Update documentation

mpavsic · Mar 18, 2024 · 890a955 · 890a955
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diff --git a/.buildinfo b/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 514f4ab7ac2ceec72bc17a36e0b7d086
+config: 056c30a74b33080c9b2c087e9ce84eb9
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/_sources/vaje/dotplot_web.md b/_sources/vaje/dotplot_web.md
@@ -5,7 +5,7 @@ Na dveh enostavnih primerih si bomo ogledali, kako lahko uporabimo točkovni dia
 ---
 ## Naloga 1: primerjava dveh krajših zaporedij
 
-S pomočjo spletnega programa [EMBOSS DotMatcher](http://emboss.bioinformatics.nl/cgi-bin/emboss/dotmatcher) primerjajte med seboj aminokislinski zaporedji proteinov:
+S pomočjo spletnega programa [EMBOSS DotMatcher](https://www.ebi.ac.uk/jdispatcher/seqstats/emboss_dotmatcher) primerjajte med seboj aminokislinski zaporedji proteinov:
 * človeški N-CAM-1 (*neural cell adhesion molecule 1*)
 * miotilin (*myotilin*)
 
@@ -16,7 +16,7 @@ Naloga:
 * Ali v točkovnem diagramu opazite kakšen izrazit vzorec? Razložite!
 * Sedaj pa primerjajte še nt-zaporedji celotne kodirajoče regije mRNA za omenjena proteina. Kakšen je rezultat take primerjave in zakaj?
 
-Na kratko o orodju DotMatcher... Orodje DotMatcher je sprogramirano tako, da za posamezne pare ij (i so ostanki iz 1. zaporedja, j pa iz 2. zaporedja) prebere vrednosti iz matrike zamenjav (privzeta EBLOSUM62 (=BLOSUM62) za ak-zaporedja, za nt-zaporedja pa EDNAFULL), nato pa izračuna vsoto nekaj zaporednih ostankov (ta parameter nastavimo z velikostjo okna – *window size*), na koncu pa znak v matriki nariše le, če je vsota enaka ali pa presega prag (*treshold*). Zaporedja, ki jih primerjate, vstavite v program v formatu FASTA.
+Na kratko o orodju DotMatcher... Orodje DotMatcher je sprogramirano tako, da za posamezne pare ij (i so ostanki iz 1. zaporedja, j pa iz 2. zaporedja) prebere vrednosti iz matrike zamenjav (privzeta EBLOSUM62 (=BLOSUM62) za ak-zaporedja, za nt-zaporedja pa EDNAFULL), nato pa izračuna vsoto nekaj zaporednih ostankov (ta parameter nastavimo z velikostjo okna – *window size*), na koncu pa znak v matriki nariše le, če je vsota enaka ali pa presega prag (*treshold*). Zaporedja, ki jih primerjate, vstavite v program v formatu FASTA. Na spodnji sliki je sicer prikazana prejšnja verzija vmesnika; nova je malce drugačna, a nudi enake parametre.
 
 ![EMBOSS DotMatcher](slike/emboss_dotmatcher.png)
 

diff --git a/....4045f2051d55cab465a707391d5b2007.min.css → ....1e8bd061cd6da7fc9cf755528e8ffc24.min.css b/....4045f2051d55cab465a707391d5b2007.min.css → ....1e8bd061cd6da7fc9cf755528e8ffc24.min.css
diff --git a/_static/basic.css b/_static/basic.css
@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -236,17 +236,11 @@ div.body p, div.body dd, div.body li, div.body blockquote {
 a.headerlink {
     visibility: hidden;
 }
-a.brackets:before,
-span.brackets > a:before{
-    content: "[";
-}
 
-a.brackets:after,
-span.brackets > a:after {
-    content: "]";
+a:visited {
+    color: #551A8B;
 }
 
-
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -334,11 +328,17 @@ aside.sidebar {
 p.sidebar-title {
     font-weight: bold;
 }
+
+nav.contents,
+aside.topic,
 div.admonition, div.topic, blockquote {
     clear: left;
 }
 
 /* -- topics ---------------------------------------------------------------- */
+
+nav.contents,
+aside.topic,
 div.topic {
     border: 1px solid #ccc;
     padding: 7px;
@@ -377,13 +377,17 @@ div.body p.centered {
 
 div.sidebar > :last-child,
 aside.sidebar > :last-child,
+nav.contents > :last-child,
+aside.topic > :last-child,
 div.topic > :last-child,
 div.admonition > :last-child {
     margin-bottom: 0;
 }
 
 div.sidebar::after,
 aside.sidebar::after,
+nav.contents::after,
+aside.topic::after,
 div.topic::after,
 div.admonition::after,
 blockquote::after {
@@ -609,25 +613,6 @@ ul.simple p {
     margin-bottom: 0;
 }
 
-/* Docutils 0.17 and older (footnotes & citations) */
-dl.footnote > dt,
-dl.citation > dt {
-    float: left;
-    margin-right: 0.5em;
-}
-
-dl.footnote > dd,
-dl.citation > dd {
-    margin-bottom: 0em;
-}
-
-dl.footnote > dd:after,
-dl.citation > dd:after {
-    content: "";
-    clear: both;
-}
-
-/* Docutils 0.18+ (footnotes & citations) */
 aside.footnote > span,
 div.citation > span {
     float: left;
@@ -652,8 +637,6 @@ div.citation > p:last-of-type:after {
     clear: both;
 }
 
-/* Footnotes & citations ends */
-
 dl.field-list {
     display: grid;
     grid-template-columns: fit-content(30%) auto;
@@ -666,10 +649,6 @@ dl.field-list > dt {
     padding-right: 5px;
 }
 
-dl.field-list > dt:after {
-    content: ":";
-}
-
 dl.field-list > dd {
     padding-left: 0.5em;
     margin-top: 0em;
@@ -695,6 +674,16 @@ dd {
     margin-left: 30px;
 }
 
+.sig dd {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
+.sig dl {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
 dl > dd:last-child,
 dl > dd:last-child > :last-child {
     margin-bottom: 0;
@@ -763,6 +752,14 @@ abbr, acronym {
     cursor: help;
 }
 
+.translated {
+    background-color: rgba(207, 255, 207, 0.2)
+}
+
+.untranslated {
+    background-color: rgba(255, 207, 207, 0.2)
+}
+
 /* -- code displays --------------------------------------------------------- */
 
 pre {

diff --git a/_static/design-style.1e8bd061cd6da7fc9cf755528e8ffc24.min.css b/_static/design-style.1e8bd061cd6da7fc9cf755528e8ffc24.min.css
diff --git a/_static/doctools.js b/_static/doctools.js
@@ -4,12 +4,19 @@
  *
  * Base JavaScript utilities for all Sphinx HTML documentation.
  *
- * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
 "use strict";
 
+const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([
+  "TEXTAREA",
+  "INPUT",
+  "SELECT",
+  "BUTTON",
+]);
+
 const _ready = (callback) => {
   if (document.readyState !== "loading") {
     callback();
@@ -18,73 +25,11 @@ const _ready = (callback) => {
   }
 };
 
-/**
- * highlight a given string on a node by wrapping it in
- * span elements with the given class name.
- */
-const _highlight = (node, addItems, text, className) => {
-  if (node.nodeType === Node.TEXT_NODE) {
-    const val = node.nodeValue;
-    const parent = node.parentNode;
-    const pos = val.toLowerCase().indexOf(text);
-    if (
-      pos >= 0 &&
-      !parent.classList.contains(className) &&
-      !parent.classList.contains("nohighlight")
-    ) {
-      let span;
-
-      const closestNode = parent.closest("body, svg, foreignObject");
-      const isInSVG = closestNode && closestNode.matches("svg");
-      if (isInSVG) {
-        span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
-      } else {
-        span = document.createElement("span");
-        span.classList.add(className);
-      }
-
-      span.appendChild(document.createTextNode(val.substr(pos, text.length)));
-      parent.insertBefore(
-        span,
-        parent.insertBefore(
-          document.createTextNode(val.substr(pos + text.length)),
-          node.nextSibling
-        )
-      );
-      node.nodeValue = val.substr(0, pos);
-
-      if (isInSVG) {
-        const rect = document.createElementNS(
-          "http://www.w3.org/2000/svg",
-          "rect"
-        );
-        const bbox = parent.getBBox();
-        rect.x.baseVal.value = bbox.x;
-        rect.y.baseVal.value = bbox.y;
-        rect.width.baseVal.value = bbox.width;
-        rect.height.baseVal.value = bbox.height;
-        rect.setAttribute("class", className);
-        addItems.push({ parent: parent, target: rect });
-      }
-    }
-  } else if (node.matches && !node.matches("button, select, textarea")) {
-    node.childNodes.forEach((el) => _highlight(el, addItems, text, className));
-  }
-};
-const _highlightText = (thisNode, text, className) => {
-  let addItems = [];
-  _highlight(thisNode, addItems, text, className);
-  addItems.forEach((obj) =>
-    obj.parent.insertAdjacentElement("beforebegin", obj.target)
-  );
-};
-
 /**
  * Small JavaScript module for the documentation.
  */
 const Documentation = {
   init: () => {
-    Documentation.highlightSearchWords();
     Documentation.initDomainIndexTable();
     Documentation.initOnKeyListeners();
   },
@@ -126,51 +71,6 @@ const Documentation = {
     Documentation.LOCALE = catalog.locale;
   },
 
