add breathe integration first attempt

.gitignore

@@ -5,4 +5,5 @@ tests/.env
 .buildpath
 .project
 .settings/
-docs/_build/
+docs/_build/
+docs/xml/

docs/api.rst

@@ -0,0 +1,4 @@
+API
+=====
+
+.. doxygenclass:: TripalImporter

docs/conf.py

@@ -17,6 +17,7 @@
 # sys.path.insert(0, os.path.abspath('.'))
 
 
+
 # -- Project information -----------------------------------------------------
 
 project = u'Tripal'
@@ -38,8 +39,7 @@ release = u'7.x-3.x'
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [
-]
+extensions =  ['breathe' ]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -153,3 +153,20 @@ texinfo_documents = [
      author, 'Tripal', 'One line description of project.',
      'Miscellaneous'),
 ]
+
+
+# ---- run doxygen if READTHEDOCS
+
+import subprocess, os
+
+read_the_docs_build = os.environ.get('READTHEDOCS', None) == 'True'
+
+if read_the_docs_build:
+
+    subprocess.call('cd ../; doxygen docs/tripal_doxygen.config', shell=True)
+
+# --- Options for breathe ------------
+
+breathe_projects = { "tripal": "xml/" }
+breathe_default_project = "tripal"
+

docs/docs/html/doxygen.css

@@ -0,0 +1,1744 @@
+/* The standard CSS for doxygen 1.8.15 */
+
+body, table, div, p, dl {
+	font: 400 14px/22px Roboto,sans-serif;
+}
+
+p.reference, p.definition {
+	font: 400 14px/22px Roboto,sans-serif;
+}
+
+/* @group Heading Levels */
+
+h1.groupheader {
+	font-size: 150%;
+}
+
+.title {
+	font: 400 14px/28px Roboto,sans-serif;
+	font-size: 150%;
+	font-weight: bold;
+	margin: 10px 2px;
+}
+
+h2.groupheader {
+	border-bottom: 1px solid #879ECB;
+	color: #354C7B;
+	font-size: 150%;
+	font-weight: normal;
+	margin-top: 1.75em;
+	padding-top: 8px;
+	padding-bottom: 4px;
+	width: 100%;
+}
+
+h3.groupheader {
+	font-size: 100%;
+}
+
+h1, h2, h3, h4, h5, h6 {
+	-webkit-transition: text-shadow 0.5s linear;
+	-moz-transition: text-shadow 0.5s linear;
+	-ms-transition: text-shadow 0.5s linear;
+	-o-transition: text-shadow 0.5s linear;
+	transition: text-shadow 0.5s linear;
+	margin-right: 15px;
+}
+
+h1.glow, h2.glow, h3.glow, h4.glow, h5.glow, h6.glow {
+	text-shadow: 0 0 15px cyan;
+}
+
+dt {
+	font-weight: bold;
+}
+
+div.multicol {
+	-moz-column-gap: 1em;
+	-webkit-column-gap: 1em;
+	-moz-column-count: 3;
+	-webkit-column-count: 3;
+}
+
+p.startli, p.startdd {
+	margin-top: 2px;
+}
+
+p.starttd {
+	margin-top: 0px;
+}
+
+p.endli {
+	margin-bottom: 0px;
+}
+
+p.enddd {
+	margin-bottom: 4px;
+}
+
+p.endtd {
+	margin-bottom: 2px;
+}
+
+/* @end */
+
+caption {
+	font-weight: bold;
+}
+
+span.legend {
+        font-size: 70%;
+        text-align: center;
+}
+
+h3.version {
+        font-size: 90%;
+        text-align: center;
+}
+
+div.qindex, div.navtab{
+	background-color: #EBEFF6;
+	border: 1px solid #A3B4D7;
+	text-align: center;
+}
+
+div.qindex, div.navpath {
+	width: 100%;
+	line-height: 140%;
+}
+
+div.navtab {
+	margin-right: 15px;
+}
+
+/* @group Link Styling */
+
+a {
+	color: #3D578C;
+	font-weight: normal;
+	text-decoration: none;
+}
+
+.contents a:visited {
+	color: #4665A2;
+}
+
+a:hover {
+	text-decoration: underline;
+}
+
+a.qindex {
+	font-weight: bold;
+}
+
+a.qindexHL {
+	font-weight: bold;
+	background-color: #9CAFD4;
+	color: #ffffff;
+	border: 1px double #869DCA;
+}
+
+.contents a.qindexHL:visited {
+        color: #ffffff;
+}
+
+a.el {
+	font-weight: bold;
+}
+
+a.elRef {
+}
+
+a.code, a.code:visited, a.line, a.line:visited {
+	color: #4665A2; 
+}
+
+a.codeRef, a.codeRef:visited, a.lineRef, a.lineRef:visited {
+	color: #4665A2; 
+}
+
+/* @end */
+
+dl.el {
+	margin-left: -1cm;
+}
+
+ul {
+  overflow: hidden; /*Fixed: list item bullets overlap floating elements*/
+}
+
+.fragment {
+  text-align: left;
+  direction: ltr;
+  overflow-x: auto; /*Fixed: fragment lines overlap floating elements*/
+  overflow-y: hidden;
+}
+
+pre.fragment {
+        border: 1px solid #C4CFE5;
+        background-color: #FBFCFD;
+        padding: 4px 6px;
+        margin: 4px 8px 4px 2px;
+        overflow: auto;
+        word-wrap: break-word;
+        font-size:  9pt;
+        line-height: 125%;
+        font-family: monospace, fixed;
+        font-size: 105%;
+}
+
+div.fragment {
+  padding: 0 0 1px 0; /*Fixed: last line underline overlap border*/
+  margin: 4px 8px 4px 2px;
+	background-color: #FBFCFD;
+	border: 1px solid #C4CFE5;
+}
+
+div.line {
+	font-family: monospace, fixed;
+        font-size: 13px;
+	min-height: 13px;
+	line-height: 1.0;
+	text-wrap: unrestricted;
+	white-space: -moz-pre-wrap; /* Moz */
+	white-space: -pre-wrap;     /* Opera 4-6 */
+	white-space: -o-pre-wrap;   /* Opera 7 */
+	white-space: pre-wrap;      /* CSS3  */
+	word-wrap: break-word;      /* IE 5.5+ */
+	text-indent: -53px;
+	padding-left: 53px;
+	padding-bottom: 0px;
+	margin: 0px;
+	-webkit-transition-property: background-color, box-shadow;
+	-webkit-transition-duration: 0.5s;
+	-moz-transition-property: background-color, box-shadow;
+	-moz-transition-duration: 0.5s;
+	-ms-transition-property: background-color, box-shadow;
+	-ms-transition-duration: 0.5s;
+	-o-transition-property: background-color, box-shadow;
+	-o-transition-duration: 0.5s;
+	transition-property: background-color, box-shadow;
+	transition-duration: 0.5s;
+}
+
+div.line:after {
+    content:"\000A";
+    white-space: pre;
+}
+
+div.line.glow {
+	background-color: cyan;
+	box-shadow: 0 0 10px cyan;
+}
+
+
+span.lineno {
+	padding-right: 4px;
+	text-align: right;
+	border-right: 2px solid #0F0;
+	background-color: #E8E8E8;
+        white-space: pre;
+}
+span.lineno a {
+	background-color: #D8D8D8;
+}
+
+span.lineno a:hover {
+	background-color: #C8C8C8;
+}
+
+.lineno {
+	-webkit-touch-callout: none;
+	-webkit-user-select: none;
+	-khtml-user-select: none;
+	-moz-user-select: none;
+	-ms-user-select: none;
+	user-select: none;
+}
+
+div.ah, span.ah {
+	background-color: black;
+	font-weight: bold;
+	color: #ffffff;
+	margin-bottom: 3px;
+	margin-top: 3px;
+	padding: 0.2em;
+	border: solid thin #333;
+	border-radius: 0.5em;
+	-webkit-border-radius: .5em;
+	-moz-border-radius: .5em;
+	box-shadow: 2px 2px 3px #999;
+	-webkit-box-shadow: 2px 2px 3px #999;
+	-moz-box-shadow: rgba(0, 0, 0, 0.15) 2px 2px 2px;
+	background-image: -webkit-gradient(linear, left top, left bottom, from(#eee), to(#000),color-stop(0.3, #444));
+	background-image: -moz-linear-gradient(center top, #eee 0%, #444 40%, #000 110%);
+}
+
+div.classindex ul {
+        list-style: none;
+        padding-left: 0;
+}
+
+div.classindex span.ai {
+        display: inline-block;
+}
+
+div.groupHeader {
+	margin-left: 16px;
+	margin-top: 12px;
+	font-weight: bold;
+}
+
+div.groupText {
+	margin-left: 16px;
+	font-style: italic;
+}
+
+body {
+	background-color: white;
+	color: black;
+        margin: 0;
+}
+
+div.contents {
+	margin-top: 10px;
+	margin-left: 12px;
+	margin-right: 8px;
+}
+
+td.indexkey {
+	background-color: #EBEFF6;
+	font-weight: bold;
+	border: 1px solid #C4CFE5;
+	margin: 2px 0px 2px 0;
+	padding: 2px 10px;
+        white-space: nowrap;
+        vertical-align: top;
+}
+
+td.indexvalue {
+	background-color: #EBEFF6;
+	border: 1px solid #C4CFE5;
+	padding: 2px 10px;
+	margin: 2px 0px;
+}
+
+tr.memlist {
+	background-color: #EEF1F7;
+}
+
+p.formulaDsp {
+	text-align: center;
+}
+
+img.formulaDsp {
+	
+}
+
+img.formulaInl {
+	vertical-align: middle;
+}
+
+div.center {
+	text-align: center;
+        margin-top: 0px;
+        margin-bottom: 0px;
+        padding: 0px;
+}
+
+div.center img {
+	border: 0px;
+}
+
+address.footer {
+	text-align: right;
+	padding-right: 12px;
+}
+
+img.footer {
+	border: 0px;
+	vertical-align: middle;
+}
+
+/* @group Code Colorization */
+
+span.keyword {
+	color: #008000
+}
+
+span.keywordtype {
+	color: #604020
+}
+
+span.keywordflow {
+	color: #e08000
+}
+
+span.comment {
+	color: #800000
+}
+
+span.preprocessor {
+	color: #806020
+}
+
+span.stringliteral {
+	color: #002080
+}
+
+span.charliteral {
+	color: #008080
+}
+
+span.vhdldigit { 
+	color: #ff00ff 
+}
+
+span.vhdlchar { 
+	color: #000000 
+}
+
+span.vhdlkeyword { 
+	color: #700070 
+}
+
+span.vhdllogic { 
+	color: #ff0000 
+}
+
+blockquote {
+        background-color: #F7F8FB;
+        border-left: 2px solid #9CAFD4;
+        margin: 0 24px 0 4px;
+        padding: 0 12px 0 16px;
+}
+
+blockquote.DocNodeRTL {
+   border-left: 0;
+   border-right: 2px solid #9CAFD4;
+   margin: 0 4px 0 24px;
+   padding: 0 16px 0 12px;
+}
+
+/* @end */
+
+/*
+.search {
+	color: #003399;
+	font-weight: bold;
+}
+
+form.search {
+	margin-bottom: 0px;
+	margin-top: 0px;
+}
+
+input.search {
+	font-size: 75%;
+	color: #000080;
+	font-weight: normal;
+	background-color: #e8eef2;
+}
+*/
+
+td.tiny {
+	font-size: 75%;
+}
+
+.dirtab {
+	padding: 4px;
+	border-collapse: collapse;
+	border: 1px solid #A3B4D7;
+}
+
+th.dirtab {
+	background: #EBEFF6;
+	font-weight: bold;
+}
+
+hr {
+	height: 0px;
+	border: none;
+	border-top: 1px solid #4A6AAA;
+}
+
+hr.footer {
+	height: 1px;
+}
+
+/* @group Member Descriptions */
+
+table.memberdecls {
+	border-spacing: 0px;
+	padding: 0px;
+}
+
+.memberdecls td, .fieldtable tr {
+	-webkit-transition-property: background-color, box-shadow;
+	-webkit-transition-duration: 0.5s;
+	-moz-transition-property: background-color, box-shadow;
+	-moz-transition-duration: 0.5s;
+	-ms-transition-property: background-color, box-shadow;
+	-ms-transition-duration: 0.5s;
+	-o-transition-property: background-color, box-shadow;
+	-o-transition-duration: 0.5s;
+	transition-property: background-color, box-shadow;
+	transition-duration: 0.5s;
+}
+
+.memberdecls td.glow, .fieldtable tr.glow {
+	background-color: cyan;
+	box-shadow: 0 0 15px cyan;
+}
+
+.mdescLeft, .mdescRight,
+.memItemLeft, .memItemRight,
+.memTemplItemLeft, .memTemplItemRight, .memTemplParams {
+	background-color: #F9FAFC;
+	border: none;
+	margin: 4px;
+	padding: 1px 0 0 8px;
+}
+
+.mdescLeft, .mdescRight {
+	padding: 0px 8px 4px 8px;
+	color: #555;
+}
+
+.memSeparator {
+        border-bottom: 1px solid #DEE4F0;
+        line-height: 1px;
+        margin: 0px;
+        padding: 0px;
+}
+
+.memItemLeft, .memTemplItemLeft {
+        white-space: nowrap;
+}
+
+.memItemRight {
+	width: 100%;
+}
+
+.memTemplParams {
+	color: #4665A2;
+        white-space: nowrap;
+	font-size: 80%;
+}
+
+/* @end */
+
+/* @group Member Details */
+
+/* Styles for detailed member documentation */
+
+.memtitle {
+	padding: 8px;
+	border-top: 1px solid #A8B8D9;
+	border-left: 1px solid #A8B8D9;
+	border-right: 1px solid #A8B8D9;
+	border-top-right-radius: 4px;
+	border-top-left-radius: 4px;
+	margin-bottom: -1px;
+	background-image: url('nav_f.png');
+	background-repeat: repeat-x;
+	background-color: #E2E8F2;
+	line-height: 1.25;
+	font-weight: 300;
+	float:left;
+}
+
+.permalink
+{
+        font-size: 65%;
+        display: inline-block;
+        vertical-align: middle;
+}
+
+.memtemplate {
+	font-size: 80%;
+	color: #4665A2;
+	font-weight: normal;
+	margin-left: 9px;
+}
+
+.memnav {
+	background-color: #EBEFF6;
+	border: 1px solid #A3B4D7;
+	text-align: center;
+	margin: 2px;
+	margin-right: 15px;
+	padding: 2px;
+}
+
+.mempage {
+	width: 100%;
+}
+
+.memitem {
+	padding: 0;
+	margin-bottom: 10px;
+	margin-right: 5px;
+        -webkit-transition: box-shadow 0.5s linear;
+        -moz-transition: box-shadow 0.5s linear;
+        -ms-transition: box-shadow 0.5s linear;
+        -o-transition: box-shadow 0.5s linear;
+        transition: box-shadow 0.5s linear;
+        display: table !important;
+        width: 100%;
+}
+
+.memitem.glow {
+         box-shadow: 0 0 15px cyan;
+}
+
+.memname {
+        font-weight: 400;
+        margin-left: 6px;
+}
+
+.memname td {
+	vertical-align: bottom;
+}
+
+.memproto, dl.reflist dt {
+        border-top: 1px solid #A8B8D9;
+        border-left: 1px solid #A8B8D9;
+        border-right: 1px solid #A8B8D9;
+        padding: 6px 0px 6px 0px;
+        color: #253555;
+        font-weight: bold;
+        text-shadow: 0px 1px 1px rgba(255, 255, 255, 0.9);
+        background-color: #DFE5F1;
+        /* opera specific markup */
+        box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+        border-top-right-radius: 4px;
+        /* firefox specific markup */
+        -moz-box-shadow: rgba(0, 0, 0, 0.15) 5px 5px 5px;
+        -moz-border-radius-topright: 4px;
+        /* webkit specific markup */
+        -webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+        -webkit-border-top-right-radius: 4px;
+
+}
+
+.overload {
+        font-family: "courier new",courier,monospace;
+	font-size: 65%;
+}
+
+.memdoc, dl.reflist dd {
+        border-bottom: 1px solid #A8B8D9;      
+        border-left: 1px solid #A8B8D9;      
+        border-right: 1px solid #A8B8D9; 
+        padding: 6px 10px 2px 10px;
+        background-color: #FBFCFD;
+        border-top-width: 0;
+        background-image:url('nav_g.png');
+        background-repeat:repeat-x;
+        background-color: #FFFFFF;
+        /* opera specific markup */
+        border-bottom-left-radius: 4px;
+        border-bottom-right-radius: 4px;
+        box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+        /* firefox specific markup */
+        -moz-border-radius-bottomleft: 4px;
+        -moz-border-radius-bottomright: 4px;
+        -moz-box-shadow: rgba(0, 0, 0, 0.15) 5px 5px 5px;
+        /* webkit specific markup */
+        -webkit-border-bottom-left-radius: 4px;
+        -webkit-border-bottom-right-radius: 4px;
+        -webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+}
+
+dl.reflist dt {
+        padding: 5px;
+}
+
+dl.reflist dd {
+        margin: 0px 0px 10px 0px;
+        padding: 5px;
+}
+
+.paramkey {
+	text-align: right;
+}
+
+.paramtype {
+	white-space: nowrap;
+}
+
+.paramname {
+	color: #602020;
+	white-space: nowrap;
+}
+.paramname em {
+	font-style: normal;
+}
+.paramname code {
+        line-height: 14px;
+}
+
+.params, .retval, .exception, .tparams {
+        margin-left: 0px;
+        padding-left: 0px;
+}       
+
+.params .paramname, .retval .paramname {
+        font-weight: bold;
+        vertical-align: top;
+}
+        
+.params .paramtype {
+        font-style: italic;
+        vertical-align: top;
+}       
+        
+.params .paramdir {
+        font-family: "courier new",courier,monospace;
+        vertical-align: top;
+}
+
+table.mlabels {
+	border-spacing: 0px;
+}
+
+td.mlabels-left {
+	width: 100%;
+	padding: 0px;
+}
+
+td.mlabels-right {
+	vertical-align: bottom;
+	padding: 0px;
+	white-space: nowrap;
+}
+
+span.mlabels {
+        margin-left: 8px;
+}
+
+span.mlabel {
+        background-color: #728DC1;
+        border-top:1px solid #5373B4;
+        border-left:1px solid #5373B4;
+        border-right:1px solid #C4CFE5;
+        border-bottom:1px solid #C4CFE5;
+	text-shadow: none;
+	color: white;
+	margin-right: 4px;
+	padding: 2px 3px;
+	border-radius: 3px;
+	font-size: 7pt;
+	white-space: nowrap;
+	vertical-align: middle;
+}
+
+
+
+/* @end */
+
+/* these are for tree view inside a (index) page */
+
+div.directory {
+        margin: 10px 0px;
+        border-top: 1px solid #9CAFD4;
+        border-bottom: 1px solid #9CAFD4;
+        width: 100%;
+}
+
+.directory table {
+        border-collapse:collapse;
+}
+
+.directory td {
+        margin: 0px;
+        padding: 0px;
+	vertical-align: top;
+}
+
+.directory td.entry {
+        white-space: nowrap;
+        padding-right: 6px;
+	padding-top: 3px;
+}
+
+.directory td.entry a {
+        outline:none;
+}
+
+.directory td.entry a img {
+        border: none;
+}
+
+.directory td.desc {
+        width: 100%;
+        padding-left: 6px;
+	padding-right: 6px;
+	padding-top: 3px;
+	border-left: 1px solid rgba(0,0,0,0.05);
+}
+
+.directory tr.even {
+	padding-left: 6px;
+	background-color: #F7F8FB;
+}
+
+.directory img {
+	vertical-align: -30%;
+}
+
+.directory .levels {
+        white-space: nowrap;
+        width: 100%;
+        text-align: right;
+        font-size: 9pt;
+}
+
+.directory .levels span {
+        cursor: pointer;
+        padding-left: 2px;
+        padding-right: 2px;
+	color: #3D578C;
+}
+
+.arrow {
+    color: #9CAFD4;
+    -webkit-user-select: none;
+    -khtml-user-select: none;
+    -moz-user-select: none;
+    -ms-user-select: none;
+    user-select: none;
+    cursor: pointer;
+    font-size: 80%;
+    display: inline-block;
+    width: 16px;
+    height: 22px;
+}
+
+.icon {
+    font-family: Arial, Helvetica;
+    font-weight: bold;
+    font-size: 12px;
+    height: 14px;
+    width: 16px;
+    display: inline-block;
+    background-color: #728DC1;
+    color: white;
+    text-align: center;
+    border-radius: 4px;
+    margin-left: 2px;
+    margin-right: 2px;
+}
+
+.icona {
+    width: 24px;
+    height: 22px;
+    display: inline-block;
+}
+
+.iconfopen {
+    width: 24px;
+    height: 18px;
+    margin-bottom: 4px;
+    background-image:url('folderopen.png');
+    background-position: 0px -4px;
+    background-repeat: repeat-y;
+    vertical-align:top;
+    display: inline-block;
+}
+
+.iconfclosed {
+    width: 24px;
+    height: 18px;
+    margin-bottom: 4px;
+    background-image:url('folderclosed.png');
+    background-position: 0px -4px;
+    background-repeat: repeat-y;
+    vertical-align:top;
+    display: inline-block;
+}
+
+.icondoc {
+    width: 24px;
+    height: 18px;
+    margin-bottom: 4px;
+    background-image:url('doc.png');
+    background-position: 0px -4px;
+    background-repeat: repeat-y;
+    vertical-align:top;
+    display: inline-block;
+}
+
+table.directory {
+    font: 400 14px Roboto,sans-serif;
+}
+
+/* @end */
+
+div.dynheader {
+        margin-top: 8px;
+	-webkit-touch-callout: none;
+	-webkit-user-select: none;
+	-khtml-user-select: none;
+	-moz-user-select: none;
+	-ms-user-select: none;
+	user-select: none;
+}
+
+address {
+	font-style: normal;
+	color: #2A3D61;
+}
+
+table.doxtable caption {
+	caption-side: top;
+}
+
+table.doxtable {
+	border-collapse:collapse;
+        margin-top: 4px;
+        margin-bottom: 4px;
+}
+
+table.doxtable td, table.doxtable th {
+	border: 1px solid #2D4068;
+	padding: 3px 7px 2px;
+}
+
+table.doxtable th {
+	background-color: #374F7F;
+	color: #FFFFFF;
+	font-size: 110%;
+	padding-bottom: 4px;
+	padding-top: 5px;
+}
+
+table.fieldtable {
+        /*width: 100%;*/
+        margin-bottom: 10px;
+        border: 1px solid #A8B8D9;
+        border-spacing: 0px;
+        -moz-border-radius: 4px;
+        -webkit-border-radius: 4px;
+        border-radius: 4px;
+        -moz-box-shadow: rgba(0, 0, 0, 0.15) 2px 2px 2px;
+        -webkit-box-shadow: 2px 2px 2px rgba(0, 0, 0, 0.15);
+        box-shadow: 2px 2px 2px rgba(0, 0, 0, 0.15);
+}
+
+.fieldtable td, .fieldtable th {
+        padding: 3px 7px 2px;
+}
+
+.fieldtable td.fieldtype, .fieldtable td.fieldname {
+        white-space: nowrap;
+        border-right: 1px solid #A8B8D9;
+        border-bottom: 1px solid #A8B8D9;
+        vertical-align: top;
+}
+
+.fieldtable td.fieldname {
+        padding-top: 3px;
+}
+
+.fieldtable td.fielddoc {
+        border-bottom: 1px solid #A8B8D9;
+        /*width: 100%;*/
+}
+
+.fieldtable td.fielddoc p:first-child {
+        margin-top: 0px;
+}       
+        
+.fieldtable td.fielddoc p:last-child {
+        margin-bottom: 2px;
+}
+
+.fieldtable tr:last-child td {
+        border-bottom: none;
+}
+
+.fieldtable th {
+        background-image:url('nav_f.png');
+        background-repeat:repeat-x;
+        background-color: #E2E8F2;
+        font-size: 90%;
+        color: #253555;
+        padding-bottom: 4px;
+        padding-top: 5px;
+        text-align:left;
+        font-weight: 400;
+        -moz-border-radius-topleft: 4px;
+        -moz-border-radius-topright: 4px;
+        -webkit-border-top-left-radius: 4px;
+        -webkit-border-top-right-radius: 4px;
+        border-top-left-radius: 4px;
+        border-top-right-radius: 4px;
+        border-bottom: 1px solid #A8B8D9;
+}
+
+
+.tabsearch {
+	top: 0px;
+	left: 10px;
+	height: 36px;
+	background-image: url('tab_b.png');
+	z-index: 101;
+	overflow: hidden;
+	font-size: 13px;
+}
+
+.navpath ul
+{
+	font-size: 11px;
+	background-image:url('tab_b.png');
+	background-repeat:repeat-x;
+	background-position: 0 -5px;
+	height:30px;
+	line-height:30px;
+	color:#8AA0CC;
+	border:solid 1px #C2CDE4;
+	overflow:hidden;
+	margin:0px;
+	padding:0px;
+}
+
+.navpath li
+{
+	list-style-type:none;
+	float:left;
+	padding-left:10px;
+	padding-right:15px;
+	background-image:url('bc_s.png');
+	background-repeat:no-repeat;
+	background-position:right;
+	color:#364D7C;
+}
+
+.navpath li.navelem a
+{
+	height:32px;
+	display:block;
+	text-decoration: none;
+	outline: none;
+	color: #283A5D;
+	font-family: 'Lucida Grande',Geneva,Helvetica,Arial,sans-serif;
+	text-shadow: 0px 1px 1px rgba(255, 255, 255, 0.9);
+	text-decoration: none;        
+}
+
+.navpath li.navelem a:hover
+{
+	color:#6884BD;
+}
+
+.navpath li.footer
+{
+        list-style-type:none;
+        float:right;
+        padding-left:10px;
+        padding-right:15px;
+        background-image:none;
+        background-repeat:no-repeat;
+        background-position:right;
+        color:#364D7C;
+        font-size: 8pt;
+}
+
+
+div.summary
+{
+	float: right;
+	font-size: 8pt;
+	padding-right: 5px;
+	width: 50%;
+	text-align: right;
+}       
+
+div.summary a
+{
+	white-space: nowrap;
+}
+
+table.classindex
+{
+        margin: 10px;
+        white-space: nowrap;
+        margin-left: 3%;
+        margin-right: 3%;
+        width: 94%;
+        border: 0;
+        border-spacing: 0; 
+        padding: 0;
+}
+
+div.ingroups
+{
+	font-size: 8pt;
+	width: 50%;
+	text-align: left;
+}
+
+div.ingroups a
+{
+	white-space: nowrap;
+}
+
+div.header
+{
+        background-image:url('nav_h.png');
+        background-repeat:repeat-x;
+	background-color: #F9FAFC;
+	margin:  0px;
+	border-bottom: 1px solid #C4CFE5;
+}
+
+div.headertitle
+{
+	padding: 5px 5px 5px 10px;
+}
+
+.PageDocRTL-title div.headertitle {
+  text-align: right;
+  direction: rtl;
+}
+
+dl
+{
+        padding: 0 0 0 10px;
+}
+
+/* dl.note, dl.warning, dl.attention, dl.pre, dl.post, dl.invariant, dl.deprecated, dl.todo, dl.test, dl.bug */
+dl.section
+{
+	margin-left: 0px;
+	padding-left: 0px;
+}
+
+dl.section.DocNodeRTL {
+  margin-right: 0px;
+  padding-right: 0px;
+}
+
+dl.note {
+  margin-left: -7px;
+  padding-left: 3px;
+  border-left: 4px solid;
+  border-color: #D0C000;
+}
+
+dl.note.DocNodeRTL {
+  margin-left: 0;
+  padding-left: 0;
+  border-left: 0;
+  margin-right: -7px;
+  padding-right: 3px;
+  border-right: 4px solid;
+  border-color: #D0C000;
+}
+
+dl.warning, dl.attention {
+  margin-left: -7px;
+  padding-left: 3px;
+  border-left: 4px solid;
+  border-color: #FF0000;
+}
+
+dl.warning.DocNodeRTL, dl.attention.DocNodeRTL {
+  margin-left: 0;
+  padding-left: 0;
+  border-left: 0;
+  margin-right: -7px;
+  padding-right: 3px;
+  border-right: 4px solid;
+  border-color: #FF0000;
+}
+
+dl.pre, dl.post, dl.invariant {
+  margin-left: -7px;
+  padding-left: 3px;
+  border-left: 4px solid;
+  border-color: #00D000;
+}
+
+dl.pre.DocNodeRTL, dl.post.DocNodeRTL, dl.invariant.DocNodeRTL {
+  margin-left: 0;
+  padding-left: 0;
+  border-left: 0;
+  margin-right: -7px;
+  padding-right: 3px;
+  border-right: 4px solid;
+  border-color: #00D000;
+}
+
+dl.deprecated {
+  margin-left: -7px;
+  padding-left: 3px;
+  border-left: 4px solid;
+  border-color: #505050;
+}
+
+dl.deprecated.DocNodeRTL {
+  margin-left: 0;
+  padding-left: 0;
+  border-left: 0;
+  margin-right: -7px;
+  padding-right: 3px;
+  border-right: 4px solid;
+  border-color: #505050;
+}
+
+dl.todo {
+  margin-left: -7px;
+  padding-left: 3px;
+  border-left: 4px solid;
+  border-color: #00C0E0;
+}
+
+dl.todo.DocNodeRTL {
+  margin-left: 0;
+  padding-left: 0;
+  border-left: 0;
+  margin-right: -7px;
+  padding-right: 3px;
+  border-right: 4px solid;
+  border-color: #00C0E0;
+}
+
+dl.test {
+  margin-left: -7px;
+  padding-left: 3px;
+  border-left: 4px solid;
+  border-color: #3030E0;
+}
+
+dl.test.DocNodeRTL {
+  margin-left: 0;
+  padding-left: 0;
+  border-left: 0;
+  margin-right: -7px;
+  padding-right: 3px;
+  border-right: 4px solid;
+  border-color: #3030E0;
+}
+
+dl.bug {
+  margin-left: -7px;
+  padding-left: 3px;
+  border-left: 4px solid;
+  border-color: #C08050;
+}
+
+dl.bug.DocNodeRTL {
+  margin-left: 0;
+  padding-left: 0;
+  border-left: 0;
+  margin-right: -7px;
+  padding-right: 3px;
+  border-right: 4px solid;
+  border-color: #C08050;
+}
+
+dl.section dd {
+	margin-bottom: 6px;
+}
+
+
+#projectlogo
+{
+	text-align: center;
+	vertical-align: bottom;
+	border-collapse: separate;
+}
+ 
+#projectlogo img
+{ 
+	border: 0px none;
+}
+ 
+#projectalign
+{
+        vertical-align: middle;
+}
+
+#projectname
+{
+	font: 300% Tahoma, Arial,sans-serif;
+	margin: 0px;
+	padding: 2px 0px;
+}
+    
+#projectbrief
+{
+	font: 120% Tahoma, Arial,sans-serif;
+	margin: 0px;
+	padding: 0px;
+}
+
+#projectnumber
+{
+	font: 50% Tahoma, Arial,sans-serif;
+	margin: 0px;
+	padding: 0px;
+}
+
+#titlearea
+{
+	padding: 0px;
+	margin: 0px;
+	width: 100%;
+	border-bottom: 1px solid #5373B4;
+}
+
+.image
+{
+        text-align: center;
+}
+
+.dotgraph
+{
+        text-align: center;
+}
+
+.mscgraph
+{
+        text-align: center;
+}
+
+.plantumlgraph
+{
+        text-align: center;
+}
+
+.diagraph
+{
+        text-align: center;
+}
+
+.caption
+{
+	font-weight: bold;
+}
+
+div.zoom
+{
+	border: 1px solid #90A5CE;
+}
+
+dl.citelist {
+        margin-bottom:50px;
+}
+
+dl.citelist dt {
+        color:#334975;
+        float:left;
+        font-weight:bold;
+        margin-right:10px;
+        padding:5px;
+}
+
+dl.citelist dd {
+        margin:2px 0;
+        padding:5px 0;
+}
+
+div.toc {
+        padding: 14px 25px;
+        background-color: #F4F6FA;
+        border: 1px solid #D8DFEE;
+        border-radius: 7px 7px 7px 7px;
+        float: right;
+        height: auto;
+        margin: 0 8px 10px 10px;
+        width: 200px;
+}
+
+.PageDocRTL-title div.toc {
+  float: left !important;
+  text-align: right;
+}
+
+div.toc li {
+        background: url("bdwn.png") no-repeat scroll 0 5px transparent;
+        font: 10px/1.2 Verdana,DejaVu Sans,Geneva,sans-serif;
+        margin-top: 5px;
+        padding-left: 10px;
+        padding-top: 2px;
+}
+
+.PageDocRTL-title div.toc li {
+  background-position-x: right !important;
+  padding-left: 0 !important;
+  padding-right: 10px;
+}
+
+div.toc h3 {
+        font: bold 12px/1.2 Arial,FreeSans,sans-serif;
+	color: #4665A2;
+        border-bottom: 0 none;
+        margin: 0;
+}
+
+div.toc ul {
+        list-style: none outside none;
+        border: medium none;
+        padding: 0px;
+}       
+
+div.toc li.level1 {
+        margin-left: 0px;
+}
+
+div.toc li.level2 {
+        margin-left: 15px;
+}
+
+div.toc li.level3 {
+        margin-left: 30px;
+}
+
+div.toc li.level4 {
+        margin-left: 45px;
+}
+
+.PageDocRTL-title div.toc li.level1 {
+  margin-left: 0 !important;
+  margin-right: 0;
+}
+
+.PageDocRTL-title div.toc li.level2 {
+  margin-left: 0 !important;
+  margin-right: 15px;
+}
+
+.PageDocRTL-title div.toc li.level3 {
+  margin-left: 0 !important;
+  margin-right: 30px;
+}
+
+.PageDocRTL-title div.toc li.level4 {
+  margin-left: 0 !important;
+  margin-right: 45px;
+}
+
+.inherit_header {
+        font-weight: bold;
+        color: gray;
+        cursor: pointer;
+	-webkit-touch-callout: none;
+	-webkit-user-select: none;
+	-khtml-user-select: none;
+	-moz-user-select: none;
+	-ms-user-select: none;
+	user-select: none;
+}
+
+.inherit_header td {
+        padding: 6px 0px 2px 5px;
+}
+
+.inherit {
+        display: none;
+}
+
+tr.heading h2 {
+        margin-top: 12px;
+        margin-bottom: 4px;
+}
+
+/* tooltip related style info */
+
+.ttc {
+        position: absolute;
+        display: none;
+}
+
+#powerTip {
+	cursor: default;
+	white-space: nowrap;
+	background-color: white;
+	border: 1px solid gray;
+	border-radius: 4px 4px 4px 4px;
+	box-shadow: 1px 1px 7px gray;
+	display: none;
+	font-size: smaller;
+	max-width: 80%;
+	opacity: 0.9;
+	padding: 1ex 1em 1em;
+	position: absolute;
+	z-index: 2147483647;
+}
+
+#powerTip div.ttdoc {
+        color: grey;
+	font-style: italic;
+}
+
+#powerTip div.ttname a {
+        font-weight: bold;
+}
+
+#powerTip div.ttname {
+        font-weight: bold;
+}
+
+#powerTip div.ttdeci {
+        color: #006318;
+}
+
+#powerTip div {
+        margin: 0px;
+        padding: 0px;
+        font: 12px/16px Roboto,sans-serif;
+}
+
+#powerTip:before, #powerTip:after {
+	content: "";
+	position: absolute;
+	margin: 0px;
+}
+
+#powerTip.n:after,  #powerTip.n:before,
+#powerTip.s:after,  #powerTip.s:before,
+#powerTip.w:after,  #powerTip.w:before,
+#powerTip.e:after,  #powerTip.e:before,
+#powerTip.ne:after, #powerTip.ne:before,
+#powerTip.se:after, #powerTip.se:before,
+#powerTip.nw:after, #powerTip.nw:before,
+#powerTip.sw:after, #powerTip.sw:before {
+	border: solid transparent;
+	content: " ";
+	height: 0;
+	width: 0;
+	position: absolute;
+}
+
+#powerTip.n:after,  #powerTip.s:after,
+#powerTip.w:after,  #powerTip.e:after,
+#powerTip.nw:after, #powerTip.ne:after,
+#powerTip.sw:after, #powerTip.se:after {
+	border-color: rgba(255, 255, 255, 0);
+}
+
+#powerTip.n:before,  #powerTip.s:before,
+#powerTip.w:before,  #powerTip.e:before,
+#powerTip.nw:before, #powerTip.ne:before,
+#powerTip.sw:before, #powerTip.se:before {
+	border-color: rgba(128, 128, 128, 0);
+}
+
+#powerTip.n:after,  #powerTip.n:before,
+#powerTip.ne:after, #powerTip.ne:before,
+#powerTip.nw:after, #powerTip.nw:before {
+	top: 100%;
+}
+
+#powerTip.n:after, #powerTip.ne:after, #powerTip.nw:after {
+	border-top-color: #ffffff;
+	border-width: 10px;
+	margin: 0px -10px;
+}
+#powerTip.n:before {
+	border-top-color: #808080;
+	border-width: 11px;
+	margin: 0px -11px;
+}
+#powerTip.n:after, #powerTip.n:before {
+	left: 50%;
+}
+
+#powerTip.nw:after, #powerTip.nw:before {
+	right: 14px;
+}
+
+#powerTip.ne:after, #powerTip.ne:before {
+	left: 14px;
+}
+
+#powerTip.s:after,  #powerTip.s:before,
+#powerTip.se:after, #powerTip.se:before,
+#powerTip.sw:after, #powerTip.sw:before {
+	bottom: 100%;
+}
+
+#powerTip.s:after, #powerTip.se:after, #powerTip.sw:after {
+	border-bottom-color: #ffffff;
+	border-width: 10px;
+	margin: 0px -10px;
+}
+
+#powerTip.s:before, #powerTip.se:before, #powerTip.sw:before {
+	border-bottom-color: #808080;
+	border-width: 11px;
+	margin: 0px -11px;
+}
+
+#powerTip.s:after, #powerTip.s:before {
+	left: 50%;
+}
+
+#powerTip.sw:after, #powerTip.sw:before {
+	right: 14px;
+}
+
+#powerTip.se:after, #powerTip.se:before {
+	left: 14px;
+}
+
+#powerTip.e:after, #powerTip.e:before {
+	left: 100%;
+}
+#powerTip.e:after {
+	border-left-color: #ffffff;
+	border-width: 10px;
+	top: 50%;
+	margin-top: -10px;
+}
+#powerTip.e:before {
+	border-left-color: #808080;
+	border-width: 11px;
+	top: 50%;
+	margin-top: -11px;
+}
+
+#powerTip.w:after, #powerTip.w:before {
+	right: 100%;
+}
+#powerTip.w:after {
+	border-right-color: #ffffff;
+	border-width: 10px;
+	top: 50%;
+	margin-top: -10px;
+}
+#powerTip.w:before {
+	border-right-color: #808080;
+	border-width: 11px;
+	top: 50%;
+	margin-top: -11px;
+}
+
+@media print
+{
+  #top { display: none; }
+  #side-nav { display: none; }
+  #nav-path { display: none; }
+  body { overflow:visible; }
+  h1, h2, h3, h4, h5, h6 { page-break-after: avoid; }
+  .summary { display: none; }
+  .memitem { page-break-inside: avoid; }
+  #doc-content
+  {
+    margin-left:0 !important;
+    height:auto !important;
+    width:auto !important;
+    overflow:inherit;
+    display:inline;
+  }
+}
+
+/* @group Markdown */
+
+/*
+table.markdownTable {
+	border-collapse:collapse;
+        margin-top: 4px;
+        margin-bottom: 4px;
+}
+
+table.markdownTable td, table.markdownTable th {
+	border: 1px solid #2D4068;
+	padding: 3px 7px 2px;
+}
+
+table.markdownTableHead tr {
+}
+
+table.markdownTableBodyLeft td, table.markdownTable th {
+	border: 1px solid #2D4068;
+	padding: 3px 7px 2px;
+}
+
+th.markdownTableHeadLeft th.markdownTableHeadRight th.markdownTableHeadCenter th.markdownTableHeadNone {
+	background-color: #374F7F;
+	color: #FFFFFF;
+	font-size: 110%;
+	padding-bottom: 4px;
+	padding-top: 5px;
+}
+
+th.markdownTableHeadLeft {
+	text-align: left
+}
+
+th.markdownTableHeadRight {
+	text-align: right
+}
+
+th.markdownTableHeadCenter {
+	text-align: center
+}
+*/
+
+table.markdownTable {
+	border-collapse:collapse;
+        margin-top: 4px;
+        margin-bottom: 4px;
+}
+
+table.markdownTable td, table.markdownTable th {
+	border: 1px solid #2D4068;
+	padding: 3px 7px 2px;
+}
+
+table.markdownTable tr {
+}
+
+th.markdownTableHeadLeft, th.markdownTableHeadRight, th.markdownTableHeadCenter, th.markdownTableHeadNone {
+	background-color: #374F7F;
+	color: #FFFFFF;
+	font-size: 110%;
+	padding-bottom: 4px;
+	padding-top: 5px;
+}
+
+th.markdownTableHeadLeft, td.markdownTableBodyLeft {
+	text-align: left
+}
+
+th.markdownTableHeadRight, td.markdownTableBodyRight {
+	text-align: right
+}
+
+th.markdownTableHeadCenter, td.markdownTableBodyCenter {
+	text-align: center
+}
+
+.DocNodeRTL {
+  text-align: right;
+  direction: rtl;
+}
+
+.DocNodeLTR {
+  text-align: left;
+  direction: ltr;
+}
+
+table.DocNodeRTL {
+   width: auto;
+   margin-right: 0;
+   margin-left: auto;
+}
+
+table.DocNodeLTR {
+   width: auto;
+   margin-right: auto;
+   margin-left: 0;
+}
+
+tt, code, kbd, samp
+{
+  display: inline-block;
+  direction:ltr; 
+}
+/* @end */

docs/docs/html/dynsections.js

@@ -0,0 +1,127 @@
+/*
+ @licstart  The following is the entire license notice for the
+ JavaScript code in this file.
+
+ Copyright (C) 1997-2017 by Dimitri van Heesch
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+ @licend  The above is the entire license notice
+ for the JavaScript code in this file
+ */
+function toggleVisibility(linkObj)
+{
+ var base = $(linkObj).attr('id');
+ var summary = $('#'+base+'-summary');
+ var content = $('#'+base+'-content');
+ var trigger = $('#'+base+'-trigger');
+ var src=$(trigger).attr('src');
+ if (content.is(':visible')===true) {
+   content.hide();
+   summary.show();
+   $(linkObj).addClass('closed').removeClass('opened');
+   $(trigger).attr('src',src.substring(0,src.length-8)+'closed.png');
+ } else {
+   content.show();
+   summary.hide();
+   $(linkObj).removeClass('closed').addClass('opened');
+   $(trigger).attr('src',src.substring(0,src.length-10)+'open.png');
+ }
+ return false;
+}
+
+function updateStripes()
+{
+  $('table.directory tr').
+       removeClass('even').filter(':visible:even').addClass('even');
+}
+
+function toggleLevel(level)
+{
+  $('table.directory tr').each(function() {
+    var l = this.id.split('_').length-1;
+    var i = $('#img'+this.id.substring(3));
+    var a = $('#arr'+this.id.substring(3));
+    if (l<level+1) {
+      i.removeClass('iconfopen iconfclosed').addClass('iconfopen');
+      a.html('&#9660;');
+      $(this).show();
+    } else if (l==level+1) {
+      i.removeClass('iconfclosed iconfopen').addClass('iconfclosed');
+      a.html('&#9654;');
+      $(this).show();
+    } else {
+      $(this).hide();
+    }
+  });
+  updateStripes();
+}
+
+function toggleFolder(id)
+{
+  // the clicked row
+  var currentRow = $('#row_'+id);
+
+  // all rows after the clicked row
+  var rows = currentRow.nextAll("tr");
+
+  var re = new RegExp('^row_'+id+'\\d+_$', "i"); //only one sub
+
+  // only match elements AFTER this one (can't hide elements before)
+  var childRows = rows.filter(function() { return this.id.match(re); });
+
+  // first row is visible we are HIDING
+  if (childRows.filter(':first').is(':visible')===true) {
+    // replace down arrow by right arrow for current row
+    var currentRowSpans = currentRow.find("span");
+    currentRowSpans.filter(".iconfopen").removeClass("iconfopen").addClass("iconfclosed");
+    currentRowSpans.filter(".arrow").html('&#9654;');
+    rows.filter("[id^=row_"+id+"]").hide(); // hide all children
+  } else { // we are SHOWING
+    // replace right arrow by down arrow for current row
+    var currentRowSpans = currentRow.find("span");
+    currentRowSpans.filter(".iconfclosed").removeClass("iconfclosed").addClass("iconfopen");
+    currentRowSpans.filter(".arrow").html('&#9660;');
+    // replace down arrows by right arrows for child rows
+    var childRowsSpans = childRows.find("span");
+    childRowsSpans.filter(".iconfopen").removeClass("iconfopen").addClass("iconfclosed");
+    childRowsSpans.filter(".arrow").html('&#9654;');
+    childRows.show(); //show all children
+  }
+  updateStripes();
+}
+
+
+function toggleInherit(id)
+{
+  var rows = $('tr.inherit.'+id);
+  var img = $('tr.inherit_header.'+id+' img');
+  var src = $(img).attr('src');
+  if (rows.filter(':first').is(':visible')===true) {
+    rows.css('display','none');
+    $(img).attr('src',src.substring(0,src.length-8)+'closed.png');
+  } else {
+    rows.css('display','table-row'); // using show() causes jump in firefox
+    $(img).attr('src',src.substring(0,src.length-10)+'open.png');
+  }
+}
+/* @license-end */
+
+$(document).ready(function() {
+  $('.code,.codeRef').each(function() {
+    $(this).data('powertip',$('#'+$(this).attr('href').replace(/.*\//,'').replace(/[^a-z_A-Z0-9]/g,'_')).html());
+    $(this).powerTip({ placement: 's', smartPlacement: true, mouseOnToPopup: true });
+  });
+});

docs/docs/html/index.html

@@ -0,0 +1,104 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.15"/>
+<meta name="viewport" content="width=device-width, initial-scale=1"/>
+<title>Tripal: Main Page</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtreedata.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
+  $(document).ready(initResizable);
+/* @license-end */</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/searchdata.js"></script>
+<script type="text/javascript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+  <td id="projectalign" style="padding-left: 0.5em;">
+   <div id="projectname">Tripal
+   &#160;<span id="projectnumber">v3.0 (7.x-3.0)</span>
+   </div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.15 -->
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+/* @license-end */
+</script>
+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
+$(function() {
+  initMenu('',true,false,'search.php','Search');
+  $(document).ready(function() { init_search(); });
+});
+/* @license-end */</script>
+<div id="main-nav"></div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+  <div id="nav-tree">
+    <div id="nav-tree-contents">
+      <div id="nav-sync" class="sync"></div>
+    </div>
+  </div>
+  <div id="splitbar" style="-moz-user-select:none;" 
+       class="ui-resizable-handle">
+  </div>
+</div>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
+$(document).ready(function(){initNavTree('index.html','');});
+/* @license-end */
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+</div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="header">
+  <div class="headertitle">
+<div class="title">Tripal Documentation</div>  </div>
+</div><!--header-->
+<div class="contents">
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="footer">Generated on Wed Aug 22 2018 12:50:41 for Tripal by
+    <a href="http://www.doxygen.org/index.html">
+    <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.15 </li>
+  </ul>
+</div>
+</body>
+</html>

docs/docs/html/menu.js

@@ -0,0 +1,50 @@
+/*
+ @licstart  The following is the entire license notice for the
+ JavaScript code in this file.
+
+ Copyright (C) 1997-2017 by Dimitri van Heesch
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+ @licend  The above is the entire license notice
+ for the JavaScript code in this file
+ */
+function initMenu(relPath,searchEnabled,serverSide,searchPage,search) {
+  function makeTree(data,relPath) {
+    var result='';
+    if ('children' in data) {
+      result+='<ul>';
+      for (var i in data.children) {
+        result+='<li><a href="'+relPath+data.children[i].url+'">'+
+                                data.children[i].text+'</a>'+
+                                makeTree(data.children[i],relPath)+'</li>';
+      }
+      result+='</ul>';
+    }
+    return result;
+  }
+
+  $('#main-nav').append(makeTree(menudata,relPath));
+  $('#main-nav').children(':first').addClass('sm sm-dox').attr('id','main-menu');
+  if (searchEnabled) {
+    if (serverSide) {
+      $('#main-menu').append('<li style="float:right"><div id="MSearchBox" class="MSearchBoxInactive"><div class="left"><form id="FSearchBox" action="'+searchPage+'" method="get"><img id="MSearchSelect" src="'+relPath+'search/mag.png" alt=""/><input type="text" id="MSearchField" name="query" value="'+search+'" size="20" accesskey="S" onfocus="searchBox.OnSearchFieldFocus(true)" onblur="searchBox.OnSearchFieldFocus(false)"></form></div><div class="right"></div></div></li>');
+    } else {
+      $('#main-menu').append('<li style="float:right"><div id="MSearchBox" class="MSearchBoxInactive"><span class="left"><img id="MSearchSelect" src="'+relPath+'search/mag_sel.png" onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" alt=""/><input type="text" id="MSearchField" value="'+search+'" accesskey="S" onfocus="searchBox.OnSearchFieldFocus(true)" onblur="searchBox.OnSearchFieldFocus(false)" onkeyup="searchBox.OnSearchFieldChange(event)"/></span><span class="right"><a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="'+relPath+'search/close.png" alt=""/></a></span></div></li>');
+    }
+  }
+  $('#main-menu').smartmenus();
+}
+/* @license-end */

docs/docs/html/menudata.js

@@ -0,0 +1,25 @@
+/*
+@ @licstart  The following is the entire license notice for the
+JavaScript code in this file.
+
+Copyright (C) 1997-2017 by Dimitri van Heesch
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+@licend  The above is the entire license notice
+for the JavaScript code in this file
+*/
+var menudata={children:[
+{text:"Main Page",url:"index.html"}]}

docs/docs/html/navtree.css

@@ -0,0 +1,146 @@
+#nav-tree .children_ul {
+  margin:0;
+  padding:4px;
+}
+
+#nav-tree ul {
+  list-style:none outside none;
+  margin:0px;
+  padding:0px;
+}
+
+#nav-tree li {
+  white-space:nowrap;
+  margin:0px;
+  padding:0px;
+}
+
+#nav-tree .plus {
+  margin:0px;
+}
+
+#nav-tree .selected {
+  background-image: url('tab_a.png');
+  background-repeat:repeat-x;
+  color: #fff;
+  text-shadow: 0px 1px 1px rgba(0, 0, 0, 1.0);
+}
+
+#nav-tree img {
+  margin:0px;
+  padding:0px;
+  border:0px;
+  vertical-align: middle;
+}
+
+#nav-tree a {
+  text-decoration:none;
+  padding:0px;
+  margin:0px;
+  outline:none;
+}
+
+#nav-tree .label {
+  margin:0px;
+  padding:0px;
+  font: 12px 'Lucida Grande',Geneva,Helvetica,Arial,sans-serif;
+}
+
+#nav-tree .label a {
+  padding:2px;
+}
+
+#nav-tree .selected a {
+  text-decoration:none;
+  color:#fff;
+}
+
+#nav-tree .children_ul {
+  margin:0px;
+  padding:0px;
+}
+
+#nav-tree .item {
+  margin:0px;
+  padding:0px;
+}
+
+#nav-tree {
+  padding: 0px 0px;
+  background-color: #FAFAFF; 
+  font-size:14px;
+  overflow:auto;
+}
+
+#doc-content {
+  overflow:auto;
+  display:block;
+  padding:0px;
+  margin:0px;
+  -webkit-overflow-scrolling : touch; /* iOS 5+ */
+}
+
+#side-nav {
+  padding:0 6px 0 0;
+  margin: 0px;
+  display:block;
+  position: absolute;
+  left: 0px;
+  width: 250px;
+}
+
+.ui-resizable .ui-resizable-handle {
+  display:block;
+}
+
+.ui-resizable-e {
+  background-image:url("splitbar.png");
+  background-size:100%;
+  background-repeat:no-repeat;
+  background-attachment: scroll;
+  cursor:ew-resize;
+  height:100%;
+  right:0;
+  top:0;
+  width:6px;
+}
+
+.ui-resizable-handle {
+  display:none;
+  font-size:0.1px;
+  position:absolute;
+  z-index:1;
+}
+
+#nav-tree-contents {
+  margin: 6px 0px 0px 0px;
+}
+
+#nav-tree {
+  background-image:url('nav_h.png');
+  background-repeat:repeat-x;
+  background-color: #F9FAFC;
+  -webkit-overflow-scrolling : touch; /* iOS 5+ */
+}
+
+#nav-sync {
+  position:absolute;
+  top:5px;
+  right:24px;
+  z-index:0;
+}
+
+#nav-sync img {
+  opacity:0.3;
+}
+
+#nav-sync img:hover {
+  opacity:0.9;
+}
+
+@media print
+{
+  #nav-tree { display: none; }
+  div.ui-resizable-handle { display: none; position: relative; }
+}
+

docs/docs/html/navtree.js

@@ -0,0 +1,540 @@
+/*
+ @licstart  The following is the entire license notice for the
+ JavaScript code in this file.
+
+ Copyright (C) 1997-2017 by Dimitri van Heesch
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+ @licend  The above is the entire license notice
+ for the JavaScript code in this file
+ */
+var navTreeSubIndices = new Array();
+var arrowDown = '▼';
+var arrowRight = '▶';
+
+function getData(varName)
+{
+  var i = varName.lastIndexOf('/');
+  var n = i>=0 ? varName.substring(i+1) : varName;
+  return eval(n.replace(/\-/g,'_'));
+}
+
+function stripPath(uri)
+{
+  return uri.substring(uri.lastIndexOf('/')+1);
+}
+
+function stripPath2(uri)
+{
+  var i = uri.lastIndexOf('/');
+  var s = uri.substring(i+1);
+  var m = uri.substring(0,i+1).match(/\/d\w\/d\w\w\/$/);
+  return m ? uri.substring(i-6) : s;
+}
+
+function hashValue()
+{
+  return $(location).attr('hash').substring(1).replace(/[^\w\-]/g,'');
+}
+
+function hashUrl()
+{
+  return '#'+hashValue();
+}
+
+function pathName()
+{
+  return $(location).attr('pathname').replace(/[^-A-Za-z0-9+&@#/%?=~_|!:,.;\(\)]/g, '');
+}
+
+function localStorageSupported()
+{
+  try {
+    return 'localStorage' in window && window['localStorage'] !== null && window.localStorage.getItem;
+  }
+  catch(e) {
+    return false;
+  }
+}
+
+
+function storeLink(link)
+{
+  if (!$("#nav-sync").hasClass('sync') && localStorageSupported()) {
+      window.localStorage.setItem('navpath',link);
+  }
+}
+
+function deleteLink()
+{
+  if (localStorageSupported()) {
+    window.localStorage.setItem('navpath','');
+  }
+}
+
+function cachedLink()
+{
+  if (localStorageSupported()) {
+    return window.localStorage.getItem('navpath');
+  } else {
+    return '';
+  }
+}
+
+function getScript(scriptName,func,show)
+{
+  var head = document.getElementsByTagName("head")[0];
+  var script = document.createElement('script');
+  script.id = scriptName;
+  script.type = 'text/javascript';
+  script.onload = func;
+  script.src = scriptName+'.js';
+  if ($.browser.msie && $.browser.version<=8) {
+    // script.onload does not work with older versions of IE
+    script.onreadystatechange = function() {
+      if (script.readyState=='complete' || script.readyState=='loaded') {
+        func(); if (show) showRoot();
+      }
+    }
+  }
+  head.appendChild(script);
+}
+
+function createIndent(o,domNode,node,level)
+{
+  var level=-1;
+  var n = node;
+  while (n.parentNode) { level++; n=n.parentNode; }
+  if (node.childrenData) {
+    var imgNode = document.createElement("span");
+    imgNode.className = 'arrow';
+    imgNode.style.paddingLeft=(16*level).toString()+'px';
+    imgNode.innerHTML=arrowRight;
+    node.plus_img = imgNode;
+    node.expandToggle = document.createElement("a");
+    node.expandToggle.href = "javascript:void(0)";
+    node.expandToggle.onclick = function() {
+      if (node.expanded) {
+        $(node.getChildrenUL()).slideUp("fast");
+        node.plus_img.innerHTML=arrowRight;
+        node.expanded = false;
+      } else {
+        expandNode(o, node, false, false);
+      }
+    }
+    node.expandToggle.appendChild(imgNode);
+    domNode.appendChild(node.expandToggle);
+  } else {
+    var span = document.createElement("span");
+    span.className = 'arrow';
+    span.style.width   = 16*(level+1)+'px';
+    span.innerHTML = '&#160;';
+    domNode.appendChild(span);
+  }
+}
+
+var animationInProgress = false;
+
+function gotoAnchor(anchor,aname,updateLocation)
+{
+  var pos, docContent = $('#doc-content');
+  var ancParent = $(anchor.parent());
+  if (ancParent.hasClass('memItemLeft') ||
+      ancParent.hasClass('fieldname') ||
+      ancParent.hasClass('fieldtype') ||
+      ancParent.is(':header'))
+  {
+    pos = ancParent.position().top;
+  } else if (anchor.position()) {
+    pos = anchor.position().top;
+  }
+  if (pos) {
+    var dist = Math.abs(Math.min(
+               pos-docContent.offset().top,
+               docContent[0].scrollHeight-
+               docContent.height()-docContent.scrollTop()));
+    animationInProgress=true;
+    docContent.animate({
+      scrollTop: pos + docContent.scrollTop() - docContent.offset().top
+    },Math.max(50,Math.min(500,dist)),function(){
+      if (updateLocation) window.location.href=aname;
+      animationInProgress=false;
+    });
+  }
+}
+
+function newNode(o, po, text, link, childrenData, lastNode)
+{
+  var node = new Object();
+  node.children = Array();
+  node.childrenData = childrenData;
+  node.depth = po.depth + 1;
+  node.relpath = po.relpath;
+  node.isLast = lastNode;
+
+  node.li = document.createElement("li");
+  po.getChildrenUL().appendChild(node.li);
+  node.parentNode = po;
+
+  node.itemDiv = document.createElement("div");
+  node.itemDiv.className = "item";
+
+  node.labelSpan = document.createElement("span");
+  node.labelSpan.className = "label";
+
+  createIndent(o,node.itemDiv,node,0);
+  node.itemDiv.appendChild(node.labelSpan);
+  node.li.appendChild(node.itemDiv);
+
+  var a = document.createElement("a");
+  node.labelSpan.appendChild(a);
+  node.label = document.createTextNode(text);
+  node.expanded = false;
+  a.appendChild(node.label);
+  if (link) {
+    var url;
+    if (link.substring(0,1)=='^') {
+      url = link.substring(1);
+      link = url;
+    } else {
+      url = node.relpath+link;
+    }
+    a.className = stripPath(link.replace('#',':'));
+    if (link.indexOf('#')!=-1) {
+      var aname = '#'+link.split('#')[1];
+      var srcPage = stripPath(pathName());
+      var targetPage = stripPath(link.split('#')[0]);
+      a.href = srcPage!=targetPage ? url : "javascript:void(0)";
+      a.onclick = function(){
+        storeLink(link);
+        if (!$(a).parent().parent().hasClass('selected'))
+        {
+          $('.item').removeClass('selected');
+          $('.item').removeAttr('id');
+          $(a).parent().parent().addClass('selected');
+          $(a).parent().parent().attr('id','selected');
+        }
+        var anchor = $(aname);
+        gotoAnchor(anchor,aname,true);
+      };
+    } else {
+      a.href = url;
+      a.onclick = function() { storeLink(link); }
+    }
+  } else {
+    if (childrenData != null)
+    {
+      a.className = "nolink";
+      a.href = "javascript:void(0)";
+      a.onclick = node.expandToggle.onclick;
+    }
+  }
+
+  node.childrenUL = null;
+  node.getChildrenUL = function() {
+    if (!node.childrenUL) {
+      node.childrenUL = document.createElement("ul");
+      node.childrenUL.className = "children_ul";
+      node.childrenUL.style.display = "none";
+      node.li.appendChild(node.childrenUL);
+    }
+    return node.childrenUL;
+  };
+
+  return node;
+}
+
+function showRoot()
+{
+  var headerHeight = $("#top").height();
+  var footerHeight = $("#nav-path").height();
+  var windowHeight = $(window).height() - headerHeight - footerHeight;
+  (function (){ // retry until we can scroll to the selected item
+    try {
+      var navtree=$('#nav-tree');
+      navtree.scrollTo('#selected',0,{offset:-windowHeight/2});
+    } catch (err) {
+      setTimeout(arguments.callee, 0);
+    }
+  })();
+}
+
+function expandNode(o, node, imm, showRoot)
+{
+  if (node.childrenData && !node.expanded) {
+    if (typeof(node.childrenData)==='string') {
+      var varName    = node.childrenData;
+      getScript(node.relpath+varName,function(){
+        node.childrenData = getData(varName);
+        expandNode(o, node, imm, showRoot);
+      }, showRoot);
+    } else {
+      if (!node.childrenVisited) {
+        getNode(o, node);
+      } if (imm || ($.browser.msie && $.browser.version>8)) {
+        // somehow slideDown jumps to the start of tree for IE9 :-(
+        $(node.getChildrenUL()).show();
+      } else {
+        $(node.getChildrenUL()).slideDown("fast");
+      }
+      node.plus_img.innerHTML = arrowDown;
+      node.expanded = true;
+    }
+  }
+}
+
+function glowEffect(n,duration)
+{
+  n.addClass('glow').delay(duration).queue(function(next){
+    $(this).removeClass('glow');next();
+  });
+}
+
+function highlightAnchor()
+{
+  var aname = hashUrl();
+  var anchor = $(aname);
+  if (anchor.parent().attr('class')=='memItemLeft'){
+    var rows = $('.memberdecls tr[class$="'+hashValue()+'"]');
+    glowEffect(rows.children(),300); // member without details
+  } else if (anchor.parent().attr('class')=='fieldname'){
+    glowEffect(anchor.parent().parent(),1000); // enum value
+  } else if (anchor.parent().attr('class')=='fieldtype'){
+    glowEffect(anchor.parent().parent(),1000); // struct field
+  } else if (anchor.parent().is(":header")) {
+    glowEffect(anchor.parent(),1000); // section header
+  } else {
+    glowEffect(anchor.next(),1000); // normal member
+  }
+  gotoAnchor(anchor,aname,false);
+}
+
+function selectAndHighlight(hash,n)
+{
+  var a;
+  if (hash) {
+    var link=stripPath(pathName())+':'+hash.substring(1);
+    a=$('.item a[class$="'+link+'"]');
+  }
+  if (a && a.length) {
+    a.parent().parent().addClass('selected');
+    a.parent().parent().attr('id','selected');
+    highlightAnchor();
+  } else if (n) {
+    $(n.itemDiv).addClass('selected');
+    $(n.itemDiv).attr('id','selected');
+  }
+  if ($('#nav-tree-contents .item:first').hasClass('selected')) {
+    $('#nav-sync').css('top','30px');
+  } else {
+    $('#nav-sync').css('top','5px');
+  }
+  showRoot();
+}
+
+function showNode(o, node, index, hash)
+{
+  if (node && node.childrenData) {
+    if (typeof(node.childrenData)==='string') {
+      var varName    = node.childrenData;
+      getScript(node.relpath+varName,function(){
+        node.childrenData = getData(varName);
+        showNode(o,node,index,hash);
+      },true);
+    } else {
+      if (!node.childrenVisited) {
+        getNode(o, node);
+      }
+      $(node.getChildrenUL()).css({'display':'block'});
+      node.plus_img.innerHTML = arrowDown;
+      node.expanded = true;
+      var n = node.children[o.breadcrumbs[index]];
+      if (index+1<o.breadcrumbs.length) {
+        showNode(o,n,index+1,hash);
+      } else {
+        if (typeof(n.childrenData)==='string') {
+          var varName = n.childrenData;
+          getScript(n.relpath+varName,function(){
+            n.childrenData = getData(varName);
+            node.expanded=false;
+            showNode(o,node,index,hash); // retry with child node expanded
+          },true);
+        } else {
+          var rootBase = stripPath(o.toroot.replace(/\..+$/, ''));
+          if (rootBase=="index" || rootBase=="pages" || rootBase=="search") {
+            expandNode(o, n, true, true);
+          }
+          selectAndHighlight(hash,n);
+        }
+      }
+    }
+  } else {
+    selectAndHighlight(hash);
+  }
+}
+
+function removeToInsertLater(element) {
+  var parentNode = element.parentNode;
+  var nextSibling = element.nextSibling;
+  parentNode.removeChild(element);
+  return function() {
+    if (nextSibling) {
+      parentNode.insertBefore(element, nextSibling);
+    } else {
+      parentNode.appendChild(element);
+    }
+  };
+}
+
+function getNode(o, po)
+{
+  var insertFunction = removeToInsertLater(po.li);
+  po.childrenVisited = true;
+  var l = po.childrenData.length-1;
+  for (var i in po.childrenData) {
+    var nodeData = po.childrenData[i];
+    po.children[i] = newNode(o, po, nodeData[0], nodeData[1], nodeData[2],
+      i==l);
+  }
+  insertFunction();
+}
+
+function gotoNode(o,subIndex,root,hash,relpath)
+{
+  var nti = navTreeSubIndices[subIndex][root+hash];
+  o.breadcrumbs = $.extend(true, [], nti ? nti : navTreeSubIndices[subIndex][root]);
+  if (!o.breadcrumbs && root!=NAVTREE[0][1]) { // fallback: show index
+    navTo(o,NAVTREE[0][1],"",relpath);
+    $('.item').removeClass('selected');
+    $('.item').removeAttr('id');
+  }
+  if (o.breadcrumbs) {
+    o.breadcrumbs.unshift(0); // add 0 for root node
+    showNode(o, o.node, 0, hash);
+  }
+}
+
+function navTo(o,root,hash,relpath)
+{
+  var link = cachedLink();
+  if (link) {
+    var parts = link.split('#');
+    root = parts[0];
+    if (parts.length>1) hash = '#'+parts[1].replace(/[^\w\-]/g,'');
+    else hash='';
+  }
+  if (hash.match(/^#l\d+$/)) {
+    var anchor=$('a[name='+hash.substring(1)+']');
+    glowEffect(anchor.parent(),1000); // line number
+    hash=''; // strip line number anchors
+  }
+  var url=root+hash;
+  var i=-1;
+  while (NAVTREEINDEX[i+1]<=url) i++;
+  if (i==-1) { i=0; root=NAVTREE[0][1]; } // fallback: show index
+  if (navTreeSubIndices[i]) {
+    gotoNode(o,i,root,hash,relpath)
+  } else {
+    getScript(relpath+'navtreeindex'+i,function(){
+      navTreeSubIndices[i] = eval('NAVTREEINDEX'+i);
+      if (navTreeSubIndices[i]) {
+        gotoNode(o,i,root,hash,relpath);
+      }
+    },true);
+  }
+}
+
+function showSyncOff(n,relpath)
+{
+    n.html('<img src="'+relpath+'sync_off.png" title="'+SYNCOFFMSG+'"/>');
+}
+
+function showSyncOn(n,relpath)
+{
+    n.html('<img src="'+relpath+'sync_on.png" title="'+SYNCONMSG+'"/>');
+}
+
+function toggleSyncButton(relpath)
+{
+  var navSync = $('#nav-sync');
+  if (navSync.hasClass('sync')) {
+    navSync.removeClass('sync');
+    showSyncOff(navSync,relpath);
+    storeLink(stripPath2(pathName())+hashUrl());
+  } else {
+    navSync.addClass('sync');
+    showSyncOn(navSync,relpath);
+    deleteLink();
+  }
+}
+
+function initNavTree(toroot,relpath)
+{
+  var o = new Object();
+  o.toroot = toroot;
+  o.node = new Object();
+  o.node.li = document.getElementById("nav-tree-contents");
+  o.node.childrenData = NAVTREE;
+  o.node.children = new Array();
+  o.node.childrenUL = document.createElement("ul");
+  o.node.getChildrenUL = function() { return o.node.childrenUL; };
+  o.node.li.appendChild(o.node.childrenUL);
+  o.node.depth = 0;
+  o.node.relpath = relpath;
+  o.node.expanded = false;
+  o.node.isLast = true;
+  o.node.plus_img = document.createElement("span");
+  o.node.plus_img.className = 'arrow';
+  o.node.plus_img.innerHTML = arrowRight;
+
+  if (localStorageSupported()) {
+    var navSync = $('#nav-sync');
+    if (cachedLink()) {
+      showSyncOff(navSync,relpath);
+      navSync.removeClass('sync');
+    } else {
+      showSyncOn(navSync,relpath);
+    }
+    navSync.click(function(){ toggleSyncButton(relpath); });
+  }
+
+  $(window).load(function(){
+    navTo(o,toroot,hashUrl(),relpath);
+    showRoot();
+  });
+
+  $(window).bind('hashchange', function(){
+     if (window.location.hash && window.location.hash.length>1){
+       var a;
+       if ($(location).attr('hash')){
+         var clslink=stripPath(pathName())+':'+hashValue();
+         a=$('.item a[class$="'+clslink.replace(/</g,'\\3c ')+'"]');
+       }
+       if (a==null || !$(a).parent().parent().hasClass('selected')){
+         $('.item').removeClass('selected');
+         $('.item').removeAttr('id');
+       }
+       var link=stripPath2(pathName());
+       navTo(o,link,hashUrl(),relpath);
+     } else if (!animationInProgress) {
+       $('#doc-content').scrollTop(0);
+       $('.item').removeClass('selected');
+       $('.item').removeAttr('id');
+       navTo(o,toroot,hashUrl(),relpath);
+     }
+  })
+}
+/* @license-end */

docs/docs/html/navtreedata.js

@@ -0,0 +1,35 @@
+/*
+@ @licstart  The following is the entire license notice for the
+JavaScript code in this file.
+
+Copyright (C) 1997-2017 by Dimitri van Heesch
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+@licend  The above is the entire license notice
+for the JavaScript code in this file
+*/
+var NAVTREE =
+[
+  [ "Tripal", "index.html", ]
+];
+
+var NAVTREEINDEX =
+[
+"index.html"
+];
+
+var SYNCONMSG = 'click to disable panel synchronisation';
+var SYNCOFFMSG = 'click to enable panel synchronisation';

docs/docs/html/navtreeindex0.js

@@ -0,0 +1,5 @@
+var NAVTREEINDEX0 =
+{
+"index.html":[],
+"pages.html":[]
+};

docs/docs/html/resize.js

@@ -0,0 +1,136 @@
+/*
+ @licstart  The following is the entire license notice for the
+ JavaScript code in this file.
+
+ Copyright (C) 1997-2017 by Dimitri van Heesch
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+ @licend  The above is the entire license notice
+ for the JavaScript code in this file
+ */
+function initResizable()
+{
+  var cookie_namespace = 'doxygen';
+  var sidenav,navtree,content,header,collapsed,collapsedWidth=0,barWidth=6,desktop_vp=768,titleHeight;
+
+  function readCookie(cookie)
+  {
+    var myCookie = cookie_namespace+"_"+cookie+"=";
+    if (document.cookie) {
+      var index = document.cookie.indexOf(myCookie);
+      if (index != -1) {
+        var valStart = index + myCookie.length;
+        var valEnd = document.cookie.indexOf(";", valStart);
+        if (valEnd == -1) {
+          valEnd = document.cookie.length;
+        }
+        var val = document.cookie.substring(valStart, valEnd);
+        return val;
+      }
+    }
+    return 0;
+  }
+
+  function writeCookie(cookie, val, expiration)
+  {
+    if (val==undefined) return;
+    if (expiration == null) {
+      var date = new Date();
+      date.setTime(date.getTime()+(10*365*24*60*60*1000)); // default expiration is one week
+      expiration = date.toGMTString();
+    }
+    document.cookie = cookie_namespace + "_" + cookie + "=" + val + "; expires=" + expiration+"; path=/";
+  }
+
+  function resizeWidth()
+  {
+    var windowWidth = $(window).width() + "px";
+    var sidenavWidth = $(sidenav).outerWidth();
+    content.css({marginLeft:parseInt(sidenavWidth)+"px"});
+    writeCookie('width',sidenavWidth-barWidth, null);
+  }
+
+  function restoreWidth(navWidth)
+  {
+    var windowWidth = $(window).width() + "px";
+    content.css({marginLeft:parseInt(navWidth)+barWidth+"px"});
+    sidenav.css({width:navWidth + "px"});
+  }
+
+  function resizeHeight()
+  {
+    var headerHeight = header.outerHeight();
+    var footerHeight = footer.outerHeight();
+    var windowHeight = $(window).height() - headerHeight - footerHeight;
+    content.css({height:windowHeight + "px"});
+    navtree.css({height:windowHeight + "px"});
+    sidenav.css({height:windowHeight + "px"});
+    var width=$(window).width();
+    if (width!=collapsedWidth) {
+      if (width<desktop_vp && collapsedWidth>=desktop_vp) {
+        if (!collapsed) {
+          collapseExpand();
+        }
+      } else if (width>desktop_vp && collapsedWidth<desktop_vp) {
+        if (collapsed) {
+          collapseExpand();
+        }
+      }
+      collapsedWidth=width;
+    }
+  }
+
+  function collapseExpand()
+  {
+    if (sidenav.width()>0) {
+      restoreWidth(0);
+      collapsed=true;
+    }
+    else {
+      var width = readCookie('width');
+      if (width>200 && width<$(window).width()) { restoreWidth(width); } else { restoreWidth(200); }
+      collapsed=false;
+    }
+  }
+
+  header  = $("#top");
+  sidenav = $("#side-nav");
+  content = $("#doc-content");
+  navtree = $("#nav-tree");
+  footer  = $("#nav-path");
+  $(".side-nav-resizable").resizable({resize: function(e, ui) { resizeWidth(); } });
+  $(sidenav).resizable({ minWidth: 0 });
+  $(window).resize(function() { resizeHeight(); });
+  var device = navigator.userAgent.toLowerCase();
+  var touch_device = device.match(/(iphone|ipod|ipad|android)/);
+  if (touch_device) { /* wider split bar for touch only devices */
+    $(sidenav).css({ paddingRight:'20px' });
+    $('.ui-resizable-e').css({ width:'20px' });
+    $('#nav-sync').css({ right:'34px' });
+    barWidth=20;
+  }
+  var width = readCookie('width');
+  if (width) { restoreWidth(width); } else { resizeWidth(); }
+  resizeHeight();
+  var url = location.href;
+  var i=url.indexOf("#");
+  if (i>=0) window.location.hash=url.substr(i);
+  var _preventDefault = function(evt) { evt.preventDefault(); };
+  $("#splitbar").bind("dragstart", _preventDefault).bind("selectstart", _preventDefault);
+  $(".ui-resizable-handle").dblclick(collapseExpand);
+  $(window).load(resizeHeight);
+}
+/* @license-end */

docs/docs/html/search/nomatches.html

@@ -0,0 +1,12 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</body>
+</html>

docs/docs/html/search/search.css

@@ -0,0 +1,271 @@
+/*---------------- Search Box */
+
+#FSearchBox {
+    float: left;
+}
+
+#MSearchBox {
+    white-space : nowrap;
+    float: none;
+    margin-top: 8px;
+    right: 0px;
+    width: 170px;
+    height: 24px;
+    z-index: 102;
+}
+
+#MSearchBox .left
+{
+    display:block;
+    position:absolute;
+    left:10px;
+    width:20px;
+    height:19px;
+    background:url('search_l.png') no-repeat;
+    background-position:right;
+}
+
+#MSearchSelect {
+    display:block;
+    position:absolute;
+    width:20px;
+    height:19px;
+}
+
+.left #MSearchSelect {
+    left:4px;
+}
+
+.right #MSearchSelect {
+    right:5px;
+}
+
+#MSearchField {
+    display:block;
+    position:absolute;
+    height:19px;
+    background:url('search_m.png') repeat-x;
+    border:none;
+    width:115px;
+    margin-left:20px;
+    padding-left:4px;
+    color: #909090;
+    outline: none;
+    font: 9pt Arial, Verdana, sans-serif;
+    -webkit-border-radius: 0px;
+}
+
+#FSearchBox #MSearchField {
+    margin-left:15px;
+}
+
+#MSearchBox .right {
+    display:block;
+    position:absolute;
+    right:10px;
+    top:8px;
+    width:20px;
+    height:19px;
+    background:url('search_r.png') no-repeat;
+    background-position:left;
+}
+
+#MSearchClose {
+    display: none;
+    position: absolute;
+    top: 4px;
+    background : none;
+    border: none;
+    margin: 0px 4px 0px 0px;
+    padding: 0px 0px;
+    outline: none;
+}
+
+.left #MSearchClose {
+    left: 6px;
+}
+
+.right #MSearchClose {
+    right: 2px;
+}
+
+.MSearchBoxActive #MSearchField {
+    color: #000000;
+}
+
+/*---------------- Search filter selection */
+
+#MSearchSelectWindow {
+    display: none;
+    position: absolute;
+    left: 0; top: 0;
+    border: 1px solid #90A5CE;
+    background-color: #F9FAFC;
+    z-index: 10001;
+    padding-top: 4px;
+    padding-bottom: 4px;
+    -moz-border-radius: 4px;
+    -webkit-border-top-left-radius: 4px;
+    -webkit-border-top-right-radius: 4px;
+    -webkit-border-bottom-left-radius: 4px;
+    -webkit-border-bottom-right-radius: 4px;
+    -webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+}
+
+.SelectItem {
+    font: 8pt Arial, Verdana, sans-serif;
+    padding-left:  2px;
+    padding-right: 12px;
+    border: 0px;
+}
+
+span.SelectionMark {
+    margin-right: 4px;
+    font-family: monospace;
+    outline-style: none;
+    text-decoration: none;
+}
+
+a.SelectItem {
+    display: block;
+    outline-style: none;
+    color: #000000; 
+    text-decoration: none;
+    padding-left:   6px;
+    padding-right: 12px;
+}
+
+a.SelectItem:focus,
+a.SelectItem:active {
+    color: #000000; 
+    outline-style: none;
+    text-decoration: none;
+}
+
+a.SelectItem:hover {
+    color: #FFFFFF;
+    background-color: #3D578C;
+    outline-style: none;
+    text-decoration: none;
+    cursor: pointer;
+    display: block;
+}
+
+/*---------------- Search results window */
+
+iframe#MSearchResults {
+    width: 60ex;
+    height: 15em;
+}
+
+#MSearchResultsWindow {
+    display: none;
+    position: absolute;
+    left: 0; top: 0;
+    border: 1px solid #000;
+    background-color: #EEF1F7;
+    z-index:10000;
+}
+
+/* ----------------------------------- */
+
+
+#SRIndex {
+    clear:both; 
+    padding-bottom: 15px;
+}
+
+.SREntry {
+    font-size: 10pt;
+    padding-left: 1ex;
+}
+
+.SRPage .SREntry {
+    font-size: 8pt;
+    padding: 1px 5px;
+}
+
+body.SRPage {
+    margin: 5px 2px;
+}
+
+.SRChildren {
+    padding-left: 3ex; padding-bottom: .5em 
+}
+
+.SRPage .SRChildren {
+    display: none;
+}
+
+.SRSymbol {
+    font-weight: bold; 
+    color: #425E97;
+    font-family: Arial, Verdana, sans-serif;
+    text-decoration: none;
+    outline: none;
+}
+
+a.SRScope {
+    display: block;
+    color: #425E97; 
+    font-family: Arial, Verdana, sans-serif;
+    text-decoration: none;
+    outline: none;
+}
+
+a.SRSymbol:focus, a.SRSymbol:active,
+a.SRScope:focus, a.SRScope:active {
+    text-decoration: underline;
+}
+
+span.SRScope {
+    padding-left: 4px;
+}
+
+.SRPage .SRStatus {
+    padding: 2px 5px;
+    font-size: 8pt;
+    font-style: italic;
+}
+
+.SRResult {
+    display: none;
+}
+
+DIV.searchresults {
+    margin-left: 10px;
+    margin-right: 10px;
+}
+
+/*---------------- External search page results */
+
+.searchresult {
+    background-color: #F0F3F8;
+}
+
+.pages b {
+   color: white;
+   padding: 5px 5px 3px 5px;
+   background-image: url("../tab_a.png");
+   background-repeat: repeat-x;
+   text-shadow: 0 1px 1px #000000;
+}
+
+.pages {
+    line-height: 17px;
+    margin-left: 4px;
+    text-decoration: none;
+}
+
+.hl {
+    font-weight: bold;
+}
+
+#searchresults {
+    margin-bottom: 20px;
+}
+
+.searchpages {
+    margin-top: 10px;
+}
+

docs/docs/html/search/search.js

@@ -0,0 +1,814 @@
+/*
+ @licstart  The following is the entire license notice for the
+ JavaScript code in this file.
+
+ Copyright (C) 1997-2017 by Dimitri van Heesch
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+ @licend  The above is the entire license notice
+ for the JavaScript code in this file
+ */
+function convertToId(search)
+{
+  var result = '';
+  for (i=0;i<search.length;i++)
+  {
+    var c = search.charAt(i);
+    var cn = c.charCodeAt(0);
+    if (c.match(/[a-z0-9\u0080-\uFFFF]/))
+    {
+      result+=c;
+    }
+    else if (cn<16)
+    {
+      result+="_0"+cn.toString(16);
+    }
+    else
+    {
+      result+="_"+cn.toString(16);
+    }
+  }
+  return result;
+}
+
+function getXPos(item)
+{
+  var x = 0;
+  if (item.offsetWidth)
+  {
+    while (item && item!=document.body)
+    {
+      x   += item.offsetLeft;
+      item = item.offsetParent;
+    }
+  }
+  return x;
+}
+
+function getYPos(item)
+{
+  var y = 0;
+  if (item.offsetWidth)
+  {
+     while (item && item!=document.body)
+     {
+       y   += item.offsetTop;
+       item = item.offsetParent;
+     }
+  }
+  return y;
+}
+
+/* A class handling everything associated with the search panel.
+
+   Parameters:
+   name - The name of the global variable that will be
+          storing this instance.  Is needed to be able to set timeouts.
+   resultPath - path to use for external files
+*/
+function SearchBox(name, resultsPath, inFrame, label)
+{
+  if (!name || !resultsPath) {  alert("Missing parameters to SearchBox."); }
+
+  // ---------- Instance variables
+  this.name                  = name;
+  this.resultsPath           = resultsPath;
+  this.keyTimeout            = 0;
+  this.keyTimeoutLength      = 500;
+  this.closeSelectionTimeout = 300;
+  this.lastSearchValue       = "";
+  this.lastResultsPage       = "";
+  this.hideTimeout           = 0;
+  this.searchIndex           = 0;
+  this.searchActive          = false;
+  this.insideFrame           = inFrame;
+  this.searchLabel           = label;
+
+  // ----------- DOM Elements
+
+  this.DOMSearchField = function()
+  {  return document.getElementById("MSearchField");  }
+
+  this.DOMSearchSelect = function()
+  {  return document.getElementById("MSearchSelect");  }
+
+  this.DOMSearchSelectWindow = function()
+  {  return document.getElementById("MSearchSelectWindow");  }
+
+  this.DOMPopupSearchResults = function()
+  {  return document.getElementById("MSearchResults");  }
+
+  this.DOMPopupSearchResultsWindow = function()
+  {  return document.getElementById("MSearchResultsWindow");  }
+
+  this.DOMSearchClose = function()
+  {  return document.getElementById("MSearchClose"); }
+
+  this.DOMSearchBox = function()
+  {  return document.getElementById("MSearchBox");  }
+
+  // ------------ Event Handlers
+
+  // Called when focus is added or removed from the search field.
+  this.OnSearchFieldFocus = function(isActive)
+  {
+    this.Activate(isActive);
+  }
+
+  this.OnSearchSelectShow = function()
+  {
+    var searchSelectWindow = this.DOMSearchSelectWindow();
+    var searchField        = this.DOMSearchSelect();
+
+    if (this.insideFrame)
+    {
+      var left = getXPos(searchField);
+      var top  = getYPos(searchField);
+      left += searchField.offsetWidth + 6;
+      top += searchField.offsetHeight;
+
+      // show search selection popup
+      searchSelectWindow.style.display='block';
+      left -= searchSelectWindow.offsetWidth;
+      searchSelectWindow.style.left =  left + 'px';
+      searchSelectWindow.style.top  =  top  + 'px';
+    }
+    else
+    {
+      var left = getXPos(searchField);
+      var top  = getYPos(searchField);
+      top += searchField.offsetHeight;
+
+      // show search selection popup
+      searchSelectWindow.style.display='block';
+      searchSelectWindow.style.left =  left + 'px';
+      searchSelectWindow.style.top  =  top  + 'px';
+    }
+
+    // stop selection hide timer
+    if (this.hideTimeout)
+    {
+      clearTimeout(this.hideTimeout);
+      this.hideTimeout=0;
+    }
+    return false; // to avoid "image drag" default event
+  }
+
+  this.OnSearchSelectHide = function()
+  {
+    this.hideTimeout = setTimeout(this.name +".CloseSelectionWindow()",
+                                  this.closeSelectionTimeout);
+  }
+
+  // Called when the content of the search field is changed.
+  this.OnSearchFieldChange = function(evt)
+  {
+    if (this.keyTimeout) // kill running timer
+    {
+      clearTimeout(this.keyTimeout);
+      this.keyTimeout = 0;
+    }
+
+    var e  = (evt) ? evt : window.event; // for IE
+    if (e.keyCode==40 || e.keyCode==13)
+    {
+      if (e.shiftKey==1)
+      {
+        this.OnSearchSelectShow();
+        var win=this.DOMSearchSelectWindow();
+        for (i=0;i<win.childNodes.length;i++)
+        {
+          var child = win.childNodes[i]; // get span within a
+          if (child.className=='SelectItem')
+          {
+            child.focus();
+            return;
+          }
+        }
+        return;
+      }
+      else if (window.frames.MSearchResults.searchResults)
+      {
+        var elem = window.frames.MSearchResults.searchResults.NavNext(0);
+        if (elem) elem.focus();
+      }
+    }
+    else if (e.keyCode==27) // Escape out of the search field
+    {
+      this.DOMSearchField().blur();
+      this.DOMPopupSearchResultsWindow().style.display = 'none';
+      this.DOMSearchClose().style.display = 'none';
+      this.lastSearchValue = '';
+      this.Activate(false);
+      return;
+    }
+
+    // strip whitespaces
+    var searchValue = this.DOMSearchField().value.replace(/ +/g, "");
+
+    if (searchValue != this.lastSearchValue) // search value has changed
+    {
+      if (searchValue != "") // non-empty search
+      {
+        // set timer for search update
+        this.keyTimeout = setTimeout(this.name + '.Search()',
+                                     this.keyTimeoutLength);
+      }
+      else // empty search field
+      {
+        this.DOMPopupSearchResultsWindow().style.display = 'none';
+        this.DOMSearchClose().style.display = 'none';
+        this.lastSearchValue = '';
+      }
+    }
+  }
+
+  this.SelectItemCount = function(id)
+  {
+    var count=0;
+    var win=this.DOMSearchSelectWindow();
+    for (i=0;i<win.childNodes.length;i++)
+    {
+      var child = win.childNodes[i]; // get span within a
+      if (child.className=='SelectItem')
+      {
+        count++;
+      }
+    }
+    return count;
+  }
+
+  this.SelectItemSet = function(id)
+  {
+    var i,j=0;
+    var win=this.DOMSearchSelectWindow();
+    for (i=0;i<win.childNodes.length;i++)
+    {
+      var child = win.childNodes[i]; // get span within a
+      if (child.className=='SelectItem')
+      {
+        var node = child.firstChild;
+        if (j==id)
+        {
+          node.innerHTML='&#8226;';
+        }
+        else
+        {
+          node.innerHTML='&#160;';
+        }
+        j++;
+      }
+    }
+  }
+
+  // Called when an search filter selection is made.
+  // set item with index id as the active item
+  this.OnSelectItem = function(id)
+  {
+    this.searchIndex = id;
+    this.SelectItemSet(id);
+    var searchValue = this.DOMSearchField().value.replace(/ +/g, "");
+    if (searchValue!="" && this.searchActive) // something was found -> do a search
+    {
+      this.Search();
+    }
+  }
+
+  this.OnSearchSelectKey = function(evt)
+  {
+    var e = (evt) ? evt : window.event; // for IE
+    if (e.keyCode==40 && this.searchIndex<this.SelectItemCount()) // Down
+    {
+      this.searchIndex++;
+      this.OnSelectItem(this.searchIndex);
+    }
+    else if (e.keyCode==38 && this.searchIndex>0) // Up
+    {
+      this.searchIndex--;
+      this.OnSelectItem(this.searchIndex);
+    }
+    else if (e.keyCode==13 || e.keyCode==27)
+    {
+      this.OnSelectItem(this.searchIndex);
+      this.CloseSelectionWindow();
+      this.DOMSearchField().focus();
+    }
+    return false;
+  }
+
+  // --------- Actions
+
+  // Closes the results window.
+  this.CloseResultsWindow = function()
+  {
+    this.DOMPopupSearchResultsWindow().style.display = 'none';
+    this.DOMSearchClose().style.display = 'none';
+    this.Activate(false);
+  }
+
+  this.CloseSelectionWindow = function()
+  {
+    this.DOMSearchSelectWindow().style.display = 'none';
+  }
+
+  // Performs a search.
+  this.Search = function()
+  {
+    this.keyTimeout = 0;
+
+    // strip leading whitespace
+    var searchValue = this.DOMSearchField().value.replace(/^ +/, "");
+
+    var code = searchValue.toLowerCase().charCodeAt(0);
+    var idxChar = searchValue.substr(0, 1).toLowerCase();
+    if ( 0xD800 <= code && code <= 0xDBFF && searchValue > 1) // surrogate pair
+    {
+      idxChar = searchValue.substr(0, 2);
+    }
+
+    var resultsPage;
+    var resultsPageWithSearch;
+    var hasResultsPage;
+
+    var idx = indexSectionsWithContent[this.searchIndex].indexOf(idxChar);
+    if (idx!=-1)
+    {
+       var hexCode=idx.toString(16);
+       resultsPage = this.resultsPath + '/' + indexSectionNames[this.searchIndex] + '_' + hexCode + '.html';
+       resultsPageWithSearch = resultsPage+'?'+escape(searchValue);
+       hasResultsPage = true;
+    }
+    else // nothing available for this search term
+    {
+       resultsPage = this.resultsPath + '/nomatches.html';
+       resultsPageWithSearch = resultsPage;
+       hasResultsPage = false;
+    }
+
+    window.frames.MSearchResults.location = resultsPageWithSearch;
+    var domPopupSearchResultsWindow = this.DOMPopupSearchResultsWindow();
+
+    if (domPopupSearchResultsWindow.style.display!='block')
+    {
+       var domSearchBox = this.DOMSearchBox();
+       this.DOMSearchClose().style.display = 'inline';
+       if (this.insideFrame)
+       {
+         var domPopupSearchResults = this.DOMPopupSearchResults();
+         domPopupSearchResultsWindow.style.position = 'relative';
+         domPopupSearchResultsWindow.style.display  = 'block';
+         var width = document.body.clientWidth - 8; // the -8 is for IE :-(
+         domPopupSearchResultsWindow.style.width    = width + 'px';
+         domPopupSearchResults.style.width          = width + 'px';
+       }
+       else
+       {
+         var domPopupSearchResults = this.DOMPopupSearchResults();
+         var left = getXPos(domSearchBox) + 150; // domSearchBox.offsetWidth;
+         var top  = getYPos(domSearchBox) + 20;  // domSearchBox.offsetHeight + 1;
+         domPopupSearchResultsWindow.style.display = 'block';
+         left -= domPopupSearchResults.offsetWidth;
+         domPopupSearchResultsWindow.style.top     = top  + 'px';
+         domPopupSearchResultsWindow.style.left    = left + 'px';
+       }
+    }
+
+    this.lastSearchValue = searchValue;
+    this.lastResultsPage = resultsPage;
+  }
+
+  // -------- Activation Functions
+
+  // Activates or deactivates the search panel, resetting things to
+  // their default values if necessary.
+  this.Activate = function(isActive)
+  {
+    if (isActive || // open it
+        this.DOMPopupSearchResultsWindow().style.display == 'block'
+       )
+    {
+      this.DOMSearchBox().className = 'MSearchBoxActive';
+
+      var searchField = this.DOMSearchField();
+
+      if (searchField.value == this.searchLabel) // clear "Search" term upon entry
+      {
+        searchField.value = '';
+        this.searchActive = true;
+      }
+    }
+    else if (!isActive) // directly remove the panel
+    {
+      this.DOMSearchBox().className = 'MSearchBoxInactive';
+      this.DOMSearchField().value   = this.searchLabel;
+      this.searchActive             = false;
+      this.lastSearchValue          = ''
+      this.lastResultsPage          = '';
+    }
+  }
+}
+
+// -----------------------------------------------------------------------
+
+// The class that handles everything on the search results page.
+function SearchResults(name)
+{
+    // The number of matches from the last run of <Search()>.
+    this.lastMatchCount = 0;
+    this.lastKey = 0;
+    this.repeatOn = false;
+
+    // Toggles the visibility of the passed element ID.
+    this.FindChildElement = function(id)
+    {
+      var parentElement = document.getElementById(id);
+      var element = parentElement.firstChild;
+
+      while (element && element!=parentElement)
+      {
+        if (element.nodeName == 'DIV' && element.className == 'SRChildren')
+        {
+          return element;
+        }
+
+        if (element.nodeName == 'DIV' && element.hasChildNodes())
+        {
+           element = element.firstChild;
+        }
+        else if (element.nextSibling)
+        {
+           element = element.nextSibling;
+        }
+        else
+        {
+          do
+          {
+            element = element.parentNode;
+          }
+          while (element && element!=parentElement && !element.nextSibling);
+
+          if (element && element!=parentElement)
+          {
+            element = element.nextSibling;
+          }
+        }
+      }
+    }
+
+    this.Toggle = function(id)
+    {
+      var element = this.FindChildElement(id);
+      if (element)
+      {
+        if (element.style.display == 'block')
+        {
+          element.style.display = 'none';
+        }
+        else
+        {
+          element.style.display = 'block';
+        }
+      }
+    }
+
+    // Searches for the passed string.  If there is no parameter,
+    // it takes it from the URL query.
+    //
+    // Always returns true, since other documents may try to call it
+    // and that may or may not be possible.
+    this.Search = function(search)
+    {
+      if (!search) // get search word from URL
+      {
+        search = window.location.search;
+        search = search.substring(1);  // Remove the leading '?'
+        search = unescape(search);
+      }
+
+      search = search.replace(/^ +/, ""); // strip leading spaces
+      search = search.replace(/ +$/, ""); // strip trailing spaces
+      search = search.toLowerCase();
+      search = convertToId(search);
+
+      var resultRows = document.getElementsByTagName("div");
+      var matches = 0;
+
+      var i = 0;
+      while (i < resultRows.length)
+      {
+        var row = resultRows.item(i);
+        if (row.className == "SRResult")
+        {
+          var rowMatchName = row.id.toLowerCase();
+          rowMatchName = rowMatchName.replace(/^sr\d*_/, ''); // strip 'sr123_'
+
+          if (search.length<=rowMatchName.length &&
+             rowMatchName.substr(0, search.length)==search)
+          {
+            row.style.display = 'block';
+            matches++;
+          }
+          else
+          {
+            row.style.display = 'none';
+          }
+        }
+        i++;
+      }
+      document.getElementById("Searching").style.display='none';
+      if (matches == 0) // no results
+      {
+        document.getElementById("NoMatches").style.display='block';
+      }
+      else // at least one result
+      {
+        document.getElementById("NoMatches").style.display='none';
+      }
+      this.lastMatchCount = matches;
+      return true;
+    }
+
+    // return the first item with index index or higher that is visible
+    this.NavNext = function(index)
+    {
+      var focusItem;
+      while (1)
+      {
+        var focusName = 'Item'+index;
+        focusItem = document.getElementById(focusName);
+        if (focusItem && focusItem.parentNode.parentNode.style.display=='block')
+        {
+          break;
+        }
+        else if (!focusItem) // last element
+        {
+          break;
+        }
+        focusItem=null;
+        index++;
+      }
+      return focusItem;
+    }
+
+    this.NavPrev = function(index)
+    {
+      var focusItem;
+      while (1)
+      {
+        var focusName = 'Item'+index;
+        focusItem = document.getElementById(focusName);
+        if (focusItem && focusItem.parentNode.parentNode.style.display=='block')
+        {
+          break;
+        }
+        else if (!focusItem) // last element
+        {
+          break;
+        }
+        focusItem=null;
+        index--;
+      }
+      return focusItem;
+    }
+
+    this.ProcessKeys = function(e)
+    {
+      if (e.type == "keydown")
+      {
+        this.repeatOn = false;
+        this.lastKey = e.keyCode;
+      }
+      else if (e.type == "keypress")
+      {
+        if (!this.repeatOn)
+        {
+          if (this.lastKey) this.repeatOn = true;
+          return false; // ignore first keypress after keydown
+        }
+      }
+      else if (e.type == "keyup")
+      {
+        this.lastKey = 0;
+        this.repeatOn = false;
+      }
+      return this.lastKey!=0;
+    }
+
+    this.Nav = function(evt,itemIndex)
+    {
+      var e  = (evt) ? evt : window.event; // for IE
+      if (e.keyCode==13) return true;
+      if (!this.ProcessKeys(e)) return false;
+
+      if (this.lastKey==38) // Up
+      {
+        var newIndex = itemIndex-1;
+        var focusItem = this.NavPrev(newIndex);
+        if (focusItem)
+        {
+          var child = this.FindChildElement(focusItem.parentNode.parentNode.id);
+          if (child && child.style.display == 'block') // children visible
+          {
+            var n=0;
+            var tmpElem;
+            while (1) // search for last child
+            {
+              tmpElem = document.getElementById('Item'+newIndex+'_c'+n);
+              if (tmpElem)
+              {
+                focusItem = tmpElem;
+              }
+              else // found it!
+              {
+                break;
+              }
+              n++;
+            }
+          }
+        }
+        if (focusItem)
+        {
+          focusItem.focus();
+        }
+        else // return focus to search field
+        {
+           parent.document.getElementById("MSearchField").focus();
+        }
+      }
+      else if (this.lastKey==40) // Down
+      {
+        var newIndex = itemIndex+1;
+        var focusItem;
+        var item = document.getElementById('Item'+itemIndex);
+        var elem = this.FindChildElement(item.parentNode.parentNode.id);
+        if (elem && elem.style.display == 'block') // children visible
+        {
+          focusItem = document.getElementById('Item'+itemIndex+'_c0');
+        }
+        if (!focusItem) focusItem = this.NavNext(newIndex);
+        if (focusItem)  focusItem.focus();
+      }
+      else if (this.lastKey==39) // Right
+      {
+        var item = document.getElementById('Item'+itemIndex);
+        var elem = this.FindChildElement(item.parentNode.parentNode.id);
+        if (elem) elem.style.display = 'block';
+      }
+      else if (this.lastKey==37) // Left
+      {
+        var item = document.getElementById('Item'+itemIndex);
+        var elem = this.FindChildElement(item.parentNode.parentNode.id);
+        if (elem) elem.style.display = 'none';
+      }
+      else if (this.lastKey==27) // Escape
+      {
+        parent.searchBox.CloseResultsWindow();
+        parent.document.getElementById("MSearchField").focus();
+      }
+      else if (this.lastKey==13) // Enter
+      {
+        return true;
+      }
+      return false;
+    }
+
+    this.NavChild = function(evt,itemIndex,childIndex)
+    {
+      var e  = (evt) ? evt : window.event; // for IE
+      if (e.keyCode==13) return true;
+      if (!this.ProcessKeys(e)) return false;
+
+      if (this.lastKey==38) // Up
+      {
+        if (childIndex>0)
+        {
+          var newIndex = childIndex-1;
+          document.getElementById('Item'+itemIndex+'_c'+newIndex).focus();
+        }
+        else // already at first child, jump to parent
+        {
+          document.getElementById('Item'+itemIndex).focus();
+        }
+      }
+      else if (this.lastKey==40) // Down
+      {
+        var newIndex = childIndex+1;
+        var elem = document.getElementById('Item'+itemIndex+'_c'+newIndex);
+        if (!elem) // last child, jump to parent next parent
+        {
+          elem = this.NavNext(itemIndex+1);
+        }
+        if (elem)
+        {
+          elem.focus();
+        }
+      }
+      else if (this.lastKey==27) // Escape
+      {
+        parent.searchBox.CloseResultsWindow();
+        parent.document.getElementById("MSearchField").focus();
+      }
+      else if (this.lastKey==13) // Enter
+      {
+        return true;
+      }
+      return false;
+    }
+}
+
+function setKeyActions(elem,action)
+{
+  elem.setAttribute('onkeydown',action);
+  elem.setAttribute('onkeypress',action);
+  elem.setAttribute('onkeyup',action);
+}
+
+function setClassAttr(elem,attr)
+{
+  elem.setAttribute('class',attr);
+  elem.setAttribute('className',attr);
+}
+
+function createResults()
+{
+  var results = document.getElementById("SRResults");
+  for (var e=0; e<searchData.length; e++)
+  {
+    var id = searchData[e][0];
+    var srResult = document.createElement('div');
+    srResult.setAttribute('id','SR_'+id);
+    setClassAttr(srResult,'SRResult');
+    var srEntry = document.createElement('div');
+    setClassAttr(srEntry,'SREntry');
+    var srLink = document.createElement('a');
+    srLink.setAttribute('id','Item'+e);
+    setKeyActions(srLink,'return searchResults.Nav(event,'+e+')');
+    setClassAttr(srLink,'SRSymbol');
+    srLink.innerHTML = searchData[e][1][0];
+    srEntry.appendChild(srLink);
+    if (searchData[e][1].length==2) // single result
+    {
+      srLink.setAttribute('href',searchData[e][1][1][0]);
+      if (searchData[e][1][1][1])
+      {
+       srLink.setAttribute('target','_parent');
+      }
+      var srScope = document.createElement('span');
+      setClassAttr(srScope,'SRScope');
+      srScope.innerHTML = searchData[e][1][1][2];
+      srEntry.appendChild(srScope);
+    }
+    else // multiple results
+    {
+      srLink.setAttribute('href','javascript:searchResults.Toggle("SR_'+id+'")');
+      var srChildren = document.createElement('div');
+      setClassAttr(srChildren,'SRChildren');
+      for (var c=0; c<searchData[e][1].length-1; c++)
+      {
+        var srChild = document.createElement('a');
+        srChild.setAttribute('id','Item'+e+'_c'+c);
+        setKeyActions(srChild,'return searchResults.NavChild(event,'+e+','+c+')');
+        setClassAttr(srChild,'SRScope');
+        srChild.setAttribute('href',searchData[e][1][c+1][0]);
+        if (searchData[e][1][c+1][1])
+        {
+         srChild.setAttribute('target','_parent');
+        }
+        srChild.innerHTML = searchData[e][1][c+1][2];
+        srChildren.appendChild(srChild);
+      }
+      srEntry.appendChild(srChildren);
+    }
+    srResult.appendChild(srEntry);
+    results.appendChild(srResult);
+  }
+}
+
+function init_search()
+{
+  var results = document.getElementById("MSearchSelectWindow");
+  for (var key in indexSectionLabels)
+  {
+    var link = document.createElement('a');
+    link.setAttribute('class','SelectItem');
+    link.setAttribute('onclick','searchBox.OnSelectItem('+key+')');
+    link.href='javascript:void(0)';
+    link.innerHTML='<span class="SelectionMark">&#160;</span>'+indexSectionLabels[key];
+    results.appendChild(link);
+  }
+  searchBox.OnSelectItem(0);
+}
+/* @license-end */

docs/docs/html/search/searchdata.js

@@ -0,0 +1,12 @@
+var indexSectionsWithContent =
+{
+};
+
+var indexSectionNames =
+{
+};
+
+var indexSectionLabels =
+{
+};
+

docs/index.rst

@@ -12,3 +12,4 @@ Welcome to Tripal's documentation!
 
    user_guide
    dev_guide
+   api

docs/tripal_doxygen.config

@@ -1906,7 +1906,7 @@ MAN_LINKS              = NO
 # captures the structure of the code including all documentation.
 # The default value is: NO.
 
-GENERATE_XML           = NO
+GENERATE_XML           = YES
 
 # 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