Merge doxygen2 into develop (#553)
* Fixed warnings and started H5Epublic.h.
* Include H5FD* headers to correctly resolve references.
* Doxygen2 (#330)
* H5Eauto_is_v2.
* Added a few more calls.
* Added a few more H5E calls.
* First cut of H5E v2.
* Added the deprecated v1 calls.
* Updated spacing.
* Once more.
* Taking some inspiration from Eigen3.
* Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pen… (#352)
* Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pencode1, H5Pget_filter_by_id1,H5Pget_version, H5Pset_file_space,H5Pget_file_space. Someone already adds H5Pget_filter1. Also fixs an extra parameter 'close' call back function for HPregister2.
* doxygen work. fixs format by using clang-format.
* doxgen work for H5Pregister1 etc. Addressed Barbara and Gerd's comments.
For Quincey's comments, since we are not supposed to change the source code.
I leave this to future improvements.
* added documentation for H5P APIs (#350)
* add documenation for H5Pget_buffer,H5Pget_data_transform,H5Pget_edc_check,H5Pget_hyper_vector_size,H5Pget_preserve,H5Pget_type_conv_cb,H5Pget_vlen_mem_manager,H5Pset_btree_ratios
* format corrections
* fixed grammer
* fixed herr_t
* Better name.
* A fresh look.
* add doxygen to H5Ppublic.h
* use attention instead of warning
* Add doxygen comments in H5Ppublic.h (#375)
* Add doxygen comments in H5Ppublic.h
* H5Pset_meta_block_size
* H5Pset_metadata_read_attempts
* H5Pset_multi_type
* H5Pset_object_flush_cb
* H5Pset_sieve_buf_size
* H5Pset_small_data_block_size
* H5Pset_all_coll_metadata_ops
* H5Pget_all_coll_metadata_ops
* Add DOXYGEN_EXAMPLES_DIR to src/CMakeLists.txt
* Fix clang-format errors
* Fix filenames in doxygen/examples
* add doxygen to H5Ppublic.h (#378)
* add doxygen to H5Ppublic.h
* use attention instead of warning
Co-authored-by: Kimmy Mu <kmu@hdfgroup.org>
* Revert "add doxygen to H5Ppublic.h (#378)"
This reverts commit 2ee1821b138a5c00b15ea57ce9e950367480f5f2.
* Updated Doxygen variables.
* I forgot to copy two images.
* Enable desktop search by default.
* Add my assigned Doxygen documentation.
* Remove whitespace at EOL. Appease clang-format.
* Addressed Chris' comments.
* Added an alias for asynchronous functions.
* One space is enough for all of us.
* Slightly restructured RM page.
* address some issues
* reformatting
* Style external links.
* reformatting
* reformatting
* Added "Metadata Caching in HDF5" as a technical note example.
* Revise this soon!
* Added specification examples.
* Fixed references.
* Added H5AC cache image stuff and file format study.
* Added older FMT versions. Where did 1.0 go?
* Updated C/C++ note and replaced ambiguous labels.
* Reformat source with clang v10.0.1.
* Added the VFL technical note.
* Added what I believe might be called version 1.0 of the format.
* Added the remaining specs.
* Added H5Z callback documentation and fixed a few mistakes.
* Added dox for deprecated H5G calls and fixed a few snippet blockIDs.
* clang-format happy?
* Ok?
* Bonus track: Deprecated H5D functions.
* Carry over the more detailed group description.
* Added documentation for the missing and deprecated H5R calls.
* Life is easier and less repetitive w/ snippets. Use them!
* Eliminate the snippet block ID artifacts in the HTML rendering.
* Fixed snippet HTML artifacts and added a few missing calls.
* Under 20 H5Ps to go!
* Almost complete!
* "This is a form of pedantry up with which I will not put." (Churchill)
* Let's not waste as much space on bulleted lists!
* First complete (?) draft of the Doxygen-based RM.
* Completeness check and minor fixes along the way.
* Pedantry.
* Adding missing H5FD calls checkpoint.
* Pedantry.
* More pedantry.
* Added H5Pset_fapl_log.
* First draft of H5ES.
* Fixed warnings.
* Prep. for map module.
* First cut of the map module.
* Pedantry.
* Possible H5F introduction.
* Fix the indentation.
* Pedantry.
* Ditto.
* Thanks to the reviewers for their comments.
* Added missing images.
* Line numbers are a distraction here.
* More examples, references, and clean-up. Don't repeat yourself!
* Clang pedantry.
* Ditto.
* More reviewer comments...
* Templatized references and cleaned up \todos.
* Committing clang-format changes
* Fixed MANIFEST.
* Addressed Quincey's comments. (OCPLs)
* Fixed a few more \todo items.
* Fixed more \todo items.
* Added attribute life cycle.
* Forgot the examples file.
* Committing clang-format changes
* Pedantry.
* Live and learn!
* Added a sample H5D life cycle.
* Committing clang-format changes
* Pedantry.
Co-authored-by: kyang2014 <kyang2014@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: Kimmy Mu <kmu@hdfgroup.org>
Co-authored-by: Christopher Hogan <ChristopherHogan@users.noreply.github.com>
Co-authored-by: jya-kmu <53388330+jya-kmu@users.noreply.github.com>
Co-authored-by: David Young <dyoung@hdfgroup.org>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2021-04-27 03:07:29 +08:00
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// generate a table of contents in the side-nav based on the h1/h2 tags of the current page.
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function generate_autotoc() {
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var headers = $("h1, h2");
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if(headers.length > 1) {
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var toc = $("#side-nav").append('<div id="nav-toc" class="toc"><h3>Table of contents</h3></div>');
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toc = $("#nav-toc");
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var footer = $("#nav-path");
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var footerHeight = footer.height();
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toc = toc.append('<ul></ul>');
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toc = toc.find('ul');
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var indices = new Array();
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indices[0] = 0;
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indices[1] = 0;
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var h1counts = $("h1").length;
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headers.each(function(i) {
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var current = $(this);
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var levelTag = current[0].tagName.charAt(1);
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if(h1counts==0)
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levelTag--;
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var cur_id = current.attr("id");
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indices[levelTag-1]+=1;
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var prefix = indices[0];
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if (levelTag >1) {
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prefix+="."+indices[1];
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}
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// Uncomment to add number prefixes
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// current.html(prefix + " " + current.html());
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for(var l = levelTag; l < 2; ++l){
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indices[l] = 0;
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}
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if(cur_id == undefined) {
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current.attr('id', 'title' + i);
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current.addClass('anchor');
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toc.append("<li class='level" + levelTag + "'><a id='link" + i + "' href='#title" +
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i + "' title='" + current.prop("tagName") + "'>" + current.text() + "</a></li>");
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} else {
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toc.append("<li class='level" + levelTag + "'><a id='" + cur_id + "' href='#title" +
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i + "' title='" + current.prop("tagName") + "'>" + current.text() + "</a></li>");
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}
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});
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resizeHeight();
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}
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}
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var global_navtree_object;
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// Overloaded to remove links to sections/subsections
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function getNode(o, po)
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{
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po.childrenVisited = true;
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var l = po.childrenData.length-1;
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for (var i in po.childrenData) {
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var nodeData = po.childrenData[i];
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if((!nodeData[1]) || (nodeData[1].indexOf('#')==-1)) // <- we added this line
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po.children[i] = newNode(o, po, nodeData[0], nodeData[1], nodeData[2], i==l);
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}
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}
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// Overloaded to adjust the size of the navtree wrt the toc
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function resizeHeight()
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{
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var header = $("#top");
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var sidenav = $("#side-nav");
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var content = $("#doc-content");
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var navtree = $("#nav-tree");
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var footer = $("#nav-path");
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var toc = $("#nav-toc");
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var headerHeight = header.outerHeight();
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var footerHeight = footer.outerHeight();
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var tocHeight = toc.height();
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var windowHeight = $(window).height() - headerHeight - footerHeight;
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content.css({height:windowHeight + "px"});
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navtree.css({height:(windowHeight-tocHeight) + "px"});
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sidenav.css({height:windowHeight + "px"});
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}
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// Overloaded to save the root node into global_navtree_object
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function initNavTree(toroot,relpath)
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{
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var o = new Object();
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global_navtree_object = o; // <- we added this line
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o.toroot = toroot;
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o.node = new Object();
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o.node.li = document.getElementById("nav-tree-contents");
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o.node.childrenData = NAVTREE;
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o.node.children = new Array();
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o.node.childrenUL = document.createElement("ul");
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o.node.getChildrenUL = function() { return o.node.childrenUL; };
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o.node.li.appendChild(o.node.childrenUL);
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o.node.depth = 0;
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o.node.relpath = relpath;
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o.node.expanded = false;
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o.node.isLast = true;
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o.node.plus_img = document.createElement("img");
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o.node.plus_img.src = relpath+"ftv2pnode.png";
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o.node.plus_img.width = 16;
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o.node.plus_img.height = 22;
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if (localStorageSupported()) {
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var navSync = $('#nav-sync');
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if (cachedLink()) {
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showSyncOff(navSync,relpath);
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navSync.removeClass('sync');
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} else {
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showSyncOn(navSync,relpath);
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}
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navSync.click(function(){ toggleSyncButton(relpath); });
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}
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navTo(o,toroot,window.location.hash,relpath);
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$(window).bind('hashchange', function(){
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if (window.location.hash && window.location.hash.length>1){
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var a;
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if ($(location).attr('hash')){
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var clslink=stripPath($(location).attr('pathname'))+':'+
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$(location).attr('hash').substring(1);
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a=$('.item a[class$="'+clslink+'"]');
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}
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if (a==null || !$(a).parent().parent().hasClass('selected')){
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$('.item').removeClass('selected');
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$('.item').removeAttr('id');
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}
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var link=stripPath2($(location).attr('pathname'));
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navTo(o,link,$(location).attr('hash'),relpath);
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} else if (!animationInProgress) {
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$('#doc-content').scrollTop(0);
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$('.item').removeClass('selected');
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$('.item').removeAttr('id');
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navTo(o,toroot,window.location.hash,relpath);
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}
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})
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$(window).on("load", showRoot);
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}
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// return false if the the node has no children at all, or has only section/subsection children
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function checkChildrenData(node) {
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if (!(typeof(node.childrenData)==='string')) {
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for (var i in node.childrenData) {
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var url = node.childrenData[i][1];
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if(url.indexOf("#")==-1)
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return true;
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}
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return false;
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}
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return (node.childrenData);
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}
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// Modified to:
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// 1 - remove the root node
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// 2 - remove the section/subsection children
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function createIndent(o,domNode,node,level)
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{
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var level=-2; // <- we replaced level=-1 by level=-2
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var n = node;
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while (n.parentNode) { level++; n=n.parentNode; }
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if (checkChildrenData(node)) { // <- we modified this line to use checkChildrenData(node) instead of node.childrenData
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var imgNode = document.createElement("span");
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imgNode.className = 'arrow';
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imgNode.style.paddingLeft=(16*level).toString()+'px';
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imgNode.innerHTML=arrowRight;
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node.plus_img = imgNode;
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node.expandToggle = document.createElement("a");
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node.expandToggle.href = "javascript:void(0)";
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node.expandToggle.onclick = function() {
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if (node.expanded) {
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$(node.getChildrenUL()).slideUp("fast");
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node.plus_img.innerHTML=arrowRight;
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node.expanded = false;
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} else {
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expandNode(o, node, false, false);
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}
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}
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node.expandToggle.appendChild(imgNode);
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domNode.appendChild(node.expandToggle);
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} else {
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var span = document.createElement("span");
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span.className = 'arrow';
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span.style.width = 16*(level+1)+'px';
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span.innerHTML = ' ';
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domNode.appendChild(span);
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}
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}
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// Overloaded to automatically expand the selected node
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function selectAndHighlight(hash,n)
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{
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var a;
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if (hash) {
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var link=stripPath($(location).attr('pathname'))+':'+hash.substring(1);
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a=$('.item a[class$="'+link+'"]');
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}
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if (a && a.length) {
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a.parent().parent().addClass('selected');
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a.parent().parent().attr('id','selected');
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highlightAnchor();
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} else if (n) {
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$(n.itemDiv).addClass('selected');
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$(n.itemDiv).attr('id','selected');
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}
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if ($('#nav-tree-contents .item:first').hasClass('selected')) {
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$('#nav-sync').css('top','30px');
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} else {
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$('#nav-sync').css('top','5px');
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}
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expandNode(global_navtree_object, n, true, true); // <- we added this line
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showRoot();
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}
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$(document).ready(function() {
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generate_autotoc();
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(function (){ // wait until the first "selected" element has been created
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try {
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2021-12-07 22:27:29 +08:00
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// this line will trigger an exception if there is no #selected element, i.e., before the tree structure is complete.
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Merge doxygen2 into develop (#553)
* Fixed warnings and started H5Epublic.h.
* Include H5FD* headers to correctly resolve references.
* Doxygen2 (#330)
* H5Eauto_is_v2.
* Added a few more calls.
* Added a few more H5E calls.
* First cut of H5E v2.
* Added the deprecated v1 calls.
* Updated spacing.
* Once more.
* Taking some inspiration from Eigen3.
* Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pen… (#352)
* Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pencode1, H5Pget_filter_by_id1,H5Pget_version, H5Pset_file_space,H5Pget_file_space. Someone already adds H5Pget_filter1. Also fixs an extra parameter 'close' call back function for HPregister2.
* doxygen work. fixs format by using clang-format.
* doxgen work for H5Pregister1 etc. Addressed Barbara and Gerd's comments.
For Quincey's comments, since we are not supposed to change the source code.
I leave this to future improvements.
* added documentation for H5P APIs (#350)
* add documenation for H5Pget_buffer,H5Pget_data_transform,H5Pget_edc_check,H5Pget_hyper_vector_size,H5Pget_preserve,H5Pget_type_conv_cb,H5Pget_vlen_mem_manager,H5Pset_btree_ratios
* format corrections
* fixed grammer
* fixed herr_t
* Better name.
* A fresh look.
* add doxygen to H5Ppublic.h
* use attention instead of warning
* Add doxygen comments in H5Ppublic.h (#375)
* Add doxygen comments in H5Ppublic.h
* H5Pset_meta_block_size
* H5Pset_metadata_read_attempts
* H5Pset_multi_type
* H5Pset_object_flush_cb
* H5Pset_sieve_buf_size
* H5Pset_small_data_block_size
* H5Pset_all_coll_metadata_ops
* H5Pget_all_coll_metadata_ops
* Add DOXYGEN_EXAMPLES_DIR to src/CMakeLists.txt
* Fix clang-format errors
* Fix filenames in doxygen/examples
* add doxygen to H5Ppublic.h (#378)
* add doxygen to H5Ppublic.h
* use attention instead of warning
Co-authored-by: Kimmy Mu <kmu@hdfgroup.org>
* Revert "add doxygen to H5Ppublic.h (#378)"
This reverts commit 2ee1821b138a5c00b15ea57ce9e950367480f5f2.
* Updated Doxygen variables.
* I forgot to copy two images.
* Enable desktop search by default.
* Add my assigned Doxygen documentation.
* Remove whitespace at EOL. Appease clang-format.
* Addressed Chris' comments.
* Added an alias for asynchronous functions.
* One space is enough for all of us.
* Slightly restructured RM page.
* address some issues
* reformatting
* Style external links.
* reformatting
* reformatting
* Added "Metadata Caching in HDF5" as a technical note example.
* Revise this soon!
* Added specification examples.
* Fixed references.
* Added H5AC cache image stuff and file format study.
* Added older FMT versions. Where did 1.0 go?
* Updated C/C++ note and replaced ambiguous labels.
* Reformat source with clang v10.0.1.
* Added the VFL technical note.
* Added what I believe might be called version 1.0 of the format.
* Added the remaining specs.
* Added H5Z callback documentation and fixed a few mistakes.
* Added dox for deprecated H5G calls and fixed a few snippet blockIDs.
* clang-format happy?
* Ok?
* Bonus track: Deprecated H5D functions.
* Carry over the more detailed group description.
* Added documentation for the missing and deprecated H5R calls.
* Life is easier and less repetitive w/ snippets. Use them!
* Eliminate the snippet block ID artifacts in the HTML rendering.
* Fixed snippet HTML artifacts and added a few missing calls.
* Under 20 H5Ps to go!
* Almost complete!
* "This is a form of pedantry up with which I will not put." (Churchill)
* Let's not waste as much space on bulleted lists!
* First complete (?) draft of the Doxygen-based RM.
* Completeness check and minor fixes along the way.
* Pedantry.
* Adding missing H5FD calls checkpoint.
* Pedantry.
* More pedantry.
* Added H5Pset_fapl_log.
* First draft of H5ES.
* Fixed warnings.
* Prep. for map module.
* First cut of the map module.
* Pedantry.
* Possible H5F introduction.
* Fix the indentation.
* Pedantry.
* Ditto.
* Thanks to the reviewers for their comments.
* Added missing images.
* Line numbers are a distraction here.
* More examples, references, and clean-up. Don't repeat yourself!
* Clang pedantry.
* Ditto.
* More reviewer comments...
* Templatized references and cleaned up \todos.
* Committing clang-format changes
* Fixed MANIFEST.
* Addressed Quincey's comments. (OCPLs)
* Fixed a few more \todo items.
* Fixed more \todo items.
* Added attribute life cycle.
* Forgot the examples file.
* Committing clang-format changes
* Pedantry.
* Live and learn!
* Added a sample H5D life cycle.
* Committing clang-format changes
* Pedantry.
Co-authored-by: kyang2014 <kyang2014@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: Kimmy Mu <kmu@hdfgroup.org>
Co-authored-by: Christopher Hogan <ChristopherHogan@users.noreply.github.com>
Co-authored-by: jya-kmu <53388330+jya-kmu@users.noreply.github.com>
Co-authored-by: David Young <dyoung@hdfgroup.org>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2021-04-27 03:07:29 +08:00
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