-  /**
-   * highlight the search words provided in the url in the text
-   */
-  highlightSearchWords: () => {
-    const highlight =
-      new URLSearchParams(window.location.search).get("highlight") || "";
-    const terms = highlight.toLowerCase().split(/\s+/).filter(x => x);
-    if (terms.length === 0) return; // nothing to do
-
-    // There should never be more than one element matching "div.body"
-    const divBody = document.querySelectorAll("div.body");
-    const body = divBody.length ? divBody[0] : document.querySelector("body");
-    window.setTimeout(() => {
-      terms.forEach((term) => _highlightText(body, term, "highlighted"));
-    }, 10);
-
-    const searchBox = document.getElementById("searchbox");
-    if (searchBox === null) return;
-    searchBox.appendChild(
-      document
-        .createRange()
-        .createContextualFragment(
-          '<p class="highlight-link">' +
-            '<a href="javascript:Documentation.hideSearchWords()">' +
-            Documentation.gettext("Hide Search Matches") +
-            "</a></p>"
-        )
-    );
-  },
-
-  /**
-   * helper function to hide the search marks again
-   */
-  hideSearchWords: () => {
-    document
-      .querySelectorAll("#searchbox .highlight-link")
-      .forEach((el) => el.remove());
-    document
-      .querySelectorAll("span.highlighted")
-      .forEach((el) => el.classList.remove("highlighted"));
-    const url = new URL(window.location);
-    url.searchParams.delete("highlight");
-    window.history.replaceState({}, "", url);
-  },
-
   /**
    * helper function to focus on search bar
    */
@@ -210,15 +110,11 @@ const Documentation = {
     )
       return;
 
-    const blacklistedElements = new Set([
-      "TEXTAREA",
-      "INPUT",
-      "SELECT",
-      "BUTTON",
-    ]);
     document.addEventListener("keydown", (event) => {
-      if (blacklistedElements.has(document.activeElement.tagName)) return; // bail for input elements
-      if (event.altKey || event.ctrlKey || event.metaKey) return; // bail with special keys
+      // bail for input elements
+      if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return;
+      // bail with special keys
+      if (event.altKey || event.ctrlKey || event.metaKey) return;
 
       if (!event.shiftKey) {
         switch (event.key) {
@@ -240,10 +136,6 @@ const Documentation = {
               event.preventDefault();
             }
             break;
-          case "Escape":
-            if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break;
-            Documentation.hideSearchWords();
-            event.preventDefault();
         }
       }
 

diff --git a/_static/documentation_options.js b/_static/documentation_options.js
@@ -1,5 +1,4 @@
-var DOCUMENTATION_OPTIONS = {
-    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
+const DOCUMENTATION_OPTIONS = {
     VERSION: '',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
@@ -10,5 +9,5 @@ var DOCUMENTATION_OPTIONS = {
     SOURCELINK_SUFFIX: '',
     NAVIGATION_WITH_KEYS: false,
     SHOW_SEARCH_SUMMARY: true,
-    ENABLE_SEARCH_SHORTCUTS: false,
+    ENABLE_SEARCH_SHORTCUTS: true,
 };
diff --git a/_static/language_data.js b/_static/language_data.js
@@ -5,7 +5,7 @@
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
  *
- * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */