updated documentation

docs/build/.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: e5d4c87dbb9b2e3a0be59da5b76a9291
+config: 2cadc0d7faf56148d7c993d240bd1a5d
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/_sources/rnalysis.filtering.CountFilter.majority_vote_intersection.rst.txt

@@ -0,0 +1,6 @@
+rnalysis.filtering.CountFilter.majority\_vote\_intersection
+===========================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: CountFilter.majority_vote_intersection

docs/build/_sources/rnalysis.filtering.CountFilter.rst.txt

@@ -1,4 +1,4 @@
-rnalysis.filtering.CountFilter
+rnalysis.filtering.CountFilter
 ==============================
 
 .. currentmodule:: rnalysis.filtering
@@ -33,6 +33,7 @@ rnalysis.filtering.CountFilter
     CountFilter.from_folder
     CountFilter.head
     CountFilter.intersection
+    CountFilter.majority_vote_intersection
     CountFilter.normalize_to_rpm
     CountFilter.normalize_with_scaling_factors
     CountFilter.number_filters

docs/build/_sources/rnalysis.filtering.DESeqFilter.majority_vote_intersection.rst.txt

@@ -0,0 +1,6 @@
+rnalysis.filtering.DESeqFilter.majority\_vote\_intersection
+===========================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: DESeqFilter.majority_vote_intersection

docs/build/_sources/rnalysis.filtering.DESeqFilter.rst.txt

@@ -1,4 +1,4 @@
-rnalysis.filtering.DESeqFilter
+rnalysis.filtering.DESeqFilter
 ==============================
 
 .. currentmodule:: rnalysis.filtering
@@ -29,6 +29,7 @@ rnalysis.filtering.DESeqFilter
     DESeqFilter.filter_top_n
     DESeqFilter.head
     DESeqFilter.intersection
+    DESeqFilter.majority_vote_intersection
     DESeqFilter.number_filters
     DESeqFilter.print_features
     DESeqFilter.save_csv

docs/build/_sources/rnalysis.filtering.Filter.majority_vote_intersection.rst.txt

@@ -0,0 +1,6 @@
+rnalysis.filtering.Filter.majority\_vote\_intersection
+======================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: Filter.majority_vote_intersection

docs/build/_sources/rnalysis.filtering.Filter.rst.txt

@@ -1,4 +1,4 @@
-rnalysis.filtering.Filter
+rnalysis.filtering.Filter
 =========================
 
 .. currentmodule:: rnalysis.filtering
@@ -26,6 +26,7 @@ rnalysis.filtering.Filter
     Filter.filter_top_n
     Filter.head
     Filter.intersection
+    Filter.majority_vote_intersection
     Filter.number_filters
     Filter.print_features
     Filter.save_csv

docs/build/_sources/rnalysis.filtering.FoldChangeFilter.majority_vote_intersection.rst.txt

@@ -0,0 +1,6 @@
+rnalysis.filtering.FoldChangeFilter.majority\_vote\_intersection
+================================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: FoldChangeFilter.majority_vote_intersection

docs/build/_sources/rnalysis.filtering.FoldChangeFilter.rst.txt

@@ -1,4 +1,4 @@
-rnalysis.filtering.FoldChangeFilter
+rnalysis.filtering.FoldChangeFilter
 ===================================
 
 .. currentmodule:: rnalysis.filtering
@@ -28,6 +28,7 @@ rnalysis.filtering.FoldChangeFilter
     FoldChangeFilter.filter_top_n
     FoldChangeFilter.head
     FoldChangeFilter.intersection
+    FoldChangeFilter.majority_vote_intersection
     FoldChangeFilter.number_filters
     FoldChangeFilter.print_features
     FoldChangeFilter.randomization_test

docs/build/_static/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -757,6 +757,7 @@ span.pre {
     -ms-hyphens: none;
     -webkit-hyphens: none;
     hyphens: none;
+    white-space: nowrap;
 }
 
 div[class*="highlight-"] {

docs/build/_static/doctools.js

@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for all documentation.
  *
- * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -154,9 +154,7 @@ var Documentation = {
     this.fixFirefoxAnchorBug();
     this.highlightSearchWords();
     this.initIndexTable();
-    if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) {
-      this.initOnKeyListeners();
-    }
+    this.initOnKeyListeners();
   },
 
   /**
@@ -264,6 +262,16 @@ var Documentation = {
   hideSearchWords : function() {
     $('#searchbox .highlight-link').fadeOut(300);
     $('span.highlighted').removeClass('highlighted');
+    var url = new URL(window.location);
+    url.searchParams.delete('highlight');
+    window.history.replaceState({}, '', url);
+  },
+
+   /**
+   * helper function to focus on search bar
+   */
+  focusSearchBar : function() {
+    $('input[name=q]').first().focus();
   },
 
   /**
@@ -288,27 +296,54 @@ var Documentation = {
   },
 
   initOnKeyListeners: function() {
+    // only install a listener if it is really needed
+    if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS &&
+        !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS)
+        return;
+
     $(document).keydown(function(event) {
       var activeElementType = document.activeElement.tagName;
       // don't navigate when in search box, textarea, dropdown or button
       if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT'
-          && activeElementType !== 'BUTTON' && !event.altKey && !event.ctrlKey && !event.metaKey
-          && !event.shiftKey) {
-        switch (event.keyCode) {
-          case 37: // left
-            var prevHref = $('link[rel="prev"]').prop('href');
-            if (prevHref) {
-              window.location.href = prevHref;
-              return false;
-            }
-            break;
-          case 39: // right
-            var nextHref = $('link[rel="next"]').prop('href');
-            if (nextHref) {
-              window.location.href = nextHref;
-              return false;
-            }
-            break;
+          && activeElementType !== 'BUTTON') {
+        if (event.altKey || event.ctrlKey || event.metaKey)
+          return;
+
+          if (!event.shiftKey) {
+            switch (event.key) {
+              case 'ArrowLeft':
+                if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS)
+                  break;
+                var prevHref = $('link[rel="prev"]').prop('href');
+                if (prevHref) {
+                  window.location.href = prevHref;
+                  return false;
+                }
+                break;
+              case 'ArrowRight':
+                if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS)
+                  break;
+                var nextHref = $('link[rel="next"]').prop('href');
+                if (nextHref) {
+                  window.location.href = nextHref;
+                  return false;
+                }
+                break;
+              case 'Escape':
+                if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS)
+                  break;
+                Documentation.hideSearchWords();
+                return false;
+          }
+        }
+
+        // some keyboard layouts may need Shift to get /
+        switch (event.key) {
+          case '/':
+            if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS)
+              break;
+            Documentation.focusSearchBar();
+            return false;
         }
       }
     });

docs/build/_static/documentation_options.js

@@ -1,12 +1,14 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '2.0.0',
+    VERSION: '2.0.1',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
     FILE_SUFFIX: '.html',
     LINK_SUFFIX: '.html',
     HAS_SOURCE: true,
     SOURCELINK_SUFFIX: '.txt',
-    NAVIGATION_WITH_KEYS: false
+    NAVIGATION_WITH_KEYS: false,
+    SHOW_SEARCH_SUMMARY: true,
+    ENABLE_SEARCH_SHORTCUTS: true,
 };

docs/build/_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 2007-2021 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */