")
- .addClass(category === "modules"
- ? "one-column-search-results"
- : "two-column-search-results");
- var col1, col2;
- if (category === "modules") {
- col1 = "Module";
- } else if (category === "packages") {
- col1 = "Module";
- col2 = "Package";
- } else if (category === "types") {
- col1 = "Package";
- col2 = "Class"
- } else if (category === "members") {
- col1 = "Class";
- col2 = "Member";
- } else if (category === "searchTags") {
- col1 = "Location";
- col2 = "Name";
- }
- $("").appendTo(table);
- if (category !== "modules") {
- $("").appendTo(table);
- }
- $.each(items, function(index, item) {
- var rowColor = index % 2 ? "odd-row-color" : "even-row-color";
- renderItem(item, table, rowColor);
- });
- return table;
- }
- function renderItem(item, table, rowColor) {
- var label = getHighlightedText(item.input, item.boundaries, item.prefix.length, item.input.length);
- var link = $("
")
- .attr("href", getURL(item.indexItem, item.category))
- .attr("tabindex", "0")
- .addClass("search-result-link")
- .html(label);
- var container = getHighlightedText(item.input, item.boundaries, 0, item.prefix.length - 1);
- if (item.category === "searchTags") {
- container = item.indexItem.h || "";
- }
- if (item.category !== "modules") {
- $("
").html(container).addClass("col-plain").addClass(rowColor).appendTo(table);
- }
- $("
").html(link).addClass("col-last").addClass(rowColor).appendTo(table);
- }
- var timeout;
- function schedulePageSearch() {
- if (timeout) {
- clearTimeout(timeout);
- }
- timeout = setTimeout(function () {
- doPageSearch()
- }, 100);
- }
- function doPageSearch() {
- setSearchUrl();
- var term = searchTerm = input.val().trim();
- if (term === "") {
- notify.html(messages.enterTerm);
- activeTab = "";
- fixedTab = false;
- resultContainer.empty();
- resultSection.hide();
- } else {
- notify.html(messages.searching);
- doSearch({ term: term, maxResults: 1200 }, renderResults);
- }
- }
- function setSearchUrl() {
- var query = input.val().trim();
- var url = document.location.pathname;
- if (query) {
- url += "?q=" + encodeURI(query);
- if (activeTab && fixedTab) {
- url += "&c=" + activeTab;
- }
- }
- history.replaceState({query: query}, "", url);
- }
- input.on("input", function(e) {
- feelingLucky = false;
- schedulePageSearch();
- });
- $(document).keydown(function(e) {
- if ((e.ctrlKey || e.metaKey) && (e.key === "ArrowLeft" || e.key === "ArrowRight")) {
- if (activeTab && visibleTabs.length > 1) {
- var idx = visibleTabs.indexOf(activeTab);
- idx += e.key === "ArrowLeft" ? visibleTabs.length - 1 : 1;
- selectTab(visibleTabs[idx % visibleTabs.length]);
- return false;
- }
- }
- });
- reset.click(function() {
- notify.html(messages.enterTerm);
- resultSection.hide();
- activeTab = "";
- fixedTab = false;
- resultContainer.empty();
- input.val('').focus();
- setSearchUrl();
- });
- input.prop("disabled", false);
- reset.prop("disabled", false);
-
- var urlParams = new URLSearchParams(window.location.search);
- if (urlParams.has("q")) {
- input.val(urlParams.get("q"))
- }
- if (urlParams.has("c")) {
- activeTab = urlParams.get("c");
- fixedTab = true;
- }
- if (urlParams.get("r")) {
- feelingLucky = true;
- }
- if (input.val()) {
- doPageSearch();
- } else {
- notify.html(messages.enterTerm);
- }
- input.select().focus();
-});
diff --git a/docs/search.html b/docs/search.html
deleted file mode 100644
index 992770e3..00000000
--- a/docs/search.html
+++ /dev/null
@@ -1,71 +0,0 @@
-
-
-
-
-
Search (ModelPolisher 2.1 API)
-
-
-
-
-
-
-
-
-
-
-
-
-
-JavaScript is disabled on your browser.
-
-
-
-
-
-Search
-
-
-Additional resources
-
-
-
-
The help page provides an introduction to the scope and syntax of JavaDoc search.
-
You can use the <ctrl> or <cmd> keys in combination with the left and right arrow keys to switch between result tabs in this page.
-
The URL template below may be used to configure this page as a search engine in browsers that support this feature. It has been tested to work in Google Chrome and Mozilla Firefox. Note that other browsers may not support this feature or require a different URL format.
-
link Copy
-
-Redirect to first result
-
Loading search index...
-
-
-
-
-
-
diff --git a/docs/search.js b/docs/search.js
deleted file mode 100644
index d3986705..00000000
--- a/docs/search.js
+++ /dev/null
@@ -1,458 +0,0 @@
-/*
- * Copyright (c) 2015, 2023, Oracle and/or its affiliates. All rights reserved.
- * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
- *
- * This code is free software; you can redistribute it and/or modify it
- * under the terms of the GNU General Public License version 2 only, as
- * published by the Free Software Foundation. Oracle designates this
- * particular file as subject to the "Classpath" exception as provided
- * by Oracle in the LICENSE file that accompanied this code.
- *
- * This code 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
- * version 2 for more details (a copy is included in the LICENSE file that
- * accompanied this code).
- *
- * You should have received a copy of the GNU General Public License version
- * 2 along with this work; if not, write to the Free Software Foundation,
- * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
- * or visit www.oracle.com if you need additional information or have any
- * questions.
- */
-"use strict";
-const messages = {
- enterTerm: "Enter a search term",
- noResult: "No results found",
- oneResult: "Found one result",
- manyResults: "Found {0} results",
- loading: "Loading search index...",
- searching: "Searching...",
- redirecting: "Redirecting to first result...",
- linkIcon: "Link icon",
- linkToSection: "Link to this section"
-}
-const categories = {
- modules: "Modules",
- packages: "Packages",
- types: "Classes and Interfaces",
- members: "Members",
- searchTags: "Search Tags"
-};
-const highlight = "
$& ";
-const NO_MATCH = {};
-const MAX_RESULTS = 300;
-function checkUnnamed(name, separator) {
- return name === "
" || !name ? "" : name + separator;
-}
-function escapeHtml(str) {
- return str.replace(//g, ">");
-}
-function getHighlightedText(str, boundaries, from, to) {
- var start = from;
- var text = "";
- for (var i = 0; i < boundaries.length; i += 2) {
- var b0 = boundaries[i];
- var b1 = boundaries[i + 1];
- if (b0 >= to || b1 <= from) {
- continue;
- }
- text += escapeHtml(str.slice(start, Math.max(start, b0)));
- text += "";
- text += escapeHtml(str.slice(Math.max(start, b0), Math.min(to, b1)));
- text += " ";
- start = Math.min(to, b1);
- }
- text += escapeHtml(str.slice(start, to));
- return text;
-}
-function getURLPrefix(item, category) {
- var urlPrefix = "";
- var slash = "/";
- if (category === "modules") {
- return item.l + slash;
- } else if (category === "packages" && item.m) {
- return item.m + slash;
- } else if (category === "types" || category === "members") {
- if (item.m) {
- urlPrefix = item.m + slash;
- } else {
- $.each(packageSearchIndex, function(index, it) {
- if (it.m && item.p === it.l) {
- urlPrefix = it.m + slash;
- }
- });
- }
- }
- return urlPrefix;
-}
-function getURL(item, category) {
- if (item.url) {
- return item.url;
- }
- var url = getURLPrefix(item, category);
- if (category === "modules") {
- url += "module-summary.html";
- } else if (category === "packages") {
- if (item.u) {
- url = item.u;
- } else {
- url += item.l.replace(/\./g, '/') + "/package-summary.html";
- }
- } else if (category === "types") {
- if (item.u) {
- url = item.u;
- } else {
- url += checkUnnamed(item.p, "/").replace(/\./g, '/') + item.l + ".html";
- }
- } else if (category === "members") {
- url += checkUnnamed(item.p, "/").replace(/\./g, '/') + item.c + ".html" + "#";
- if (item.u) {
- url += item.u;
- } else {
- url += item.l;
- }
- } else if (category === "searchTags") {
- url += item.u;
- }
- item.url = url;
- return url;
-}
-function createMatcher(term, camelCase) {
- if (camelCase && !isUpperCase(term)) {
- return null; // no need for camel-case matcher for lower case query
- }
- var pattern = "";
- var upperCase = [];
- term.trim().split(/\s+/).forEach(function(w, index, array) {
- var tokens = w.split(/(?=[A-Z,.()<>?[\/])/);
- for (var i = 0; i < tokens.length; i++) {
- var s = tokens[i];
- // ',' and '?' are the only delimiters commonly followed by space in java signatures
- pattern += "(" + $.ui.autocomplete.escapeRegex(s).replace(/[,?]/g, "$&\\s*?") + ")";
- upperCase.push(false);
- var isWordToken = /\w$/.test(s);
- if (isWordToken) {
- if (i === tokens.length - 1 && index < array.length - 1) {
- // space in query string matches all delimiters
- pattern += "(.*?)";
- upperCase.push(isUpperCase(s[0]));
- } else {
- if (!camelCase && isUpperCase(s) && s.length === 1) {
- pattern += "()";
- } else {
- pattern += "([a-z0-9$<>?[\\]]*?)";
- }
- upperCase.push(isUpperCase(s[0]));
- }
- } else {
- pattern += "()";
- upperCase.push(false);
- }
- }
- });
- var re = new RegExp(pattern, "gi");
- re.upperCase = upperCase;
- return re;
-}
-function findMatch(matcher, input, startOfName, endOfName) {
- var from = startOfName;
- matcher.lastIndex = from;
- var match = matcher.exec(input);
- // Expand search area until we get a valid result or reach the beginning of the string
- while (!match || match.index + match[0].length < startOfName || endOfName < match.index) {
- if (from === 0) {
- return NO_MATCH;
- }
- from = input.lastIndexOf(".", from - 2) + 1;
- matcher.lastIndex = from;
- match = matcher.exec(input);
- }
- var boundaries = [];
- var matchEnd = match.index + match[0].length;
- var score = 5;
- var start = match.index;
- var prevEnd = -1;
- for (var i = 1; i < match.length; i += 2) {
- var isUpper = isUpperCase(input[start]);
- var isMatcherUpper = matcher.upperCase[i];
- // capturing groups come in pairs, match and non-match
- boundaries.push(start, start + match[i].length);
- // make sure groups are anchored on a left word boundary
- var prevChar = input[start - 1] || "";
- var nextChar = input[start + 1] || "";
- if (start !== 0 && !/[\W_]/.test(prevChar) && !/[\W_]/.test(input[start])) {
- if (isUpper && (isLowerCase(prevChar) || isLowerCase(nextChar))) {
- score -= 0.1;
- } else if (isMatcherUpper && start === prevEnd) {
- score -= isUpper ? 0.1 : 1.0;
- } else {
- return NO_MATCH;
- }
- }
- prevEnd = start + match[i].length;
- start += match[i].length + match[i + 1].length;
-
- // lower score for parts of the name that are missing
- if (match[i + 1] && prevEnd < endOfName) {
- score -= rateNoise(match[i + 1]);
- }
- }
- // lower score if a type name contains unmatched camel-case parts
- if (input[matchEnd - 1] !== "." && endOfName > matchEnd)
- score -= rateNoise(input.slice(matchEnd, endOfName));
- score -= rateNoise(input.slice(0, Math.max(startOfName, match.index)));
-
- if (score <= 0) {
- return NO_MATCH;
- }
- return {
- input: input,
- score: score,
- boundaries: boundaries
- };
-}
-function isUpperCase(s) {
- return s !== s.toLowerCase();
-}
-function isLowerCase(s) {
- return s !== s.toUpperCase();
-}
-function rateNoise(str) {
- return (str.match(/([.(])/g) || []).length / 5
- + (str.match(/([A-Z]+)/g) || []).length / 10
- + str.length / 20;
-}
-function doSearch(request, response) {
- var term = request.term.trim();
- var maxResults = request.maxResults || MAX_RESULTS;
- if (term.length === 0) {
- return this.close();
- }
- var matcher = {
- plainMatcher: createMatcher(term, false),
- camelCaseMatcher: createMatcher(term, true)
- }
- var indexLoaded = indexFilesLoaded();
-
- function getPrefix(item, category) {
- switch (category) {
- case "packages":
- return checkUnnamed(item.m, "/");
- case "types":
- return checkUnnamed(item.p, ".");
- case "members":
- return checkUnnamed(item.p, ".") + item.c + ".";
- default:
- return "";
- }
- }
- function useQualifiedName(category) {
- switch (category) {
- case "packages":
- return /[\s/]/.test(term);
- case "types":
- case "members":
- return /[\s.]/.test(term);
- default:
- return false;
- }
- }
- function searchIndex(indexArray, category) {
- var matches = [];
- if (!indexArray) {
- if (!indexLoaded) {
- matches.push({ l: messages.loading, category: category });
- }
- return matches;
- }
- $.each(indexArray, function (i, item) {
- var prefix = getPrefix(item, category);
- var simpleName = item.l;
- var qualifiedName = prefix + simpleName;
- var useQualified = useQualifiedName(category);
- var input = useQualified ? qualifiedName : simpleName;
- var startOfName = useQualified ? prefix.length : 0;
- var endOfName = category === "members" && input.indexOf("(", startOfName) > -1
- ? input.indexOf("(", startOfName) : input.length;
- var m = findMatch(matcher.plainMatcher, input, startOfName, endOfName);
- if (m === NO_MATCH && matcher.camelCaseMatcher) {
- m = findMatch(matcher.camelCaseMatcher, input, startOfName, endOfName);
- }
- if (m !== NO_MATCH) {
- m.indexItem = item;
- m.prefix = prefix;
- m.category = category;
- if (!useQualified) {
- m.input = qualifiedName;
- m.boundaries = m.boundaries.map(function(b) {
- return b + prefix.length;
- });
- }
- matches.push(m);
- }
- return true;
- });
- return matches.sort(function(e1, e2) {
- return e2.score - e1.score;
- }).slice(0, maxResults);
- }
-
- var result = searchIndex(moduleSearchIndex, "modules")
- .concat(searchIndex(packageSearchIndex, "packages"))
- .concat(searchIndex(typeSearchIndex, "types"))
- .concat(searchIndex(memberSearchIndex, "members"))
- .concat(searchIndex(tagSearchIndex, "searchTags"));
-
- if (!indexLoaded) {
- updateSearchResults = function() {
- doSearch(request, response);
- }
- } else {
- updateSearchResults = function() {};
- }
- response(result);
-}
-// JQuery search menu implementation
-$.widget("custom.catcomplete", $.ui.autocomplete, {
- _create: function() {
- this._super();
- this.widget().menu("option", "items", "> .result-item");
- // workaround for search result scrolling
- this.menu._scrollIntoView = function _scrollIntoView( item ) {
- var borderTop, paddingTop, offset, scroll, elementHeight, itemHeight;
- if ( this._hasScroll() ) {
- borderTop = parseFloat( $.css( this.activeMenu[ 0 ], "borderTopWidth" ) ) || 0;
- paddingTop = parseFloat( $.css( this.activeMenu[ 0 ], "paddingTop" ) ) || 0;
- offset = item.offset().top - this.activeMenu.offset().top - borderTop - paddingTop;
- scroll = this.activeMenu.scrollTop();
- elementHeight = this.activeMenu.height() - 26;
- itemHeight = item.outerHeight();
-
- if ( offset < 0 ) {
- this.activeMenu.scrollTop( scroll + offset );
- } else if ( offset + itemHeight > elementHeight ) {
- this.activeMenu.scrollTop( scroll + offset - elementHeight + itemHeight );
- }
- }
- };
- },
- _renderMenu: function(ul, items) {
- var currentCategory = "";
- var widget = this;
- widget.menu.bindings = $();
- $.each(items, function(index, item) {
- if (item.category && item.category !== currentCategory) {
- ul.append("" + categories[item.category] + " ");
- currentCategory = item.category;
- }
- var li = widget._renderItemData(ul, item);
- if (item.category) {
- li.attr("aria-label", categories[item.category] + " : " + item.l);
- } else {
- li.attr("aria-label", item.l);
- }
- li.attr("class", "result-item");
- });
- ul.append("Go to search page
").appendTo(li);
- var label = item.l
- ? item.l
- : getHighlightedText(item.input, item.boundaries, 0, item.input.length);
- var idx = item.indexItem;
- if (item.category === "searchTags" && idx && idx.h) {
- if (idx.d) {
- div.html(label + " (" + idx.h + ") "
- + idx.d + " (" + idx.h + ") ");
- }
- } else {
- div.html(label);
- }
- return li;
- }
-});
-$(function() {
- var expanded = false;
- var windowWidth;
- function collapse() {
- if (expanded) {
- $("div#navbar-top").removeAttr("style");
- $("button#navbar-toggle-button")
- .removeClass("expanded")
- .attr("aria-expanded", "false");
- expanded = false;
- }
- }
- $("button#navbar-toggle-button").click(function (e) {
- if (expanded) {
- collapse();
- } else {
- var navbar = $("div#navbar-top");
- navbar.height(navbar.prop("scrollHeight"));
- $("button#navbar-toggle-button")
- .addClass("expanded")
- .attr("aria-expanded", "true");
- expanded = true;
- windowWidth = window.innerWidth;
- }
- });
- $("ul.sub-nav-list-small li a").click(collapse);
- $("input#search-input").focus(collapse);
- $("main").click(collapse);
- $("section[id] > :header, :header[id], :header:has(a[id])").each(function(idx, el) {
- // Create anchor links for headers with an associated id attribute
- var hdr = $(el);
- var id = hdr.attr("id") || hdr.parent("section").attr("id") || hdr.children("a").attr("id");
- if (id) {
- hdr.append(" \
- ');
- background-size:100% 100%;
- width:9px;
- height:14px;
- margin-left:4px;
- margin-bottom:-3px;
-}
-.table-header[onclick].sort-asc::after {
- background-image:url('data:image/svg+xml; utf8, \
- \
- ');
-
-}
-.table-header[onclick].sort-desc::after {
- background-image:url('data:image/svg+xml; utf8, \
- \
- ');
-}
-.col-first, .col-first {
- font-size:0.93em;
-}
-.col-second, .col-second, .col-last, .col-constructor-name, .col-summary-item-name, .col-last {
- font-size:0.93em;
-}
-.col-first, .col-second, .col-constructor-name {
- vertical-align:top;
- overflow: auto;
-}
-.col-last {
- white-space:normal;
-}
-.col-first a:link, .col-first a:visited,
-.col-second a:link, .col-second a:visited,
-.col-first a:link, .col-first a:visited,
-.col-second a:link, .col-second a:visited,
-.col-constructor-name a:link, .col-constructor-name a:visited,
-.col-summary-item-name a:link, .col-summary-item-name a:visited {
- font-weight:bold;
-}
-.even-row-color, .even-row-color .table-header {
- background-color:var(--even-row-color);
-}
-.odd-row-color, .odd-row-color .table-header {
- background-color:var(--odd-row-color);
-}
-/*
- * Styles for contents.
- */
-div.block {
- font-size:var(--body-font-size);
- font-family:var(--block-font-family);
-}
-.col-last div {
- padding-top:0;
-}
-.col-last a {
- padding-bottom:3px;
-}
-.module-signature,
-.package-signature,
-.type-signature,
-.member-signature {
- font-family:var(--code-font-family);
- font-size:1em;
- margin:14px 0;
- white-space: pre-wrap;
-}
-.module-signature,
-.package-signature,
-.type-signature {
- margin-top: 0;
-}
-.member-signature .type-parameters-long,
-.member-signature .parameters,
-.member-signature .exceptions {
- display: inline-block;
- vertical-align: top;
- white-space: pre;
-}
-.member-signature .type-parameters {
- white-space: normal;
-}
-/*
- * Styles for formatting effect.
- */
-.source-line-no {
- /* Color of line numbers in source pages can be set via custom property below */
- color:var(--source-linenumber-color, green);
- padding:0 30px 0 0;
-}
-.block {
- display:block;
- margin:0 10px 5px 0;
- color:var(--block-text-color);
-}
-.deprecated-label, .description-from-type-label, .implementation-label, .member-name-link,
-.module-label-in-package, .module-label-in-type, .package-label-in-type,
-.package-hierarchy-label, .type-name-label, .type-name-link, .search-tag-link, .preview-label {
- font-weight:bold;
-}
-.deprecation-comment, .help-footnote, .preview-comment {
- font-style:italic;
-}
-.deprecation-block {
- font-size:1em;
- font-family:var(--block-font-family);
- border-style:solid;
- border-width:thin;
- border-radius:10px;
- padding:10px;
- margin-bottom:10px;
- margin-right:10px;
- display:inline-block;
-}
-.preview-block {
- font-size:1em;
- font-family:var(--block-font-family);
- border-style:solid;
- border-width:thin;
- border-radius:10px;
- padding:10px;
- margin-bottom:10px;
- margin-right:10px;
- display:inline-block;
-}
-div.block div.deprecation-comment {
- font-style:normal;
-}
-details.invalid-tag, span.invalid-tag {
- font-size:1em;
- font-family:var(--block-font-family);
- color: var(--invalid-tag-text-color);
- background: var(--invalid-tag-background-color);
- border: thin solid var(--table-border-color);
- border-radius:2px;
- padding: 2px 4px;
- display:inline-block;
-}
-details summary {
- cursor: pointer;
-}
-/*
- * Styles specific to HTML5 elements.
- */
-main, nav, header, footer, section {
- display:block;
-}
-/*
- * Styles for javadoc search.
- */
-.ui-state-active {
- /* Overrides the color of selection used in jQuery UI */
- background: var(--selected-background-color);
- border: 1px solid var(--selected-background-color);
- color: var(--selected-text-color);
-}
-.ui-autocomplete-category {
- font-weight:bold;
- font-size:15px;
- padding:7px 0 7px 3px;
- background-color:var(--navbar-background-color);
- color:var(--navbar-text-color);
-}
-.ui-autocomplete {
- max-height:85%;
- max-width:65%;
- overflow-y:auto;
- overflow-x:auto;
- scrollbar-width: thin;
- white-space:nowrap;
- box-shadow: 0 3px 6px rgba(0,0,0,0.16), 0 3px 6px rgba(0,0,0,0.23);
-}
-ul.ui-autocomplete {
- position:fixed;
- z-index:1;
- background-color: var(--body-background-color);
-}
-ul.ui-autocomplete li {
- float:left;
- clear:both;
- min-width:100%;
-}
-ul.ui-autocomplete li.ui-static-link {
- position:sticky;
- bottom:0;
- left:0;
- background: var(--subnav-background-color);
- padding: 5px 0;
- font-family: var(--body-font-family);
- font-size: 0.93em;
- font-weight: bolder;
- z-index: 2;
-}
-li.ui-static-link a, li.ui-static-link a:visited {
- text-decoration:none;
- color:var(--link-color);
- float:right;
- margin-right:20px;
-}
-.ui-autocomplete .result-item {
- font-size: inherit;
-}
-.ui-autocomplete .result-highlight {
- font-weight:bold;
-}
-#search-input, #page-search-input {
- background-image:url('resources/glass.png');
- background-size:13px;
- background-repeat:no-repeat;
- background-position:2px 3px;
- background-color: var(--search-input-background-color);
- color: var(--search-input-text-color);
- border-color: var(--border-color);
- padding-left:20px;
- width: 250px;
- margin: 0;
-}
-#search-input {
- margin-left: 4px;
-}
-#reset-button {
- background-color: transparent;
- background-image:url('resources/x.png');
- background-repeat:no-repeat;
- background-size:contain;
- border:0;
- border-radius:0;
- width:12px;
- height:12px;
- position:absolute;
- right:12px;
- top:10px;
- font-size:0;
-}
-::placeholder {
- color:var(--search-input-placeholder-color);
- opacity: 1;
-}
-.search-tag-desc-result {
- font-style:italic;
- font-size:11px;
-}
-.search-tag-holder-result {
- font-style:italic;
- font-size:12px;
-}
-.search-tag-result:target {
- background-color:var(--search-tag-highlight-color);
-}
-details.page-search-details {
- display: inline-block;
-}
-div#result-container {
- font-size: 1em;
-}
-div#result-container a.search-result-link {
- padding: 0;
- margin: 4px 0;
- width: 100%;
-}
-#result-container .result-highlight {
- font-weight:bolder;
-}
-.page-search-info {
- background-color: var(--subnav-background-color);
- border-radius: 3px;
- border: 0 solid var(--border-color);
- padding: 0 8px;
- overflow: hidden;
- height: 0;
- transition: all 0.2s ease;
-}
-div.table-tabs > button.table-tab {
- background: var(--navbar-background-color);
- color: var(--navbar-text-color);
-}
-.page-search-header {
- padding: 5px 12px 7px 12px;
- font-weight: bold;
- margin-right: 3px;
- background-color:var(--navbar-background-color);
- color:var(--navbar-text-color);
- display: inline-block;
-}
-button.page-search-header {
- border: none;
- cursor: pointer;
-}
-span#page-search-link {
- text-decoration: underline;
-}
-.module-graph span, .sealed-graph span {
- display:none;
- position:absolute;
-}
-.module-graph:hover span, .sealed-graph:hover span {
- display:block;
- margin: -100px 0 0 100px;
- z-index: 1;
-}
-.inherited-list {
- margin: 10px 0 10px 0;
-}
-section.class-description {
- line-height: 1.4;
-}
-.summary section[class$="-summary"], .details section[class$="-details"],
-.class-uses .detail, .serialized-class-details {
- padding: 0 20px 5px 10px;
- border: 1px solid var(--border-color);
- background-color: var(--section-background-color);
-}
-.inherited-list, section[class$="-details"] .detail {
- padding:0 0 5px 8px;
- background-color:var(--detail-background-color);
- border:none;
-}
-.vertical-separator {
- padding: 0 5px;
-}
-ul.help-section-list {
- margin: 0;
-}
-ul.help-subtoc > li {
- display: inline-block;
- padding-right: 5px;
- font-size: smaller;
-}
-ul.help-subtoc > li::before {
- content: "\2022" ;
- padding-right:2px;
-}
-.help-note {
- font-style: italic;
-}
-/*
- * Indicator icon for external links.
- */
-main a[href*="://"]::after {
- content:"";
- display:inline-block;
- background-image:url('data:image/svg+xml; utf8, \
- \
- ');
- background-size:100% 100%;
- width:7px;
- height:7px;
- margin-left:2px;
- margin-bottom:4px;
-}
-main a[href*="://"]:hover::after,
-main a[href*="://"]:focus::after {
- background-image:url('data:image/svg+xml; utf8, \
- \
- ');
-}
-/*
- * Styles for header/section anchor links
- */
-a.anchor-link {
- opacity: 0;
- transition: opacity 0.1s;
-}
-:hover > a.anchor-link {
- opacity: 80%;
-}
-a.anchor-link:hover,
-a.anchor-link:focus-visible,
-a.anchor-link.visible {
- opacity: 100%;
-}
-a.anchor-link > img {
- width: 0.9em;
- height: 0.9em;
-}
-/*
- * Styles for copy-to-clipboard buttons
- */
-button.copy {
- opacity: 70%;
- border: none;
- border-radius: 3px;
- position: relative;
- background:none;
- transition: opacity 0.3s;
- cursor: pointer;
-}
-:hover > button.copy {
- opacity: 80%;
-}
-button.copy:hover,
-button.copy:active,
-button.copy:focus-visible,
-button.copy.visible {
- opacity: 100%;
-}
-button.copy img {
- position: relative;
- background: none;
- filter: brightness(var(--copy-icon-brightness));
-}
-button.copy:active {
- background-color: var(--copy-button-background-color-active);
-}
-button.copy span {
- color: var(--body-text-color);
- position: relative;
- top: -0.1em;
- transition: all 0.1s;
- font-size: 0.76rem;
- line-height: 1.2em;
- opacity: 0;
-}
-button.copy:hover span,
-button.copy:focus-visible span,
-button.copy.visible span {
- opacity: 100%;
-}
-/* search page copy button */
-button#page-search-copy {
- margin-left: 0.4em;
- padding:0.3em;
- top:0.13em;
-}
-button#page-search-copy img {
- width: 1.2em;
- height: 1.2em;
- padding: 0.01em 0;
- top: 0.15em;
-}
-button#page-search-copy span {
- color: var(--body-text-color);
- line-height: 1.2em;
- padding: 0.2em;
- top: -0.18em;
-}
-div.page-search-info:hover button#page-search-copy span {
- opacity: 100%;
-}
-/* snippet copy button */
-button.snippet-copy {
- position: absolute;
- top: 6px;
- right: 6px;
- height: 1.7em;
- padding: 2px;
-}
-button.snippet-copy img {
- width: 18px;
- height: 18px;
- padding: 0.05em 0;
-}
-button.snippet-copy span {
- line-height: 1.2em;
- padding: 0.2em;
- position: relative;
- top: -0.5em;
-}
-div.snippet-container:hover button.snippet-copy span {
- opacity: 100%;
-}
-/*
- * Styles for user-provided tables.
- *
- * borderless:
- * No borders, vertical margins, styled caption.
- * This style is provided for use with existing doc comments.
- * In general, borderless tables should not be used for layout purposes.
- *
- * plain:
- * Plain borders around table and cells, vertical margins, styled caption.
- * Best for small tables or for complex tables for tables with cells that span
- * rows and columns, when the "striped" style does not work well.
- *
- * striped:
- * Borders around the table and vertical borders between cells, striped rows,
- * vertical margins, styled caption.
- * Best for tables that have a header row, and a body containing a series of simple rows.
- */
-
-table.borderless,
-table.plain,
-table.striped {
- margin-top: 10px;
- margin-bottom: 10px;
-}
-table.borderless > caption,
-table.plain > caption,
-table.striped > caption {
- font-weight: bold;
- font-size: smaller;
-}
-table.borderless th, table.borderless td,
-table.plain th, table.plain td,
-table.striped th, table.striped td {
- padding: 2px 5px;
-}
-table.borderless,
-table.borderless > thead > tr > th, table.borderless > tbody > tr > th, table.borderless > tr > th,
-table.borderless > thead > tr > td, table.borderless > tbody > tr > td, table.borderless > tr > td {
- border: none;
-}
-table.borderless > thead > tr, table.borderless > tbody > tr, table.borderless > tr {
- background-color: transparent;
-}
-table.plain {
- border-collapse: collapse;
- border: 1px solid var(--table-border-color);
-}
-table.plain > thead > tr, table.plain > tbody tr, table.plain > tr {
- background-color: transparent;
-}
-table.plain > thead > tr > th, table.plain > tbody > tr > th, table.plain > tr > th,
-table.plain > thead > tr > td, table.plain > tbody > tr > td, table.plain > tr > td {
- border: 1px solid var(--table-border-color);
-}
-table.striped {
- border-collapse: collapse;
- border: 1px solid var(--table-border-color);
-}
-table.striped > thead {
- background-color: var(--subnav-background-color);
-}
-table.striped > thead > tr > th, table.striped > thead > tr > td {
- border: 1px solid var(--table-border-color);
-}
-table.striped > tbody > tr:nth-child(even) {
- background-color: var(--odd-row-color)
-}
-table.striped > tbody > tr:nth-child(odd) {
- background-color: var(--even-row-color)
-}
-table.striped > tbody > tr > th, table.striped > tbody > tr > td {
- border-left: 1px solid var(--table-border-color);
- border-right: 1px solid var(--table-border-color);
-}
-table.striped > tbody > tr > th {
- font-weight: normal;
-}
-/**
- * Tweak style for small screens.
- */
-@media screen and (max-width: 920px) {
- header.flex-header {
- max-height: 100vh;
- overflow-y: auto;
- }
- div#navbar-top {
- height: 2.8em;
- transition: height 0.35s ease;
- }
- ul.nav-list {
- display: block;
- width: 40%;
- float:left;
- clear: left;
- margin: 10px 0 0 0;
- padding: 0;
- }
- ul.nav-list li {
- float: none;
- padding: 6px;
- margin-left: 10px;
- margin-top: 2px;
- }
- ul.sub-nav-list-small {
- display:block;
- height: 100%;
- width: 50%;
- float: right;
- clear: right;
- background-color: var(--subnav-background-color);
- color: var(--body-text-color);
- margin: 6px 0 0 0;
- padding: 0;
- }
- ul.sub-nav-list-small ul {
- padding-left: 20px;
- }
- ul.sub-nav-list-small a:link, ul.sub-nav-list-small a:visited {
- color:var(--link-color);
- }
- ul.sub-nav-list-small a:hover {
- color:var(--link-color-active);
- }
- ul.sub-nav-list-small li {
- list-style:none;
- float:none;
- padding: 6px;
- margin-top: 1px;
- text-transform:uppercase;
- }
- ul.sub-nav-list-small > li {
- margin-left: 10px;
- }
- ul.sub-nav-list-small li p {
- margin: 5px 0;
- }
- div#navbar-sub-list {
- display: none;
- }
- .top-nav a:link, .top-nav a:active, .top-nav a:visited {
- display: block;
- }
- button#navbar-toggle-button {
- width: 3.4em;
- height: 2.8em;
- background-color: transparent;
- display: block;
- float: left;
- border: 0;
- margin: 0 10px;
- cursor: pointer;
- font-size: 10px;
- }
- button#navbar-toggle-button .nav-bar-toggle-icon {
- display: block;
- width: 24px;
- height: 3px;
- margin: 1px 0 4px 0;
- border-radius: 2px;
- transition: all 0.1s;
- background-color: var(--navbar-text-color);
- }
- button#navbar-toggle-button.expanded span.nav-bar-toggle-icon:nth-child(1) {
- transform: rotate(45deg);
- transform-origin: 10% 10%;
- width: 26px;
- }
- button#navbar-toggle-button.expanded span.nav-bar-toggle-icon:nth-child(2) {
- opacity: 0;
- }
- button#navbar-toggle-button.expanded span.nav-bar-toggle-icon:nth-child(3) {
- transform: rotate(-45deg);
- transform-origin: 10% 90%;
- width: 26px;
- }
-}
-@media screen and (max-width: 800px) {
- .about-language {
- padding-right: 16px;
- }
- ul.nav-list li {
- margin-left: 5px;
- }
- ul.sub-nav-list-small > li {
- margin-left: 5px;
- }
- main {
- padding: 10px;
- }
- .summary section[class$="-summary"], .details section[class$="-details"],
- .class-uses .detail, .serialized-class-details {
- padding: 0 8px 5px 8px;
- }
- body {
- -webkit-text-size-adjust: none;
- }
-}
-@media screen and (max-width: 400px) {
- .about-language {
- font-size: 10px;
- padding-right: 12px;
- }
-}
-@media screen and (max-width: 400px) {
- .nav-list-search {
- width: 94%;
- }
- #search-input, #page-search-input {
- width: 70%;
- }
-}
-@media screen and (max-width: 320px) {
- .nav-list-search > label {
- display: none;
- }
- .nav-list-search {
- width: 90%;
- }
- #search-input, #page-search-input {
- width: 80%;
- }
-}
-
-pre.snippet {
- background-color: var(--snippet-background-color);
- color: var(--snippet-text-color);
- padding: 10px;
- margin: 12px 0;
- overflow: auto;
- white-space: pre;
-}
-div.snippet-container {
- position: relative;
-}
-@media screen and (max-width: 800px) {
- pre.snippet {
- padding-top: 26px;
- }
- button.snippet-copy {
- top: 4px;
- right: 4px;
- }
-}
-pre.snippet .italic {
- font-style: italic;
-}
-pre.snippet .bold {
- font-weight: bold;
-}
-pre.snippet .highlighted {
- background-color: var(--snippet-highlight-color);
- border-radius: 10%;
-}
diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
index e6441136..d64cd491 100644
Binary files a/gradle/wrapper/gradle-wrapper.jar and b/gradle/wrapper/gradle-wrapper.jar differ
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
index a4413138..1af9e093 100644
--- a/gradle/wrapper/gradle-wrapper.properties
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -1,6 +1,6 @@
distributionBase=GRADLE_USER_HOME
distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.8-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-bin.zip
networkTimeout=10000
validateDistributionUrl=true
zipStoreBase=GRADLE_USER_HOME
diff --git a/gradlew b/gradlew
index b740cf13..1aa94a42 100755
--- a/gradlew
+++ b/gradlew
@@ -55,7 +55,7 @@
# Darwin, MinGW, and NonStop.
#
# (3) This script is generated from the Groovy template
-# https://github.com/gradle/gradle/blob/HEAD/platforms/jvm/plugins-application/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+# https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
# within the Gradle project.
#
# You can find Gradle at https://github.com/gradle/gradle/.
diff --git a/gradlew.bat b/gradlew.bat
index 7101f8e4..6689b85b 100644
--- a/gradlew.bat
+++ b/gradlew.bat
@@ -43,11 +43,11 @@ set JAVA_EXE=java.exe
%JAVA_EXE% -version >NUL 2>&1
if %ERRORLEVEL% equ 0 goto execute
-echo. 1>&2
-echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. 1>&2
-echo. 1>&2
-echo Please set the JAVA_HOME variable in your environment to match the 1>&2
-echo location of your Java installation. 1>&2
+echo.
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
goto fail
@@ -57,11 +57,11 @@ set JAVA_EXE=%JAVA_HOME%/bin/java.exe
if exist "%JAVA_EXE%" goto execute
-echo. 1>&2
-echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% 1>&2
-echo. 1>&2
-echo Please set the JAVA_HOME variable in your environment to match the 1>&2
-echo location of your Java installation. 1>&2
+echo.
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
goto fail
diff --git a/lib/de/zbit/SysBio/1390/SysBio-1390.jar b/lib/de/zbit/SysBio/1390/SysBio-1390.jar
deleted file mode 100644
index 41eddc08..00000000
Binary files a/lib/de/zbit/SysBio/1390/SysBio-1390.jar and /dev/null differ
diff --git a/doc/img/ModelPolisherIcon.png b/public/img/ModelPolisherIcon.png
similarity index 100%
rename from doc/img/ModelPolisherIcon.png
rename to public/img/ModelPolisherIcon.png
diff --git a/doc/img/ModelPolisherIcon.psd b/public/img/ModelPolisherIcon.psd
similarity index 100%
rename from doc/img/ModelPolisherIcon.psd
rename to public/img/ModelPolisherIcon.psd
diff --git a/doc/img/ModelPolisherIcon256.png b/public/img/ModelPolisherIcon256.png
similarity index 100%
rename from doc/img/ModelPolisherIcon256.png
rename to public/img/ModelPolisherIcon256.png
diff --git a/docs/allclasses-index.html b/public/javadoc/allclasses-index.html
similarity index 96%
rename from docs/allclasses-index.html
rename to public/javadoc/allclasses-index.html
index f3ea6ad7..ca3e5f93 100644
--- a/docs/allclasses-index.html
+++ b/public/javadoc/allclasses-index.html
@@ -1,7 +1,7 @@
-
+
All Classes and Interfaces (ModelPolisher 2.1 API)
JavaScript is disabled on your browser.
@@ -23,7 +28,7 @@
-*Authors:* [Andreas Dräger](https://github.com/draeger/), [Thomas J. Zajac](https://github.com/mephenor/), [Matthias König](https://github.com/matthiaskoenig), [Kaustubh Trivedi](https://github.com/codekaust)
-
-[](https://travis-ci.org/draeger-lab/ModelPolisher)
-[](https://github.com/draeger-lab/ModelPolisher/releases/)
+[](https://github.com/draeger-lab/ModelPolisher/releases/)
[](https://doi.org/10.1371/journal.pone.0149263)
[](http://opensource.org/licenses/MIT)
-ModelPolisher accesses the [BiGG Models knowledgebase](http://bigg.ucsd.edu) to annotate and autocomplete [SBML](http://sbml.org) models.
-Thereby, the program mainly relies on [BiGG identifiers](https://github.com/SBRG/bigg_models/wiki/BiGG-Models-ID-Specification-and-Guidelines) for model components.
-Moreover, it fixes some apparent errors in the models and uses mappings from [AnnotateDB](https://github.com/matthiaskoenig/annotatedb) to further add annotations.
+ModelPolisher is a simple single-purpose automated curation tool for SBML models.
+It
+
+- improves the adherence to FAIR data standards as practiced in the SBML modelling community,
+- implements non-binding best practices as defined by the [SBML specification]() documents,
+- adds MIRIAM-style semantic annotations to models, using the [BiGG Models knowledgebase](http://bigg.ucsd.edu) and [AnnotateDB]().
+
+You can find comprehensive documentation on what ModelPolisher does in [our Wiki](https://github.com/draeger-lab/ModelPolisher/wiki).
+
+Furthermore, it can, on a best effort basis, attempt to perform minimal fixes on a model to make it valid with regards to the [SBMLValidator]().
+Note however, that it will not perform curation on a model that cannot be brought into a valid state.
+
+Again, you find comprehensive documentation on this in [our Wiki](https://github.com/draeger-lab/ModelPolisher/wiki).
+
+Currently supported versions of the SBML standard are:
-ModelPolisher is primarily a command-line based tool. You can run ModelPolisher locally [using `Docker`](#using-docker) or using your installation of BiGG Models database (see https://github.com/SBRG/bigg_models).
+- Version 3 Level 1
+ - FBC Version 2
+
+You can use ModelPolisher as a tool via its [Python API client]() to our HTTP server, or locally using Docker or as a Standalone JAR.
+
+ModelPolisher can also be used as a Java library, building on the [JSBML]() project.
# Table of Contents
-* [Usage Notes](#run-ModelPolisher)
+* [Performance](#performance)
+* [Using ModelPolisher as a Tool](#using-modelpolisher-as-a-tool)
+ * [Parameters](#parameters)
+ * [Using the Python API package](#using-the-python-api-client-
+ package)
* [Using Docker](#using-docker)
- * [Using ModelPolisher jar](#using-jar)
-* [How to cite ModelPolisher?](#cite-ModelPolisher)
+ * [Using ModelPolisher Jar](#using-modepolisher-jar)
+* [Using ModelPolisher as a Java library](#using-modelpolisher-as-a-java-library)
+* [How to cite ModelPolisher](#how-to-cite-ModelPolisher)
* [Licenses](#licenses)
-# Usage Notes
+# Performance
+We have run ModelPolisher on all models in the BiGG Database and on 3000 models available on Biomodels. Furthermore, we have evaluated it's performance on newly generated models using [CarveMe](), [Reconstructor]() and the [KBase Create Metabolic Model App](), with regards to [MEMOTE]() scores.
-We recommend users to run ModelPolisher [using `docker`](#using-docker), though ModelPolisher can be run [from ModelPolisher `jar`](#using-jar), which is preferred for developers.
+Here you can see a brief overview of its impact:
-NOTE: ModelPolisher provides various command line arguments which can be seen using arguments `-?` and `--help`:
-```
-java -jar