Add dot plot documentation

src/dgenies/md/doc_dotplot.md

+# Dot plot
+
+In bioinformatics a dot plot is a graphical method that allows the comparison of two biological sequences and identify regions of close similarity between them. It is a type of recurrence plot.
+
+More details of dot plot [here](https://en.wikipedia.org/wiki/Dot_plot_(bioinformatics)). Below, some examples of events which can be detected by dot plots.
+
+## Match
+
+When two samples sequence are identical, it's a match.
+
+![match](/static/images/dotplot/match.png)
+
+## Gap
+
+Dot plots can be used to detect a gap between two samples: small sequence which exists only in one sample, between two matching regions.
+
+![gap](/static/images/dotplot/gap.png)
+
+## Inversion
+
+Sequence which exists in the two samples but not in the same order.
+
+![inversion](/static/images/dotplot/inversion.png)
+
+## Repeats
+
+Dot plot can be used to detect repeated regions: a sequence which is repeated several times in a sample.
+
+![repeats](/static/images/dotplot/repeat2.png)
\ No newline at end of file

src/dgenies/templates/base.html

@@ -63,6 +63,7 @@
                             <ul class="dropdown-menu" role="menu">
                                 <li><a href="/documentation/run">Launch a job</a></li>
                                 <li><a href="/documentation/result">Results</a></li>
+                                <li><a href="/documentation/dotplot">Dot plot</a></li>
                                 <li><a href="/documentation/formats">File formats</a></li>
                             </ul>
                         </li>

src/dgenies/templates/documentation.html

@@ -28,10 +28,17 @@
             color: #ffffff;
             font-weight: bold;
         }
+        {% if toc %}
         #body {
             width: calc(100% - 300px);
             margin-left: 295px !important;
         }
+        {% else %}
+        #body {
+            width: calc(100% - 300px);
+            margin-left: 145px !important;
+        }
+        {% endif %}
     </style>
 
     <script type="text/javascript">
@@ -42,11 +49,13 @@
 {% endblock %}
 {% block content %}
 
-    <div id="plan-back">
-        <div id="plan">
-            {{ toc }}
+    {% if toc %}
+        <div id="plan-back">
+            <div id="plan">
+                {{ toc }}
+            </div>
         </div>
-    </div>
+    {% endif %}
 
     <div id="body">
         {{ content }}

src/dgenies/views.py

@@ -361,7 +361,7 @@ def documentation_result():
 
 @app.route("/documentation/formats", methods=['GET'])
 def documentation_formats():
-    with open(os.path.join(app_folder, "md", "formats.md"), "r",
+    with open(os.path.join(app_folder, "md", "doc_formats.md"), "r",
               encoding='utf-8') as install_instr:
         content = install_instr.read()
     md = Markdown(extensions=[TocExtension(baselevel=1), TableExtension()])
@@ -370,6 +370,17 @@ def documentation_formats():
     return render_template("documentation.html", menu="documentation", content=content, toc=toc)
 
 
+@app.route("/documentation/dotplot", methods=['GET'])
+def documentation_dotplot():
+    with open(os.path.join(app_folder, "md", "doc_dotplot.md"), "r",
+              encoding='utf-8') as install_instr:
+        content = install_instr.read()
+    md = Markdown(extensions=[TocExtension(baselevel=1)])
+    content = Markup(md.convert(content))
+    toc = Markup(md.toc)
+    return render_template("documentation.html", menu="documentation", content=content, toc=toc)
+
+
 @app.route("/install", methods=['GET'])
 def install():
     with open(os.path.join(app_folder, "md", "INSTALL.md"), "r", encoding='utf-8') as install_instr: