From ad41709fc6f56a181dde3fdc8e3f07d8911d776e Mon Sep 17 00:00:00 2001
From: domonik <schdruzzi@gmail.com>
Date: Fri, 13 Oct 2023 15:44:42 +0200
Subject: [PATCH] added initial sheet0

---
 _navbar.html                    |   1 +
 assets/html/removeSolution.html |   1 +
 assets/img/bat.svg              | 106 ++++++++++++++++
 assets/img/pumpkin.svg          | 156 ++++++++++++++++++++++++
 assets/img/witch.svg            | 206 ++++++++++++++++++++++++++++++++
 assets/js/recursions.js         | 183 ++++++++++++++++++++++++++++
 assets/js/restylePage.js        |  66 ++++++++++
 bioinf-style.css                |  30 ++++-
 exercise-sheet-0.Rmd            |  58 +++++++++
 figures/bioinf-fr-logo-blau.svg |  49 ++++----
 header.html                     |   1 +
 html/linearRecursion.html       |  26 ++++
 html/matrixMax.html             |  16 +++
 13 files changed, 875 insertions(+), 24 deletions(-)
 create mode 100644 assets/img/bat.svg
 create mode 100644 assets/img/pumpkin.svg
 create mode 100644 assets/img/witch.svg
 create mode 100644 assets/js/recursions.js
 create mode 100644 assets/js/restylePage.js
 create mode 100644 exercise-sheet-0.Rmd
 create mode 100644 html/linearRecursion.html
 create mode 100644 html/matrixMax.html

diff --git a/_navbar.html b/_navbar.html
index 0842598..78bd908 100644
--- a/_navbar.html
+++ b/_navbar.html
@@ -23,6 +23,7 @@
       <ul class="nav navbar-nav">
         <li><a href="index.html">Intro</a></li>
         <li><a href="howto.html">HowTo</a></li>
+        <li><a href="exercise-sheet-0.html">ES 0</a></li>
         <li><a href="exercise-sheet-1.html">ES 1</a></li>
         <li><a href="exercise-sheet-2.html">ES 2</a></li>
         <li><a href="exercise-sheet-3.html">ES 3</a></li>
diff --git a/assets/html/removeSolution.html b/assets/html/removeSolution.html
index 7911e7c..2e2ecf4 100644
--- a/assets/html/removeSolution.html
+++ b/assets/html/removeSolution.html
@@ -1 +1,2 @@
+<script src="assets/js/restylePage.js"></script>
 <script src="assets/js/removeSolution.js"></script>
diff --git a/assets/img/bat.svg b/assets/img/bat.svg
new file mode 100644
index 0000000..d98348c
--- /dev/null
+++ b/assets/img/bat.svg
@@ -0,0 +1,106 @@
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+
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+   height="52.474468mm"
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+   inkscape:version="1.3 (1:1.3+202307231459+0e150ed6c4)"
+   sodipodi:docname="bat.svg"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:svg="http://www.w3.org/2000/svg">
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+     inkscape:snap-nodes="true"
+     inkscape:zoom="0.83991382"
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+     inkscape:cy="204.18762"
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+     inkscape:window-height="991"
+     inkscape:window-x="26"
+     inkscape:window-y="23"
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+     inkscape:current-layer="layer1"
+     inkscape:showpageshadow="2"
+     inkscape:deskcolor="#d1d1d1" />
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+       sodipodi:type="inkscape:persp3d"
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+       inkscape:vp_z="210 : -96.025533 : 1"
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+       id="path6"
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+  </g>
+</svg>
diff --git a/assets/img/witch.svg b/assets/img/witch.svg
new file mode 100644
index 0000000..a8817f7
--- /dev/null
+++ b/assets/img/witch.svg
@@ -0,0 +1,206 @@
+<?xml version="1.0" standalone="no"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 20010904//EN"
+ "http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd">
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+ width="1280.000000pt" height="1009.000000pt" viewBox="0 0 1280.000000 1009.000000"
+ preserveAspectRatio="xMidYMid meet">
+<metadata>
+Created by potrace 1.15, written by Peter Selinger 2001-2017
+</metadata>
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diff --git a/assets/js/recursions.js b/assets/js/recursions.js
new file mode 100644
index 0000000..db1cac7
--- /dev/null
+++ b/assets/js/recursions.js
@@ -0,0 +1,183 @@
+
+function getRandomNumber(min, max) {
+            return Math.floor(Math.random() * (max - min + 1)) + min;
+        }
+
+function createArray(table, size, name) {
+  // Create a table element
+
+  // Create a table row (the header row)
+  var headrow = table.insertRow(0)
+  var row = table.insertRow(1)
+  row.id = name
+
+
+  // Add header cells with integers from 0 to 10
+  for (var i = 0; i <= size; i++) {
+    td = document.createElement('td');
+    th = document.createElement('th')
+
+    var input = document.createElement("input");
+    input.type = "number";
+    input.id = name + i;
+    input.style.backgroundColor = "transparent"
+    td.appendChild(input);
+    row.appendChild(td)
+    th = document.createElement('th');
+    var subscript = document.createElement('sub');
+    th.textContent = "a";
+    subscript.textContent = i;
+    th.appendChild(subscript);
+    headrow.appendChild(th);
+
+  }
+
+}
+
+function accessArray(arrayName) {
+  var tableRow = document.getElementById(arrayName);
+  var rowDataArray = [];
+
+  // Iterate through the table cells within the row.
+  var cells = tableRow.getElementsByTagName('td');
+  for (var i = 0; i < cells.length; i++) {
+    rowDataArray.push(cells[i].childNodes[0].value);
+  }
+  return rowDataArray;
+}
+
+function linearRecursion(a0, d, x) {
+  if (x <= 1) {
+    return [a0];
+  }
+
+  const sequence = [a0];
+
+  for (let n = 2; n < x; n++) {
+    const an = sequence[n - 2] + d;
+    sequence.push(an);
+  }
+
+  return sequence;
+}
+
+
+
+function checkLinearRecursion(){
+  a0 = document.getElementById("linRecA0").value;
+  x = document.getElementById("linRecX").value;
+  d = document.getElementById("linRecD").value;
+  const lrtable = document.getElementById('lin-rec-table');
+  array = accessArray("linRecTable");
+  expected = linearRecursion(a0, d, x);
+  console.log("expected ",expected)
+  for (var i = 0; i < array.length; i++) {
+    const cellElement = lrtable.rows[1].cells[i];
+    let current = cellElement.childNodes[0].value
+    var ei = expected[i]
+    if (i >= x){
+      if (current == "" || current == null) {
+          cellElement.style.backgroundColor = "var(--right-answer)"
+      }
+      else {
+          cellElement.style.backgroundColor = "var(--wrong-answer)"
+      }
+    } else {
+      if (current == "" || current == null) {
+          cellElement.style.backgroundColor = "var(--wrong-answer)"
+      }
+      else if (current == array[i]) {
+          cellElement.style.backgroundColor = "var(--right-answer)"
+      } else {
+          cellElement.style.backgroundColor = "var(--wrong-answer)"
+      }
+
+    }
+  }
+}
+
+function createMaxMatrix() {
+    const table = document.getElementById('maxTable');
+    table.style.margin = "auto"
+    while (table.firstChild) {
+        table.removeChild(table.firstChild);
+    }
+    for (let row = 0; row <= 2; row++) {
+        const tr = document.createElement('tr');
+        for (let col = 0; col <= 2; col++) {
+            var td;
+            if ( row == 0 && col == 0 ) {
+                td = document.createElement('th')
+                var subscript = document.createElement('sub');
+                subscript.textContent = "i,j";
+                td.textContent = "D";
+                td.appendChild(subscript);
+
+            } else if (row == 0) {
+                td = document.createElement('th');
+
+                td.textContent = col;
+            } else if (col == 0) {
+                td = document.createElement('td');
+
+                td.textContent = row;
+                td.style.fontWeight = "bold";
+                td.style.width = "10%"
+                td.style.textAlign = "center";
+                td.style.border = "2px solid";
+
+            } else {
+                td = document.createElement('td');
+
+                var input = document.createElement("input");
+                input.type = "number";
+                input.name = "member" + row + "-" + col;
+                input.style.backgroundColor = "transparent"
+                if ((row != 2) || (col != 2)) {
+                  input.disabled = true;
+                  input.value = getRandomNumber(0, 10);
+                }
+                td.appendChild(input);
+
+            }
+            tr.appendChild(td);
+        }
+        table.appendChild(tr);
+    }
+}
+
+function checkMaxMatrix(){
+  const maxTable = document.getElementById('maxTable');
+  console.log(maxTable.rows[1].cells[2].children[0].value)
+  first = parseInt(maxTable.rows[1].cells[1].children[0].value) + 2;
+  second = parseInt(maxTable.rows[1].cells[2].children[0].value) + 3;
+  third = parseInt(maxTable.rows[1].cells[2].children[0].value) + 1;
+  result = Math.max(first, second, third);
+  cellElement = maxTable.rows[2].cells[2];
+  current = parseInt(cellElement.children[0].value);
+  console.log(current, result)
+  if (current == "" || current == null) {
+      cellElement.style.backgroundColor = "var(--wrong-answer)";
+  } else if (current == result){
+          cellElement.style.backgroundColor = "var(--right-answer)";
+
+
+  } else {
+    cellElement.style.backgroundColor = "var(--wrong-answer)";
+  }
+
+
+
+
+}
+
+
+// To add the table to a specific HTML element, you can do something like this:
+var lrTable = document.getElementById('lin-rec-table');
+createArray(lrTable, 10, "linRecTable")// Replace 'table-container' with the ID of the element where you want to insert the table-container
+createMaxMatrix()
+
+
+        // Function to display a random SVG image at a random position
+
+
diff --git a/assets/js/restylePage.js b/assets/js/restylePage.js
new file mode 100644
index 0000000..db0abf1
--- /dev/null
+++ b/assets/js/restylePage.js
@@ -0,0 +1,66 @@
+
+ function getRandomNumber(min, max) {
+            return Math.floor(Math.random() * (max - min + 1)) + min;
+        }
+
+function displayRandomImage(svgImage, left, top, scale, rotation, zindex=-99) {
+    // Get a reference to the "img" folder
+    var imgFolder = "assets/img/";
+
+    // List of SVG image file names in the "img" folder
+    // Choose a random SVG image from the list
+    // Create an image element and set its attributes
+    var image = new Image();
+    image.src = imgFolder + svgImage;
+    image.style.width = "100px"
+    image.style.transform = `rotate(${rotation}deg)`;
+    image.style.transform += ` scale(${scale})`;
+    image.className = "random-image";
+    image.style.position = "fixed";
+    image.style.zIndex = zindex;
+    image.style.left = left + "%"; // Adjust as needed
+    image.style.top = top + "%"; // Adjust as needed
+
+    // Add a click event listener to make the image disappear
+    image.addEventListener("click", function() {
+        document.body.removeChild(image);
+    });
+
+    // Append the image to the body
+    document.body.appendChild(image);
+}
+
+function determineTheme(){
+  const currentTime = new Date();
+  const currentMonth = currentTime.getMonth(); // Get the month (0-11)
+  if (currentMonth == 9){
+    halloweenTheme()
+  }
+
+}
+function changeFontFamily(fontFamily) {
+  const headerElements = document.querySelectorAll('h1, h2, h3, h4, h5, h6');
+
+  headerElements.forEach(element => {
+    element.style.fontFamily = fontFamily;
+  });
+}
+
+function halloweenTheme(){
+  displayRandomImage("bat.svg", 10, 10, 1.5, 25);
+  displayRandomImage("bat.svg", 2, 30, 2, -30);
+  displayRandomImage("bat.svg", 25, 60, 1, 10);
+  displayRandomImage("bat.svg", 7, 70, 0.5, -5);
+  displayRandomImage("bat.svg", 5, 73, 0.7, 8);
+  displayRandomImage("witch.svg", 90, 20, 1.5, 8);
+  displayRandomImage("pumpkin.svg", 90, 85, 3, 8, zindex=1);
+  document.documentElement.style.setProperty('--ufr-main-blue', "#171512");
+  document.documentElement.style.setProperty('--active-item-color', "rgb(219, 134, 7)");
+  document.documentElement.style.setProperty('--selector-color', "rgba(219, 134, 7, 0.3)");
+  document.documentElement.style.setProperty('--font-family', 'Creepster,"Source Sans Pro",Calibri,Candara,Arial,sans-serif');
+
+
+
+}
+
+window.onload = determineTheme()
diff --git a/bioinf-style.css b/bioinf-style.css
index b4ea18d..dd5e251 100644
--- a/bioinf-style.css
+++ b/bioinf-style.css
@@ -1,6 +1,30 @@
+:root {
+  --wrong-answer: rgba(255, 0, 0, 0.4);
+  --right-answer: rgb(221,255,221);
+  --ufr-main-blue: rgb(52, 74, 154);
+  --active-item-color: #00a082;
+  --selector-color: #ebf5fb;
+  --font-family: "Source Sans Pro",Calibri,Candara,Arial,sans-serif;
+}
+h1, h2, h3, h4, h5, h6, .h1, .h2, .h3, .h4, .h5, .h6 {
+  font-family: var(--font-family);
+}
+a {
+  color: var(--active-item-color);
+}
+a:hover {
+  color: var(--active-item-color);
+}
+.toc-content {
+  background-color: white;
+}
+.list-group-item.active, .list-group-item.active:hover, .list-group-item.active:focus {
+  background-color: var(--active-item-color);
+}
+
 table td:first-child { border-right:  1px solid; }
 table th {border-bottom: 1px solid;}
-.navbar-default {background-color: #003591ff}
+.navbar-default {background-color: var(--ufr-main-blue)}
 .navbar .navbar-brand {
   vertical-align: middle;
 }
@@ -292,7 +316,7 @@ label, input, button {
   margin: 10px auto;
   width: 90%;
   align-items: right;
-  background-color: #2780e3;
+  background-color: var(--active-item-color);
   border: 0px;
   padding: 5px;
   border-radius: 5px;
@@ -305,7 +329,7 @@ label, input, button {
 }
 
 .selectordiv {
-  background-color:  #ebf5fb ;
+  background-color:  var(--selector-color);
   margin-top: 20px;
   margin-bottom: 20px;
   padding: 10px 10px 10px 10px;
diff --git a/exercise-sheet-0.Rmd b/exercise-sheet-0.Rmd
new file mode 100644
index 0000000..1d2fdb7
--- /dev/null
+++ b/exercise-sheet-0.Rmd
@@ -0,0 +1,58 @@
+---
+title: "Exercise sheet 0: Math"
+---
+
+---------------------------------
+
+# Exercise 1 - Recursions
+
+
+### 1a)
+
+Given the recursive Formulation, fill in the array underneath:
+
+$$
+a_n = a_{n-1} + d\ \forall \ 2\leq n < x
+$$
+
+```{r, echo=FALSE}
+htmltools::includeHTML("html/linearRecursion.html")
+```
+
+
+
+
+### 1b)
+
+Given the recursive formulation, fill in the missing cell underneath:
+
+
+:::: {#explaining .message-box }
+
+::: {#note-exp .note-header}
+```{r, include=knitr::is_html_output(), echo=FALSE,}
+knitr::include_graphics("figures/infoicon.svg")
+```
+**Note**
+:::
+::: {#note-exp .note-body}
+
+
+During the course of Bioinformatics we will use $i$ as the row and $j$ as the
+column index
+
+:::
+
+::::
+
+
+$$
+D_{i, j} = max (D_{i-1. j-1} + 2, D_{i-1, j} + 3, D_{i, j-1} + 1)\ \forall i\ge j > 1
+$$
+```{r, echo=FALSE}
+htmltools::includeHTML("html/matrixMax.html")
+```
+
+```{r, echo=FALSE}
+htmltools::tags$script(src = "assets/js/recursions.js", type= "text/javascript")
+```
diff --git a/figures/bioinf-fr-logo-blau.svg b/figures/bioinf-fr-logo-blau.svg
index af3b632..7be9e96 100644
--- a/figures/bioinf-fr-logo-blau.svg
+++ b/figures/bioinf-fr-logo-blau.svg
@@ -2,22 +2,22 @@
 <!-- Created with Inkscape (http://www.inkscape.org/) -->
 
 <svg
-   xmlns:dc="http://purl.org/dc/elements/1.1/"
-   xmlns:cc="http://creativecommons.org/ns#"
-   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-   xmlns:svg="http://www.w3.org/2000/svg"
-   xmlns="http://www.w3.org/2000/svg"
-   xmlns:xlink="http://www.w3.org/1999/xlink"
-   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
-   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
    width="513.7851"
    height="494.38583"
    id="svg3183"
    sodipodi:version="0.32"
-   inkscape:version="0.92.5 (2060ec1f9f, 2020-04-08)"
+   inkscape:version="1.3 (1:1.3+202307231459+0e150ed6c4)"
    version="1.0"
    sodipodi:docname="bioinf-fr-logo-blau.svg"
-   inkscape:output_extension="org.inkscape.output.svgz.inkscape">
+   inkscape:output_extension="org.inkscape.output.svgz.inkscape"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:xlink="http://www.w3.org/1999/xlink"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:dc="http://purl.org/dc/elements/1.1/">
   <defs
      id="defs3185">
     <linearGradient
@@ -97,21 +97,29 @@
      inkscape:pageopacity="0.0"
      inkscape:pageshadow="2"
      inkscape:zoom="0.49497475"
-     inkscape:cx="-20.725981"
-     inkscape:cy="515.95939"
+     inkscape:cx="-20.203051"
+     inkscape:cy="514.16764"
      inkscape:document-units="px"
      inkscape:current-layer="layer1"
      showgrid="false"
-     inkscape:window-width="1042"
-     inkscape:window-height="974"
-     inkscape:window-x="0"
-     inkscape:window-y="25"
-     inkscape:window-maximized="0">
+     inkscape:window-width="1452"
+     inkscape:window-height="991"
+     inkscape:window-x="26"
+     inkscape:window-y="23"
+     inkscape:window-maximized="0"
+     inkscape:showpageshadow="2"
+     inkscape:pagecheckerboard="0"
+     inkscape:deskcolor="#d1d1d1">
     <inkscape:grid
        type="xygrid"
        id="grid3217"
-       visible="true"
-       enabled="true" />
+       visible="false"
+       enabled="true"
+       originx="0"
+       originy="0"
+       spacingy="1"
+       spacingx="1"
+       units="px" />
   </sodipodi:namedview>
   <metadata
      id="metadata3188">
@@ -121,7 +129,6 @@
         <dc:format>image/svg+xml</dc:format>
         <dc:type
            rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
-        <dc:title></dc:title>
       </cc:Work>
     </rdf:RDF>
   </metadata>
@@ -132,7 +139,7 @@
      style="display:inline"
      transform="translate(-82.25032,-239.45496)">
     <rect
-       style="opacity:1;fill:#003592;fill-opacity:1;fill-rule:nonzero;stroke:none;stroke-width:0.17100000000000001;stroke-linecap:butt;stroke-linejoin:miter;marker:none;marker-start:none;marker-mid:none;marker-end:none;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;visibility:visible;display:inline;overflow:visible;enable-background:accumulate"
+       style="opacity:1;fill:#003592;fill-opacity:0;fill-rule:nonzero;stroke:none;stroke-width:0.171;stroke-linecap:butt;stroke-linejoin:miter;marker:none;marker-start:none;marker-mid:none;marker-end:none;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;visibility:visible;display:inline;overflow:visible;enable-background:accumulate"
        id="rect3244"
        width="513.7851"
        height="494.38583"
diff --git a/header.html b/header.html
index de61747..5833a68 100644
--- a/header.html
+++ b/header.html
@@ -1,3 +1,4 @@
 <head>
 <link rel="shortcut icon" href="figures/favicon.svg" />
+<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Creepster">
 </head>
diff --git a/html/linearRecursion.html b/html/linearRecursion.html
new file mode 100644
index 0000000..22a9092
--- /dev/null
+++ b/html/linearRecursion.html
@@ -0,0 +1,26 @@
+<div class="selectordiv">
+
+
+    <div class="nwselector">
+      <label for="a0">a<sub>0:</sub></label>
+      <input type="number" id="linRecA0" name="fname" value=1><br>
+    </div>
+    <div class="nwselector">
+      <label for="x">x:</label>
+      <input type="number" id="linRecX" name="fname" value="5" min=1 max=10 step=1><br>
+    </div>
+    <div class="nwselector">
+      <label for="d">d:</label>
+      <input type="number" id="linRecD" name="fname" value="5" min=0 max=100 step=1><br>
+    </div>
+
+    <div class="nwselector">
+
+    <button class="checker" onclick="checkLinearRecursion()">Check Array</button>
+    </div>
+
+</div>
+
+<div class="nwtablediv">
+  <table id="lin-rec-table"></table>
+</div>
diff --git a/html/matrixMax.html b/html/matrixMax.html
new file mode 100644
index 0000000..f5eaecc
--- /dev/null
+++ b/html/matrixMax.html
@@ -0,0 +1,16 @@
+
+<div class="selectordiv">
+    <div class="nwselector">
+
+    <button class="checker" onclick="createMaxMatrix()">New Numbers</button>
+    </div>
+    <div class="nwselector">
+
+    <button class="checker" onclick="checkMaxMatrix()">Check Result</button>
+    </div>
+
+</div>
+
+<div class="nwtablediv">
+  <table id="maxTable"></table>
+</div>