[med-svn] [qualimap] 01/01: Imported Upstream version 2.1.3+dfsg
Andreas Tille
tille at debian.org
Wed Nov 18 08:51:17 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch upstream
in repository qualimap.
commit f3f40045001db742829aadd468793705272c751a
Author: Andreas Tille <tille at debian.org>
Date: Wed Nov 18 09:48:08 2015 +0100
Imported Upstream version 2.1.3+dfsg
---
doc/count-data/_static/agogo.css | 471 ------------
doc/count-data/_static/ajax-loader.gif | Bin 673 -> 0 bytes
doc/count-data/_static/basic.css | 540 --------------
doc/count-data/_static/bgfooter.png | Bin 434 -> 0 bytes
doc/count-data/_static/bgtop.png | Bin 430 -> 0 bytes
doc/count-data/_static/comment-bright.png | Bin 3500 -> 0 bytes
doc/count-data/_static/comment-close.png | Bin 3578 -> 0 bytes
doc/count-data/_static/comment.png | Bin 3445 -> 0 bytes
doc/count-data/_static/doctools.js | 247 -------
doc/count-data/_static/down-pressed.png | Bin 368 -> 0 bytes
doc/count-data/_static/down.png | Bin 363 -> 0 bytes
doc/count-data/_static/file.png | Bin 392 -> 0 bytes
doc/count-data/_static/jquery.js | 154 ----
doc/count-data/_static/minus.png | Bin 199 -> 0 bytes
doc/count-data/_static/plus.png | Bin 199 -> 0 bytes
doc/count-data/_static/pygments.css | 62 --
doc/count-data/_static/qualimap_logo_small.png | Bin 2922 -> 0 bytes
doc/count-data/_static/report.css | 50 --
doc/count-data/_static/searchtools.js | 560 --------------
doc/count-data/_static/underscore.js | 23 -
doc/count-data/_static/up-pressed.png | Bin 372 -> 0 bytes
doc/count-data/_static/up.png | Bin 363 -> 0 bytes
doc/count-data/_static/websupport.js | 808 ---------------------
doc/plasmodium/_static/agogo.css | 471 ------------
doc/plasmodium/_static/ajax-loader.gif | Bin 673 -> 0 bytes
doc/plasmodium/_static/basic.css | 540 --------------
doc/plasmodium/_static/bgfooter.png | Bin 434 -> 0 bytes
doc/plasmodium/_static/bgtop.png | Bin 430 -> 0 bytes
doc/plasmodium/_static/comment-bright.png | Bin 3500 -> 0 bytes
doc/plasmodium/_static/comment-close.png | Bin 3578 -> 0 bytes
doc/plasmodium/_static/comment.png | Bin 3445 -> 0 bytes
doc/plasmodium/_static/doctools.js | 247 -------
doc/plasmodium/_static/down-pressed.png | Bin 368 -> 0 bytes
doc/plasmodium/_static/down.png | Bin 363 -> 0 bytes
doc/plasmodium/_static/file.png | Bin 392 -> 0 bytes
doc/plasmodium/_static/jquery.js | 154 ----
doc/plasmodium/_static/minus.png | Bin 199 -> 0 bytes
doc/plasmodium/_static/plus.png | Bin 199 -> 0 bytes
doc/plasmodium/_static/pygments.css | 62 --
doc/plasmodium/_static/qualimap_logo_small.png | Bin 2922 -> 0 bytes
doc/plasmodium/_static/report.css | 50 --
doc/plasmodium/_static/searchtools.js | 560 --------------
doc/plasmodium/_static/underscore.js | 23 -
doc/plasmodium/_static/up-pressed.png | Bin 372 -> 0 bytes
doc/plasmodium/_static/up.png | Bin 363 -> 0 bytes
doc/plasmodium/_static/websupport.js | 808 ---------------------
doc/plasmodium_RNA-seq/_static/agogo.css | 471 ------------
doc/plasmodium_RNA-seq/_static/ajax-loader.gif | Bin 673 -> 0 bytes
doc/plasmodium_RNA-seq/_static/basic.css | 540 --------------
doc/plasmodium_RNA-seq/_static/bgfooter.png | Bin 434 -> 0 bytes
doc/plasmodium_RNA-seq/_static/bgtop.png | Bin 430 -> 0 bytes
doc/plasmodium_RNA-seq/_static/comment-bright.png | Bin 3500 -> 0 bytes
doc/plasmodium_RNA-seq/_static/comment-close.png | Bin 3578 -> 0 bytes
doc/plasmodium_RNA-seq/_static/comment.png | Bin 3445 -> 0 bytes
doc/plasmodium_RNA-seq/_static/doctools.js | 247 -------
doc/plasmodium_RNA-seq/_static/down-pressed.png | Bin 368 -> 0 bytes
doc/plasmodium_RNA-seq/_static/down.png | Bin 363 -> 0 bytes
doc/plasmodium_RNA-seq/_static/file.png | Bin 392 -> 0 bytes
doc/plasmodium_RNA-seq/_static/jquery.js | 154 ----
doc/plasmodium_RNA-seq/_static/minus.png | Bin 199 -> 0 bytes
doc/plasmodium_RNA-seq/_static/plus.png | Bin 199 -> 0 bytes
doc/plasmodium_RNA-seq/_static/pygments.css | 62 --
.../_static/qualimap_logo_small.png | Bin 2922 -> 0 bytes
doc/plasmodium_RNA-seq/_static/report.css | 50 --
doc/plasmodium_RNA-seq/_static/searchtools.js | 560 --------------
doc/plasmodium_RNA-seq/_static/underscore.js | 23 -
doc/plasmodium_RNA-seq/_static/up-pressed.png | Bin 372 -> 0 bytes
doc/plasmodium_RNA-seq/_static/up.png | Bin 363 -> 0 bytes
doc/plasmodium_RNA-seq/_static/websupport.js | 808 ---------------------
doc/rna-seq-example/_static/agogo.css | 471 ------------
doc/rna-seq-example/_static/ajax-loader.gif | Bin 673 -> 0 bytes
doc/rna-seq-example/_static/basic.css | 540 --------------
doc/rna-seq-example/_static/bgfooter.png | Bin 434 -> 0 bytes
doc/rna-seq-example/_static/bgtop.png | Bin 430 -> 0 bytes
doc/rna-seq-example/_static/comment-bright.png | Bin 3500 -> 0 bytes
doc/rna-seq-example/_static/comment-close.png | Bin 3578 -> 0 bytes
doc/rna-seq-example/_static/comment.png | Bin 3445 -> 0 bytes
doc/rna-seq-example/_static/doctools.js | 247 -------
doc/rna-seq-example/_static/down-pressed.png | Bin 368 -> 0 bytes
doc/rna-seq-example/_static/down.png | Bin 363 -> 0 bytes
doc/rna-seq-example/_static/file.png | Bin 392 -> 0 bytes
doc/rna-seq-example/_static/jquery.js | 154 ----
doc/rna-seq-example/_static/minus.png | Bin 199 -> 0 bytes
doc/rna-seq-example/_static/plus.png | Bin 199 -> 0 bytes
doc/rna-seq-example/_static/pygments.css | 62 --
.../_static/qualimap_logo_small.png | Bin 2922 -> 0 bytes
doc/rna-seq-example/_static/report.css | 50 --
doc/rna-seq-example/_static/searchtools.js | 560 --------------
doc/rna-seq-example/_static/underscore.js | 23 -
doc/rna-seq-example/_static/up-pressed.png | Bin 372 -> 0 bytes
doc/rna-seq-example/_static/up.png | Bin 363 -> 0 bytes
doc/rna-seq-example/_static/websupport.js | 808 ---------------------
92 files changed, 11660 deletions(-)
diff --git a/doc/count-data/_static/agogo.css b/doc/count-data/_static/agogo.css
deleted file mode 100644
index 3e96e34..0000000
--- a/doc/count-data/_static/agogo.css
+++ /dev/null
@@ -1,471 +0,0 @@
-/*
- * agogo.css_t
- * ~~~~~~~~~~~
- *
- * Sphinx stylesheet -- agogo theme.
- *
- * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
-
-* {
- margin: 0px;
- padding: 0px;
-}
-
-body {
- font-family: "Verdana", Arial, sans-serif;
- line-height: 1.4em;
- color: black;
- background-color: #eeeeec;
-}
-
-
-/* Page layout */
-
-div.header, div.content, div.footer {
- width: 70em;
- margin-left: auto;
- margin-right: auto;
-}
-
-div.header-wrapper {
- background: url(bgtop.png) top left repeat-x;
- border-bottom: 3px solid #2e3436;
-}
-
-
-/* Default body styles */
-a {
- color: #ce5c00;
-}
-
-div.bodywrapper a, div.footer a {
- text-decoration: underline;
-}
-
-.clearer {
- clear: both;
-}
-
-.left {
- float: left;
-}
-
-.right {
- float: right;
-}
-
-.line-block {
- display: block;
- margin-top: 1em;
- margin-bottom: 1em;
-}
-
-.line-block .line-block {
- margin-top: 0;
- margin-bottom: 0;
- margin-left: 1.5em;
-}
-
-h1, h2, h3, h4 {
- font-family: "Georgia", "Times New Roman", serif;
- font-weight: normal;
- color: #3465a4;
- margin-bottom: .8em;
-}
-
-h1 {
- color: #204a87;
-}
-
-h2 {
- padding-bottom: .5em;
- border-bottom: 1px solid #3465a4;
-}
-
-a.headerlink {
- visibility: hidden;
- color: #dddddd;
- padding-left: .3em;
-}
-
-h1:hover > a.headerlink,
-h2:hover > a.headerlink,
-h3:hover > a.headerlink,
-h4:hover > a.headerlink,
-h5:hover > a.headerlink,
-h6:hover > a.headerlink,
-dt:hover > a.headerlink {
- visibility: visible;
-}
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-img {
- border: 0;
-}
-
-div.admonition {
- margin-top: 10px;
- margin-bottom: 10px;
- padding: 2px 7px 1px 7px;
- border-left: 0.2em solid black;
-}
-
-p.admonition-title {
- margin: 0px 10px 5px 0px;
- font-weight: bold;
-}
-
-dt:target, .highlighted {
- background-color: #fbe54e;
-}
-
-/* Header */
-
-div.header {
- padding-top: 10px;
- padding-bottom: 10px;
-}
-
-div.header .headertitle {
- font-family: "Georgia", "Times New Roman", serif;
- font-weight: normal;
- font-size: 180%;
- letter-spacing: .08em;
- margin-bottom: .8em;
-}
-
-div.header .headertitle a {
- color: white;
-}
-
-div.header div.rel {
- margin-top: 1em;
-}
-
-div.header div.rel a {
- color: #fcaf3e;
- letter-spacing: .1em;
- text-transform: uppercase;
-}
-
-p.logo {
- float: right;
-}
-
-img.logo {
- border: 0;
-}
-
-
-/* Content */
-div.content-wrapper {
- background-color: white;
- padding-top: 20px;
- padding-bottom: 20px;
-}
-
-div.document {
- width: 50em;
- float: left;
-}
-
-div.body {
- padding-right: 2em;
- text-align: justify;
-}
-
-div.document h1 {
- line-height: 120%;
-}
-
-div.document ul {
- margin: 1.5em;
- list-style-type: square;
-}
-
-div.document dd {
- margin-left: 1.2em;
- margin-top: .4em;
- margin-bottom: 1em;
-}
-
-div.document .section {
- margin-top: 1.7em;
-}
-div.document .section:first-child {
- margin-top: 0px;
-}
-
-div.document div.highlight {
- padding: 3px;
- background-color: #eeeeec;
- border-top: 2px solid #dddddd;
- border-bottom: 2px solid #dddddd;
- margin-top: .8em;
- margin-bottom: .8em;
-}
-
-div.document h2 {
- margin-top: .7em;
-}
-
-div.document p {
- margin-bottom: .5em;
-}
-
-div.document li.toctree-l1 {
- margin-bottom: 1em;
-}
-
-div.document .descname {
- font-weight: bold;
-}
-
-div.document .docutils.literal {
- background-color: #eeeeec;
- padding: 1px;
-}
-
-div.document .docutils.xref.literal {
- background-color: transparent;
- padding: 0px;
-}
-
-div.document blockquote {
- margin: 1em;
-}
-
-div.document ol {
- margin: 1.5em;
-}
-
-
-/* Sidebar */
-
-div.sidebar {
- width: 20em;
- float: right;
- font-size: .9em;
-}
-
-div.sidebar a, div.header a {
- text-decoration: none;
-}
-
-div.sidebar a:hover, div.header a:hover {
- text-decoration: underline;
-}
-
-div.sidebar h3 {
- color: #2e3436;
- text-transform: uppercase;
- font-size: 130%;
- letter-spacing: .1em;
-}
-
-div.sidebar ul {
- list-style-type: none;
-}
-
-div.sidebar li.toctree-l1 a {
- display: block;
- padding: 1px;
- border: 1px solid #dddddd;
- background-color: #eeeeec;
- margin-bottom: .4em;
- padding-left: 3px;
- color: #2e3436;
-}
-
-div.sidebar li.toctree-l2 a {
- background-color: transparent;
- border: none;
- margin-left: 1em;
- border-bottom: 1px solid #dddddd;
-}
-
-div.sidebar li.toctree-l3 a {
- background-color: transparent;
- border: none;
- margin-left: 2em;
- border-bottom: 1px solid #dddddd;
-}
-
-div.sidebar li.toctree-l2:last-child a {
- border-bottom: none;
-}
-
-div.sidebar li.toctree-l1.current a {
- border-right: 5px solid #fcaf3e;
-}
-
-div.sidebar li.toctree-l1.current li.toctree-l2 a {
- border-right: none;
-}
-
-div.sidebar input[type="text"] {
- width: 170px;
-}
-
-div.sidebar input[type="submit"] {
- width: 30px;
-}
-
-
-/* Footer */
-
-div.footer-wrapper {
- background: url(bgfooter.png) top left repeat-x;
- border-top: 4px solid #babdb6;
- padding-top: 10px;
- padding-bottom: 10px;
- min-height: 80px;
-}
-
-div.footer, div.footer a {
- color: #888a85;
-}
-
-div.footer .right {
- text-align: right;
-}
-
-div.footer .left {
- text-transform: uppercase;
-}
-
-
-/* Styles copied from basic theme */
-
-img.align-left, .figure.align-left, object.align-left {
- clear: left;
- float: left;
- margin-right: 1em;
-}
-
-img.align-right, .figure.align-right, object.align-right {
- clear: right;
- float: right;
- margin-left: 1em;
-}
-
-img.align-center, .figure.align-center, object.align-center {
- display: block;
- margin-left: auto;
- margin-right: auto;
-}
-
-img.align-center-qualimap {
- display: block;
- margin-left: auto;
- margin-right: auto;
- width: 100%
-}
-
-.align-left {
- text-align: left;
-}
-
-.align-center {
- text-align: center;
-}
-
-.align-right {
- text-align: right;
-}
-
-/* -- search page ----------------------------------------------------------- */
-
-ul.search {
- margin: 10px 0 0 20px;
- padding: 0;
-}
-
-ul.search li {
- padding: 5px 0 5px 20px;
- background-image: url(file.png);
- background-repeat: no-repeat;
- background-position: 0 7px;
-}
-
-ul.search li a {
- font-weight: bold;
-}
-
-ul.search li div.context {
- color: #888;
- margin: 2px 0 0 30px;
- text-align: left;
-}
-
-ul.keywordmatches li.goodmatch a {
- font-weight: bold;
-}
-
-/* -- index page ------------------------------------------------------------ */
-
-table.contentstable {
- width: 90%;
-}
-
-table.contentstable p.biglink {
- line-height: 150%;
-}
-
-a.biglink {
- font-size: 1.3em;
-}
-
-span.linkdescr {
- font-style: italic;
- padding-top: 5px;
- font-size: 90%;
-}
-
-/* -- general index --------------------------------------------------------- */
-
-table.indextable td {
- text-align: left;
- vertical-align: top;
-}
-
-table.indextable dl, table.indextable dd {
- margin-top: 0;
- margin-bottom: 0;
-}
-
-table.indextable tr.pcap {
- height: 10px;
-}
-
-table.indextable tr.cap {
- margin-top: 10px;
- background-color: #f2f2f2;
-}
-
-img.toggler {
- margin-right: 3px;
- margin-top: 3px;
- cursor: pointer;
-}
-
-/* -- viewcode extension ---------------------------------------------------- */
-
-.viewcode-link {
- float: right;
-}
-
-.viewcode-back {
- float: right;
- font-family:: "Verdana", Arial, sans-serif;
-}
-
-div.viewcode-block:target {
- margin: -1px -3px;
- padding: 0 3px;
- background-color: #f4debf;
- border-top: 1px solid #ac9;
- border-bottom: 1px solid #ac9;
-}
diff --git a/doc/count-data/_static/ajax-loader.gif b/doc/count-data/_static/ajax-loader.gif
deleted file mode 100644
index 61faf8c..0000000
Binary files a/doc/count-data/_static/ajax-loader.gif and /dev/null differ
diff --git a/doc/count-data/_static/basic.css b/doc/count-data/_static/basic.css
deleted file mode 100644
index 1e02c5d..0000000
--- a/doc/count-data/_static/basic.css
+++ /dev/null
@@ -1,540 +0,0 @@
-/*
- * basic.css
- * ~~~~~~~~~
- *
- * Sphinx stylesheet -- basic theme.
- *
- * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
-
-/* -- main layout ----------------------------------------------------------- */
-
-div.clearer {
- clear: both;
-}
-
-/* -- relbar ---------------------------------------------------------------- */
-
-div.related {
- width: 100%;
- font-size: 90%;
-}
-
-div.related h3 {
- display: none;
-}
-
-div.related ul {
- margin: 0;
- padding: 0 0 0 10px;
- list-style: none;
-}
-
-div.related li {
- display: inline;
-}
-
-div.related li.right {
- float: right;
- margin-right: 5px;
-}
-
-/* -- sidebar --------------------------------------------------------------- */
-
-div.sphinxsidebarwrapper {
- padding: 10px 5px 0 10px;
-}
-
-div.sphinxsidebar {
- float: left;
- width: 0px;
- margin-left: -100%;
- font-size: 90%;
-}
-
-div.sphinxsidebar ul {
- list-style: none;
-}
-
-div.sphinxsidebar ul ul,
-div.sphinxsidebar ul.want-points {
- margin-left: 20px;
- list-style: square;
-}
-
-div.sphinxsidebar ul ul {
- margin-top: 0;
- margin-bottom: 0;
-}
-
-div.sphinxsidebar form {
- margin-top: 10px;
-}
-
-div.sphinxsidebar input {
- border: 1px solid #98dbcc;
- font-family: sans-serif;
- font-size: 1em;
-}
-
-div.sphinxsidebar #searchbox input[type="text"] {
- width: 170px;
-}
-
-div.sphinxsidebar #searchbox input[type="submit"] {
- width: 30px;
-}
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-img {
- border: 0;
-}
-
-/* -- search page ----------------------------------------------------------- */
-
-ul.search {
- margin: 10px 0 0 20px;
- padding: 0;
-}
-
-ul.search li {
- padding: 5px 0 5px 20px;
- background-image: url(file.png);
- background-repeat: no-repeat;
- background-position: 0 7px;
-}
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-ul.search li a {
- font-weight: bold;
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-ul.search li div.context {
- color: #888;
- margin: 2px 0 0 30px;
- text-align: left;
-}
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-ul.keywordmatches li.goodmatch a {
- font-weight: bold;
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-/* -- index page ------------------------------------------------------------ */
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-table.contentstable {
- width: 90%;
-}
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-a.biglink {
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-span.linkdescr {
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- padding-top: 5px;
- font-size: 90%;
-}
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-/* -- general index --------------------------------------------------------- */
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- visibility: visible;
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-div.body p.caption {
- text-align: inherit;
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-div.body td {
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-.field-list ul {
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-.first {
- margin-top: 0 !important;
-}
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-p.rubric {
- margin-top: 30px;
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-}
-
-img.align-left, .figure.align-left, object.align-left {
- clear: left;
- float: left;
- margin-right: 1em;
-}
-
-img.align-right, .figure.align-right, object.align-right {
- clear: right;
- float: right;
- margin-left: 1em;
-}
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-img.align-center, .figure.align-center, object.align-center {
- display: block;
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-.align-left {
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-
-.align-center {
- text-align: center;
-}
-
-.align-right {
- text-align: right;
-}
-
-/* -- sidebars -------------------------------------------------------------- */
-
-div.sidebar {
- margin: 0 0 0.5em 1em;
- border: 1px solid #ddb;
- padding: 7px 7px 0 7px;
- background-color: #ffe;
- width: 40%;
- float: right;
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-p.sidebar-title {
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-
-/* -- topics ---------------------------------------------------------------- */
-
-div.topic {
- border: 1px solid #ccc;
- padding: 7px 7px 0 7px;
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-}
-
-p.topic-title {
- font-size: 1.1em;
- font-weight: bold;
- margin-top: 10px;
-}
-
-/* -- admonitions ----------------------------------------------------------- */
-
-div.admonition {
- margin-top: 10px;
- margin-bottom: 10px;
- padding: 7px;
-}
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-div.admonition dt {
- font-weight: bold;
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-
-div.admonition dl {
- margin-bottom: 0;
-}
-
-p.admonition-title {
- margin: 0px 10px 5px 0px;
- font-weight: bold;
-}
-
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-/*
- * searchtools.js_t
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- *
- * Sphinx JavaScript utilties for the full-text search.
- *
- * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
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- * helper function to return a node containing the
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- * of stemmed words, hlwords is the list of normal, unstemmed
- * words. the first one is used to find the occurance, the
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-
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- iciti: 'ic',
- ical: 'ic',
- ful: '',
- ness: ''
- };
-
- var c = "[^aeiou]"; // consonant
- var v = "[aeiouy]"; // vowel
- var C = c + "[^aeiouy]*"; // consonant sequence
- var V = v + "[aeiou]*"; // vowel sequence
-
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- var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1
- var s_v = "^(" + C + ")?" + v; // vowel in stem
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- this.stemWord = function (w) {
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-
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- re2 = /^(.+?)([^s])s$/;
-
- if (re.test(w))
- w = w.replace(re,"$1$2");
- else if (re2.test(w))
- w = w.replace(re2,"$1$2");
-
- // Step 1b
- re = /^(.+?)eed$/;
- re2 = /^(.+?)(ed|ing)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- re = new RegExp(mgr0);
- if (re.test(fp[1])) {
- re = /.$/;
- w = w.replace(re,"");
- }
- }
- else if (re2.test(w)) {
- var fp = re2.exec(w);
- stem = fp[1];
- re2 = new RegExp(s_v);
- if (re2.test(stem)) {
- w = stem;
- re2 = /(at|bl|iz)$/;
- re3 = new RegExp("([^aeiouylsz])\\1$");
- re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
- if (re2.test(w))
- w = w + "e";
- else if (re3.test(w)) {
- re = /.$/;
- w = w.replace(re,"");
- }
- else if (re4.test(w))
- w = w + "e";
- }
- }
-
- // Step 1c
- re = /^(.+?)y$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(s_v);
- if (re.test(stem))
- w = stem + "i";
- }
-
- // Step 2
- re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- suffix = fp[2];
- re = new RegExp(mgr0);
- if (re.test(stem))
- w = stem + step2list[suffix];
- }
-
- // Step 3
- re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- suffix = fp[2];
- re = new RegExp(mgr0);
- if (re.test(stem))
- w = stem + step3list[suffix];
- }
-
- // Step 4
- re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
- re2 = /^(.+?)(s|t)(ion)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(mgr1);
- if (re.test(stem))
- w = stem;
- }
- else if (re2.test(w)) {
- var fp = re2.exec(w);
- stem = fp[1] + fp[2];
- re2 = new RegExp(mgr1);
- if (re2.test(stem))
- w = stem;
- }
-
- // Step 5
- re = /^(.+?)e$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(mgr1);
- re2 = new RegExp(meq1);
- re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
- if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
- w = stem;
- }
- re = /ll$/;
- re2 = new RegExp(mgr1);
- if (re.test(w) && re2.test(w)) {
- re = /.$/;
- w = w.replace(re,"");
- }
-
- // and turn initial Y back to y
- if (firstch == "y")
- w = firstch.toLowerCase() + w.substr(1);
- return w;
- }
-}
-
-
-/**
- * Search Module
- */
-var Search = {
-
- _index : null,
- _queued_query : null,
- _pulse_status : -1,
-
- init : function() {
- var params = $.getQueryParameters();
- if (params.q) {
- var query = params.q[0];
- $('input[name="q"]')[0].value = query;
- this.performSearch(query);
- }
- },
-
- loadIndex : function(url) {
- $.ajax({type: "GET", url: url, data: null, success: null,
- dataType: "script", cache: true});
- },
-
- setIndex : function(index) {
- var q;
- this._index = index;
- if ((q = this._queued_query) !== null) {
- this._queued_query = null;
- Search.query(q);
- }
- },
-
- hasIndex : function() {
- return this._index !== null;
- },
-
- deferQuery : function(query) {
- this._queued_query = query;
- },
-
- stopPulse : function() {
- this._pulse_status = 0;
- },
-
- startPulse : function() {
- if (this._pulse_status >= 0)
- return;
- function pulse() {
- Search._pulse_status = (Search._pulse_status + 1) % 4;
- var dotString = '';
- for (var i = 0; i < Search._pulse_status; i++)
- dotString += '.';
- Search.dots.text(dotString);
- if (Search._pulse_status > -1)
- window.setTimeout(pulse, 500);
- };
- pulse();
- },
-
- /**
- * perform a search for something
- */
- performSearch : function(query) {
- // create the required interface elements
- this.out = $('#search-results');
- this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
- this.dots = $('<span></span>').appendTo(this.title);
- this.status = $('<p style="display: none"></p>').appendTo(this.out);
- this.output = $('<ul class="search"/>').appendTo(this.out);
-
- $('#search-progress').text(_('Preparing search...'));
- this.startPulse();
-
- // index already loaded, the browser was quick!
- if (this.hasIndex())
- this.query(query);
- else
- this.deferQuery(query);
- },
-
- query : function(query) {
- var stopwords = ["and","then","into","it","as","are","in","if","for","no","there","their","was","is","be","to","that","but","they","not","such","with","by","a","on","these","of","will","this","near","the","or","at"];
-
- // Stem the searchterms and add them to the correct list
- var stemmer = new Stemmer();
- var searchterms = [];
- var excluded = [];
- var hlterms = [];
- var tmp = query.split(/\s+/);
- var objectterms = [];
- for (var i = 0; i < tmp.length; i++) {
- if (tmp[i] != "") {
- objectterms.push(tmp[i].toLowerCase());
- }
-
- if ($u.indexOf(stopwords, tmp[i]) != -1 || tmp[i].match(/^\d+$/) ||
- tmp[i] == "") {
- // skip this "word"
- continue;
- }
- // stem the word
- var word = stemmer.stemWord(tmp[i]).toLowerCase();
- // select the correct list
- if (word[0] == '-') {
- var toAppend = excluded;
- word = word.substr(1);
- }
- else {
- var toAppend = searchterms;
- hlterms.push(tmp[i].toLowerCase());
- }
- // only add if not already in the list
- if (!$.contains(toAppend, word))
- toAppend.push(word);
- };
- var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
-
- // console.debug('SEARCH: searching for:');
- // console.info('required: ', searchterms);
- // console.info('excluded: ', excluded);
-
- // prepare search
- var filenames = this._index.filenames;
- var titles = this._index.titles;
- var terms = this._index.terms;
- var fileMap = {};
- var files = null;
- // different result priorities
- var importantResults = [];
- var objectResults = [];
- var regularResults = [];
- var unimportantResults = [];
- $('#search-progress').empty();
-
- // lookup as object
- for (var i = 0; i < objectterms.length; i++) {
- var others = [].concat(objectterms.slice(0,i),
- objectterms.slice(i+1, objectterms.length))
- var results = this.performObjectSearch(objectterms[i], others);
- // Assume first word is most likely to be the object,
- // other words more likely to be in description.
- // Therefore put matches for earlier words first.
- // (Results are eventually used in reverse order).
- objectResults = results[0].concat(objectResults);
- importantResults = results[1].concat(importantResults);
- unimportantResults = results[2].concat(unimportantResults);
- }
-
- // perform the search on the required terms
- for (var i = 0; i < searchterms.length; i++) {
- var word = searchterms[i];
- // no match but word was a required one
- if ((files = terms[word]) == null)
- break;
- if (files.length == undefined) {
- files = [files];
- }
- // create the mapping
- for (var j = 0; j < files.length; j++) {
- var file = files[j];
- if (file in fileMap)
- fileMap[file].push(word);
- else
- fileMap[file] = [word];
- }
- }
-
- // now check if the files don't contain excluded terms
- for (var file in fileMap) {
- var valid = true;
-
- // check if all requirements are matched
- if (fileMap[file].length != searchterms.length)
- continue;
-
- // ensure that none of the excluded terms is in the
- // search result.
- for (var i = 0; i < excluded.length; i++) {
- if (terms[excluded[i]] == file ||
- $.contains(terms[excluded[i]] || [], file)) {
- valid = false;
- break;
- }
- }
-
- // if we have still a valid result we can add it
- // to the result list
- if (valid)
- regularResults.push([filenames[file], titles[file], '', null]);
- }
-
- // delete unused variables in order to not waste
- // memory until list is retrieved completely
- delete filenames, titles, terms;
-
- // now sort the regular results descending by title
- regularResults.sort(function(a, b) {
- var left = a[1].toLowerCase();
- var right = b[1].toLowerCase();
- return (left > right) ? -1 : ((left < right) ? 1 : 0);
- });
-
- // combine all results
- var results = unimportantResults.concat(regularResults)
- .concat(objectResults).concat(importantResults);
-
- // print the results
- var resultCount = results.length;
- function displayNextItem() {
- // results left, load the summary and display it
- if (results.length) {
- var item = results.pop();
- var listItem = $('<li style="display:none"></li>');
- if (DOCUMENTATION_OPTIONS.FILE_SUFFIX == '') {
- // dirhtml builder
- var dirname = item[0] + '/';
- if (dirname.match(/\/index\/$/)) {
- dirname = dirname.substring(0, dirname.length-6);
- } else if (dirname == 'index/') {
- dirname = '';
- }
- listItem.append($('<a/>').attr('href',
- DOCUMENTATION_OPTIONS.URL_ROOT + dirname +
- highlightstring + item[2]).html(item[1]));
- } else {
- // normal html builders
- listItem.append($('<a/>').attr('href',
- item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
- highlightstring + item[2]).html(item[1]));
- }
- if (item[3]) {
- listItem.append($('<span> (' + item[3] + ')</span>'));
- Search.output.append(listItem);
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
- $.get(DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' +
- item[0] + '.txt', function(data) {
- if (data != '') {
- listItem.append($.makeSearchSummary(data, searchterms, hlterms));
- Search.output.append(listItem);
- }
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- }, "text");
- } else {
- // no source available, just display title
- Search.output.append(listItem);
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- }
- }
- // search finished, update title and status message
- else {
- Search.stopPulse();
- Search.title.text(_('Search Results'));
- if (!resultCount)
- Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
- else
- Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
- Search.status.fadeIn(500);
- }
- }
- displayNextItem();
- },
-
- performObjectSearch : function(object, otherterms) {
- var filenames = this._index.filenames;
- var objects = this._index.objects;
- var objnames = this._index.objnames;
- var titles = this._index.titles;
-
- var importantResults = [];
- var objectResults = [];
- var unimportantResults = [];
-
- for (var prefix in objects) {
- for (var name in objects[prefix]) {
- var fullname = (prefix ? prefix + '.' : '') + name;
- if (fullname.toLowerCase().indexOf(object) > -1) {
- var match = objects[prefix][name];
- var objname = objnames[match[1]][2];
- var title = titles[match[0]];
- // If more than one term searched for, we require other words to be
- // found in the name/title/description
- if (otherterms.length > 0) {
- var haystack = (prefix + ' ' + name + ' ' +
- objname + ' ' + title).toLowerCase();
- var allfound = true;
- for (var i = 0; i < otherterms.length; i++) {
- if (haystack.indexOf(otherterms[i]) == -1) {
- allfound = false;
- break;
- }
- }
- if (!allfound) {
- continue;
- }
- }
- var descr = objname + _(', in ') + title;
- anchor = match[3];
- if (anchor == '')
- anchor = fullname;
- else if (anchor == '-')
- anchor = objnames[match[1]][1] + '-' + fullname;
- result = [filenames[match[0]], fullname, '#'+anchor, descr];
- switch (match[2]) {
- case 1: objectResults.push(result); break;
- case 0: importantResults.push(result); break;
- case 2: unimportantResults.push(result); break;
- }
- }
- }
- }
-
- // sort results descending
- objectResults.sort(function(a, b) {
- return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
- });
-
- importantResults.sort(function(a, b) {
- return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
- });
-
- unimportantResults.sort(function(a, b) {
- return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
- });
-
- return [importantResults, objectResults, unimportantResults]
- }
-}
-
-$(document).ready(function() {
- Search.init();
-});
\ No newline at end of file
diff --git a/doc/count-data/_static/underscore.js b/doc/count-data/_static/underscore.js
deleted file mode 100644
index 5d89914..0000000
--- a/doc/count-data/_static/underscore.js
+++ /dev/null
@@ -1,23 +0,0 @@
-// Underscore.js 0.5.5
-// (c) 2009 Jeremy Ashkenas, DocumentCloud Inc.
-// Underscore is freely distributable under the terms of the MIT license.
-// Portions of Underscore are inspired by or borrowed from Prototype.js,
-// Oliver Steele's Functional, and John Resig's Micro-Templating.
-// For all details and documentation:
-// http://documentcloud.github.com/underscore/
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-a.test&&a.exec&&(a.ignoreCase||a.ignoreCase===false))};b.isNaN=function(a){return b.isNumber(a)&&isNaN(a)};b.isNull=function(a){return a===null};b.isUndefined=function(a){return typeof a=="undefined"};b.noConflict=function(){j._=n;return this};b.identity=function(a){return a};b.breakLoop=function(){throw m;};var s=0;b.uniqueId=function(a){var c=s++;return a?a+c:c};b.template=function(a,c){a=new Function("obj","var p=[],print=function(){p.push.apply(p,arguments);};with(obj){p.push('"+a.re [...]
-" ").replace(/'(?=[^%]*%>)/g,"\t").split("'").join("\\'").split("\t").join("'").replace(/<%=(.+?)%>/g,"',$1,'").split("<%").join("');").split("%>").join("p.push('")+"');}return p.join('');");return c?a(c):a};b.forEach=b.each;b.foldl=b.inject=b.reduce;b.foldr=b.reduceRight;b.filter=b.select;b.every=b.all;b.some=b.any;b.head=b.first;b.tail=b.rest;b.methods=b.functions;var l=function(a,c){return c?b(a).chain():a};b.each(b.functions(b),function(a){var c=b[a];i.prototype[a]=function(){var d=b [...]
-o.call(d,this._wrapped);return l(c.apply(b,d),this._chain)}});b.each(["pop","push","reverse","shift","sort","splice","unshift"],function(a){var c=Array.prototype[a];i.prototype[a]=function(){c.apply(this._wrapped,arguments);return l(this._wrapped,this._chain)}});b.each(["concat","join","slice"],function(a){var c=Array.prototype[a];i.prototype[a]=function(){return l(c.apply(this._wrapped,arguments),this._chain)}});i.prototype.chain=function(){this._chain=true;return this};i.prototype.valu [...]
diff --git a/doc/count-data/_static/up-pressed.png b/doc/count-data/_static/up-pressed.png
deleted file mode 100644
index 8bd587a..0000000
Binary files a/doc/count-data/_static/up-pressed.png and /dev/null differ
diff --git a/doc/count-data/_static/up.png b/doc/count-data/_static/up.png
deleted file mode 100644
index b946256..0000000
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diff --git a/doc/count-data/_static/websupport.js b/doc/count-data/_static/websupport.js
deleted file mode 100644
index e9bd1b8..0000000
--- a/doc/count-data/_static/websupport.js
+++ /dev/null
@@ -1,808 +0,0 @@
-/*
- * websupport.js
- * ~~~~~~~~~~~~~
- *
- * sphinx.websupport utilties for all documentation.
- *
- * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
-
-(function($) {
- $.fn.autogrow = function() {
- return this.each(function() {
- var textarea = this;
-
- $.fn.autogrow.resize(textarea);
-
- $(textarea)
- .focus(function() {
- textarea.interval = setInterval(function() {
- $.fn.autogrow.resize(textarea);
- }, 500);
- })
- .blur(function() {
- clearInterval(textarea.interval);
- });
- });
- };
-
- $.fn.autogrow.resize = function(textarea) {
- var lineHeight = parseInt($(textarea).css('line-height'), 10);
- var lines = textarea.value.split('\n');
- var columns = textarea.cols;
- var lineCount = 0;
- $.each(lines, function() {
- lineCount += Math.ceil(this.length / columns) || 1;
- });
- var height = lineHeight * (lineCount + 1);
- $(textarea).css('height', height);
- };
-})(jQuery);
-
-(function($) {
- var comp, by;
-
- function init() {
- initEvents();
- initComparator();
- }
-
- function initEvents() {
- $('a.comment-close').live("click", function(event) {
- event.preventDefault();
- hide($(this).attr('id').substring(2));
- });
- $('a.vote').live("click", function(event) {
- event.preventDefault();
- handleVote($(this));
- });
- $('a.reply').live("click", function(event) {
- event.preventDefault();
- openReply($(this).attr('id').substring(2));
- });
- $('a.close-reply').live("click", function(event) {
- event.preventDefault();
- closeReply($(this).attr('id').substring(2));
- });
- $('a.sort-option').live("click", function(event) {
- event.preventDefault();
- handleReSort($(this));
- });
- $('a.show-proposal').live("click", function(event) {
- event.preventDefault();
- showProposal($(this).attr('id').substring(2));
- });
- $('a.hide-proposal').live("click", function(event) {
- event.preventDefault();
- hideProposal($(this).attr('id').substring(2));
- });
- $('a.show-propose-change').live("click", function(event) {
- event.preventDefault();
- showProposeChange($(this).attr('id').substring(2));
- });
- $('a.hide-propose-change').live("click", function(event) {
- event.preventDefault();
- hideProposeChange($(this).attr('id').substring(2));
- });
- $('a.accept-comment').live("click", function(event) {
- event.preventDefault();
- acceptComment($(this).attr('id').substring(2));
- });
- $('a.delete-comment').live("click", function(event) {
- event.preventDefault();
- deleteComment($(this).attr('id').substring(2));
- });
- $('a.comment-markup').live("click", function(event) {
- event.preventDefault();
- toggleCommentMarkupBox($(this).attr('id').substring(2));
- });
- }
-
- /**
- * Set comp, which is a comparator function used for sorting and
- * inserting comments into the list.
- */
- function setComparator() {
- // If the first three letters are "asc", sort in ascending order
- // and remove the prefix.
- if (by.substring(0,3) == 'asc') {
- var i = by.substring(3);
- comp = function(a, b) { return a[i] - b[i]; };
- } else {
- // Otherwise sort in descending order.
- comp = function(a, b) { return b[by] - a[by]; };
- }
-
- // Reset link styles and format the selected sort option.
- $('a.sel').attr('href', '#').removeClass('sel');
- $('a.by' + by).removeAttr('href').addClass('sel');
- }
-
- /**
- * Create a comp function. If the user has preferences stored in
- * the sortBy cookie, use those, otherwise use the default.
- */
- function initComparator() {
- by = 'rating'; // Default to sort by rating.
- // If the sortBy cookie is set, use that instead.
- if (document.cookie.length > 0) {
- var start = document.cookie.indexOf('sortBy=');
- if (start != -1) {
- start = start + 7;
- var end = document.cookie.indexOf(";", start);
- if (end == -1) {
- end = document.cookie.length;
- by = unescape(document.cookie.substring(start, end));
- }
- }
- }
- setComparator();
- }
-
- /**
- * Show a comment div.
- */
- function show(id) {
- $('#ao' + id).hide();
- $('#ah' + id).show();
- var context = $.extend({id: id}, opts);
- var popup = $(renderTemplate(popupTemplate, context)).hide();
- popup.find('textarea[name="proposal"]').hide();
- popup.find('a.by' + by).addClass('sel');
- var form = popup.find('#cf' + id);
- form.submit(function(event) {
- event.preventDefault();
- addComment(form);
- });
- $('#s' + id).after(popup);
- popup.slideDown('fast', function() {
- getComments(id);
- });
- }
-
- /**
- * Hide a comment div.
- */
- function hide(id) {
- $('#ah' + id).hide();
- $('#ao' + id).show();
- var div = $('#sc' + id);
- div.slideUp('fast', function() {
- div.remove();
- });
- }
-
- /**
- * Perform an ajax request to get comments for a node
- * and insert the comments into the comments tree.
- */
- function getComments(id) {
- $.ajax({
- type: 'GET',
- url: opts.getCommentsURL,
- data: {node: id},
- success: function(data, textStatus, request) {
- var ul = $('#cl' + id);
- var speed = 100;
- $('#cf' + id)
- .find('textarea[name="proposal"]')
- .data('source', data.source);
-
- if (data.comments.length === 0) {
- ul.html('<li>No comments yet.</li>');
- ul.data('empty', true);
- } else {
- // If there are comments, sort them and put them in the list.
- var comments = sortComments(data.comments);
- speed = data.comments.length * 100;
- appendComments(comments, ul);
- ul.data('empty', false);
- }
- $('#cn' + id).slideUp(speed + 200);
- ul.slideDown(speed);
- },
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem retrieving the comments.');
- },
- dataType: 'json'
- });
- }
-
- /**
- * Add a comment via ajax and insert the comment into the comment tree.
- */
- function addComment(form) {
- var node_id = form.find('input[name="node"]').val();
- var parent_id = form.find('input[name="parent"]').val();
- var text = form.find('textarea[name="comment"]').val();
- var proposal = form.find('textarea[name="proposal"]').val();
-
- if (text == '') {
- showError('Please enter a comment.');
- return;
- }
-
- // Disable the form that is being submitted.
- form.find('textarea,input').attr('disabled', 'disabled');
-
- // Send the comment to the server.
- $.ajax({
- type: "POST",
- url: opts.addCommentURL,
- dataType: 'json',
- data: {
- node: node_id,
- parent: parent_id,
- text: text,
- proposal: proposal
- },
- success: function(data, textStatus, error) {
- // Reset the form.
- if (node_id) {
- hideProposeChange(node_id);
- }
- form.find('textarea')
- .val('')
- .add(form.find('input'))
- .removeAttr('disabled');
- var ul = $('#cl' + (node_id || parent_id));
- if (ul.data('empty')) {
- $(ul).empty();
- ul.data('empty', false);
- }
- insertComment(data.comment);
- var ao = $('#ao' + node_id);
- ao.find('img').attr({'src': opts.commentBrightImage});
- if (node_id) {
- // if this was a "root" comment, remove the commenting box
- // (the user can get it back by reopening the comment popup)
- $('#ca' + node_id).slideUp();
- }
- },
- error: function(request, textStatus, error) {
- form.find('textarea,input').removeAttr('disabled');
- showError('Oops, there was a problem adding the comment.');
- }
- });
- }
-
- /**
- * Recursively append comments to the main comment list and children
- * lists, creating the comment tree.
- */
- function appendComments(comments, ul) {
- $.each(comments, function() {
- var div = createCommentDiv(this);
- ul.append($(document.createElement('li')).html(div));
- appendComments(this.children, div.find('ul.comment-children'));
- // To avoid stagnating data, don't store the comments children in data.
- this.children = null;
- div.data('comment', this);
- });
- }
-
- /**
- * After adding a new comment, it must be inserted in the correct
- * location in the comment tree.
- */
- function insertComment(comment) {
- var div = createCommentDiv(comment);
-
- // To avoid stagnating data, don't store the comments children in data.
- comment.children = null;
- div.data('comment', comment);
-
- var ul = $('#cl' + (comment.node || comment.parent));
- var siblings = getChildren(ul);
-
- var li = $(document.createElement('li'));
- li.hide();
-
- // Determine where in the parents children list to insert this comment.
- for(i=0; i < siblings.length; i++) {
- if (comp(comment, siblings[i]) <= 0) {
- $('#cd' + siblings[i].id)
- .parent()
- .before(li.html(div));
- li.slideDown('fast');
- return;
- }
- }
-
- // If we get here, this comment rates lower than all the others,
- // or it is the only comment in the list.
- ul.append(li.html(div));
- li.slideDown('fast');
- }
-
- function acceptComment(id) {
- $.ajax({
- type: 'POST',
- url: opts.acceptCommentURL,
- data: {id: id},
- success: function(data, textStatus, request) {
- $('#cm' + id).fadeOut('fast');
- $('#cd' + id).removeClass('moderate');
- },
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem accepting the comment.');
- }
- });
- }
-
- function deleteComment(id) {
- $.ajax({
- type: 'POST',
- url: opts.deleteCommentURL,
- data: {id: id},
- success: function(data, textStatus, request) {
- var div = $('#cd' + id);
- if (data == 'delete') {
- // Moderator mode: remove the comment and all children immediately
- div.slideUp('fast', function() {
- div.remove();
- });
- return;
- }
- // User mode: only mark the comment as deleted
- div
- .find('span.user-id:first')
- .text('[deleted]').end()
- .find('div.comment-text:first')
- .text('[deleted]').end()
- .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id +
- ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id)
- .remove();
- var comment = div.data('comment');
- comment.username = '[deleted]';
- comment.text = '[deleted]';
- div.data('comment', comment);
- },
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem deleting the comment.');
- }
- });
- }
-
- function showProposal(id) {
- $('#sp' + id).hide();
- $('#hp' + id).show();
- $('#pr' + id).slideDown('fast');
- }
-
- function hideProposal(id) {
- $('#hp' + id).hide();
- $('#sp' + id).show();
- $('#pr' + id).slideUp('fast');
- }
-
- function showProposeChange(id) {
- $('#pc' + id).hide();
- $('#hc' + id).show();
- var textarea = $('#pt' + id);
- textarea.val(textarea.data('source'));
- $.fn.autogrow.resize(textarea[0]);
- textarea.slideDown('fast');
- }
-
- function hideProposeChange(id) {
- $('#hc' + id).hide();
- $('#pc' + id).show();
- var textarea = $('#pt' + id);
- textarea.val('').removeAttr('disabled');
- textarea.slideUp('fast');
- }
-
- function toggleCommentMarkupBox(id) {
- $('#mb' + id).toggle();
- }
-
- /** Handle when the user clicks on a sort by link. */
- function handleReSort(link) {
- var classes = link.attr('class').split(/\s+/);
- for (var i=0; i<classes.length; i++) {
- if (classes[i] != 'sort-option') {
- by = classes[i].substring(2);
- }
- }
- setComparator();
- // Save/update the sortBy cookie.
