the HTML
+# output directory using the MATHJAX_RELPATH option. The destination directory
+# should contain the MathJax.js script. For instance, if the mathjax directory
+# is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
+# Content Delivery Network so you can quickly see the result without installing
+# MathJax. However, it is strongly recommended to install a local copy of
+# MathJax from http://www.mathjax.org before deployment.
+# The default value is: http://cdn.mathjax.org/mathjax/latest.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest
+
+# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
+# extension names that should be enabled during MathJax rendering. For example
+# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_EXTENSIONS =
+
+# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
+# of code that will be used on startup of the MathJax code. See the MathJax site
+# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
+# example see the documentation.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_CODEFILE =
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
+# the HTML output. The underlying search engine uses javascript and DHTML and
+# should work on any modern browser. Note that when using HTML help
+# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
+# there is already a search function so this one should typically be disabled.
+# For large projects the javascript based search engine can be slow, then
+# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
+# search using the keyboard; to jump to the search box use <access key> + S
+# (what the <access key> is depends on the OS and browser, but it is typically
+# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
+# key> to jump into the search results window, the results can be navigated
+# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
+# the search. The filter options can be selected when the cursor is inside the
+# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
+# to select a filter and <Enter> or <escape> to activate or cancel the filter
+# option.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+SEARCHENGINE = YES
+
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
+# implemented using a web server instead of a web client using Javascript. There
+# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
+# setting. When disabled, doxygen will generate a PHP script for searching and
+# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
+# and searching needs to be provided by external tools. See the section
+# "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SERVER_BASED_SEARCH = NO
+
+# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
+# script for searching. Instead the search results are written to an XML file
+# which needs to be processed by an external indexer. Doxygen will invoke an
+# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
+# search results.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: http://xapian.org/).
+#
+# See the section "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH = NO
+
+# The SEARCHENGINE_URL should point to a search engine hosted by a web server
+# which will return the search results when EXTERNAL_SEARCH is enabled.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: http://xapian.org/). See the section "External Indexing and
+# Searching" for details.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHENGINE_URL =
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
+# search data is written to a file for indexing by an external tool. With the
+# SEARCHDATA_FILE tag the name of this file can be specified.
+# The default file is: searchdata.xml.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHDATA_FILE = searchdata.xml
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
+# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
+# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
+# projects and redirect the results back to the right project.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH_ID =
+
+# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
+# projects other than the one defined by this configuration file, but that are
+# all added to the same external search index. Each project needs to have a
+# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
+# to a relative location where the documentation can be found. The format is:
+# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTRA_SEARCH_MAPPINGS =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
+# The default value is: YES.
+
+GENERATE_LATEX = NO
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_OUTPUT = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked.
+#
+# Note that when enabling USE_PDFLATEX this option is only used for generating
+# bitmaps for formulas in the HTML output, but not in the Makefile that is
+# written to the output directory.
+# The default file is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_CMD_NAME = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
+# index for LaTeX.
+# The default file is: makeindex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+MAKEINDEX_CMD_NAME = makeindex
+
+# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+COMPACT_LATEX = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used by the
+# printer.
+# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
+# 14 inches) and executive (7.25 x 10.5 inches).
+# The default value is: a4.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PAPER_TYPE = a4
+
+# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
+# that should be included in the LaTeX output. The package can be specified just
+# by its name or with the correct syntax as to be used with the LaTeX
+# \usepackage command. To get the times font for instance you can specify :
+# EXTRA_PACKAGES=times or EXTRA_PACKAGES={times}
+# To use the option intlimits with the amsmath package you can specify:
+# EXTRA_PACKAGES=[intlimits]{amsmath}
+# If left blank no extra packages will be included.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+EXTRA_PACKAGES =
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
+# generated LaTeX document. The header should contain everything until the first
+# chapter. If it is left blank doxygen will generate a standard header. See
+# section "Doxygen usage" for information on how to let doxygen write the
+# default header to a separate file.
+#
+# Note: Only use a user-defined header if you know what you are doing! The
+# following commands have a special meaning inside the header: $title,
+# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
+# $projectbrief, $projectlogo. Doxygen will replace $title with the empty
+# string, for the replacement values of the other commands the user is referred
+# to HTML_HEADER.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HEADER =
+
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
+# generated LaTeX document. The footer should contain everything after the last
+# chapter. If it is left blank doxygen will generate a standard footer. See
+# LATEX_HEADER for more information on how to generate a default footer and what
+# special commands can be used inside the footer.
+#
+# Note: Only use a user-defined footer if you know what you are doing!
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_FOOTER =
+
+# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# LaTeX style sheets that are included after the standard style sheets created
+# by doxygen. Using this option one can overrule certain style aspects. Doxygen
+# will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list).
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_STYLESHEET =
+
+# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the LATEX_OUTPUT output
+# directory. Note that the files will be copied as-is; there are no commands or
+# markers available.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_FILES =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
+# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
+# contain links (just like the HTML output) instead of page references. This
+# makes the output suitable for online browsing using a PDF viewer.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PDF_HYPERLINKS = YES
+
+# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
+# the PDF file directly from the LaTeX files. Set this option to YES, to get a
+# higher quality PDF documentation.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+USE_PDFLATEX = YES
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
+# command to the generated LaTeX files. This will instruct LaTeX to keep running
+# if errors occur, instead of asking the user for help. This option is also used
+# when generating formulas in HTML.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BATCHMODE = NO
+
+# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
+# index chapters (such as File Index, Compound Index, etc.) in the output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HIDE_INDICES = NO
+
+# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
+# code with syntax highlighting in the LaTeX output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_SOURCE_CODE = NO
+
+# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
+# bibliography, e.g. plainnat, or ieeetr. See
+# http://en.wikipedia.org/wiki/BibTeX and \cite for more info.
+# The default value is: plain.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BIB_STYLE = plain
+
+# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated
+# page will contain the date and time when the page was generated. Setting this
+# to NO can help when comparing the output of multiple runs.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_TIMESTAMP = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The
+# RTF output is optimized for Word 97 and may not look too pretty with other RTF
+# readers/editors.
+# The default value is: NO.
+
+GENERATE_RTF = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: rtf.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_OUTPUT = rtf
+
+# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+COMPACT_RTF = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
+# contain hyperlink fields. The RTF file will contain links (just like the HTML
+# output) instead of page references. This makes the output suitable for online
+# browsing using Word or some other Word compatible readers that support those
+# fields.
+#
+# Note: WordPad (write) and others do not support links.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_HYPERLINKS = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's config
+# file, i.e. a series of assignments. You only have to provide replacements,
+# missing definitions are set to their default value.
+#
+# See also section "Doxygen usage" for information on how to generate the
+# default style sheet that doxygen normally uses.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_STYLESHEET_FILE =
+
+# Set optional variables used in the generation of an RTF document. Syntax is
+# similar to doxygen's config file. A template extensions file can be generated
+# using doxygen -e rtf extensionFile.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_EXTENSIONS_FILE =
+
+# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
+# with syntax highlighting in the RTF output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_SOURCE_CODE = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for
+# classes and files.
+# The default value is: NO.
+
+GENERATE_MAN = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it. A directory man3 will be created inside the directory specified by
+# MAN_OUTPUT.
+# The default directory is: man.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_OUTPUT = man
+
+# The MAN_EXTENSION tag determines the extension that is added to the generated
+# man pages. In case the manual section does not start with a number, the number
+# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
+# optional.
+# The default value is: .3.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_EXTENSION = .3
+
+# The MAN_SUBDIR tag determines the name of the directory created within
+# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
+# MAN_EXTENSION with the initial . removed.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_SUBDIR =
+
+# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
+# will generate one additional man file for each entity documented in the real
+# man page(s). These additional files only source the real man page, but without
+# them the man command would be unable to find the correct page.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_LINKS = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that
+# captures the structure of the code including all documentation.
+# The default value is: NO.
+
+GENERATE_XML = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: xml.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_OUTPUT = xml
+
+# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program
+# listings (including syntax highlighting and cross-referencing information) to
+# the XML output. Note that enabling this will significantly increase the size
+# of the XML output.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_PROGRAMLISTING = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to the DOCBOOK output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files
+# that can be used to generate PDF.
+# The default value is: NO.
+
+GENERATE_DOCBOOK = NO
+
+# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
+# front of it.
+# The default directory is: docbook.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_OUTPUT = docbook
+
+# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
+# program listings (including syntax highlighting and cross-referencing
+# information) to the DOCBOOK output. Note that enabling this will significantly
+# increase the size of the DOCBOOK output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_PROGRAMLISTING = NO
+
+#---------------------------------------------------------------------------
+# Configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
+# AutoGen Definitions (see http://autogen.sf.net) file that captures the
+# structure of the code including all documentation. Note that this feature is
+# still experimental and incomplete at the moment.
+# The default value is: NO.
+
+GENERATE_AUTOGEN_DEF = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module
+# file that captures the structure of the code including all documentation.
+#
+# Note that this feature is still experimental and incomplete at the moment.
+# The default value is: NO.
+
+GENERATE_PERLMOD = NO
+
+# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary
+# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
+# output from the Perl module output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_LATEX = NO
+
+# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely
+# formatted so it can be parsed by a human reader. This is useful if you want to
+# understand what is going on. On the other hand, if this tag is set to NO, the
+# size of the Perl module output will be much smaller and Perl will parse it
+# just the same.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_PRETTY = YES
+
+# The names of the make variables in the generated doxyrules.make file are
+# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
+# so different doxyrules.make files included by the same Makefile don't
+# overwrite each other's variables.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_MAKEVAR_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all
+# C-preprocessor directives found in the sources and include files.
+# The default value is: YES.
+
+ENABLE_PREPROCESSING = YES
+
+# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
+# in the source code. If set to NO, only conditional compilation will be
+# performed. Macro expansion can be done in a controlled way by setting
+# EXPAND_ONLY_PREDEF to YES.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+MACRO_EXPANSION = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
+# the macro expansion is limited to the macros specified with the PREDEFINED and
+# EXPAND_AS_DEFINED tags.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_ONLY_PREDEF = NO
+
+# If the SEARCH_INCLUDES tag is set to YES, the include files in the
+# INCLUDE_PATH will be searched if a #include is found.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SEARCH_INCLUDES = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by the
+# preprocessor.
+# This tag requires that the tag SEARCH_INCLUDES is set to YES.
+
+INCLUDE_PATH =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will be
+# used.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+INCLUDE_FILE_PATTERNS =
+
+# The PREDEFINED tag can be used to specify one or more macro names that are
+# defined before the preprocessor is started (similar to the -D option of e.g.
+# gcc). The argument of the tag is a list of macros of the form: name or
+# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
+# is assumed. To prevent a macro definition from being undefined via #undef or
+# recursively expanded use the := operator instead of the = operator.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+PREDEFINED = DOXY
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
+# tag can be used to specify a list of macro names that should be expanded. The
+# macro definition that is found in the sources will be used. Use the PREDEFINED
+# tag if you want to use a different macro definition that overrules the
+# definition found in the source code.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_AS_DEFINED =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
+# remove all references to function-like macros that are alone on a line, have
+# an all uppercase name, and do not end with a semicolon. Such function macros
+# are typically used for boiler-plate code, and will confuse the parser if not
+# removed.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SKIP_FUNCTION_MACROS = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to external references
+#---------------------------------------------------------------------------
+
+# The TAGFILES tag can be used to specify one or more tag files. For each tag
+# file the location of the external documentation should be added. The format of
+# a tag file without this location is as follows:
+# TAGFILES = file1 file2 ...
+# Adding location for the tag files is done as follows:
+# TAGFILES = file1=loc1 "file2 = loc2" ...
+# where loc1 and loc2 can be relative or absolute paths or URLs. See the
+# section "Linking to external documentation" for more information about the use
+# of tag files.
+# Note: Each tag file must have a unique name (where the name does NOT include
+# the path). If a tag file is not located in the directory in which doxygen is
+# run, you must also specify the path to the tagfile here.
+
+TAGFILES =
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
+# tag file that is based on the input files it reads. See section "Linking to
+# external documentation" for more information about the usage of tag files.
+
+GENERATE_TAGFILE =
+
+# If the ALLEXTERNALS tag is set to YES, all external class will be listed in
+# the class index. If set to NO, only the inherited external classes will be
+# listed.
+# The default value is: NO.
+
+ALLEXTERNALS = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES, all external groups will be listed
+# in the modules index. If set to NO, only the current project's groups will be
+# listed.
+# The default value is: YES.
+
+EXTERNAL_GROUPS = YES
+
+# If the EXTERNAL_PAGES tag is set to YES, all external pages will be listed in
+# the related pages index. If set to NO, only the current project's pages will
+# be listed.
+# The default value is: YES.
+
+EXTERNAL_PAGES = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script
+# interpreter (i.e. the result of 'which perl').
+# The default file (with absolute path) is: /usr/bin/perl.
+
+PERL_PATH = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES, doxygen will generate a class diagram
+# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to
+# NO turns the diagrams off. Note that this option also works with HAVE_DOT
+# disabled, but it is recommended to install and use dot, since it yields more
+# powerful graphs.
+# The default value is: YES.
+
+CLASS_DIAGRAMS = YES
+
+# You can define message sequence charts within doxygen comments using the \msc
+# command. Doxygen will then run the mscgen tool (see:
+# http://www.mcternan.me.uk/mscgen/)) to produce the chart and insert it in the
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where
+# the mscgen tool resides. If left empty the tool is assumed to be found in the
+# default search path.
+
+MSCGEN_PATH =
+
+# You can include diagrams made with dia in doxygen documentation. Doxygen will
+# then run dia to produce the diagram and insert it in the documentation. The
+# DIA_PATH tag allows you to specify the directory where the dia binary resides.
+# If left empty dia is assumed to be found in the default search path.
+
+DIA_PATH =
+
+# If set to YES the inheritance and collaboration graphs will hide inheritance
+# and usage relations if the target is undocumented or is not a class.
+# The default value is: YES.
+
+HIDE_UNDOC_RELATIONS = YES
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
+# available from the path. This tool is part of Graphviz (see:
+# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
+# Bell Labs. The other options in this section have no effect if this option is
+# set to NO
+# The default value is: YES.
+
+HAVE_DOT = YES
+
+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
+# to run in parallel. When set to 0 doxygen will base this on the number of
+# processors available in the system. You can set it explicitly to a value
+# larger than 0 to get control over the balance between CPU load and processing
+# speed.
+# Minimum value: 0, maximum value: 32, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_NUM_THREADS = 0
+
+# When you want a differently looking font in the dot files that doxygen
+# generates you can specify the font name using DOT_FONTNAME. You need to make
+# sure dot is able to find the font, which can be done by putting it in a
+# standard location or by setting the DOTFONTPATH environment variable or by
+# setting DOT_FONTPATH to the directory containing the font.
+# The default value is: Helvetica.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_FONTNAME = Helvetica
+
+# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
+# dot graphs.
+# Minimum value: 4, maximum value: 24, default value: 10.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_FONTSIZE = 10
+
+# By default doxygen will tell dot to use the default font as specified with
+# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set
+# the path where dot can find it using this tag.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_FONTPATH =
+
+# If the CLASS_GRAPH tag is set to YES then doxygen will generate a graph for
+# each documented class showing the direct and indirect inheritance relations.
+# Setting this tag to YES will force the CLASS_DIAGRAMS tag to NO.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+CLASS_GRAPH = YES
+
+# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a
+# graph for each documented class showing the direct and indirect implementation
+# dependencies (inheritance, containment, and class references variables) of the
+# class with other documented classes.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+COLLABORATION_GRAPH = YES
+
+# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for
+# groups, showing the direct groups dependencies.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+GROUP_GRAPHS = YES
+
+# If the UML_LOOK tag is set to YES, doxygen will generate inheritance and
+# collaboration diagrams in a style similar to the OMG's Unified Modeling
+# Language.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+UML_LOOK = NO
+
+# If the UML_LOOK tag is enabled, the fields and methods are shown inside the
+# class node. If there are many fields or methods and many nodes the graph may
+# become too big to be useful. The UML_LIMIT_NUM_FIELDS threshold limits the
+# number of items for each type to make the size more manageable. Set this to 0
+# for no limit. Note that the threshold may be exceeded by 50% before the limit
+# is enforced. So when you set the threshold to 10, up to 15 fields may appear,
+# but if the number exceeds 15, the total amount of fields shown is limited to
+# 10.
+# Minimum value: 0, maximum value: 100, default value: 10.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+UML_LIMIT_NUM_FIELDS = 10
+
+# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and
+# collaboration graphs will show the relations between templates and their
+# instances.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+TEMPLATE_RELATIONS = NO
+
+# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to
+# YES then doxygen will generate a graph for each documented file showing the
+# direct and indirect include dependencies of the file with other documented
+# files.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+INCLUDE_GRAPH = YES
+
+# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
+# set to YES then doxygen will generate a graph for each documented file showing
+# the direct and indirect include dependencies of the file with other documented
+# files.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+INCLUDED_BY_GRAPH = YES
+
+# If the CALL_GRAPH tag is set to YES then doxygen will generate a call
+# dependency graph for every global function or class method.
+#
+# Note that enabling this option will significantly increase the time of a run.
+# So in most cases it will be better to enable call graphs for selected
+# functions only using the \callgraph command. Disabling a call graph can be
+# accomplished by means of the command \hidecallgraph.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+CALL_GRAPH = NO
+
+# If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
+# dependency graph for every global function or class method.
+#
+# Note that enabling this option will significantly increase the time of a run.
+# So in most cases it will be better to enable caller graphs for selected
+# functions only using the \callergraph command. Disabling a caller graph can be
+# accomplished by means of the command \hidecallergraph.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+CALLER_GRAPH = NO
+
+# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
+# hierarchy of all classes instead of a textual one.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+GRAPHICAL_HIERARCHY = YES
+
+# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the
+# dependencies a directory has on other directories in a graphical way. The
+# dependency relations are determined by the #include relations between the
+# files in the directories.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DIRECTORY_GRAPH = YES
+
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
+# generated by dot. For an explanation of the image formats see the section
+# output formats in the documentation of the dot tool (Graphviz (see:
+# http://www.graphviz.org/)).
+# Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order
+# to make the SVG files visible in IE 9+ (other browsers do not have this
+# requirement).
+# Possible values are: png, png:cairo, png:cairo:cairo, png:cairo:gd, png:gd,
+# png:gd:gd, jpg, jpg:cairo, jpg:cairo:gd, jpg:gd, jpg:gd:gd, gif, gif:cairo,
+# gif:cairo:gd, gif:gd, gif:gd:gd, svg, png:gd, png:gd:gd, png:cairo,
+# png:cairo:gd, png:cairo:cairo, png:cairo:gdiplus, png:gdiplus and
+# png:gdiplus:gdiplus.
+# The default value is: png.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_IMAGE_FORMAT = png
+
+# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
+# enable generation of interactive SVG images that allow zooming and panning.
+#
+# Note that this requires a modern browser other than Internet Explorer. Tested
+# and working are Firefox, Chrome, Safari, and Opera.
+# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make
+# the SVG files visible. Older versions of IE do not have SVG support.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+INTERACTIVE_SVG = NO
+
+# The DOT_PATH tag can be used to specify the path where the dot tool can be
+# found. If left blank, it is assumed the dot tool can be found in the path.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_PATH =
+
+# The DOTFILE_DIRS tag can be used to specify one or more directories that
+# contain dot files that are included in the documentation (see the \dotfile
+# command).
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOTFILE_DIRS =
+
+# The MSCFILE_DIRS tag can be used to specify one or more directories that
+# contain msc files that are included in the documentation (see the \mscfile
+# command).
+
+MSCFILE_DIRS =
+
+# The DIAFILE_DIRS tag can be used to specify one or more directories that
+# contain dia files that are included in the documentation (see the \diafile
+# command).
+
+DIAFILE_DIRS =
+
+# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the
+# path where java can find the plantuml.jar file. If left blank, it is assumed
+# PlantUML is not used or called during a preprocessing step. Doxygen will
+# generate a warning when it encounters a \startuml command in this case and
+# will not generate output for the diagram.
+
+PLANTUML_JAR_PATH =
+
+# When using plantuml, the specified paths are searched for files specified by
+# the !include statement in a plantuml block.
+
+PLANTUML_INCLUDE_PATH =
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes
+# that will be shown in the graph. If the number of nodes in a graph becomes
+# larger than this value, doxygen will truncate the graph, which is visualized
+# by representing a node as a red box. Note that doxygen if the number of direct
+# children of the root node in a graph is already larger than
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note that
+# the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+# Minimum value: 0, maximum value: 10000, default value: 50.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_GRAPH_MAX_NODES = 50
+
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs
+# generated by dot. A depth value of 3 means that only nodes reachable from the
+# root by following a path via at most 3 edges will be shown. Nodes that lay
+# further from the root node will be omitted. Note that setting this option to 1
+# or 2 may greatly reduce the computation time needed for large code bases. Also
+# note that the size of a graph can be further restricted by
+# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+# Minimum value: 0, maximum value: 1000, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+MAX_DOT_GRAPH_DEPTH = 0
+
+# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
+# background. This is disabled by default, because dot on Windows does not seem
+# to support this out of the box.
+#
+# Warning: Depending on the platform used, enabling this option may lead to
+# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
+# read).
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_TRANSPARENT = NO
+
+# Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output
+# files in one run (i.e. multiple -o and -T options on the command line). This
+# makes dot run faster, but since only newer versions of dot (>1.8.10) support
+# this, this feature is disabled by default.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_MULTI_TARGETS = NO
+
+# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page
+# explaining the meaning of the various boxes and arrows in the dot generated
+# graphs.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+GENERATE_LEGEND = YES
+
+# If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate dot
+# files that are used to generate the various graphs.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_CLEANUP = YES
diff --git a/README.org b/README.org
index bd589ba..6436e3b 100644
--- a/README.org
+++ b/README.org
@@ -12,7 +12,7 @@ A lightweight C++ library for accessing Oxford Nanopore Technologies sequencing
The core library is written in header-only C++11, and it enables read-write access to fast5 files from C++ code.
-The core library requires no installation, other than setting the compiler's include path to find [[file:src/fast5.hpp][fast5.hpp]]. See [[file:src/f5ls-full.cpp][f5ls-full.cpp]] for an example.
+The core library requires no installation, other than setting the compiler's include path to find [[file:include/fast5.hpp][fast5.hpp]]. See [[file:src/f5ls-full.cpp][f5ls-full.cpp]] for an example.
The core library is built on top the HDF5 C API, so the compiler must also be able to find the HDF5 headers and libraries. See the project's Travis CI [[file:.travis.Dockerfile.in][Dockerfile]] for an example of how to install prerequisites on Debian Jessie.
diff --git a/src/fast5.hpp b/include/fast5.hpp
similarity index 99%
rename from src/fast5.hpp
rename to include/fast5.hpp
index db6eb1d..9216c43 100644
--- a/src/fast5.hpp
+++ b/include/fast5.hpp
@@ -22,11 +22,11 @@
#include <map>
#include <stdexcept>
-#include "logger.hpp"
-#include "fast5_version.hpp"
-#include "hdf5_tools.hpp"
-#include "Huffman_Packer.hpp"
-#include "Bit_Packer.hpp"
+#include "fast5/logger.hpp"
+#include "fast5/fast5_version.hpp"
+#include "fast5/hdf5_tools.hpp"
+#include "fast5/Huffman_Packer.hpp"
+#include "fast5/Bit_Packer.hpp"
#define MAX_K_LEN 8
@@ -1566,7 +1566,19 @@ private:
{
std::string tmp;
Base::read(path, tmp);
- auto pref = basecall_root_path().substr(1) + "/" + basecall_group_prefix();
+
+ // Metrichor writes "Analyses" before the group, Albacore does not
+ std::string possible_prefix = "Analyses";
+ std::string pref = "";
+
+ if(tmp.substr(0, possible_prefix.length()) == possible_prefix) {
+ // metrichor version
+ pref = possible_prefix + "/" + basecall_group_prefix();
+ } else {
+ // albacore version
+ pref = basecall_group_prefix();
+ }
+
if (tmp.size() >= pref.size()
and tmp.substr(0, pref.size()) == pref)
{
diff --git a/src/Bit_Packer.hpp b/include/fast5/Bit_Packer.hpp
similarity index 100%
rename from src/Bit_Packer.hpp
rename to include/fast5/Bit_Packer.hpp
diff --git a/src/Huffman_Packer.hpp b/include/fast5/Huffman_Packer.hpp
similarity index 100%
rename from src/Huffman_Packer.hpp
rename to include/fast5/Huffman_Packer.hpp
diff --git a/src/cwmap.fast5_ed_len_1.inl b/include/fast5/cwmap.fast5_ed_len_1.inl
similarity index 100%
rename from src/cwmap.fast5_ed_len_1.inl
rename to include/fast5/cwmap.fast5_ed_len_1.inl
diff --git a/src/cwmap.fast5_ed_skip_1.inl b/include/fast5/cwmap.fast5_ed_skip_1.inl
similarity index 100%
rename from src/cwmap.fast5_ed_skip_1.inl
rename to include/fast5/cwmap.fast5_ed_skip_1.inl
diff --git a/src/cwmap.fast5_ev_move_1.inl b/include/fast5/cwmap.fast5_ev_move_1.inl
similarity index 100%
rename from src/cwmap.fast5_ev_move_1.inl
rename to include/fast5/cwmap.fast5_ev_move_1.inl
diff --git a/src/cwmap.fast5_ev_rel_skip_1.inl b/include/fast5/cwmap.fast5_ev_rel_skip_1.inl
similarity index 100%
rename from src/cwmap.fast5_ev_rel_skip_1.inl
rename to include/fast5/cwmap.fast5_ev_rel_skip_1.inl
diff --git a/src/cwmap.fast5_fq_bp_1.inl b/include/fast5/cwmap.fast5_fq_bp_1.inl
similarity index 100%
rename from src/cwmap.fast5_fq_bp_1.inl
rename to include/fast5/cwmap.fast5_fq_bp_1.inl
diff --git a/src/cwmap.fast5_fq_qv_1.inl b/include/fast5/cwmap.fast5_fq_qv_1.inl
similarity index 100%
rename from src/cwmap.fast5_fq_qv_1.inl
rename to include/fast5/cwmap.fast5_fq_qv_1.inl
diff --git a/src/cwmap.fast5_rw_1.inl b/include/fast5/cwmap.fast5_rw_1.inl
similarity index 100%
rename from src/cwmap.fast5_rw_1.inl
rename to include/fast5/cwmap.fast5_rw_1.inl
diff --git a/src/fast5_version.hpp b/include/fast5/fast5_version.hpp
similarity index 100%
rename from src/fast5_version.hpp
rename to include/fast5/fast5_version.hpp
diff --git a/src/hdf5_tools.hpp b/include/fast5/hdf5_tools.hpp
similarity index 55%
rename from src/hdf5_tools.hpp
rename to include/fast5/hdf5_tools.hpp
index 6fa9124..7d17116 100644
--- a/src/hdf5_tools.hpp
+++ b/include/fast5/hdf5_tools.hpp
@@ -25,11 +25,15 @@
#include <limits>
#include <type_traits>
+/// Original HDF5 C API.
namespace hdf5
{
+#ifndef DOXY
#include <hdf5.h>
+#endif
}
+/// New C++ wrapper for the HDF5 C API.
namespace hdf5_tools
{
using namespace hdf5;
@@ -39,9 +43,15 @@ class Exception
: public std::exception
{
public:
- Exception(const std::string& msg) : _msg(active_path() + ": " + msg) {}
- const char* what() const noexcept { return _msg.c_str(); }
- static std::string& active_path()
+ /// Ctor: from message @p msg.
+ Exception(std::string const & msg) : _msg(active_path() + ": " + msg) {}
+ /// Get exception message.
+ char const * what() const noexcept { return _msg.c_str(); }
+ /**
+ * Active HDF5 operation path.
+ * If set during a high-level HDF5 operation, it will be printed as part of any exception message.
+ */
+ static std::string & active_path()
{
static thread_local std::string _active_path;
return _active_path;
@@ -53,99 +63,132 @@ private:
// Forward declaration
class Compound_Map;
+/// Internal constructs.
namespace detail
{
-/// Compute offset of a struct member from a member pointer (runtime version).
-template < typename T, typename U >
+/**
+ * Compute offset of a struct member from a member pointer (runtime version).
+ * @tparam T Struct type.
+ * @tparam U Member type.
+ */
+template <typename T, typename U>
std::size_t offset_of(U T::* mem_ptr)
{
- return reinterpret_cast< std::size_t >(&(((T*)0)->*mem_ptr));
+ return reinterpret_cast<std::size_t>(&(((T*)0)->*mem_ptr));
}
-/// TempMetaFunc: Given destination type, deduce memory type to be used in hdf5 read operation.
-/// Only useful for numeric types.
-/// HDF5 idiosyncracy:
-/// Types such as H5T_NATIVE_INT are not constants(!?), so id() is not a constexpr.
-template < typename T > struct get_mem_type { static hid_t id() { return -1; } };
-// signed integral:
-template <> struct get_mem_type< char > { static hid_t id() { return H5T_NATIVE_CHAR; } };
-template <> struct get_mem_type< short > { static hid_t id() { return H5T_NATIVE_SHORT; } };
-template <> struct get_mem_type< int > { static hid_t id() { return H5T_NATIVE_INT; } };
-template <> struct get_mem_type< long > { static hid_t id() { return H5T_NATIVE_LONG; } };
-template <> struct get_mem_type< long long > { static hid_t id() { return H5T_NATIVE_LLONG; } };
-// unsigned integral:
-template <> struct get_mem_type< unsigned char > { static hid_t id() { return H5T_NATIVE_UCHAR; } };
-template <> struct get_mem_type< unsigned short > { static hid_t id() { return H5T_NATIVE_USHORT; } };
-template <> struct get_mem_type< unsigned > { static hid_t id() { return H5T_NATIVE_UINT; } };
-template <> struct get_mem_type< unsigned long > { static hid_t id() { return H5T_NATIVE_ULONG; } };
-template <> struct get_mem_type< unsigned long long > { static hid_t id() { return H5T_NATIVE_ULLONG; } };
-// float:
-template <> struct get_mem_type< float > { static hid_t id() { return H5T_NATIVE_FLOAT; } };
-template <> struct get_mem_type< double > { static hid_t id() { return H5T_NATIVE_DOUBLE; } };
-template <> struct get_mem_type< long double > { static hid_t id() { return H5T_NATIVE_LDOUBLE; } };
+/**
+ * TMF: Get HDF5 memory type for native numeric destination type.
+ * Note HDF5 idiosyncrasy:
+ * Types such as H5T_NATIVE_INT are not constants(!?), so id() is not a constexpr.
+ */
+template <typename T>
+struct get_mem_type
+{
+ /// Id
+ static hid_t id()
+ {
+ return -1;
+ }
+};
+#ifndef DOXY
+// signed integral
+template <> struct get_mem_type<char> { static hid_t id() { return H5T_NATIVE_CHAR; } };
+template <> struct get_mem_type<short> { static hid_t id() { return H5T_NATIVE_SHORT; } };
+template <> struct get_mem_type<int> { static hid_t id() { return H5T_NATIVE_INT; } };
+template <> struct get_mem_type<long> { static hid_t id() { return H5T_NATIVE_LONG; } };
+template <> struct get_mem_type<long long> { static hid_t id() { return H5T_NATIVE_LLONG; } };
+// unsigned integral
+template <> struct get_mem_type<unsigned char> { static hid_t id() { return H5T_NATIVE_UCHAR; } };
+template <> struct get_mem_type<unsigned short> { static hid_t id() { return H5T_NATIVE_USHORT; } };
+template <> struct get_mem_type<unsigned> { static hid_t id() { return H5T_NATIVE_UINT; } };
+template <> struct get_mem_type<unsigned long> { static hid_t id() { return H5T_NATIVE_ULONG; } };
+template <> struct get_mem_type<unsigned long long> { static hid_t id() { return H5T_NATIVE_ULLONG; } };
+// float
+template <> struct get_mem_type<float> { static hid_t id() { return H5T_NATIVE_FLOAT; } };
+template <> struct get_mem_type<double> { static hid_t id() { return H5T_NATIVE_DOUBLE; } };
+template <> struct get_mem_type<long double> { static hid_t id() { return H5T_NATIVE_LDOUBLE; } };
+#endif
/**
- * Class of memory type:
- * 0 - unknown
- * 1 - numeric (signed/unsigned integer or float)
- * 2 - fixed length string (char array)
- * 3 - variable length string (std::string)
- * 4 - class
+ * TMF: Get class of memory type.
+ * Results:
+ * - 0: unknown
+ * - 1: numeric (signed/unsigned integer or float)
+ * - 2: fixed length string (char array)
+ * - 3: variable length string (std::string)
+ * - 4: struct/class
*/
-template < typename T >
+template <typename T>
struct mem_type_class
{
- static const int value =
- std::conditional< std::is_integral< T >::value or std::is_floating_point< T >::value,
- std::integral_constant< int, 1 >,
- typename std::conditional< std::is_class< T >::value,
- std::integral_constant< int, 4 >,
- std::integral_constant< int, 0 > >::type >::type::value;
+#ifndef DOXY
+ static int const value =
+ std::conditional<std::is_integral<T>::value or std::is_floating_point<T>::value,
+ std::integral_constant<int, 1>,
+ typename std::conditional<std::is_class<T>::value,
+ std::integral_constant<int, 4>,
+ std::integral_constant<int, 0>>::type>::type::value;
+#else
+ /// Value
+ static int const value = 0;
+#endif
};
-template < size_t Size >
-struct mem_type_class< char[Size] >
+#ifndef DOXY
+template <size_t Size>
+struct mem_type_class<char[Size]>
{
- static const int value = 2;
+ static int const value = 2;
};
-template < size_t Size >
-struct mem_type_class< const char[Size] >
+template <size_t Size>
+struct mem_type_class<char const[Size]>
{
- static const int value = 2;
+ static int const value = 2;
};
-template < size_t Size >
-struct mem_type_class< std::array< char, Size > >
+template <size_t Size>
+struct mem_type_class<std::array<char, Size>>
{
- static const int value = 2;
+ static int const value = 2;
};
-template < size_t Size >
-struct mem_type_class< std::array< const char, Size > >
+template <size_t Size>
+struct mem_type_class<std::array<char const, Size>>
{
- static const int value = 2;
+ static int const value = 2;
};
template <>
-struct mem_type_class< std::string >
+struct mem_type_class<std::string>
{
- static const int value = 3;
+ static int const value = 3;
};
+#endif
-// Struct whose purpuse is to destroy the HDF object during destruction
+/**
+ * HDF5 object holder.
+ * Upon destruction, deallocate the held HDF5 object, check the HDF5 API return value, and throw exception on error.
+ */
struct HDF_Object_Holder
{
+ /// HDF5 object
hid_t id;
- std::function< herr_t(hid_t) > dtor;
+ /// HDF5 object deallocator
+ std::function<herr_t(hid_t)> dtor;
+
+ /// Ctor: default
HDF_Object_Holder()
: id(0) {}
- HDF_Object_Holder(const HDF_Object_Holder&) = delete;
- HDF_Object_Holder(HDF_Object_Holder&& other)
+ /// Ctor: copy
+ HDF_Object_Holder(HDF_Object_Holder const &) = delete;
+ /// Ctor: move
+ HDF_Object_Holder(HDF_Object_Holder && other)
: id(0)
{
- load(std::move(other));
- }
- HDF_Object_Holder(hid_t _id, std::function< herr_t(hid_t) > _dtor)
- {
- load(_id, _dtor);
+ *this = std::move(other);
}
+ /// Ctor: from HDF5 object and destructor
+ HDF_Object_Holder(hid_t _id, std::function<herr_t(hid_t)> _dtor)
+ : id(_id), dtor(_dtor) {}
+ /// Dtor: throw on HDF5 errors
~HDF_Object_Holder() noexcept(false)
{
if (id > 0)
@@ -157,8 +200,10 @@ struct HDF_Object_Holder
id = 0;
}
}
- HDF_Object_Holder& operator = (const HDF_Object_Holder&) = delete;
- HDF_Object_Holder& operator = (HDF_Object_Holder&& other)
+ /// Asop: copy
+ HDF_Object_Holder & operator = (HDF_Object_Holder const &) = delete;
+ /// Asop: move
+ HDF_Object_Holder & operator = (HDF_Object_Holder && other)
{
if (&other != this)
{
@@ -167,24 +212,18 @@ struct HDF_Object_Holder
}
return *this;
}
- void load(hid_t _id, std::function< herr_t(hid_t) > _dtor)
- {
- id = _id;
- dtor = _dtor;
- }
- void load(HDF_Object_Holder&& other)
- {
- *this = std::move(other);
- }
}; // struct HDF_Object_Holder
+/// Holder of static methods
struct Util
{
/**
- * Make hdf5 string type.
- * @param sz If negative, make varlen string; else make fixlen string of size sz.
+ * Create HDF5 string type.
+ * @param sz If nonnegative, create fixed length string type of size @p sz;
+ * else create variable length string type.
*/
- static HDF_Object_Holder make_str_type(long sz)
+ static HDF_Object_Holder
+ make_str_type(long sz)
{
assert(sz != 0);
HDF_Object_Holder res(
@@ -193,362 +232,406 @@ struct Util
size_t tmp = sz < 0? H5T_VARIABLE : sz;
wrap(H5Tset_size, res.id, tmp);
return res;
- } // make_str_type
+ } // make_str_type()
+
+ /**
+ * Wrapper of HDF5 calls.
+ * Apply HDF5 call and check return value for validity.
+ * @tparam Function HDF5 function type.
+ * @tparam Args Variable arguments type.
+ * @param f HDF5 function.
+ * @param args Variable arguments.
+ */
+ template <typename Function, typename... Args>
+ static typename std::result_of<Function(Args...)>::type
+ wrap(Function && f, Args && ...args)
+ {
+ auto res = f(args...);
+ auto const & f_info = get_fcn_info((void(*)())&f);
+ if (not f_info.second((void*)&res)) throw Exception(std::string("error in ") + f_info.first);
+ return res;
+ }
+
+ /**
+ * Wrapped closer function.
+ * Create and return a wrapped closer function.
+ * @tparam Function HDF5 closer function type.
+ * @param f HDF5 closer function.
+ */
+ template <typename Function>
+ static std::function<herr_t(hid_t)>
+ wrapped_closer(Function && f)
+ {
+ return [&] (hid_t id) { return wrap(f, id); };
+ }
+private:
/**
- * Get name and return value checker for hdf5 function.
+ * Get name and return value checker for HDF5 function.
+ * Maintain a static map of HDF5 functions and corresponding checks for return value validity.
*/
- static const std::pair< const char *, std::function< bool(void *) > >&
+ static std::pair<char const *, std::function<bool(void *)>> const &
get_fcn_info(void (*fcn_ptr)())
{
- static const std::map< void (*)(), std::pair< const char *, std::function< bool(void *) > > > fcn_info_m =
+ static std::map<void (*)(), std::pair<char const *, std::function<bool(void *)>>> const fcn_info_m =
{
{ (void(*)())&H5Aclose,
{ "H5Aclose",
- [] (void * vp) { return *reinterpret_cast< herr_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<herr_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Acreate2,
{ "H5Acreate2",
- [] (void * vp) { return *reinterpret_cast< hid_t * >(vp) > 0; }
+ [] (void * vp) { return *reinterpret_cast<hid_t *>(vp) > 0; }
}
},
{ (void(*)())&H5Aexists_by_name,
{ "H5Aexists_by_name",
- [] (void * vp) { return *reinterpret_cast< htri_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<htri_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Aget_name_by_idx,
{ "H5Aget_name_by_idx",
- [] (void * vp) { return *reinterpret_cast< ssize_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<ssize_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Aget_space,
{ "H5Aget_space",
- [] (void * vp) { return *reinterpret_cast< hid_t * >(vp) > 0; }
+ [] (void * vp) { return *reinterpret_cast<hid_t *>(vp) > 0; }
}
},
{ (void(*)())&H5Aget_type,
{ "H5Aget_type",
- [] (void * vp) { return *reinterpret_cast< hid_t * >(vp) > 0; }
+ [] (void * vp) { return *reinterpret_cast<hid_t *>(vp) > 0; }
}
},
{ (void(*)())&H5Aopen,
{ "H5Aopen",
- [] (void * vp) { return *reinterpret_cast< hid_t * >(vp) > 0; }
+ [] (void * vp) { return *reinterpret_cast<hid_t *>(vp) > 0; }
}
},
{ (void(*)())&H5Aopen_by_name,
{ "H5Aopen_by_name",
- [] (void * vp) { return *reinterpret_cast< hid_t * >(vp) > 0; }
+ [] (void * vp) { return *reinterpret_cast<hid_t *>(vp) > 0; }
}
},
{ (void(*)())&H5Aread,
{ "H5Aread",
- [] (void * vp) { return *reinterpret_cast< herr_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<herr_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Awrite,
{ "H5Awrite",
- [] (void * vp) { return *reinterpret_cast< herr_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<herr_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Dclose,
{ "H5Dclose",
- [] (void * vp) { return *reinterpret_cast< herr_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<herr_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Dcreate2,
{ "H5Dcreate2",
- [] (void * vp) { return *reinterpret_cast< hid_t * >(vp) > 0; }
+ [] (void * vp) { return *reinterpret_cast<hid_t *>(vp) > 0; }
}
},
{ (void(*)())&H5Dget_space,
{ "H5Dget_space",
- [] (void * vp) { return *reinterpret_cast< hid_t * >(vp) > 0; }
+ [] (void * vp) { return *reinterpret_cast<hid_t *>(vp) > 0; }
}
},
{ (void(*)())&H5Dget_type,
{ "H5Dget_type",
- [] (void * vp) { return *reinterpret_cast< hid_t * >(vp) > 0; }
+ [] (void * vp) { return *reinterpret_cast<hid_t *>(vp) > 0; }
}
},
{ (void(*)())&H5Dopen,
{ "H5Dopen",
- [] (void * vp) { return *reinterpret_cast< hid_t * >(vp) > 0; }
+ [] (void * vp) { return *reinterpret_cast<hid_t *>(vp) > 0; }
}
},
{ (void(*)())&H5Dread,
{ "H5Dread",
- [] (void * vp) { return *reinterpret_cast< herr_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<herr_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Dvlen_reclaim,
{ "H5Dvlen_reclaim",
- [] (void * vp) { return *reinterpret_cast< herr_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<herr_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Dwrite,
{ "H5Dwrite",
- [] (void * vp) { return *reinterpret_cast< herr_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<herr_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Gclose,
{ "H5Gclose",
- [] (void * vp) { return *reinterpret_cast< herr_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<herr_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Gcreate2,
{ "H5Gcreate2",
- [] (void * vp) { return *reinterpret_cast< hid_t * >(vp) > 0; }
+ [] (void * vp) { return *reinterpret_cast<hid_t *>(vp) > 0; }
}
},
{ (void(*)())&H5Gget_info,
{ "H5Gget_info",
- [] (void * vp) { return *reinterpret_cast< herr_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<herr_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Gopen2,
{ "H5Gopen2",
- [] (void * vp) { return *reinterpret_cast< hid_t * >(vp) > 0; }
+ [] (void * vp) { return *reinterpret_cast<hid_t *>(vp) > 0; }
}
},
{ (void(*)())&H5Lexists,
{ "H5Lexists",
- [] (void * vp) { return *reinterpret_cast< htri_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<htri_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Lget_name_by_idx,
{ "H5Lget_name_by_idx",
- [] (void * vp) { return *reinterpret_cast< ssize_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<ssize_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Oclose,
{ "H5Oclose",
- [] (void * vp) { return *reinterpret_cast< herr_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<herr_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Oexists_by_name,
{ "H5Oexists_by_name",
- [] (void * vp) { return *reinterpret_cast< htri_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<htri_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Oget_info,
{ "H5Oget_info",
- [] (void * vp) { return *reinterpret_cast< herr_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<herr_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Oopen,
{ "H5Oopen",
- [] (void * vp) { return *reinterpret_cast< hid_t * >(vp) > 0; }
+ [] (void * vp) { return *reinterpret_cast<hid_t *>(vp) > 0; }
}
},
{ (void(*)())&H5Pclose,
{ "H5Pclose",
- [] (void * vp) { return *reinterpret_cast< herr_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<herr_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Pcreate,
{ "H5Pcreate",
- [] (void * vp) { return *reinterpret_cast< hid_t * >(vp) > 0; }
+ [] (void * vp) { return *reinterpret_cast<hid_t *>(vp) > 0; }
}
},
{ (void(*)())&H5Pset_create_intermediate_group,
{ "H5Pset_create_intermediate_group",
- [] (void * vp) { return *reinterpret_cast< herr_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<herr_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Sclose,
{ "H5Sclose",
- [] (void * vp) { return *reinterpret_cast< herr_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<herr_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Screate,
{ "H5Screate",
- [] (void * vp) { return *reinterpret_cast< hid_t * >(vp) > 0; }
+ [] (void * vp) { return *reinterpret_cast<hid_t *>(vp) > 0; }
}
},
{ (void(*)())&H5Screate_simple,
{ "H5Screate_simple",
- [] (void * vp) { return *reinterpret_cast< hid_t * >(vp) > 0; }
+ [] (void * vp) { return *reinterpret_cast<hid_t *>(vp) > 0; }
}
},
{ (void(*)())&H5Sget_simple_extent_dims,
{ "H5Sget_simple_extent_dims",
- [] (void * vp) { return *reinterpret_cast< int * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<int *>(vp) >= 0; }
}
},
{ (void(*)())&H5Sget_simple_extent_ndims,
{ "H5Sget_simple_extent_ndims",
- [] (void * vp) { return *reinterpret_cast< int * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<int *>(vp) >= 0; }
}
},
{ (void(*)())&H5Sget_simple_extent_type,
{ "H5Sget_simple_extent_type",
- [] (void * vp) { return *reinterpret_cast< H5S_class_t * >(vp) != H5S_NO_CLASS; }
+ [] (void * vp) { return *reinterpret_cast<H5S_class_t *>(vp) != H5S_NO_CLASS; }
}
},
{ (void(*)())&H5Tclose,
{ "H5Tclose",
- [] (void * vp) { return *reinterpret_cast< herr_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<herr_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Tcopy,
{ "H5Tcopy",
- [] (void * vp) { return *reinterpret_cast< hid_t * >(vp) > 0; }
+ [] (void * vp) { return *reinterpret_cast<hid_t *>(vp) > 0; }
}
},
{ (void(*)())&H5Tcreate,
{ "H5Tcreate",
- [] (void * vp) { return *reinterpret_cast< hid_t * >(vp) > 0; }
+ [] (void * vp) { return *reinterpret_cast<hid_t *>(vp) > 0; }
}
},
{ (void(*)())&H5Tget_class,
{ "H5Tget_class",
- [] (void * vp) { return *reinterpret_cast< H5T_class_t * >(vp) != H5T_NO_CLASS; }
+ [] (void * vp) { return *reinterpret_cast<H5T_class_t *>(vp) != H5T_NO_CLASS; }
}
},
{ (void(*)())&H5Tget_cset,
{ "H5Tget_cset",
- [] (void * vp) { return *reinterpret_cast< H5T_cset_t * >(vp) != H5T_CSET_ERROR; }
+ [] (void * vp) { return *reinterpret_cast<H5T_cset_t *>(vp) != H5T_CSET_ERROR; }
}
},
{ (void(*)())&H5Tget_member_index,
{ "H5Tget_member_index",
- [] (void * vp) { return *reinterpret_cast< int * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<int *>(vp) >= 0; }
}
},
{ (void(*)())&H5Tget_member_name,
{ "H5Tget_member_name",
- [] (void * vp) { return *reinterpret_cast< char* * >(vp) != nullptr; }
+ [] (void * vp) { return *reinterpret_cast<char* *>(vp) != nullptr; }
}
},
{ (void(*)())&H5Tget_member_type,
{ "H5Tget_member_type",
- [] (void * vp) { return *reinterpret_cast< hid_t * >(vp) > 0; }
+ [] (void * vp) { return *reinterpret_cast<hid_t *>(vp) > 0; }
}
},
{ (void(*)())&H5Tget_nmembers,
{ "H5Tget_nmembers",
- [] (void * vp) { return *reinterpret_cast< int * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<int *>(vp) >= 0; }
}
},
{ (void(*)())&H5Tget_sign,
{ "H5Tget_sign",
- [] (void * vp) { return *reinterpret_cast< H5T_sign_t * >(vp) != H5T_SGN_ERROR; }
+ [] (void * vp) { return *reinterpret_cast<H5T_sign_t *>(vp) != H5T_SGN_ERROR; }
}
},
{ (void(*)())&H5Tget_size,
{ "H5Tget_size",
- [] (void * vp) { return *reinterpret_cast< size_t * >(vp) > 0; }
+ [] (void * vp) { return *reinterpret_cast<size_t *>(vp) > 0; }
}
},
{ (void(*)())&H5Tinsert,
{ "H5Tinsert",
- [] (void * vp) { return *reinterpret_cast< herr_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<herr_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Tis_variable_str,
{ "H5Tis_variable_str",
- [] (void * vp) { return *reinterpret_cast< htri_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<htri_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Tset_cset,
{ "H5Tset_cset",
- [] (void * vp) { return *reinterpret_cast< herr_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<herr_t *>(vp) >= 0; }
}
},
{ (void(*)())&H5Tset_size,
{ "H5Tset_size",
- [] (void * vp) { return *reinterpret_cast< herr_t * >(vp) >= 0; }
+ [] (void * vp) { return *reinterpret_cast<herr_t *>(vp) >= 0; }
}
},
};
return fcn_info_m.at(fcn_ptr);
}
- /**
- * General-purpose wrapper of hdf5 calls that checks return value for validity.
- */
- template < typename Function, typename... Args >
- static typename std::result_of< Function(Args...) >::type
- wrap(Function&& f, Args&& ...args)
- {
- auto res = f(args...);
- const auto& f_info = get_fcn_info((void(*)())&f);
- if (not f_info.second((void*)&res)) throw Exception(std::string("error in ") + f_info.first);
- return res;
- }
-
- /**
- * Wrap closer function.
- */
- template < typename Function >
- static std::function< herr_t(hid_t) > wrapped_closer(Function&& f)
- {
- return [&] (hid_t id) { return wrap(f, id); };
- }
}; // struct Util
-/// Description of a member inside a compound
-/// Only works with numeric, string, and struct types.
+/**
+ * Description of a compound member.
+ * Only for numeric, string, and struct member types.
+ */
struct Compound_Member_Description
{
public:
- Compound_Member_Description(const std::string& _name, size_t _offset, hid_t _numeric_type_id)
+ /**
+ * Ctor: numeric compound member
+ * @param _name Compound member name
+ * @param _offset Compound member offset
+ * @param _numeric_type_id HDF5 numeric type
+ */
+ Compound_Member_Description(std::string const & _name, size_t _offset, hid_t _numeric_type_id)
: type(numeric),
name(_name),
offset(_offset),
numeric_type_id(_numeric_type_id) {}
- Compound_Member_Description(const std::string& _name, size_t _offset, size_t _char_array_size)
+ /**
+ * Ctor: fixed-length string compound member
+ * @param _name Compound member name
+ * @param _offset Compound member offset
+ * @param _char_array_size Fixed length string size
+ */
+ Compound_Member_Description(std::string const & _name, size_t _offset, size_t _char_array_size)
: type(char_array),
name(_name),
offset(_offset),
char_array_size(_char_array_size) {}
- Compound_Member_Description(const std::string& _name, size_t _offset)
+ /**
+ * Ctor: variable-length string compound member
+ * @param _name Compound member name
+ * @param _offset Compound member offset
+ */
+ Compound_Member_Description(std::string const & _name, size_t _offset)
: type(string),
name(_name),
offset(_offset) {}
- Compound_Member_Description(const std::string& _name, size_t _offset,
- const Compound_Map* _compound_map_ptr, size_t _compound_size)
+ /**
+ * Ctor: struct compound member
+ * @param _name Compound member name
+ * @param _offset Compound member offset
+ * @param _compound_map_ptr Inner compound map
+ * @param _compound_size Inner compound size
+ */
+ Compound_Member_Description(std::string const & _name, size_t _offset,
+ Compound_Map const * _compound_map_ptr, size_t _compound_size)
: type(compound),
name(_name),
offset(_offset),
compound_map_ptr(_compound_map_ptr),
compound_size(_compound_size) {}
+ /// Is member a numeric
bool is_numeric() const { return type == numeric; }
+ /// Is member a fixed-length string
bool is_char_array() const { return type == char_array; }
+ /// Is member a variable-length string
bool is_string() const { return type == string; }
+ /// Is member a compound
bool is_compound() const { return type == compound; }
+ /// Create and return a holder for the HDF5 type of this compound member.
HDF_Object_Holder get_type() const
{
assert(not is_compound());
HDF_Object_Holder res;
if (is_numeric())
{
- res.load(numeric_type_id, nullptr);
+ res = HDF_Object_Holder(numeric_type_id, nullptr);
}
else if (is_char_array())
{
- res.load(Util::make_str_type(char_array_size));
+ res = Util::make_str_type(char_array_size);
}
else if (is_string())
{
- res.load(Util::make_str_type(-1));
+ res = Util::make_str_type(-1);
}
return res;
- }
+ } // get_type()
- friend std::ostream& operator << (std::ostream& os, const Compound_Member_Description& e)
+ /// Write compound member description to stream
+ friend std::ostream & operator << (std::ostream & os, Compound_Member_Description const & e)
{
os << "(&=" << (void*)&e
<< ",name=\"" << e.name
@@ -562,6 +645,7 @@ public:
return os;
}
+ /// Compound member type enum
enum member_type
{
numeric,
@@ -569,17 +653,25 @@ public:
string,
compound
};
+
+ /// Compound member type
member_type type;
+ /// Compound member name
std::string name;
+ /// Compound member offset
size_t offset;
union
{
+ /// For numeric types: HDF5 type
hid_t numeric_type_id;
+ /// For string types: size of string type, 0 if variable-length.
size_t char_array_size;
- const Compound_Map* compound_map_ptr;
+ /// For compound types: inner compound map
+ Compound_Map const * compound_map_ptr;
};
+ /// For compound types: inner compound size
size_t compound_size;
-}; // Compound_Member_Description
+}; // struct Compound_Member_Description
} // namespace detail
@@ -587,54 +679,76 @@ public:
class Compound_Map
{
public:
+ /// Ctor: default
Compound_Map() = default;
- Compound_Map(const Compound_Map&) = delete;
- Compound_Map(Compound_Map&&) = default;
- Compound_Map& operator = (const Compound_Map&) = delete;
- Compound_Map& operator = (Compound_Map&&) = default;
- ~Compound_Map() = default;
-
- template < typename T, typename U >
- void add_member(const std::string& name, U T::* mem_ptr)
+ /// Ctor: copy
+ Compound_Map(Compound_Map const &) = delete;
+ /// Ctor: move
+ Compound_Map(Compound_Map &&) = default;
+ /// Asop: copy
+ Compound_Map & operator = (Compound_Map const &) = delete;
+ /// Asop: move
+ Compound_Map & operator = (Compound_Map &&) = default;
+
+ /**
+ * Add numeric/string compound member.
+ * @tparam T struct type
+ * @tparam U member type
+ * @param name HDF5 compound member name
+ * @param mem_ptr struct member pointer
+ */
+ template <typename T, typename U>
+ void add_member(std::string const & name, U T::* mem_ptr)
{
- static_assert(detail::mem_type_class< U >::value == 1
- or detail::mem_type_class< U >::value == 2
- or detail::mem_type_class< U >::value == 3,
+ static_assert(detail::mem_type_class<U>::value == 1
+ or detail::mem_type_class<U>::value == 2
+ or detail::mem_type_class<U>::value == 3,
"add_member(name, mem_ptr) overload expects numerical or string types only");
- if (detail::mem_type_class< U >::value == 1)
+ if (detail::mem_type_class<U>::value == 1)
{
- _members.emplace_back(name, detail::offset_of(mem_ptr), detail::get_mem_type< U >::id());
+ _members.emplace_back(name, detail::offset_of(mem_ptr), detail::get_mem_type<U>::id());
}
- else if (detail::mem_type_class< U >::value == 2)
+ else if (detail::mem_type_class<U>::value == 2)
{
_members.emplace_back(name, detail::offset_of(mem_ptr), sizeof(U));
}
- else if (detail::mem_type_class< U >::value == 3)
+ else if (detail::mem_type_class<U>::value == 3)
{
_members.emplace_back(name, detail::offset_of(mem_ptr));
}
}
- template < typename T, typename U >
- void add_member(const std::string& name, U T::* mem_ptr, const Compound_Map* compound_map_ptr)
+ /**
+ * Add compound compound member.
+ * @tparam T struct type
+ * @tparam U member type
+ * @param name HDF5 compound member name
+ * @param mem_ptr struct member pointer
+ * @param compound_map_ptr inner compound map
+ */
+ template <typename T, typename U>
+ void add_member(std::string const & name, U T::* mem_ptr, Compound_Map const * compound_map_ptr)
{
- static_assert(detail::mem_type_class< U >::value == 4,
+ static_assert(detail::mem_type_class<U>::value == 4,
"add_member(name, mem_ptr, compound_map_ptr) overload expects class types only");
_members.emplace_back(name, detail::offset_of(mem_ptr), compound_map_ptr, sizeof(U));
}
- const std::vector< detail::Compound_Member_Description >& members() const { return _members; }
+ /// Get list of compound members.
+ std::vector<detail::Compound_Member_Description> const & members() const { return _members; }
+ /// Type returned by @p get_member_ptr_list().
+ typedef std::deque<std::pair<std::deque<detail::Compound_Member_Description const *>,
+ size_t>> member_ptr_list_type;
/**
- * Get list of non-compound member types.
- * @return A list of pairs; first: list of member ptrs followed; second: absolute offset.
+ * Get list of inner non-compound member types.
+ * If members of the top-level compound are also compounds, they are traversed recursively.
+ * @return A list of pairs; first: list of member ptrs followed; second: absolute offset
*/
- typedef std::deque< std::pair< std::deque< const detail::Compound_Member_Description* >,
- size_t > > member_ptr_list_type;
member_ptr_list_type get_member_ptr_list() const
{
member_ptr_list_type res;
- for (const auto& e : members())
+ for (auto const & e : members())
{
member_ptr_list_type::value_type p;
if (not e.is_compound())
@@ -647,7 +761,7 @@ public:
else
{
auto tmp = e.compound_map_ptr->get_member_ptr_list();
- for (auto& tmp_p : tmp)
+ for (auto & tmp_p : tmp)
{
member_ptr_list_type::value_type p;
p.first = std::move(tmp_p.first);
@@ -661,21 +775,21 @@ public:
}
/**
- * Produce hdf5 compound datatype for this map.
+ * Create an HDF5 compound type for this map.
* @param compound_size Extrenally-tracked compound size
- * @param selector If empty, use all elements; if not empty, use only elements that pass selection.
- * @fill If true, type offsets follow compound map offsets, allowing for gaps;
- * if false: type offsets are minimal values required to fit members.
+ * @param selector If empty, use all elements; if not empty, use only elements that pass selection
+ * @param fill If true, type offsets follow compound map offsets, allowing for gaps;
+ * if false: type offsets are minimal values required to fit members
*/
detail::HDF_Object_Holder build_type(
size_t compound_size,
- std::function< bool(const detail::Compound_Member_Description&) > selector = nullptr,
+ std::function<bool(detail::Compound_Member_Description const &)> selector = nullptr,
bool fill = true) const
{
//std::clog << "===== build_type (" << (void*)this << ") start" << std::endl;
- std::deque< std::tuple< std::string, detail::HDF_Object_Holder, size_t > > stype_id_holder_l;
+ std::deque<std::tuple<std::string, detail::HDF_Object_Holder, size_t>> stype_id_holder_l;
size_t compressed_size = 0;
- for (const auto& e : members())
+ for (auto const & e : members())
{
detail::HDF_Object_Holder stype_id_holder;
if (selector and not e.is_compound() and not selector(e)) continue;
@@ -705,7 +819,7 @@ public:
detail::HDF_Object_Holder res(
detail::Util::wrap(H5Tcreate, H5T_COMPOUND, fill? compound_size : compressed_size),
detail::Util::wrapped_closer(H5Tclose));
- for (const auto& t : stype_id_holder_l)
+ for (auto const & t : stype_id_holder_l)
{
//std::clog << "===== build_type (" << (void*)this << ") adding name=\"" << std::get<0>(t) << "\", offset=" << std::get<2>(t) << std::endl;
detail::Util::wrap(H5Tinsert, res.id, std::get<0>(t).c_str(), std::get<2>(t), std::get<1>(t).id);
@@ -714,14 +828,19 @@ public:
return res;
}
+ /**
+ * Create a flat HDF5 compound type for members in the given list
+ * @param l List of compound member descriptions
+ * @param id If non-zero, HDF5 id of compound type to extend
+ */
static detail::HDF_Object_Holder build_flat_type(
- const member_ptr_list_type::value_type::first_type& l, hid_t id = 0)
+ member_ptr_list_type::value_type::first_type const & l, hid_t id = 0)
{
detail::HDF_Object_Holder res;
size_t sz = 0;
for (auto it = l.rbegin(); it != l.rend(); ++it)
{
- const detail::Compound_Member_Description& e = **it;
+ auto const & e = **it;
assert((it == l.rbegin()) == (not e.is_compound()));
assert((it == l.rbegin()) == (res.id == 0));
assert((it == l.rbegin()) == (sz == 0));
@@ -729,11 +848,11 @@ public:
{
if (id == 0)
{
- res.load(e.get_type());
+ res = e.get_type();
}
else
{
- res.load(
+ res = detail::HDF_Object_Holder(
detail::Util::wrap(H5Tcopy, id),
detail::Util::wrapped_closer(H5Tclose));
}
@@ -749,17 +868,21 @@ public:
}
/**
- * Get compound member from an existing compound type.
+ * Extract inner compound member type.
+ * Given an existing compound type and a list of member compound pointers to follow,
+ * extract inner compound type.
+ * @param id HDF5 compound type
+ * @param l List of inner compound members to follow (all but the last must be compounds)
*/
static detail::HDF_Object_Holder get_compound_member(
- hid_t id, const member_ptr_list_type::value_type::first_type& l)
+ hid_t id, member_ptr_list_type::value_type::first_type const & l)
{
detail::HDF_Object_Holder res(
detail::Util::wrap(H5Tcopy, id),
detail::Util::wrapped_closer(H5Tclose));
for (auto it = l.begin(); it != l.end(); ++it)
{
- const detail::Compound_Member_Description& e = **it;
+ auto const & e = **it;
assert(detail::Util::wrap(H5Tget_class, res.id) == H5T_COMPOUND);
unsigned idx = detail::Util::wrap(H5Tget_member_index, res.id, e.name.c_str());
detail::HDF_Object_Holder tmp(
@@ -772,46 +895,55 @@ public:
}
private:
- std::vector< detail::Compound_Member_Description > _members;
+ std::vector<detail::Compound_Member_Description> _members;
}; // Compound_Map
namespace detail
{
-// open object to be read, return dspace_id, file_dtype_id, reader fcn, reader fcn name, and is_ds
+/**
+ * Manage HDF5 file object access during a read operation.
+ * Opens a file object, and retrieves various attributes.
+ * Note: called by @p Reader; level 2 below @p File::read().
+ */
struct Reader_Base
{
- Reader_Base(hid_t grp_id, const std::string& name)
+ /**
+ * Ctor: from HDF5 group and name.
+ * @param grp_id HDF5 group id
+ * @param name HDF5 object name (dataset or attribute)
+ */
+ Reader_Base(hid_t grp_id, std::string const & name)
{
int status = Util::wrap(H5Aexists_by_name, grp_id, ".", name.c_str(), H5P_DEFAULT);
is_ds = status == 0;
if (is_ds)
{
- obj_id_holder.load(
+ obj_id_holder = HDF_Object_Holder(
Util::wrap(H5Dopen, grp_id, name.c_str(), H5P_DEFAULT),
Util::wrapped_closer(H5Dclose));
- dspace_id_holder.load(
+ dspace_id_holder = HDF_Object_Holder(
Util::wrap(H5Dget_space, obj_id_holder.id),
Util::wrapped_closer(H5Sclose));
- file_dtype_id_holder.load(
+ file_dtype_id_holder = HDF_Object_Holder(
Util::wrap(H5Dget_type, obj_id_holder.id),
Util::wrapped_closer(H5Tclose));
- reader = [&] (hid_t mem_dtype_id, void* dest) {
+ reader = [&] (hid_t mem_dtype_id, void * dest) {
return Util::wrap(H5Dread, obj_id_holder.id, mem_dtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, dest);
};
}
else
{
- obj_id_holder.load(
+ obj_id_holder = HDF_Object_Holder(
Util::wrap(H5Aopen, grp_id, name.c_str(), H5P_DEFAULT),
Util::wrapped_closer(H5Aclose));
- dspace_id_holder.load(
+ dspace_id_holder = HDF_Object_Holder(
Util::wrap(H5Aget_space, obj_id_holder.id),
Util::wrapped_closer(H5Sclose));
- file_dtype_id_holder.load(
+ file_dtype_id_holder = HDF_Object_Holder(
Util::wrap(H5Aget_type, obj_id_holder.id),
Util::wrapped_closer(H5Tclose));
- reader = [&] (hid_t mem_dtype_id, void* dest) {
+ reader = [&] (hid_t mem_dtype_id, void * dest) {
return Util::wrap(H5Aread, obj_id_holder.id, mem_dtype_id, dest);
};
}
@@ -846,25 +978,48 @@ struct Reader_Base
// datatype size
file_dtype_size = Util::wrap(H5Tget_size, file_dtype_id_holder.id);
}
+ /// Object holder
HDF_Object_Holder obj_id_holder;
+ /// Dataspace holder
HDF_Object_Holder dspace_id_holder;
+ /// Datatype holder
HDF_Object_Holder file_dtype_id_holder;
- std::function< void(hid_t, void*) > reader;
+ /// Reader function
+ std::function<void(hid_t, void *)> reader;
+ /// Dataspace class
H5S_class_t dspace_class;
+ /// Dataspace size
size_t dspace_size;
+ /// Datatype class
H5T_class_t file_dtype_class;
+ /// Variable-length string flag
htri_t file_dtype_is_vlen_str;
+ /// Datatype size
size_t file_dtype_size;
+ /// Is-dataset flag
bool is_ds;
}; // struct Reader_Base
-struct String_reader
+/**
+ * Read a vector of strings.
+ */
+struct String_Reader
{
- std::vector< std::string > operator () (
- Reader_Base& reader_base,
- const Compound_Map::member_ptr_list_type::value_type::first_type* mptr_l_ptr = nullptr) const
+ /**
+ * Perform read.
+ * Given a file object and an optional inner member pointer selector,
+ * read extent into vector of strings.
+ * The function converts numeric and fixed/variable-length string HDF5 types to string.
+ * @param reader_base File object read manager.
+ * @param mptr_l_ptr Optional inner compound member selector. If file object is a compound,
+ * the list should specify which inner compound members to follow to get to a base
+ * non-compound member to read.
+ */
+ std::vector<std::string> operator () (
+ Reader_Base const & reader_base,
+ Compound_Map::member_ptr_list_type::value_type::first_type const * mptr_l_ptr = nullptr) const
{
- std::vector< std::string > res(reader_base.dspace_size);
+ std::vector<std::string> res(reader_base.dspace_size);
assert((mptr_l_ptr != nullptr) == (reader_base.file_dtype_class == H5T_COMPOUND));
HDF_Object_Holder file_stype_id_holder;
hid_t file_stype_id = 0;
@@ -879,7 +1034,7 @@ struct String_reader
{
file_stype_id = reader_base.file_dtype_id_holder.id;
}
- auto mem_type_wrapper = [&] (HDF_Object_Holder&& id_holder) {
+ auto mem_type_wrapper = [&] (HDF_Object_Holder && id_holder) {
HDF_Object_Holder tmp(std::move(id_holder));
return (mptr_l_ptr != nullptr
? Compound_Map::build_flat_type(*mptr_l_ptr, tmp.id)
@@ -898,7 +1053,7 @@ struct String_reader
Util::wrap(H5Tset_cset, mem_stype_id_holder.id, file_stype_cset);
mem_dtype_id_holder = mem_type_wrapper(std::move(mem_stype_id_holder));
// prepare buffer to receive data
- std::vector< char * > charptr_buff(res.size(), nullptr);
+ std::vector<char *> charptr_buff(res.size(), nullptr);
// perform the read
reader_base.reader(mem_dtype_id_holder.id, charptr_buff.data());
// transfer strings to destination
@@ -919,7 +1074,7 @@ struct String_reader
Util::wrap(H5Tset_cset, mem_stype_id_holder.id, file_stype_cset);
mem_dtype_id_holder = mem_type_wrapper(std::move(mem_stype_id_holder));
// prepare buffer to receieve data
- std::vector< char > char_buff(res.size() * (file_stype_size + 1), '\0');
+ std::vector<char> char_buff(res.size() * (file_stype_size + 1), '\0');
// perform the read
reader_base.reader(mem_dtype_id_holder.id, char_buff.data());
// transfer strings to destination
@@ -940,9 +1095,9 @@ struct String_reader
{
// compute mem_type
mem_dtype_id_holder = mem_type_wrapper(
- HDF_Object_Holder(get_mem_type< unsigned long long >::id(), nullptr));
+ HDF_Object_Holder(get_mem_type<unsigned long long>::id(), nullptr));
// prepare buffer to read data
- std::vector< unsigned long long > ull_buff(res.size());
+ std::vector<unsigned long long> ull_buff(res.size());
// perform the read
reader_base.reader(mem_dtype_id_holder.id, ull_buff.data());
// transfer to destination
@@ -957,9 +1112,9 @@ struct String_reader
{
// compute mem_type
mem_dtype_id_holder = mem_type_wrapper(
- HDF_Object_Holder(get_mem_type< long long >::id(), nullptr));
+ HDF_Object_Holder(get_mem_type<long long>::id(), nullptr));
// prepare buffer to read data
- std::vector< long long > ll_buff(res.size());
+ std::vector<long long> ll_buff(res.size());
// perform the read
reader_base.reader(mem_dtype_id_holder.id, ll_buff.data());
// transfer to destination
@@ -975,9 +1130,9 @@ struct String_reader
{
// compute mem_type
mem_dtype_id_holder = mem_type_wrapper(
- HDF_Object_Holder(get_mem_type< double >::id(), nullptr));
+ HDF_Object_Holder(get_mem_type<double>::id(), nullptr));
// prepare buffer to read data
- std::vector< double > d_buff(res.size());
+ std::vector<double> d_buff(res.size());
// perform the read
reader_base.reader(mem_dtype_id_holder.id, d_buff.data());
// transfer to destination
@@ -990,28 +1145,55 @@ struct String_reader
}
return res;
}
-};
+}; // struct String_Reader
-// Reader_helper
-// Branch on memory type classes
-template < int, typename >
-struct Reader_helper;
-// numeric
-template < typename Data_Type >
-struct Reader_helper< 1, Data_Type >
+/**
+ * Construct memory data type and invoke @p Reader_Base reader.
+ * Note: called by @p Reader; level 2 below @p File::read().
+ */
+template <int Mem_Type_Class, typename Data_Type>
+struct Reader_Helper;
+
+/// @details @em Specialization_Numeric: @p Mem_Type_Class = 1.
+#ifndef DOXY
+template <typename Data_Type>
+struct Reader_Helper<1, Data_Type>
+#else
+template <int Mem_Type_Class, typename Data_Type>
+struct Reader_Helper
+#endif
{
- void operator () (Reader_Base& reader_base, Data_Type * out) const
+ /**
+ * Functor operator. @em Specialization_Numeric.
+ * Obtain memory type from @p get_mem_type.
+ * @param reader_base File object read manager
+ * @param out Destination
+ */
+ void operator () (Reader_Base const & reader_base, Data_Type * out) const
{
- assert(std::is_integral< Data_Type >::value or std::is_floating_point< Data_Type >::value);
- hid_t mem_dtype_id = get_mem_type< Data_Type >::id();
+ assert(std::is_integral<Data_Type>::value or std::is_floating_point<Data_Type>::value);
+ hid_t mem_dtype_id = get_mem_type<Data_Type>::id();
reader_base.reader(mem_dtype_id, out);
}
};
-// char array
-template < typename Data_Type >
-struct Reader_helper< 2, Data_Type >
+
+/// @details @em Specialization_Fix_Len_String: @p Mem_Type_Class = 2.
+#ifndef DOXY
+template <typename Data_Type>
+struct Reader_Helper<2, Data_Type>
+#else
+template <int Mem_Type_Class, typename Data_Type>
+struct Reader_Helper
+#endif
{
- void operator () (Reader_Base& reader_base, Data_Type * out) const
+ /**
+ * Functor operator. @em Specialization_Fix_Len_String.
+ * If the file datatype is also fixed-length, use @p Reader_Base reader directly.
+ * Else, use @p String_Reader.
+ * @param reader_base File object read manager
+ * @param out Destination
+ */
+ void operator () (Reader_Base const & reader_base, Data_Type * out) const
{
if (reader_base.file_dtype_class == H5T_STRING
and not reader_base.file_dtype_is_vlen_str)
@@ -1023,7 +1205,7 @@ struct Reader_helper< 2, Data_Type >
}
else // conversion needed
{
- auto tmp = String_reader()(reader_base);
+ auto tmp = String_Reader()(reader_base);
for (size_t i = 0; i < tmp.size(); ++i)
{
std::memset(&out[i][0], '\0', sizeof(Data_Type));
@@ -1032,31 +1214,58 @@ struct Reader_helper< 2, Data_Type >
}
}
};
-// string
-template < typename Data_Type >
-struct Reader_helper< 3, Data_Type >
+
+/// @details @em Specialization_Var_Len_String: @p Mem_Type_Class = 3.
+#ifndef DOXY
+template <typename Data_Type>
+struct Reader_Helper<3, Data_Type>
+#else
+template <int Mem_Type_Class, typename Data_Type>
+struct Reader_Helper
+#endif
{
- void operator () (Reader_Base& reader_base, Data_Type * out) const
+ /**
+ * Functor operator. @em Specialization_Var_Len_String.
+ * Use @p String_Reader.
+ * @param reader_base File object read manager
+ * @param out Destination
+ */
+ void operator () (Reader_Base const & reader_base, Data_Type * out) const
{
- static_assert(std::is_same< Data_Type, std::string >::value, "Data_Type not std::string");
- auto tmp = String_reader()(reader_base);
+ static_assert(std::is_same<Data_Type, std::string>::value, "Data_Type not std::string");
+ auto tmp = String_Reader()(reader_base);
for (size_t i = 0; i < tmp.size(); ++i)
{
std::swap(out[i], tmp[i]);
}
}
};
-// compound
-template < typename Data_Type >
-struct Reader_helper< 4, Data_Type >
+
+/// @details @em Specialization_Compound: @p Mem_Type_Class = 4.
+#ifndef DOXY
+template <typename Data_Type>
+struct Reader_Helper<4, Data_Type>
+#else
+template <int Mem_Type_Class, typename Data_Type>
+struct Reader_Helper
+#endif
{
- void operator () (Reader_Base& reader_base, Data_Type * out, const Compound_Map & cm) const
+ /**
+ * Functor operator. @em Specialization_Compound.
+ * Go through the list of compound members;
+ * read all of the ones that don't need conversion in one go;
+ * read the remaining ones one at a time.
+ * @param reader_base File object read manager
+ * @param out Destination
+ * @param cm Compound map
+ */
+ void operator () (Reader_Base const & reader_base, Data_Type * out, Compound_Map const & cm) const
{
// get member list
auto mptr_l = cm.get_member_ptr_list();
// go through members, check they exist, decide if they need conversion
- std::set< const detail::Compound_Member_Description * > conversion_needed_s;
- for (const auto& p : mptr_l)
+ std::set<detail::Compound_Member_Description const *> conversion_needed_s;
+ for (auto const & p : mptr_l)
{
HDF_Object_Holder file_stype_id_holder(
Compound_Map::get_compound_member(reader_base.file_dtype_id_holder.id, p.first));
@@ -1069,7 +1278,7 @@ struct Reader_helper< 4, Data_Type >
}
}
// read all members that do not need conversion all-at-once
- auto implicit_conversion = [&] (const detail::Compound_Member_Description& e) {
+ auto implicit_conversion = [&] (detail::Compound_Member_Description const & e) {
return conversion_needed_s.count(&e) == 0;
};
HDF_Object_Holder mem_dtype_id_holder(cm.build_type(sizeof(Data_Type), implicit_conversion, true));
@@ -1078,12 +1287,12 @@ struct Reader_helper< 4, Data_Type >
reader_base.reader(mem_dtype_id_holder.id, out);
}
// read members that need conversion one-by-one
- for (const auto& p : mptr_l)
+ for (auto const & p : mptr_l)
{
- const detail::Compound_Member_Description& e = *p.first.back();
+ auto const & e = *p.first.back();
if (implicit_conversion(e)) continue;
// read member into vector of strings
- auto tmp = String_reader()(reader_base, &p.first);
+ auto tmp = String_Reader()(reader_base, &p.first);
assert(tmp.size() == reader_base.dspace_size);
// write it to destination
assert(e.is_char_array() or e.is_string());
@@ -1091,8 +1300,8 @@ struct Reader_helper< 4, Data_Type >
{
for (size_t i = 0; i < tmp.size(); ++i)
{
- std::memset(reinterpret_cast< char * >(&out[i]) + p.second, '\0', e.char_array_size);
- std::memcpy(reinterpret_cast< char * >(&out[i]) + p.second,
+ std::memset(reinterpret_cast<char *>(&out[i]) + p.second, '\0', e.char_array_size);
+ std::memcpy(reinterpret_cast<char *>(&out[i]) + p.second,
tmp[i].data(),
std::min(tmp[i].size(), e.char_array_size - 1));
}
@@ -1102,7 +1311,7 @@ struct Reader_helper< 4, Data_Type >
for (size_t i = 0; i < tmp.size(); ++i)
{
std::swap(
- *reinterpret_cast< std::string * >(reinterpret_cast< char * >(&out[i]) + p.second),
+ *reinterpret_cast<std::string *>(reinterpret_cast<char *>(&out[i]) + p.second),
tmp[i]);
}
}
@@ -1110,28 +1319,58 @@ struct Reader_helper< 4, Data_Type >
}
};
-template < typename Data_Type >
+/**
+ * Prepare destination for a read operation.
+ * Branch statically on the destination data type @p Dest_Type.
+ * Use @p Reader_Base to open file object, then pass control to @p Reader_Helper.
+ * Note: called by @p File::read.
+ */
+template <typename Dest_Type>
+struct Reader;
+
+/**
+ * @struct Reader
+ * @details @em Specialization_Default: @p Dest_Type = @p Data_Type.
+ */
+#ifndef DOXY
+template <typename Data_Type>
+struct Reader
+#else
+template <typename Dest_Type>
struct Reader
+#endif
{
- template < typename ...Args >
- void operator () (hid_t grp_id, const std::string& name,
- Data_Type & out, Args&& ...args) const
+ /**
+ * Functor operator.
+ * @em Specialization_Default.
+ * Check file object is scalar (dspace_size == 1).
+ * Quirk: If reading a @p std::string, allow for file object to be an extent
+ * of size 1 characters.
+ * @param grp_id HDF5 group object
+ * @param name HDF5 object name to read
+ * @param out Destination (single address)
+ * @param args Optional reading arguments passed to @p Reader_Helper
+ */
+ template <typename ...Args>
+ void operator () (hid_t grp_id, std::string const & name,
+ Data_Type & out,
+ Args && ...args) const
{
Reader_Base reader_base(grp_id, name);
if (reader_base.dspace_size == 1)
{
- Reader_helper< mem_type_class< Data_Type >::value, Data_Type >()(
- reader_base, &out, std::forward< Args >(args)...);
+ Reader_Helper<mem_type_class<Data_Type>::value, Data_Type>()(
+ reader_base, &out, std::forward<Args>(args)...);
}
- else if (std::is_same< Data_Type, std::string >::value
+ else if (std::is_same<Data_Type, std::string>::value
and reader_base.file_dtype_class == H5T_STRING
and not reader_base.file_dtype_is_vlen_str
and reader_base.file_dtype_size == 1)
{
- std::vector< std::array< char, 1 > > char_buff(reader_base.dspace_size);
- Reader_helper< 2, std::array< char, 1 > >()(
- reader_base, char_buff.data(), std::forward< Args >(args)...);
- reinterpret_cast< std::string& >(out).assign(&char_buff[0][0], reader_base.dspace_size);
+ std::vector<std::array<char, 1>> char_buff(reader_base.dspace_size);
+ Reader_Helper<2, std::array<char, 1>>()(
+ reader_base, char_buff.data(), std::forward<Args>(args)...);
+ reinterpret_cast<std::string &>(out).assign(&char_buff[0][0], reader_base.dspace_size);
}
else
{
@@ -1139,46 +1378,81 @@ struct Reader
}
}
};
-template < typename Data_Type >
-struct Reader< std::vector< Data_Type > >
+/**
+ * @struct Reader
+ * @details @em Specialization_Vector: @p Dest_Type = @p std::vector<Data_Type>.
+ */
+#ifndef DOXY
+template <typename Data_Type>
+struct Reader<std::vector<Data_Type>>
+#else
+template <typename Dest_Type>
+struct Reader
+#endif
{
- template < typename ...Args >
- void operator () (hid_t grp_id, const std::string& name,
- std::vector< Data_Type> & out, Args&& ...args) const
+ /**
+ * Functor operator.
+ * @em Specialization_Vector.
+ * Clear and resize destination vector.
+ * @param grp_id HDF5 group object
+ * @param name HDF5 object name to read
+ * @param out Destination (vector)
+ * @param args Optional reading arguments passed to @p Reader_Helper
+ */
+ template <typename ...Args>
+ void operator () (hid_t grp_id, std::string const & name,
+ std::vector<Data_Type> & out,
+ Args && ...args) const
{
Reader_Base reader_base(grp_id, name);
out.clear();
out.resize(reader_base.dspace_size);
- Reader_helper< mem_type_class< Data_Type >::value, Data_Type >()(
- reader_base, out.data(), std::forward< Args >(args)...);
+ Reader_Helper<mem_type_class<Data_Type>::value, Data_Type>()(
+ reader_base, out.data(), std::forward<Args>(args)...);
}
};
-// Writer_helper_base
-// Common base for Write_helper atomic/compound
-struct Writer_helper_base
+/**
+ * Holder of HDF5 access methods used during a write operation.
+ */
+struct Writer_Base
{
- static HDF_Object_Holder create(hid_t grp_id, const std::string& loc_name, bool as_ds,
+ /**
+ * Create a dataset/attribute.
+ * @param grp_id Parent group object.
+ * @param loc_name dataset/attribute name.
+ * @param as_ds Flag; create dataset iff true.
+ * @param dspace_id HDF5 dataspace.
+ * @param file_dtype_id HDF5 file datatype.
+ */
+ static HDF_Object_Holder create(hid_t grp_id, std::string const & loc_name, bool as_ds,
hid_t dspace_id, hid_t file_dtype_id)
{
HDF_Object_Holder obj_id_holder;
if (as_ds)
{
- obj_id_holder.load(
+ obj_id_holder = HDF_Object_Holder(
Util::wrap(H5Dcreate2, grp_id, loc_name.c_str(), file_dtype_id, dspace_id,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT),
Util::wrapped_closer(H5Dclose));
}
else
{
- obj_id_holder.load(
+ obj_id_holder = HDF_Object_Holder(
Util::wrap(H5Acreate2, grp_id, loc_name.c_str(), file_dtype_id, dspace_id,
H5P_DEFAULT, H5P_DEFAULT),
Util::wrapped_closer(H5Aclose));
}
return obj_id_holder;
}
- static void write(hid_t obj_id, bool as_ds, hid_t mem_dtype_id, const void* in)
+ /**
+ * Write dataset/attribute to file.
+ * @param obj_id Destination object.
+ * @param as_ds Flag; write dataset iff true.
+ * @param mem_dtype_id HDF5 memory datatype.
+ * @param in Source memory address.
+ */
+ static void write(hid_t obj_id, bool as_ds, hid_t mem_dtype_id, void const * in)
{
if (as_ds)
{
@@ -1189,55 +1463,101 @@ struct Writer_helper_base
Util::wrap(H5Awrite, obj_id, mem_dtype_id, in);
}
}
- static void create_and_write(hid_t grp_id, const std::string& loc_name, bool as_ds,
+ /**
+ * Create and write dataset/attribute.
+ * @param grp_id Parent group object.
+ * @param loc_name dataset/attribute name.
+ * @param as_ds Flag; create dataset iff true.
+ * @param dspace_id HDF5 dataspace.
+ * @param mem_dtype_id HDF5 memory datatype.
+ * @param file_dtype_id HDF5 file datatype.
+ * @param in Source memory address.
+ */
+ static void create_and_write(hid_t grp_id, std::string const & loc_name, bool as_ds,
hid_t dspace_id, hid_t mem_dtype_id, hid_t file_dtype_id,
- const void* in)
+ void const * in)
{
HDF_Object_Holder obj_id_holder(create(grp_id, loc_name, as_ds, dspace_id, file_dtype_id));
write(obj_id_holder.id, as_ds, mem_dtype_id, in);
}
-}; // struct Writer_helper_base
+}; // struct Writer_Base
-// Writer_helper
-// Branch on memory type classes
-template < int, typename >
-struct Writer_helper;
-// numeric
-template < typename In_Data_Type >
-struct Writer_helper< 1, In_Data_Type >
- : public Writer_helper_base
+/**
+ * Manage calls to Write_Base methods.
+ * Note: called by @p Writer; level 2 below @p File::write().
+ */
+template <int, typename>
+struct Writer_Helper;
+
+/// @details @em Specialization_Numeric: @p Mem_Type_Class = 1.
+#ifndef DOXY
+template <typename In_Data_Type>
+struct Writer_Helper<1, In_Data_Type>
+#else
+template <int Mem_Type_Class, typename In_Data_Type>
+struct Writer_Helper
+#endif
{
- void operator () (hid_t grp_id, const std::string& loc_name, bool as_ds,
- hid_t dspace_id, size_t,
- const In_Data_Type * in, hid_t file_dtype_id = 0) const
+ /**
+ * Functor operator. @em Specialization_Numeric.
+ * Obtain memory type from @p get_mem_type.
+ * @param grp_id Parent group object.
+ * @param loc_name dataset/attribute name.
+ * @param as_ds Flag; create dataset iff true.
+ * @param dspace_id HDF5 dataspace.
+ * @param in Source memory address.
+ * @param file_dtype_id HDF5 file datatype;
+ * if 0, use @p mem_dtype_id.
+ */
+ void operator () (hid_t grp_id, std::string const & loc_name,
+ bool as_ds, hid_t dspace_id, size_t,
+ In_Data_Type const * in, hid_t file_dtype_id = 0) const
{
- assert(std::is_integral< In_Data_Type >::value or std::is_floating_point< In_Data_Type >::value);
- hid_t mem_dtype_id = get_mem_type< In_Data_Type >::id();
+ assert(std::is_integral<In_Data_Type>::value or std::is_floating_point<In_Data_Type>::value);
+ hid_t mem_dtype_id = get_mem_type<In_Data_Type>::id();
if (file_dtype_id == 0)
{
file_dtype_id = mem_dtype_id;
}
- Writer_helper_base::create_and_write(
+ Writer_Base::create_and_write(
grp_id, loc_name, as_ds,
dspace_id, mem_dtype_id, file_dtype_id,
in);
}
-};
-
-// fixed-length string
-template < typename In_Data_Type >
-struct Writer_helper< 2, In_Data_Type >
- : public Writer_helper_base
+}; // struct Writer_Helper<1, In_Data_Type>
+
+/// @details @em Specialization_Fix_Len_String: @p Mem_Type_Class = 2.
+#ifndef DOXY
+template <typename In_Data_Type>
+struct Writer_Helper<2, In_Data_Type>
+#else
+template <int Mem_Type_Class, typename In_Data_Type>
+struct Writer_Helper
+#endif
{
- void operator () (hid_t grp_id, const std::string& loc_name, bool as_ds,
- hid_t dspace_id, size_t sz,
- const In_Data_Type * in, hid_t file_dtype_id = 0) const
+ /**
+ * Functor operator. @em Specialization_Fix_Len_String.
+ * Write as fixed-length or variable-length strings.
+ * @param grp_id Parent group object.
+ * @param loc_name dataset/attribute name.
+ * @param as_ds Flag; create dataset iff true.
+ * @param dspace_id HDF5 dataspace.
+ * @param sz Number of elements.
+ * @param in Source memory address.
+ * @param file_dtype_id HDF5 file datatype:
+ * if 0, use @p mem_dtype_id;
+ * if >0, write as fixed-length strings of this size;
+ * if <0, write as variable-length strings.
+ */
+ void operator () (hid_t grp_id, std::string const & loc_name,
+ bool as_ds, hid_t dspace_id, size_t sz,
+ In_Data_Type const * in, hid_t file_dtype_id = 0) const
{
HDF_Object_Holder mem_dtype_id_holder;
HDF_Object_Holder file_dtype_id_holder;
- std::vector< const char * > charptr_buff;
- const void * vptr_in = in;
+ std::vector<char const *> charptr_buff;
+ void const * vptr_in = in;
if (file_dtype_id >= 0)
{
mem_dtype_id_holder = Util::make_str_type(sizeof(In_Data_Type));
@@ -1263,26 +1583,43 @@ struct Writer_helper< 2, In_Data_Type >
}
vptr_in = charptr_buff.data();
}
- Writer_helper_base::create_and_write(
+ Writer_Base::create_and_write(
grp_id, loc_name, as_ds,
dspace_id, mem_dtype_id_holder.id, file_dtype_id,
vptr_in);
}
-};
+}; // struct Writer_Helper<2, In_Data_Type>
-// variable-length string
+/// @details @em Specialization_Var_Len_String: @p Mem_Type_Class = 3.
+#ifndef DOXY
template <>
-struct Writer_helper< 3, std::string >
- : public Writer_helper_base
+struct Writer_Helper<3, std::string>
+#else
+template <int Mem_Type_Class, typename In_Data_Type>
+struct Writer_Helper
+#endif
{
- void operator () (hid_t grp_id, const std::string& loc_name, bool as_ds,
- hid_t dspace_id, size_t sz,
- const std::string * in, hid_t file_dtype_id = -1) const
+ /**
+ * Functor operator. @em Specialization_Var_Len_String.
+ * Write as fixed-length or variable-length strings.
+ * @param grp_id Parent group object.
+ * @param loc_name dataset/attribute name.
+ * @param as_ds Flag; create dataset iff true.
+ * @param dspace_id HDF5 dataspace.
+ * @param sz Number of elements.
+ * @param in Source memory address.
+ * @param file_dtype_id HDF5 file datatype:
+ * if -1, write variable-length strings;
+ * if >=0, write as fixed-length strings of that size.
+ */
+ void operator () (hid_t grp_id, std::string const & loc_name,
+ bool as_ds, hid_t dspace_id, size_t sz,
+ std::string const * in, hid_t file_dtype_id = -1) const
{
HDF_Object_Holder mem_dtype_id_holder;
- std::vector< const char * > charptr_buff;
- std::vector< char > char_buff;
- const void * vptr_in;
+ std::vector<char const *> charptr_buff;
+ std::vector<char> char_buff;
+ void const * vptr_in;
if (file_dtype_id == -1) // varlen to varlen
{
mem_dtype_id_holder = Util::make_str_type(-1);
@@ -1297,7 +1634,7 @@ struct Writer_helper< 3, std::string >
{
assert(file_dtype_id > 0 or sz == 1); // file_dtype_id == 0 only allowed for single strings
size_t slen = file_dtype_id > 0 ? file_dtype_id : in[0].size() + 1;
- assert(slen <= std::numeric_limits< long >::max());
+ assert(slen <= std::numeric_limits<long>::max());
mem_dtype_id_holder = Util::make_str_type(slen);
char_buff.resize(sz * slen);
for (hsize_t i = 0; i < sz; ++i)
@@ -1310,21 +1647,38 @@ struct Writer_helper< 3, std::string >
}
vptr_in = char_buff.data();
}
- Writer_helper_base::create_and_write(
+ Writer_Base::create_and_write(
grp_id, loc_name, as_ds,
dspace_id, mem_dtype_id_holder.id, mem_dtype_id_holder.id,
vptr_in);
}
-};
-
-// compound
-template < typename In_Data_Type >
-struct Writer_helper< 4, In_Data_Type >
- : public Writer_helper_base
+}; // struct Writer_Helper<3, std::string>
+
+/// @details @em Specialization_Compound: @p Mem_Type_Class = 4.
+#ifndef DOXY
+template <typename In_Data_Type>
+struct Writer_Helper<4, In_Data_Type>
+#else
+template <int Mem_Type_Class, typename In_Data_Type>
+struct Writer_Helper
+#endif
{
- void operator () (hid_t grp_id, const std::string& loc_name, bool as_ds,
- hid_t dspace_id, size_t sz,
- const In_Data_Type * in, const Compound_Map& cm) const
+ /**
+ * Functor operator. @em Specialization_Compound.
+ * Go through the list of compound members;
+ * write all of the ones that don't need conversion in one go;
+ * write the remaining ones one at a time.
+ * @param grp_id Parent group object.
+ * @param loc_name dataset/attribute name.
+ * @param as_ds Flag; create dataset iff true.
+ * @param dspace_id HDF5 dataspace.
+ * @param sz Number of elements.
+ * @param in Source memory address.
+ * @param cm Compound map.
+ */
+ void operator () (hid_t grp_id, std::string const & loc_name,
+ bool as_ds, hid_t dspace_id, size_t sz,
+ In_Data_Type const * in, Compound_Map const & cm) const
{
HDF_Object_Holder obj_id_holder;
// create object
@@ -1332,83 +1686,125 @@ struct Writer_helper< 4, In_Data_Type >
// create the file type
HDF_Object_Holder file_dtype_id_holder(
cm.build_type(sizeof(In_Data_Type), nullptr, false));
- obj_id_holder = Writer_helper_base::create(
+ obj_id_holder = Writer_Base::create(
grp_id, loc_name, as_ds,
dspace_id, file_dtype_id_holder.id);
}
// define functor that selects members which can be written with implicit conversion
- auto implicit_conversion = [] (const detail::Compound_Member_Description& e) {
- return (e.is_numeric()
- or e.is_char_array());
+ auto implicit_conversion = [] (detail::Compound_Member_Description const & e) {
+ return (e.is_numeric() or e.is_char_array());
};
// write fields which do not need conversion, all-in-one
{
HDF_Object_Holder mem_dtype_id_holder(
cm.build_type(sizeof(In_Data_Type), implicit_conversion, true));
- Writer_helper_base::write(obj_id_holder.id, as_ds, mem_dtype_id_holder.id, in);
+ Writer_Base::write(obj_id_holder.id, as_ds, mem_dtype_id_holder.id, in);
}
// write fields which need conversion, one-by-one
{
auto mptr_l = cm.get_member_ptr_list();
- for (const auto& p : mptr_l)
+ for (auto const & p : mptr_l)
{
- const detail::Compound_Member_Description& e = *p.first.back();
+ auto const & e = *p.first.back();
if (implicit_conversion(e)) continue;
if (not as_ds) throw Exception("string in compound is supported in datasets, but not attributes");
size_t mem_offset = p.second;
if (e.is_string())
{
// prepare memory vector of char*
- std::vector< const char * > charptr_buff(sz);
+ std::vector<char const *> charptr_buff(sz);
for (size_t i = 0; i < sz; ++i)
{
- charptr_buff[i] = reinterpret_cast< const std::string * >(
- reinterpret_cast< const char * >(&in[i]) + mem_offset)->data();
+ charptr_buff[i] = reinterpret_cast<std::string const *>(
+ reinterpret_cast<char const *>(&in[i]) + mem_offset)->data();
}
// create flat hdf5 type
//HDF_Object_Holder mem_dtype_id_holder(Compound_Map::build_flat_type(p.first));
HDF_Object_Holder mem_dtype_id_holder(
cm.build_type(sizeof(In_Data_Type),
- [&e] (const detail::Compound_Member_Description& _e) {
+ [&e] (detail::Compound_Member_Description const & _e) {
return &_e == &e;
},
false));
- Writer_helper_base::write(obj_id_holder.id, as_ds, mem_dtype_id_holder.id, charptr_buff.data());
+ Writer_Base::write(obj_id_holder.id, as_ds, mem_dtype_id_holder.id, charptr_buff.data());
}
}
}
}
-};
+}; // struct Writer_Helper<4, In_Data_Type>
+
+/**
+ * Prepare for a write operation.
+ * Branch statically on the source data type @p Src_Type:
+ * if object is a vector, write a simple extent;
+ * if object is not a vector, write a scalar.
+ * Pass control to appropriate @p Writer_Helper.
+ * Note: called by @p File::write.
+ */
+template <typename Src_Type>
+struct Writer;
-// Writer
-// Struct branches on data argument type:
-// if std::vector, it writes a simple extent;
-// if not std::vector, it writes a scalar.
-template < typename In_Data_Type >
+/**
+ * @struct Writer
+ * @details @em Specialization_Default: @p Src_Type = @p In_Data_Type.
+ */
+#ifndef DOXY
+template <typename In_Data_Type>
+struct Writer
+#else
+template <typename Src_Type>
struct Writer
+#endif
{
- template < typename ...Args >
- void operator () (hid_t grp_id, const std::string& loc_name, bool as_ds,
- const In_Data_Type & in, Args&& ...args) const
+ /**
+ * Functor operator.
+ * @em Specialization_Default.
+ * Create dataspace and invoke @p Writer_Helper.
+ * @param grp_id HDF5 parent group
+ * @param loc_name Object name to write
+ * @param as_ds Flag; create dataset iff true.
+ * @param in Source (single address).
+ * @param args Optional reading arguments passed to @p Writer_Helper.
+ */
+ template <typename ...Args>
+ void operator () (hid_t grp_id, std::string const & loc_name,
+ bool as_ds, In_Data_Type const & in, Args && ...args) const
{
// create dataspace
HDF_Object_Holder dspace_id_holder(
Util::wrap(H5Screate, H5S_SCALAR),
Util::wrapped_closer(H5Sclose));
- Writer_helper< mem_type_class< In_Data_Type >::value, In_Data_Type >()(
+ Writer_Helper<mem_type_class<In_Data_Type>::value, In_Data_Type>()(
grp_id, loc_name, as_ds,
dspace_id_holder.id, 1,
- &in, std::forward< Args >(args)...);
+ &in, std::forward<Args>(args)...);
}
-};
-
-
-template < typename In_Data_Type >
-struct Writer< std::vector< In_Data_Type > >
+}; // struct Writer<In_Data_Type>
+/**
+ * @struct Writer
+ * @details @em Specialization_Vector: @p Src_Type = @p std::vector<In_Data_Type>.
+ */
+#ifndef DOXY
+template <typename In_Data_Type>
+struct Writer<std::vector<In_Data_Type>>
+#else
+template <typename Src_Type>
+struct Writer
+#endif
{
- template < typename ...Args >
- void operator () (hid_t grp_id, const std::string& loc_name, bool as_ds,
- const std::vector< In_Data_Type > & in, Args&& ...args) const
+ /**
+ * Functor operator.
+ * @em Specialization_Vector.
+ * Create dataspace and invoke @p Writer_Helper.
+ * @param grp_id HDF5 parent group
+ * @param loc_name Object name to write
+ * @param as_ds Flag; create dataset iff true.
+ * @param in Source.
+ * @param args Optional reading arguments passed to @p Writer_Helper.
+ */
+ template <typename ...Args>
+ void operator () (hid_t grp_id, std::string const & loc_name,
+ bool as_ds, std::vector<In_Data_Type> const & in, Args && ...args) const
{
assert(not in.empty());
// create dataspace
@@ -1416,12 +1812,12 @@ struct Writer< std::vector< In_Data_Type > >
HDF_Object_Holder dspace_id_holder(
Util::wrap(H5Screate_simple, 1, &sz, nullptr),
Util::wrapped_closer(H5Sclose));
- Writer_helper< mem_type_class< In_Data_Type >::value, In_Data_Type >()(
+ Writer_Helper<mem_type_class<In_Data_Type>::value, In_Data_Type>()(
grp_id, loc_name, as_ds,
dspace_id_holder.id, sz,
- in.data(), std::forward< Args >(args)...);
+ in.data(), std::forward<Args>(args)...);
}
-};
+}; // struct Writer<std::vector<In_Data_Type>>
} // namespace detail
@@ -1429,34 +1825,58 @@ struct Writer< std::vector< In_Data_Type > >
class File
{
public:
- typedef std::map< std::string, std::string > Attr_Map;
+ /// A map of attributes of string type.
+ typedef std::map<std::string, std::string> Attr_Map;
+ /// Ctor: default
File() : _file_id(0) {}
- File(const std::string& file_name, bool rw = false) : _file_id(0) { open(file_name, rw); }
- File(const File&) = delete;
- File& operator = (const File&) = delete;
+ /**
+ * Ctor: from file name
+ * @param file_name File name to open.
+ * @param rw Flag: open for writing iff true.
+ */
+ File(std::string const & file_name, bool rw = false) : _file_id(0) { open(file_name, rw); }
+ /// Ctor: copy
+ File(File const &) = delete;
+ /// Asop: copy
+ File & operator = (File const &) = delete;
+ /// Dtor
~File() { if (is_open()) close(); }
+ /// Check if file is open.
bool is_open() const { return _file_id > 0; }
+ /// Check if file is open for writing.
bool is_rw() const { return _rw; }
- const std::string& file_name() const { return _file_name; }
+ /// Get file name.
+ std::string const & file_name() const { return _file_name; }
- void create(const std::string& file_name, bool truncate = false)
+ /**
+ * Create file.
+ * @param file_name File name to create.
+ * @param truncate Control behaviour if file exists: if true, truncate; if false, fail.
+ */
+ void create(std::string const & file_name, bool truncate = false)
{
if (is_open()) close();
_file_name = file_name;
_rw = true;
_file_id = H5Fcreate(file_name.c_str(), truncate? H5F_ACC_TRUNC : H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
if (not is_open()) throw Exception(_file_name + ": error in H5Fcreate");
- }
- void open(const std::string& file_name, bool rw = false)
+ } // create()
+ /**
+ * Open file.
+ * @param file_name File name to open.
+ * @param rw Flag: open for writing iff true.
+ */
+ void open(std::string const & file_name, bool rw = false)
{
if (is_open()) close();
_file_name = file_name;
_rw = rw;
_file_id = H5Fopen(file_name.c_str(), not rw? H5F_ACC_RDONLY : H5F_ACC_RDWR, H5P_DEFAULT);
if (not is_open()) throw Exception(_file_name + ": error in H5Fopen");
- }
+ } // open()
+ /// Close file
void close()
{
if (not is_open()) return;
@@ -1465,8 +1885,9 @@ public:
if (status < 0) throw Exception(_file_name + ": error in H5Fclose");
_file_id = 0;
_file_name.clear();
- }
- static bool is_valid_file(const std::string& file_name)
+ } // close()
+ /// Check if file name is a valid HDF5 file.
+ static bool is_valid_file(std::string const & file_name)
{
std::ifstream ifs(file_name);
if (not ifs) return false;
@@ -1480,15 +1901,20 @@ public:
status = H5Fclose(file_id);
if (status < 0) throw Exception(file_name + ": error in H5Fclose");
return 1;
- }
+ } // is_valid_file()
+ /// Get HDF5 object count.
static int get_object_count()
{
return H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL);
- }
+ } // get_object_count()
- /// Check if a group exists
- bool group_exists(std::string const & loc_full_name) const
+ /**
+ * Check if an object exists that is a group.
+ * @param loc_full_name Full path.
+ */
+ bool
+ group_exists(std::string const & loc_full_name) const
{
assert(is_open());
assert(not loc_full_name.empty() and loc_full_name.front() == '/');
@@ -1497,9 +1923,13 @@ public:
// check all path elements exist, except for what is to the right of the last '/'
// sets active path
return path_exists(loc.first) and check_object_type(loc_full_name, H5O_TYPE_GROUP);
- }
- /// Check if a dataset exists
- bool dataset_exists(std::string const & loc_full_name) const
+ } // group_exists()
+ /**
+ * Check if an object exists that is a dataset.
+ * @param loc_full_name Full path.
+ */
+ bool
+ dataset_exists(std::string const & loc_full_name) const
{
assert(is_open());
assert(not loc_full_name.empty() and loc_full_name.front() == '/');
@@ -1508,8 +1938,13 @@ public:
// check all path elements exist, except for what is to the right of the last '/'
// sets active path
return path_exists(loc.first) and check_object_type(loc_full_name, H5O_TYPE_DATASET);
- }
- bool group_or_dataset_exists(std::string const & loc_full_name) const
+ } // dataset_exists()
+ /**
+ * Check if an object exists that is a group or a dataset.
+ * @param loc_full_name Full path.
+ */
+ bool
+ group_or_dataset_exists(std::string const & loc_full_name) const
{
assert(is_open());
assert(not loc_full_name.empty() and loc_full_name.front() == '/');
@@ -1520,9 +1955,13 @@ public:
return (path_exists(loc.first) and
(check_object_type(loc_full_name, H5O_TYPE_DATASET) or
check_object_type(loc_full_name, H5O_TYPE_GROUP)));
- }
- /// Check if attribute exists
- bool attribute_exists(std::string const & loc_full_name) const
+ } // group_or_dataset_exists()
+ /**
+ * Check if an object exists that is an attribute.
+ * @param loc_full_name Full path.
+ */
+ bool
+ attribute_exists(std::string const & loc_full_name) const
{
assert(is_open());
assert(not loc_full_name.empty() and loc_full_name.front() == '/');
@@ -1535,15 +1974,26 @@ public:
int status = H5Aexists_by_name(_file_id, loc.first.c_str(), loc.second.c_str(), H5P_DEFAULT);
if (status < 0) throw Exception("error in H5Aexists_by_name");
return status > 0;
- }
- bool exists(std::string const & loc_full_name) const
+ } // attribute_exists()
+ /**
+ * Check if an object exists.
+ * @param loc_full_name Full path.
+ */
+ bool
+ exists(std::string const & loc_full_name) const
{
return attribute_exists(loc_full_name) or dataset_exists(loc_full_name);
- }
+ } // exists()
- /// Read attribute or dataset at address
- template < typename Data_Storage, typename ...Args >
- void read(const std::string& loc_full_name, Data_Storage& out, Args&& ...args) const
+ /**
+ * Read dataset/attribute.
+ * @param loc_full_name Full path.
+ * @param out Destination (single address or vector reference).
+ * @param args Extra arguments to pass on to @p Reader.
+ */
+ template <typename Data_Storage, typename ...Args>
+ void
+ read(std::string const & loc_full_name, Data_Storage & out, Args && ...args) const
{
assert(is_open());
assert(not loc_full_name.empty() and loc_full_name[0] == '/');
@@ -1552,12 +2002,19 @@ public:
detail::HDF_Object_Holder grp_id_holder(
detail::Util::wrap(H5Oopen, _file_id, loc.first.c_str(), H5P_DEFAULT),
detail::Util::wrapped_closer(H5Oclose));
- detail::Reader< Data_Storage >()(grp_id_holder.id, loc.second,
- out, std::forward< Args >(args)...);
- }
- /// Write attribute or dataset
- template < typename In_Data_Storage, typename ...Args >
- void write(const std::string& loc_full_name, bool as_ds, const In_Data_Storage& in, Args&& ...args) const
+ detail::Reader<Data_Storage>()(grp_id_holder.id, loc.second,
+ out, std::forward<Args>(args)...);
+ } // read()
+ /**
+ * Write dataset/attribute.
+ * @param loc_full_name Full path.
+ * @param as_ds Flag; create dataset iff true.
+ * @param in Source (single address or vector reference).
+ * @param args Extra arguments to pass on to @p Writer.
+ */
+ template <typename In_Data_Storage, typename ...Args>
+ void
+ write(std::string const & loc_full_name, bool as_ds, In_Data_Storage const & in, Args && ...args) const
{
assert(is_open());
assert(is_rw());
@@ -1568,7 +2025,7 @@ public:
detail::HDF_Object_Holder grp_id_holder;
if (group_or_dataset_exists(loc.first))
{
- grp_id_holder.load(
+ grp_id_holder = detail::HDF_Object_Holder(
detail::Util::wrap(H5Oopen, _file_id, loc.first.c_str(), H5P_DEFAULT),
detail::Util::wrapped_closer(H5Oclose));
}
@@ -1578,27 +2035,46 @@ public:
detail::Util::wrap(H5Pcreate, H5P_LINK_CREATE),
detail::Util::wrapped_closer(H5Pclose));
detail::Util::wrap(H5Pset_create_intermediate_group, lcpl_id_holder.id, 1);
- grp_id_holder.load(
+ grp_id_holder = detail::HDF_Object_Holder(
detail::Util::wrap(H5Gcreate2, _file_id, loc.first.c_str(), lcpl_id_holder.id, H5P_DEFAULT, H5P_DEFAULT),
detail::Util::wrapped_closer(H5Gclose));
}
- detail::Writer< In_Data_Storage >()(grp_id_holder.id, loc.second, as_ds, in, std::forward< Args >(args)...);
- }
- template < typename In_Data_Storage, typename ...Args >
- void write_dataset(const std::string& loc_full_name, const In_Data_Storage& in, Args&& ...args) const
+ detail::Writer<In_Data_Storage>()(grp_id_holder.id, loc.second, as_ds, in, std::forward<Args>(args)...);
+ } // write()
+ /**
+ * Write dataset.
+ * @param loc_full_name Full path.
+ * @param in Source (single address or vector reference).
+ * @param args Extra arguments to pass on to @p Writer.
+ */
+ template <typename In_Data_Storage, typename ...Args>
+ void
+ write_dataset(std::string const & loc_full_name, In_Data_Storage const & in, Args && ...args) const
{
- write(loc_full_name, true, in, std::forward< Args >(args)...);
- }
- template < typename In_Data_Storage, typename ...Args >
- void write_attribute(const std::string& loc_full_name, const In_Data_Storage& in, Args&& ...args) const
+ write(loc_full_name, true, in, std::forward<Args>(args)...);
+ } // write_dataset()
+ /**
+ * Write attribute.
+ * @param loc_full_name Full path.
+ * @param in Source (single address or vector reference).
+ * @param args Extra arguments to pass on to @p Writer.
+ */
+ template <typename In_Data_Storage, typename ...Args>
+ void
+ write_attribute(std::string const & loc_full_name, In_Data_Storage const & in, Args && ...args) const
{
- write(loc_full_name, false, in, std::forward< Args >(args)...);
- }
+ write(loc_full_name, false, in, std::forward<Args>(args)...);
+ } // write_attribute()
- /// Return a list of names (groups/datasets) in the given group
- std::vector< std::string > list_group(const std::string& group_full_name) const
+ /**
+ * List group.
+ * Return a list of names (groups/datasets) in the given group.
+ * @param group_full_name Full path.
+ */
+ std::vector<std::string>
+ list_group(std::string const & group_full_name) const
{
- std::vector< std::string > res;
+ std::vector<std::string> res;
Exception::active_path() = group_full_name;
assert(group_exists(group_full_name));
detail::HDF_Object_Holder g_id_holder(
@@ -1618,11 +2094,16 @@ public:
if (sz1 != sz2) throw Exception("error in H5Lget_name_by_idx: sz1!=sz2");
}
return res;
- } // list_group
- /// Return a list of attributes of the given object
- std::vector< std::string > get_attr_list(const std::string& loc_full_name) const
+ } // list_group()
+ /**
+ * List attributes.
+ * Return a list of attribute names of the given object.
+ * @param loc_full_name Full path.
+ */
+ std::vector<std::string>
+ get_attr_list(std::string const & loc_full_name) const
{
- std::vector< std::string > res;
+ std::vector<std::string> res;
Exception::active_path() = loc_full_name;
assert(group_or_dataset_exists(loc_full_name));
detail::HDF_Object_Holder id_holder(
@@ -1641,12 +2122,17 @@ public:
res.emplace_back(std::move(tmp));
}
return res;
- } // get_attr_list
+ } // get_attr_list()
+ /**
+ * Read attribute map.
+ * @param path Full path.
+ * @param recurse Flag: if true, recurse into subgroups.
+ */
Attr_Map
get_attr_map(std::string const & path, bool recurse = false) const
{
Attr_Map res;
- std::queue< std::string > q;
+ std::queue<std::string> q;
q.push("");
while (not q.empty())
{
@@ -1671,6 +2157,11 @@ public:
}
return res;
} // get_attr_map()
+ /**
+ * Write attribute map.
+ * @param path Full path.
+ * @param attr_m Attribute map.
+ */
void
add_attr_map(std::string const & path, Attr_Map const & attr_m) const
{
@@ -1679,10 +2170,15 @@ public:
write_attribute(path + "/" + p.first, p.second);
}
} // add_attr_map()
- /// Return a list of struct field names in the given dataset/attribute
- std::vector< std::string > get_struct_members(const std::string& loc_full_name) const
+ /**
+ * List field names.
+ * Return a list of struct field names in the given compound dataset/attribute.
+ * @param loc_full_name Full path.
+ */
+ std::vector<std::string>
+ get_struct_members(std::string const & loc_full_name) const
{
- std::vector< std::string > res;
+ std::vector<std::string> res;
Exception::active_path() = loc_full_name;
assert(attribute_exists(loc_full_name) or dataset_exists(loc_full_name));
detail::HDF_Object_Holder attr_id_holder;
@@ -1691,20 +2187,20 @@ public:
if (attribute_exists(loc_full_name))
{
auto && loc = split_full_name(loc_full_name);
- attr_id_holder.load(
+ attr_id_holder = detail::HDF_Object_Holder(
detail::Util::wrap(H5Aopen_by_name, _file_id, loc.first.c_str(), loc.second.c_str(),
H5P_DEFAULT, H5P_DEFAULT),
detail::Util::wrapped_closer(H5Aclose));
- type_id_holder.load(
+ type_id_holder = detail::HDF_Object_Holder(
detail::Util::wrap(H5Aget_type, attr_id_holder.id),
detail::Util::wrapped_closer(H5Tclose));
}
else
{
- ds_id_holder.load(
+ ds_id_holder = detail::HDF_Object_Holder(
detail::Util::wrap(H5Oopen, _file_id, loc_full_name.c_str(), H5P_DEFAULT),
detail::Util::wrapped_closer(H5Oclose));
- type_id_holder.load(
+ type_id_holder = detail::HDF_Object_Holder(
detail::Util::wrap(H5Dget_type, ds_id_holder.id),
detail::Util::wrapped_closer(H5Tclose));
}
@@ -1720,35 +2216,18 @@ public:
}
}
return res;
- } // get_struct_members
+ } // get_struct_members()
- /*
- static void copy(File & src_f, File & dst_f, std::string const & path, bool shallow = false)
- {
- assert(src_f.is_open());
- assert(dst_f.is_open());
- assert(dst_f.is_rw());
- assert(src_f.group_exists(path) or src_f.dataset_exists(path));
- assert(not (dst_f.group_exists(path) or dst_f.dataset_exists(path)));
- detail::HDF_Object_Holder ocpypl_id_holder(
- detail::Util::wrap(H5Pcreate, H5P_OBJECT_COPY),
- detail::Util::wrapped_closer(H5Pclose));
- auto status = hdf5::H5Pset_copy_object(ocpypl_id_holder.id, H5O_COPY_MERGE_COMMITTED_DTYPE_FLAG);
- if (status < 0) throw Exception("error in H5Pset_copy_object");
- if (shallow)
- {
- status = hdf5::H5Pset_copy_object(ocpypl_id_holder.id, H5O_COPY_SHALLOW_HIERARCHY_FLAG);
- if (status < 0) throw Exception("error in H5Pset_copy_object");
- }
- auto res = hdf5::H5Ocopy(src_f._file_id, path.c_str(),
- dst_f._file_id, path.c_str(),
- ocpypl_id_holder.id, H5P_DEFAULT);
- if (res < 0) throw Exception("error in H5Ocopy");
- } // copy
- */
-
- static void copy_attribute(File const & src_f, File const & dst_f,
- std::string const & src_full_path, std::string const & _dst_full_path = std::string())
+ /**
+ * Copy an attribute between files.
+ * @param src_f Source file.
+ * @param dst_f Destination file.
+ * @param src_full_path Source path.
+ * @param _dst_full_path Destination path; if empty, use @p src_full_path.
+ */
+ static void
+ copy_attribute(File const & src_f, File const & dst_f,
+ std::string const & src_full_path, std::string const & _dst_full_path = std::string())
{
if (not src_f.is_open()) throw Exception("source file not open");
if (not dst_f.is_open()) throw Exception("destination file not open");
@@ -1820,7 +2299,7 @@ public:
else if (dspace_type == H5S_SIMPLE)
{
if (sz != 1) throw Exception("unsupported attribute type for copying: extent of string of size > 1");
- std::vector< char[1] > tmp_v(tmp.size());
+ std::vector<std::array<char, 1>> tmp_v(tmp.size());
for (unsigned i = 0; i < tmp.size(); ++i)
{
tmp_v[i][0] = tmp[i];
@@ -1837,8 +2316,15 @@ public:
{
throw Exception("unsupported attribute type for copying");
}
- } // copy_attribute
+ } // copy_attribute()
+ /**
+ * Copy attributes between files.
+ * @param src_f Source file.
+ * @param dst_f Destination file.
+ * @param path Source path.
+ * @param recurse Flag; if true, recurse.
+ */
static void
copy_attributes(File const & src_f, File const & dst_f, std::string const & path, bool recurse = false)
{
@@ -1862,9 +2348,12 @@ private:
hid_t _file_id;
bool _rw;
- /// Split a full name into path and name
- /// full_name must begin with '/', and not end with '/' unless it equals "/"
- static std::pair< std::string, std::string > split_full_name(const std::string& full_name)
+ /**
+ * Split a full name into path and name.
+ * Note: @p full_name must begin with '/', and not end with '/' unless it equals "/".
+ */
+ static std::pair<std::string, std::string>
+ split_full_name(std::string const & full_name)
{
assert(not full_name.empty() and
full_name.front() == '/' and
@@ -1874,10 +2363,11 @@ private:
return (pos != std::string::npos
? std::make_pair(full_name.substr(0, pos > 0? pos : 1), full_name.substr(pos + 1))
: std::make_pair(std::string(), std::string()));
- } // split_full_name
+ } // split_full_name()
/// Determine if a path to an element exists
- bool path_exists(std::string const & full_path_name) const
+ bool
+ path_exists(std::string const & full_path_name) const
{
assert(is_open());
assert(not full_path_name.empty() and full_path_name.front() == '/');
@@ -1906,8 +2396,9 @@ private:
return true;
} // path_exists()
- /// Check if a group exists
- bool check_object_type(std::string const & loc_full_name, H5O_type_t type_id) const
+ /// Check if HDF5 object has given type
+ bool
+ check_object_type(std::string const & loc_full_name, H5O_type_t type_id) const
{
// check link exists
if (loc_full_name != "/"
@@ -1922,7 +2413,7 @@ private:
H5O_info_t o_info;
detail::Util::wrap(H5Oget_info, o_id_holder.id, &o_info);
return o_info.type == type_id;
- }
+ } // check_object_type()
}; // class File
} // namespace hdf5_tools
diff --git a/src/logger.hpp b/include/fast5/logger.hpp
similarity index 99%
rename from src/logger.hpp
rename to include/fast5/logger.hpp
index 2c69592..c6b44c2 100644
--- a/src/logger.hpp
+++ b/include/fast5/logger.hpp
@@ -72,6 +72,7 @@
#include <iostream>
#include <mutex>
#include <stdexcept>
+#include <functional>
namespace logger
{
diff --git a/python/bin/f5ls b/python/bin/f5ls
index 14e78fc..514e771 100755
--- a/python/bin/f5ls
+++ b/python/bin/f5ls
@@ -98,8 +98,8 @@ def stat_file(ifn, args):
for st in [0, 1, 2]:
d["bc"][gr]["packed_fastq"][st] = not f.have_basecall_fastq_unpack(st, gr)
if st < 2:
- d["bc"][gr]["packed_events"][st] = not f.have_basecall_events_unpack(st, gr)
if d["bc"][gr]["desc"]["have_events"][st]:
+ d["bc"][gr]["packed_events"][st] = not f.have_basecall_events_unpack(st, gr)
ev_params = f.get_basecall_events_params(st, gr)
d["bc"][gr]["start"][st] = ev_params["start_time"]
d["bc"][gr]["length"][st] = ev_params["duration"]
@@ -192,8 +192,8 @@ def list_file(ifn, include_fn, args):
fq_len = d["bc"][gr]["summary"][fk]
if st < 2:
# events
- print_path(["bc", gr, st, "events", "packed"], int(d["bc"][gr]["packed_events"][st]), args)
if d["bc"][gr]["desc"]["have_events"][st]:
+ print_path(["bc", gr, st, "events", "packed"], int(d["bc"][gr]["packed_events"][st]), args)
for k in ["start", "length"]:
print_path(["bc", gr, st, "events", k], as_time(float(d["bc"][gr][k][st]), 1.0), args)
if st in d["bc"][gr]["count"]:
diff --git a/python/setup.py b/python/setup.py
index f969514..bcf18df 100755
--- a/python/setup.py
+++ b/python/setup.py
@@ -26,7 +26,8 @@ if (not os.path.isfile(os.path.join(hdf5_lib_dir, 'lib' + hdf5_lib + '.so'))
sys.exit(hdf5_lib_dir + ': could not find HDF5 library file; use HDF5_DIR or HDF5_LIB_DIR/HDF5_LIB')
fast5_dir = os.environ.get('FAST5_DIR', '..')
-fast5_src_dir = os.path.join(fast5_dir, 'src')
+fast5pack_src_dir = os.path.join(fast5_dir, 'src')
+fast5_src_dir = os.path.join(fast5_dir, 'include')
fast5_version = open(os.path.join(fast5_dir, 'VERSION')).readline().strip()
extra_compile_args = [
@@ -51,7 +52,7 @@ extensions = [
'fast5',
language='c++',
sources=['fast5/fast5.' + ['cpp', 'pyx'][use_cython]],
- include_dirs=[fast5_src_dir],
+ include_dirs=[fast5_src_dir, fast5pack_src_dir],
library_dirs=[hdf5_lib_dir],
runtime_library_dirs=[hdf5_lib_dir],
libraries=[hdf5_lib],
diff --git a/src/File_Packer.hpp b/src/File_Packer.hpp
index 990cc38..14eaf6e 100644
--- a/src/File_Packer.hpp
+++ b/src/File_Packer.hpp
@@ -11,8 +11,7 @@
#include <string>
#include <set>
-#include "fast5.hpp"
-#include "logger.hpp"
+#include <fast5.hpp>
#define STATIC_MEMBER_WRAPPER(_type, _id, _init) \
static _type & _id() { static _type _ ## _id = _init; return _ ## _id; }
diff --git a/src/Makefile b/src/Makefile
index 0d64a1e..0b0d73a 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -17,13 +17,14 @@ HDF5_LIB_DIR ?= ${HDF5_DIR}/lib
HDF5_LIB ?= hdf5
TCLAP_DIR ?= tclap
HPPTOOLS_DIR ?= hpptools
+FAST5_DIR ?= ${CURDIR}/../include
TARGETS = f5ls f5ls-full hdf5-mod f5-mod
EXTRA_TARGETS = f5dump f5pack
-HPP_FILES := fast5.hpp hdf5_tools.hpp Huffman_Packer.hpp Bit_Packer.hpp
+HPP_FILES := $(addprefix ${FAST5_DIR}/, fast5.hpp fast5/hdf5_tools.hpp fast5/Huffman_Packer.hpp fast5/Bit_Packer.hpp)
CXXFLAGS := -std=c++11 -O0 -g3 -ggdb -fno-eliminate-unused-debug-types -Wall -Wextra -Wpedantic
-CPPFLAGS := -isystem ${HDF5_INCLUDE_DIR}
+CPPFLAGS := -isystem ${HDF5_INCLUDE_DIR} -I $(FAST5_DIR)
EXTRA_CPPFLAGS := -isystem ${TCLAP_DIR}/include -I ${HPPTOOLS_DIR}/include
LDFLAGS := -L${HDF5_LIB_DIR} -Wl,--rpath=${HDF5_LIB_DIR} -l${HDF5_LIB} -lpthread -lz -ldl
diff --git a/src/f5-mod.cpp b/src/f5-mod.cpp
index 5d510ae..39e2b38 100644
--- a/src/f5-mod.cpp
+++ b/src/f5-mod.cpp
@@ -9,7 +9,7 @@
#include <iostream>
#include <string>
-#include "fast5.hpp"
+#include <fast5.hpp>
using namespace std;
diff --git a/src/f5dump.cpp b/src/f5dump.cpp
index 3d18351..4be1b96 100644
--- a/src/f5dump.cpp
+++ b/src/f5dump.cpp
@@ -13,7 +13,7 @@
#include <tclap/CmdLine.h>
#include "alg.hpp"
-#include "fast5.hpp"
+#include <fast5.hpp>
using namespace std;
diff --git a/src/f5ls-full.cpp b/src/f5ls-full.cpp
index 48dd47a..181a74b 100644
--- a/src/f5ls-full.cpp
+++ b/src/f5ls-full.cpp
@@ -9,7 +9,7 @@
#include <iostream>
#include <string>
-#include "fast5.hpp"
+#include <fast5.hpp>
using namespace std;
diff --git a/src/f5ls.cpp b/src/f5ls.cpp
index c485ab7..318aeeb 100644
--- a/src/f5ls.cpp
+++ b/src/f5ls.cpp
@@ -9,7 +9,7 @@
#include <iostream>
#include <string>
-#include "fast5.hpp"
+#include <fast5.hpp>
using namespace std;
diff --git a/src/f5pack.cpp b/src/f5pack.cpp
index 9afd30f..27f4fd2 100644
--- a/src/f5pack.cpp
+++ b/src/f5pack.cpp
@@ -11,9 +11,8 @@
#include <string>
#include <tclap/CmdLine.h>
-#include "logger.hpp"
-#include "fast5.hpp"
+#include <fast5.hpp>
#include "File_Packer.hpp"
using namespace std;
diff --git a/src/hdf5-mod.cpp b/src/hdf5-mod.cpp
index 818d36d..5074462 100644
--- a/src/hdf5-mod.cpp
+++ b/src/hdf5-mod.cpp
@@ -9,7 +9,7 @@
#include <iostream>
#include <string>
-#include "hdf5_tools.hpp"
+#include <fast5/hdf5_tools.hpp>
using namespace std;
using namespace hdf5;
diff --git a/src/huffman-decode.cpp b/src/huffman-decode.cpp
index 80af4a7..14a02e0 100644
--- a/src/huffman-decode.cpp
+++ b/src/huffman-decode.cpp
@@ -10,8 +10,8 @@
#include <string>
#include <vector>
-#include "fast5_pack.hpp"
-#include "logger.hpp"
+#include <fast5/fast5_pack.hpp>
+#include <fast5/logger.hpp>
using namespace std;
diff --git a/src/huffman-encode.cpp b/src/huffman-encode.cpp
index 20e4c33..ca4e463 100644
--- a/src/huffman-encode.cpp
+++ b/src/huffman-encode.cpp
@@ -10,8 +10,8 @@
#include <string>
#include <vector>
-#include "fast5_pack.hpp"
-#include "logger.hpp"
+#include <fast5/fast5_pack.hpp>
+#include <fast5/logger.hpp>
using namespace std;
--
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