- var expiration = new Date();
- expiration.setDate(expiration.getDate() + 365);
- document.cookie= 'sortBy=' + escape(by) +
- ';expires=' + expiration.toUTCString();
- $('ul.comment-ul').each(function(index, ul) {
- var comments = getChildren($(ul), true);
- comments = sortComments(comments);
- appendComments(comments, $(ul).empty());
- });
- }
-
- /**
- * Function to process a vote when a user clicks an arrow.
- */
- function handleVote(link) {
- if (!opts.voting) {
- showError("You'll need to login to vote.");
- return;
- }
-
- var id = link.attr('id');
- if (!id) {
- // Didn't click on one of the voting arrows.
- return;
- }
- // If it is an unvote, the new vote value is 0,
- // Otherwise it's 1 for an upvote, or -1 for a downvote.
- var value = 0;
- if (id.charAt(1) != 'u') {
- value = id.charAt(0) == 'u' ? 1 : -1;
- }
- // The data to be sent to the server.
- var d = {
- comment_id: id.substring(2),
- value: value
- };
-
- // Swap the vote and unvote links.
- link.hide();
- $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id)
- .show();
-
- // The div the comment is displayed in.
- var div = $('div#cd' + d.comment_id);
- var data = div.data('comment');
-
- // If this is not an unvote, and the other vote arrow has
- // already been pressed, unpress it.
- if ((d.value !== 0) && (data.vote === d.value * -1)) {
- $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide();
- $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show();
- }
-
- // Update the comments rating in the local data.
- data.rating += (data.vote === 0) ? d.value : (d.value - data.vote);
- data.vote = d.value;
- div.data('comment', data);
-
- // Change the rating text.
- div.find('.rating:first')
- .text(data.rating + ' point' + (data.rating == 1 ? '' : 's'));
-
- // Send the vote information to the server.
- $.ajax({
- type: "POST",
- url: opts.processVoteURL,
- data: d,
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem casting that vote.');
- }
- });
- }
-
- /**
- * Open a reply form used to reply to an existing comment.
- */
- function openReply(id) {
- // Swap out the reply link for the hide link
- $('#rl' + id).hide();
- $('#cr' + id).show();
-
- // Add the reply li to the children ul.
- var div = $(renderTemplate(replyTemplate, {id: id})).hide();
- $('#cl' + id)
- .prepend(div)
- // Setup the submit handler for the reply form.
- .find('#rf' + id)
- .submit(function(event) {
- event.preventDefault();
- addComment($('#rf' + id));
- closeReply(id);
- })
- .find('input[type=button]')
- .click(function() {
- closeReply(id);
- });
- div.slideDown('fast', function() {
- $('#rf' + id).find('textarea').focus();
- });
- }
-
- /**
- * Close the reply form opened with openReply.
- */
- function closeReply(id) {
- // Remove the reply div from the DOM.
- $('#rd' + id).slideUp('fast', function() {
- $(this).remove();
- });
-
- // Swap out the hide link for the reply link
- $('#cr' + id).hide();
- $('#rl' + id).show();
- }
-
- /**
- * Recursively sort a tree of comments using the comp comparator.
- */
- function sortComments(comments) {
- comments.sort(comp);
- $.each(comments, function() {
- this.children = sortComments(this.children);
- });
- return comments;
- }
-
- /**
- * Get the children comments from a ul. If recursive is true,
- * recursively include childrens' children.
- */
- function getChildren(ul, recursive) {
- var children = [];
- ul.children().children("[id^='cd']")
- .each(function() {
- var comment = $(this).data('comment');
- if (recursive)
- comment.children = getChildren($(this).find('#cl' + comment.id), true);
- children.push(comment);
- });
- return children;
- }
-
- /** Create a div to display a comment in. */
- function createCommentDiv(comment) {
- if (!comment.displayed && !opts.moderator) {
- return $('<div class="moderate">Thank you! Your comment will show up '
- + 'once it is has been approved by a moderator.</div>');
- }
- // Prettify the comment rating.
- comment.pretty_rating = comment.rating + ' point' +
- (comment.rating == 1 ? '' : 's');
- // Make a class (for displaying not yet moderated comments differently)
- comment.css_class = comment.displayed ? '' : ' moderate';
- // Create a div for this comment.
- var context = $.extend({}, opts, comment);
- var div = $(renderTemplate(commentTemplate, context));
-
- // If the user has voted on this comment, highlight the correct arrow.
- if (comment.vote) {
- var direction = (comment.vote == 1) ? 'u' : 'd';
- div.find('#' + direction + 'v' + comment.id).hide();
- div.find('#' + direction + 'u' + comment.id).show();
- }
-
- if (opts.moderator || comment.text != '[deleted]') {
- div.find('a.reply').show();
- if (comment.proposal_diff)
- div.find('#sp' + comment.id).show();
- if (opts.moderator && !comment.displayed)
- div.find('#cm' + comment.id).show();
- if (opts.moderator || (opts.username == comment.username))
- div.find('#dc' + comment.id).show();
- }
- return div;
- }
-
- /**
- * A simple template renderer. Placeholders such as <%id%> are replaced
- * by context['id'] with items being escaped. Placeholders such as <#id#>
- * are not escaped.
- */
- function renderTemplate(template, context) {
- var esc = $(document.createElement('div'));
-
- function handle(ph, escape) {
- var cur = context;
- $.each(ph.split('.'), function() {
- cur = cur[this];
- });
- return escape ? esc.text(cur || "").html() : cur;
- }
-
- return template.replace(/<([%#])([\w\.]*)\1>/g, function() {
- return handle(arguments[2], arguments[1] == '%' ? true : false);
- });
- }
-
- /** Flash an error message briefly. */
- function showError(message) {
- $(document.createElement('div')).attr({'class': 'popup-error'})
- .append($(document.createElement('div'))
- .attr({'class': 'error-message'}).text(message))
- .appendTo('body')
- .fadeIn("slow")
- .delay(2000)
- .fadeOut("slow");
- }
-
- /** Add a link the user uses to open the comments popup. */
- $.fn.comment = function() {
- return this.each(function() {
- var id = $(this).attr('id').substring(1);
- var count = COMMENT_METADATA[id];
- var title = count + ' comment' + (count == 1 ? '' : 's');
- var image = count > 0 ? opts.commentBrightImage : opts.commentImage;
- var addcls = count == 0 ? ' nocomment' : '';
- $(this)
- .append(
- $(document.createElement('a')).attr({
- href: '#',
- 'class': 'sphinx-comment-open' + addcls,
- id: 'ao' + id
- })
- .append($(document.createElement('img')).attr({
- src: image,
- alt: 'comment',
- title: title
- }))
- .click(function(event) {
- event.preventDefault();
- show($(this).attr('id').substring(2));
- })
- )
- .append(
- $(document.createElement('a')).attr({
- href: '#',
- 'class': 'sphinx-comment-close hidden',
- id: 'ah' + id
- })
- .append($(document.createElement('img')).attr({
- src: opts.closeCommentImage,
- alt: 'close',
- title: 'close'
- }))
- .click(function(event) {
- event.preventDefault();
- hide($(this).attr('id').substring(2));
- })
- );
- });
- };
-
- var opts = {
- processVoteURL: '/_process_vote',
- addCommentURL: '/_add_comment',
- getCommentsURL: '/_get_comments',
- acceptCommentURL: '/_accept_comment',
- deleteCommentURL: '/_delete_comment',
- commentImage: '/static/_static/comment.png',
- closeCommentImage: '/static/_static/comment-close.png',
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diff --git a/doc/plasmodium/_static/agogo.css b/doc/plasmodium/_static/agogo.css
deleted file mode 100644
index 3e96e34..0000000
--- a/doc/plasmodium/_static/agogo.css
+++ /dev/null
@@ -1,471 +0,0 @@
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diff --git a/doc/plasmodium/_static/ajax-loader.gif b/doc/plasmodium/_static/ajax-loader.gif
deleted file mode 100644
index 61faf8c..0000000
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diff --git a/doc/plasmodium/_static/basic.css b/doc/plasmodium/_static/basic.css
deleted file mode 100644
index 1e02c5d..0000000
--- a/doc/plasmodium/_static/basic.css
+++ /dev/null
@@ -1,540 +0,0 @@
-/*
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-/*
- * searchtools.js_t
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- * Sphinx JavaScript utilties for the full-text search.
- *
- * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
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- * words. the first one is used to find the occurance, the
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- alize: 'al',
- iciti: 'ic',
- ical: 'ic',
- ful: '',
- ness: ''
- };
-
- var c = "[^aeiou]"; // consonant
- var v = "[aeiouy]"; // vowel
- var C = c + "[^aeiouy]*"; // consonant sequence
- var V = v + "[aeiou]*"; // vowel sequence
-
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- var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1
- var s_v = "^(" + C + ")?" + v; // vowel in stem
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- this.stemWord = function (w) {
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- }
- else if (re2.test(w)) {
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- stem = fp[1];
- re2 = new RegExp(s_v);
- if (re2.test(stem)) {
- w = stem;
- re2 = /(at|bl|iz)$/;
- re3 = new RegExp("([^aeiouylsz])\\1$");
- re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
- if (re2.test(w))
- w = w + "e";
- else if (re3.test(w)) {
- re = /.$/;
- w = w.replace(re,"");
- }
- else if (re4.test(w))
- w = w + "e";
- }
- }
-
- // Step 1c
- re = /^(.+?)y$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(s_v);
- if (re.test(stem))
- w = stem + "i";
- }
-
- // Step 2
- re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- suffix = fp[2];
- re = new RegExp(mgr0);
- if (re.test(stem))
- w = stem + step2list[suffix];
- }
-
- // Step 3
- re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- suffix = fp[2];
- re = new RegExp(mgr0);
- if (re.test(stem))
- w = stem + step3list[suffix];
- }
-
- // Step 4
- re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
- re2 = /^(.+?)(s|t)(ion)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(mgr1);
- if (re.test(stem))
- w = stem;
- }
- else if (re2.test(w)) {
- var fp = re2.exec(w);
- stem = fp[1] + fp[2];
- re2 = new RegExp(mgr1);
- if (re2.test(stem))
- w = stem;
- }
-
- // Step 5
- re = /^(.+?)e$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(mgr1);
- re2 = new RegExp(meq1);
- re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
- if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
- w = stem;
- }
- re = /ll$/;
- re2 = new RegExp(mgr1);
- if (re.test(w) && re2.test(w)) {
- re = /.$/;
- w = w.replace(re,"");
- }
-
- // and turn initial Y back to y
- if (firstch == "y")
- w = firstch.toLowerCase() + w.substr(1);
- return w;
- }
-}
-
-
-/**
- * Search Module
- */
-var Search = {
-
- _index : null,
- _queued_query : null,
- _pulse_status : -1,
-
- init : function() {
- var params = $.getQueryParameters();
- if (params.q) {
- var query = params.q[0];
- $('input[name="q"]')[0].value = query;
- this.performSearch(query);
- }
- },
-
- loadIndex : function(url) {
- $.ajax({type: "GET", url: url, data: null, success: null,
- dataType: "script", cache: true});
- },
-
- setIndex : function(index) {
- var q;
- this._index = index;
- if ((q = this._queued_query) !== null) {
- this._queued_query = null;
- Search.query(q);
- }
- },
-
- hasIndex : function() {
- return this._index !== null;
- },
-
- deferQuery : function(query) {
- this._queued_query = query;
- },
-
- stopPulse : function() {
- this._pulse_status = 0;
- },
-
- startPulse : function() {
- if (this._pulse_status >= 0)
- return;
- function pulse() {
- Search._pulse_status = (Search._pulse_status + 1) % 4;
- var dotString = '';
- for (var i = 0; i < Search._pulse_status; i++)
- dotString += '.';
- Search.dots.text(dotString);
- if (Search._pulse_status > -1)
- window.setTimeout(pulse, 500);
- };
- pulse();
- },
-
- /**
- * perform a search for something
- */
- performSearch : function(query) {
- // create the required interface elements
- this.out = $('#search-results');
- this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
- this.dots = $('<span></span>').appendTo(this.title);
- this.status = $('<p style="display: none"></p>').appendTo(this.out);
- this.output = $('<ul class="search"/>').appendTo(this.out);
-
- $('#search-progress').text(_('Preparing search...'));
- this.startPulse();
-
- // index already loaded, the browser was quick!
- if (this.hasIndex())
- this.query(query);
- else
- this.deferQuery(query);
- },
-
- query : function(query) {
- var stopwords = ["and","then","into","it","as","are","in","if","for","no","there","their","was","is","be","to","that","but","they","not","such","with","by","a","on","these","of","will","this","near","the","or","at"];
-
- // Stem the searchterms and add them to the correct list
- var stemmer = new Stemmer();
- var searchterms = [];
- var excluded = [];
- var hlterms = [];
- var tmp = query.split(/\s+/);
- var objectterms = [];
- for (var i = 0; i < tmp.length; i++) {
- if (tmp[i] != "") {
- objectterms.push(tmp[i].toLowerCase());
- }
-
- if ($u.indexOf(stopwords, tmp[i]) != -1 || tmp[i].match(/^\d+$/) ||
- tmp[i] == "") {
- // skip this "word"
- continue;
- }
- // stem the word
- var word = stemmer.stemWord(tmp[i]).toLowerCase();
- // select the correct list
- if (word[0] == '-') {
- var toAppend = excluded;
- word = word.substr(1);
- }
- else {
- var toAppend = searchterms;
- hlterms.push(tmp[i].toLowerCase());
- }
- // only add if not already in the list
- if (!$.contains(toAppend, word))
- toAppend.push(word);
- };
- var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
-
- // console.debug('SEARCH: searching for:');
- // console.info('required: ', searchterms);
- // console.info('excluded: ', excluded);
-
- // prepare search
- var filenames = this._index.filenames;
- var titles = this._index.titles;
- var terms = this._index.terms;
- var fileMap = {};
- var files = null;
- // different result priorities
- var importantResults = [];
- var objectResults = [];
- var regularResults = [];
- var unimportantResults = [];
- $('#search-progress').empty();
-
- // lookup as object
- for (var i = 0; i < objectterms.length; i++) {
- var others = [].concat(objectterms.slice(0,i),
- objectterms.slice(i+1, objectterms.length))
- var results = this.performObjectSearch(objectterms[i], others);
- // Assume first word is most likely to be the object,
- // other words more likely to be in description.
- // Therefore put matches for earlier words first.
- // (Results are eventually used in reverse order).
- objectResults = results[0].concat(objectResults);
- importantResults = results[1].concat(importantResults);
- unimportantResults = results[2].concat(unimportantResults);
- }
-
- // perform the search on the required terms
- for (var i = 0; i < searchterms.length; i++) {
- var word = searchterms[i];
- // no match but word was a required one
- if ((files = terms[word]) == null)
- break;
- if (files.length == undefined) {
- files = [files];
- }
- // create the mapping
- for (var j = 0; j < files.length; j++) {
- var file = files[j];
- if (file in fileMap)
- fileMap[file].push(word);
- else
- fileMap[file] = [word];
- }
- }
-
- // now check if the files don't contain excluded terms
- for (var file in fileMap) {
- var valid = true;
-
- // check if all requirements are matched
- if (fileMap[file].length != searchterms.length)
- continue;
-
- // ensure that none of the excluded terms is in the
- // search result.
- for (var i = 0; i < excluded.length; i++) {
- if (terms[excluded[i]] == file ||
- $.contains(terms[excluded[i]] || [], file)) {
- valid = false;
- break;
- }
- }
-
- // if we have still a valid result we can add it
- // to the result list
- if (valid)
- regularResults.push([filenames[file], titles[file], '', null]);
- }
-
- // delete unused variables in order to not waste
- // memory until list is retrieved completely
- delete filenames, titles, terms;
-
- // now sort the regular results descending by title
- regularResults.sort(function(a, b) {
- var left = a[1].toLowerCase();
- var right = b[1].toLowerCase();
- return (left > right) ? -1 : ((left < right) ? 1 : 0);
- });
-
- // combine all results
- var results = unimportantResults.concat(regularResults)
- .concat(objectResults).concat(importantResults);
-
- // print the results
- var resultCount = results.length;
- function displayNextItem() {
- // results left, load the summary and display it
- if (results.length) {
- var item = results.pop();
- var listItem = $('<li style="display:none"></li>');
- if (DOCUMENTATION_OPTIONS.FILE_SUFFIX == '') {
- // dirhtml builder
- var dirname = item[0] + '/';
- if (dirname.match(/\/index\/$/)) {
- dirname = dirname.substring(0, dirname.length-6);
- } else if (dirname == 'index/') {
- dirname = '';
- }
- listItem.append($('<a/>').attr('href',
- DOCUMENTATION_OPTIONS.URL_ROOT + dirname +
- highlightstring + item[2]).html(item[1]));
- } else {
- // normal html builders
- listItem.append($('<a/>').attr('href',
- item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
- highlightstring + item[2]).html(item[1]));
- }
- if (item[3]) {
- listItem.append($('<span> (' + item[3] + ')</span>'));
- Search.output.append(listItem);
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
- $.get(DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' +
- item[0] + '.txt', function(data) {
- if (data != '') {
- listItem.append($.makeSearchSummary(data, searchterms, hlterms));
- Search.output.append(listItem);
- }
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- }, "text");
- } else {
- // no source available, just display title
- Search.output.append(listItem);
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- }
- }
- // search finished, update title and status message
- else {
- Search.stopPulse();
- Search.title.text(_('Search Results'));
- if (!resultCount)
- Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
- else
- Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
- Search.status.fadeIn(500);
- }
- }
- displayNextItem();
- },
-
- performObjectSearch : function(object, otherterms) {
- var filenames = this._index.filenames;
- var objects = this._index.objects;
- var objnames = this._index.objnames;
- var titles = this._index.titles;
-
- var importantResults = [];
- var objectResults = [];
- var unimportantResults = [];
-
- for (var prefix in objects) {
- for (var name in objects[prefix]) {
- var fullname = (prefix ? prefix + '.' : '') + name;
- if (fullname.toLowerCase().indexOf(object) > -1) {
- var match = objects[prefix][name];
- var objname = objnames[match[1]][2];
- var title = titles[match[0]];
- // If more than one term searched for, we require other words to be
- // found in the name/title/description
- if (otherterms.length > 0) {
- var haystack = (prefix + ' ' + name + ' ' +
- objname + ' ' + title).toLowerCase();
- var allfound = true;
- for (var i = 0; i < otherterms.length; i++) {
- if (haystack.indexOf(otherterms[i]) == -1) {
- allfound = false;
- break;
- }
- }
- if (!allfound) {
- continue;
- }
- }
- var descr = objname + _(', in ') + title;
- anchor = match[3];
- if (anchor == '')
- anchor = fullname;
- else if (anchor == '-')
- anchor = objnames[match[1]][1] + '-' + fullname;
- result = [filenames[match[0]], fullname, '#'+anchor, descr];
- switch (match[2]) {
- case 1: objectResults.push(result); break;
- case 0: importantResults.push(result); break;
- case 2: unimportantResults.push(result); break;
- }
- }
- }
- }
-
- // sort results descending
- objectResults.sort(function(a, b) {
- return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
- });
-
- importantResults.sort(function(a, b) {
- return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
- });
-
- unimportantResults.sort(function(a, b) {
- return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
- });
-
- return [importantResults, objectResults, unimportantResults]
- }
-}
-
-$(document).ready(function() {
- Search.init();
-});
\ No newline at end of file
diff --git a/doc/plasmodium/_static/underscore.js b/doc/plasmodium/_static/underscore.js
deleted file mode 100644
index 5d89914..0000000
--- a/doc/plasmodium/_static/underscore.js
+++ /dev/null
@@ -1,23 +0,0 @@
-// Underscore.js 0.5.5
-// (c) 2009 Jeremy Ashkenas, DocumentCloud Inc.
-// Underscore is freely distributable under the terms of the MIT license.
-// Portions of Underscore are inspired by or borrowed from Prototype.js,
-// Oliver Steele's Functional, and John Resig's Micro-Templating.
-// For all details and documentation:
-// http://documentcloud.github.com/underscore/
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-" ").replace(/'(?=[^%]*%>)/g,"\t").split("'").join("\\'").split("\t").join("'").replace(/<%=(.+?)%>/g,"',$1,'").split("<%").join("');").split("%>").join("p.push('")+"');}return p.join('');");return c?a(c):a};b.forEach=b.each;b.foldl=b.inject=b.reduce;b.foldr=b.reduceRight;b.filter=b.select;b.every=b.all;b.some=b.any;b.head=b.first;b.tail=b.rest;b.methods=b.functions;var l=function(a,c){return c?b(a).chain():a};b.each(b.functions(b),function(a){var c=b[a];i.prototype[a]=function(){var d=b [...]
-o.call(d,this._wrapped);return l(c.apply(b,d),this._chain)}});b.each(["pop","push","reverse","shift","sort","splice","unshift"],function(a){var c=Array.prototype[a];i.prototype[a]=function(){c.apply(this._wrapped,arguments);return l(this._wrapped,this._chain)}});b.each(["concat","join","slice"],function(a){var c=Array.prototype[a];i.prototype[a]=function(){return l(c.apply(this._wrapped,arguments),this._chain)}});i.prototype.chain=function(){this._chain=true;return this};i.prototype.valu [...]
diff --git a/doc/plasmodium/_static/up-pressed.png b/doc/plasmodium/_static/up-pressed.png
deleted file mode 100644
index 8bd587a..0000000
Binary files a/doc/plasmodium/_static/up-pressed.png and /dev/null differ
diff --git a/doc/plasmodium/_static/up.png b/doc/plasmodium/_static/up.png
deleted file mode 100644
index b946256..0000000
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diff --git a/doc/plasmodium/_static/websupport.js b/doc/plasmodium/_static/websupport.js
deleted file mode 100644
index e9bd1b8..0000000
--- a/doc/plasmodium/_static/websupport.js
+++ /dev/null
@@ -1,808 +0,0 @@
-/*
- * websupport.js
- * ~~~~~~~~~~~~~
- *
- * sphinx.websupport utilties for all documentation.
- *
- * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
-
-(function($) {
- $.fn.autogrow = function() {
- return this.each(function() {
- var textarea = this;
-
- $.fn.autogrow.resize(textarea);
-
- $(textarea)
- .focus(function() {
- textarea.interval = setInterval(function() {
- $.fn.autogrow.resize(textarea);
- }, 500);
- })
- .blur(function() {
- clearInterval(textarea.interval);
- });
- });
- };
-
- $.fn.autogrow.resize = function(textarea) {
- var lineHeight = parseInt($(textarea).css('line-height'), 10);
- var lines = textarea.value.split('\n');
- var columns = textarea.cols;
- var lineCount = 0;
- $.each(lines, function() {
- lineCount += Math.ceil(this.length / columns) || 1;
- });
- var height = lineHeight * (lineCount + 1);
- $(textarea).css('height', height);
- };
-})(jQuery);
-
-(function($) {
- var comp, by;
-
- function init() {
- initEvents();
- initComparator();
- }
-
- function initEvents() {
- $('a.comment-close').live("click", function(event) {
- event.preventDefault();
- hide($(this).attr('id').substring(2));
- });
- $('a.vote').live("click", function(event) {
- event.preventDefault();
- handleVote($(this));
- });
- $('a.reply').live("click", function(event) {
- event.preventDefault();
- openReply($(this).attr('id').substring(2));
- });
- $('a.close-reply').live("click", function(event) {
- event.preventDefault();
- closeReply($(this).attr('id').substring(2));
- });
- $('a.sort-option').live("click", function(event) {
- event.preventDefault();
- handleReSort($(this));
- });
- $('a.show-proposal').live("click", function(event) {
- event.preventDefault();
- showProposal($(this).attr('id').substring(2));
- });
- $('a.hide-proposal').live("click", function(event) {
- event.preventDefault();
- hideProposal($(this).attr('id').substring(2));
- });
- $('a.show-propose-change').live("click", function(event) {
- event.preventDefault();
- showProposeChange($(this).attr('id').substring(2));
- });
- $('a.hide-propose-change').live("click", function(event) {
- event.preventDefault();
- hideProposeChange($(this).attr('id').substring(2));
- });
- $('a.accept-comment').live("click", function(event) {
- event.preventDefault();
- acceptComment($(this).attr('id').substring(2));
- });
- $('a.delete-comment').live("click", function(event) {
- event.preventDefault();
- deleteComment($(this).attr('id').substring(2));
- });
- $('a.comment-markup').live("click", function(event) {
- event.preventDefault();
- toggleCommentMarkupBox($(this).attr('id').substring(2));
- });
- }
-
- /**
- * Set comp, which is a comparator function used for sorting and
- * inserting comments into the list.
- */
- function setComparator() {
- // If the first three letters are "asc", sort in ascending order
- // and remove the prefix.
- if (by.substring(0,3) == 'asc') {
- var i = by.substring(3);
- comp = function(a, b) { return a[i] - b[i]; };
- } else {
- // Otherwise sort in descending order.
- comp = function(a, b) { return b[by] - a[by]; };
- }
-
- // Reset link styles and format the selected sort option.
- $('a.sel').attr('href', '#').removeClass('sel');
- $('a.by' + by).removeAttr('href').addClass('sel');
- }
-
- /**
- * Create a comp function. If the user has preferences stored in
- * the sortBy cookie, use those, otherwise use the default.
- */
- function initComparator() {
- by = 'rating'; // Default to sort by rating.
- // If the sortBy cookie is set, use that instead.
- if (document.cookie.length > 0) {
- var start = document.cookie.indexOf('sortBy=');
- if (start != -1) {
- start = start + 7;
- var end = document.cookie.indexOf(";", start);
- if (end == -1) {
- end = document.cookie.length;
- by = unescape(document.cookie.substring(start, end));
- }
- }
- }
- setComparator();
- }
-
- /**
- * Show a comment div.
- */
- function show(id) {
- $('#ao' + id).hide();
- $('#ah' + id).show();
- var context = $.extend({id: id}, opts);
- var popup = $(renderTemplate(popupTemplate, context)).hide();
- popup.find('textarea[name="proposal"]').hide();
- popup.find('a.by' + by).addClass('sel');
- var form = popup.find('#cf' + id);
- form.submit(function(event) {
- event.preventDefault();
- addComment(form);
- });
- $('#s' + id).after(popup);
- popup.slideDown('fast', function() {
- getComments(id);
- });
- }
-
- /**
- * Hide a comment div.
- */
- function hide(id) {
- $('#ah' + id).hide();
- $('#ao' + id).show();
- var div = $('#sc' + id);
- div.slideUp('fast', function() {
- div.remove();
- });
- }
-
- /**
- * Perform an ajax request to get comments for a node
- * and insert the comments into the comments tree.
- */
- function getComments(id) {
- $.ajax({
- type: 'GET',
- url: opts.getCommentsURL,
- data: {node: id},
- success: function(data, textStatus, request) {
- var ul = $('#cl' + id);
- var speed = 100;
- $('#cf' + id)
- .find('textarea[name="proposal"]')
- .data('source', data.source);
-
- if (data.comments.length === 0) {
- ul.html('<li>No comments yet.</li>');
- ul.data('empty', true);
- } else {
- // If there are comments, sort them and put them in the list.
- var comments = sortComments(data.comments);
- speed = data.comments.length * 100;
- appendComments(comments, ul);
- ul.data('empty', false);
- }
- $('#cn' + id).slideUp(speed + 200);
- ul.slideDown(speed);
- },
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem retrieving the comments.');
- },
- dataType: 'json'
- });
- }
-
- /**
- * Add a comment via ajax and insert the comment into the comment tree.
- */
- function addComment(form) {
- var node_id = form.find('input[name="node"]').val();
- var parent_id = form.find('input[name="parent"]').val();
- var text = form.find('textarea[name="comment"]').val();
- var proposal = form.find('textarea[name="proposal"]').val();
-
- if (text == '') {
- showError('Please enter a comment.');
- return;
- }
-
- // Disable the form that is being submitted.
- form.find('textarea,input').attr('disabled', 'disabled');
-
- // Send the comment to the server.
- $.ajax({
- type: "POST",
- url: opts.addCommentURL,
- dataType: 'json',
- data: {
- node: node_id,
- parent: parent_id,
- text: text,
- proposal: proposal
- },
- success: function(data, textStatus, error) {
- // Reset the form.
- if (node_id) {
- hideProposeChange(node_id);
- }
- form.find('textarea')
- .val('')
- .add(form.find('input'))
- .removeAttr('disabled');
- var ul = $('#cl' + (node_id || parent_id));
- if (ul.data('empty')) {
- $(ul).empty();
- ul.data('empty', false);
- }
- insertComment(data.comment);
- var ao = $('#ao' + node_id);
- ao.find('img').attr({'src': opts.commentBrightImage});
- if (node_id) {
- // if this was a "root" comment, remove the commenting box
- // (the user can get it back by reopening the comment popup)
- $('#ca' + node_id).slideUp();
- }
- },
- error: function(request, textStatus, error) {
- form.find('textarea,input').removeAttr('disabled');
- showError('Oops, there was a problem adding the comment.');
- }
- });
- }
-
- /**
- * Recursively append comments to the main comment list and children
- * lists, creating the comment tree.
- */
- function appendComments(comments, ul) {
- $.each(comments, function() {
- var div = createCommentDiv(this);
- ul.append($(document.createElement('li')).html(div));
- appendComments(this.children, div.find('ul.comment-children'));
- // To avoid stagnating data, don't store the comments children in data.
- this.children = null;
- div.data('comment', this);
- });
- }
-
- /**
- * After adding a new comment, it must be inserted in the correct
- * location in the comment tree.
- */
- function insertComment(comment) {
- var div = createCommentDiv(comment);
-
- // To avoid stagnating data, don't store the comments children in data.
- comment.children = null;
- div.data('comment', comment);
-
- var ul = $('#cl' + (comment.node || comment.parent));
- var siblings = getChildren(ul);
-
- var li = $(document.createElement('li'));
- li.hide();
-
- // Determine where in the parents children list to insert this comment.
- for(i=0; i < siblings.length; i++) {
- if (comp(comment, siblings[i]) <= 0) {
- $('#cd' + siblings[i].id)
- .parent()
- .before(li.html(div));
- li.slideDown('fast');
- return;
- }
- }
-
- // If we get here, this comment rates lower than all the others,
- // or it is the only comment in the list.
- ul.append(li.html(div));
- li.slideDown('fast');
- }
-
- function acceptComment(id) {
- $.ajax({
- type: 'POST',
- url: opts.acceptCommentURL,
- data: {id: id},
- success: function(data, textStatus, request) {
- $('#cm' + id).fadeOut('fast');
- $('#cd' + id).removeClass('moderate');
- },
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem accepting the comment.');
- }
- });
- }
-
- function deleteComment(id) {
- $.ajax({
- type: 'POST',
- url: opts.deleteCommentURL,
- data: {id: id},
- success: function(data, textStatus, request) {
- var div = $('#cd' + id);
- if (data == 'delete') {
- // Moderator mode: remove the comment and all children immediately
- div.slideUp('fast', function() {
- div.remove();
- });
- return;
- }
- // User mode: only mark the comment as deleted
- div
- .find('span.user-id:first')
- .text('[deleted]').end()
- .find('div.comment-text:first')
- .text('[deleted]').end()
- .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id +
- ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id)
- .remove();
- var comment = div.data('comment');
- comment.username = '[deleted]';
- comment.text = '[deleted]';
- div.data('comment', comment);
- },
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem deleting the comment.');
- }
- });
- }
-
- function showProposal(id) {
- $('#sp' + id).hide();
- $('#hp' + id).show();
- $('#pr' + id).slideDown('fast');
- }
-
- function hideProposal(id) {
- $('#hp' + id).hide();
- $('#sp' + id).show();
- $('#pr' + id).slideUp('fast');
- }
-
- function showProposeChange(id) {
- $('#pc' + id).hide();
- $('#hc' + id).show();
- var textarea = $('#pt' + id);
- textarea.val(textarea.data('source'));
- $.fn.autogrow.resize(textarea[0]);
- textarea.slideDown('fast');
- }
-
- function hideProposeChange(id) {
- $('#hc' + id).hide();
- $('#pc' + id).show();
- var textarea = $('#pt' + id);
- textarea.val('').removeAttr('disabled');
- textarea.slideUp('fast');
- }
-
- function toggleCommentMarkupBox(id) {
- $('#mb' + id).toggle();
- }
-
- /** Handle when the user clicks on a sort by link. */
- function handleReSort(link) {
- var classes = link.attr('class').split(/\s+/);
- for (var i=0; i<classes.length; i++) {
- if (classes[i] != 'sort-option') {
- by = classes[i].substring(2);
- }
- }
- setComparator();
- // Save/update the sortBy cookie.
- var expiration = new Date();
- expiration.setDate(expiration.getDate() + 365);
- document.cookie= 'sortBy=' + escape(by) +
- ';expires=' + expiration.toUTCString();
- $('ul.comment-ul').each(function(index, ul) {
- var comments = getChildren($(ul), true);
- comments = sortComments(comments);
- appendComments(comments, $(ul).empty());
- });
- }
-
- /**
- * Function to process a vote when a user clicks an arrow.
- */
- function handleVote(link) {
- if (!opts.voting) {
- showError("You'll need to login to vote.");
- return;
- }
-
- var id = link.attr('id');
- if (!id) {
- // Didn't click on one of the voting arrows.
- return;
- }
- // If it is an unvote, the new vote value is 0,
- // Otherwise it's 1 for an upvote, or -1 for a downvote.
- var value = 0;
- if (id.charAt(1) != 'u') {
- value = id.charAt(0) == 'u' ? 1 : -1;
- }
- // The data to be sent to the server.
- var d = {
- comment_id: id.substring(2),
- value: value
- };
-
- // Swap the vote and unvote links.
- link.hide();
- $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id)
- .show();
-
- // The div the comment is displayed in.
- var div = $('div#cd' + d.comment_id);
- var data = div.data('comment');
-
- // If this is not an unvote, and the other vote arrow has
- // already been pressed, unpress it.
- if ((d.value !== 0) && (data.vote === d.value * -1)) {
- $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide();
- $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show();
- }
-
- // Update the comments rating in the local data.
- data.rating += (data.vote === 0) ? d.value : (d.value - data.vote);
- data.vote = d.value;
- div.data('comment', data);
-
- // Change the rating text.
- div.find('.rating:first')
- .text(data.rating + ' point' + (data.rating == 1 ? '' : 's'));
-
- // Send the vote information to the server.
- $.ajax({
- type: "POST",
- url: opts.processVoteURL,
- data: d,
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem casting that vote.');
- }
- });
- }
-
- /**
- * Open a reply form used to reply to an existing comment.
- */
- function openReply(id) {
- // Swap out the reply link for the hide link
- $('#rl' + id).hide();
- $('#cr' + id).show();
-
- // Add the reply li to the children ul.
- var div = $(renderTemplate(replyTemplate, {id: id})).hide();
- $('#cl' + id)
- .prepend(div)
- // Setup the submit handler for the reply form.
- .find('#rf' + id)
- .submit(function(event) {
- event.preventDefault();
- addComment($('#rf' + id));
- closeReply(id);
- })
- .find('input[type=button]')
- .click(function() {
- closeReply(id);
- });
- div.slideDown('fast', function() {
- $('#rf' + id).find('textarea').focus();
- });
- }
-
- /**
- * Close the reply form opened with openReply.
- */
- function closeReply(id) {
- // Remove the reply div from the DOM.
- $('#rd' + id).slideUp('fast', function() {
- $(this).remove();
- });
-
- // Swap out the hide link for the reply link
- $('#cr' + id).hide();
- $('#rl' + id).show();
- }
-
- /**
- * Recursively sort a tree of comments using the comp comparator.
- */
- function sortComments(comments) {
- comments.sort(comp);
- $.each(comments, function() {
- this.children = sortComments(this.children);
- });
- return comments;
- }
-
- /**
- * Get the children comments from a ul. If recursive is true,
- * recursively include childrens' children.
- */
- function getChildren(ul, recursive) {
- var children = [];
- ul.children().children("[id^='cd']")
- .each(function() {
- var comment = $(this).data('comment');
- if (recursive)
- comment.children = getChildren($(this).find('#cl' + comment.id), true);
- children.push(comment);
- });
- return children;
- }
-
- /** Create a div to display a comment in. */
- function createCommentDiv(comment) {
- if (!comment.displayed && !opts.moderator) {
- return $('<div class="moderate">Thank you! Your comment will show up '
- + 'once it is has been approved by a moderator.</div>');
- }
- // Prettify the comment rating.
- comment.pretty_rating = comment.rating + ' point' +
- (comment.rating == 1 ? '' : 's');
- // Make a class (for displaying not yet moderated comments differently)
- comment.css_class = comment.displayed ? '' : ' moderate';
- // Create a div for this comment.
- var context = $.extend({}, opts, comment);
- var div = $(renderTemplate(commentTemplate, context));
-
- // If the user has voted on this comment, highlight the correct arrow.
- if (comment.vote) {
- var direction = (comment.vote == 1) ? 'u' : 'd';
- div.find('#' + direction + 'v' + comment.id).hide();
- div.find('#' + direction + 'u' + comment.id).show();
- }
-
- if (opts.moderator || comment.text != '[deleted]') {
- div.find('a.reply').show();
- if (comment.proposal_diff)
- div.find('#sp' + comment.id).show();
- if (opts.moderator && !comment.displayed)
- div.find('#cm' + comment.id).show();
- if (opts.moderator || (opts.username == comment.username))
- div.find('#dc' + comment.id).show();
- }
- return div;
- }
-
- /**
- * A simple template renderer. Placeholders such as <%id%> are replaced
- * by context['id'] with items being escaped. Placeholders such as <#id#>
- * are not escaped.
- */
- function renderTemplate(template, context) {
- var esc = $(document.createElement('div'));
-
- function handle(ph, escape) {
- var cur = context;
- $.each(ph.split('.'), function() {
- cur = cur[this];
- });
- return escape ? esc.text(cur || "").html() : cur;
- }
-
- return template.replace(/<([%#])([\w\.]*)\1>/g, function() {
- return handle(arguments[2], arguments[1] == '%' ? true : false);
- });
- }
-
- /** Flash an error message briefly. */
- function showError(message) {
- $(document.createElement('div')).attr({'class': 'popup-error'})
- .append($(document.createElement('div'))
- .attr({'class': 'error-message'}).text(message))
- .appendTo('body')
- .fadeIn("slow")
- .delay(2000)
- .fadeOut("slow");
- }
-
- /** Add a link the user uses to open the comments popup. */
- $.fn.comment = function() {
- return this.each(function() {
- var id = $(this).attr('id').substring(1);
- var count = COMMENT_METADATA[id];
- var title = count + ' comment' + (count == 1 ? '' : 's');
- var image = count > 0 ? opts.commentBrightImage : opts.commentImage;
- var addcls = count == 0 ? ' nocomment' : '';
- $(this)
- .append(
- $(document.createElement('a')).attr({
- href: '#',
- 'class': 'sphinx-comment-open' + addcls,
- id: 'ao' + id
- })
- .append($(document.createElement('img')).attr({
- src: image,
- alt: 'comment',
- title: title
- }))
- .click(function(event) {
- event.preventDefault();
- show($(this).attr('id').substring(2));
- })
- )
- .append(
- $(document.createElement('a')).attr({
- href: '#',
- 'class': 'sphinx-comment-close hidden',
- id: 'ah' + id
- })
- .append($(document.createElement('img')).attr({
- src: opts.closeCommentImage,
- alt: 'close',
- title: 'close'
- }))
- .click(function(event) {
- event.preventDefault();
- hide($(this).attr('id').substring(2));
- })
- );
- });
- };
-
- var opts = {
- processVoteURL: '/_process_vote',
- addCommentURL: '/_add_comment',
- getCommentsURL: '/_get_comments',
- acceptCommentURL: '/_accept_comment',
- deleteCommentURL: '/_delete_comment',
- commentImage: '/static/_static/comment.png',
- closeCommentImage: '/static/_static/comment-close.png',
- loadingImage: '/static/_static/ajax-loader.gif',
- commentBrightImage: '/static/_static/comment-bright.png',
- upArrow: '/static/_static/up.png',
- downArrow: '/static/_static/down.png',
- upArrowPressed: '/static/_static/up-pressed.png',
- downArrowPressed: '/static/_static/down-pressed.png',
- voting: false,
- moderator: false
- };
-
- if (typeof COMMENT_OPTIONS != "undefined") {
- opts = jQuery.extend(opts, COMMENT_OPTIONS);
- }
-
- var popupTemplate = '\
- <div class="sphinx-comments" id="sc<%id%>">\
- <p class="sort-options">\
- Sort by:\
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- var fp = re2.exec(w);
- stem = fp[1];
- re2 = new RegExp(s_v);
- if (re2.test(stem)) {
- w = stem;
- re2 = /(at|bl|iz)$/;
- re3 = new RegExp("([^aeiouylsz])\\1$");
- re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
- if (re2.test(w))
- w = w + "e";
- else if (re3.test(w)) {
- re = /.$/;
- w = w.replace(re,"");
- }
- else if (re4.test(w))
- w = w + "e";
- }
- }
-
- // Step 1c
- re = /^(.+?)y$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(s_v);
- if (re.test(stem))
- w = stem + "i";
- }
-
- // Step 2
- re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- suffix = fp[2];
- re = new RegExp(mgr0);
- if (re.test(stem))
- w = stem + step2list[suffix];
- }
-
- // Step 3
- re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- suffix = fp[2];
- re = new RegExp(mgr0);
- if (re.test(stem))
- w = stem + step3list[suffix];
- }
-
- // Step 4
- re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
- re2 = /^(.+?)(s|t)(ion)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(mgr1);
- if (re.test(stem))
- w = stem;
- }
- else if (re2.test(w)) {
- var fp = re2.exec(w);
- stem = fp[1] + fp[2];
- re2 = new RegExp(mgr1);
- if (re2.test(stem))
- w = stem;
- }
-
- // Step 5
- re = /^(.+?)e$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(mgr1);
- re2 = new RegExp(meq1);
- re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
- if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
- w = stem;
- }
- re = /ll$/;
- re2 = new RegExp(mgr1);
- if (re.test(w) && re2.test(w)) {
- re = /.$/;
- w = w.replace(re,"");
- }
-
- // and turn initial Y back to y
- if (firstch == "y")
- w = firstch.toLowerCase() + w.substr(1);
- return w;
- }
-}
-
-
-/**
- * Search Module
- */
-var Search = {
-
- _index : null,
- _queued_query : null,
- _pulse_status : -1,
-
- init : function() {
- var params = $.getQueryParameters();
- if (params.q) {
- var query = params.q[0];
- $('input[name="q"]')[0].value = query;
- this.performSearch(query);
- }
- },
-
- loadIndex : function(url) {
- $.ajax({type: "GET", url: url, data: null, success: null,
- dataType: "script", cache: true});
- },
-
- setIndex : function(index) {
- var q;
- this._index = index;
- if ((q = this._queued_query) !== null) {
- this._queued_query = null;
- Search.query(q);
- }
- },
-
- hasIndex : function() {
- return this._index !== null;
- },
-
- deferQuery : function(query) {
- this._queued_query = query;
- },
-
- stopPulse : function() {
- this._pulse_status = 0;
- },
-
- startPulse : function() {
- if (this._pulse_status >= 0)
- return;
- function pulse() {
- Search._pulse_status = (Search._pulse_status + 1) % 4;
- var dotString = '';
- for (var i = 0; i < Search._pulse_status; i++)
- dotString += '.';
- Search.dots.text(dotString);
- if (Search._pulse_status > -1)
- window.setTimeout(pulse, 500);
- };
- pulse();
- },
-
- /**
- * perform a search for something
- */
- performSearch : function(query) {
- // create the required interface elements
- this.out = $('#search-results');
- this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
- this.dots = $('<span></span>').appendTo(this.title);
- this.status = $('<p style="display: none"></p>').appendTo(this.out);
- this.output = $('<ul class="search"/>').appendTo(this.out);
-
- $('#search-progress').text(_('Preparing search...'));
- this.startPulse();
-
- // index already loaded, the browser was quick!
- if (this.hasIndex())
- this.query(query);
- else
- this.deferQuery(query);
- },
-
- query : function(query) {
- var stopwords = ["and","then","into","it","as","are","in","if","for","no","there","their","was","is","be","to","that","but","they","not","such","with","by","a","on","these","of","will","this","near","the","or","at"];
-
- // Stem the searchterms and add them to the correct list
- var stemmer = new Stemmer();
- var searchterms = [];
- var excluded = [];
- var hlterms = [];
- var tmp = query.split(/\s+/);
- var objectterms = [];
- for (var i = 0; i < tmp.length; i++) {
- if (tmp[i] != "") {
- objectterms.push(tmp[i].toLowerCase());
- }
-
- if ($u.indexOf(stopwords, tmp[i]) != -1 || tmp[i].match(/^\d+$/) ||
- tmp[i] == "") {
- // skip this "word"
- continue;
- }
- // stem the word
- var word = stemmer.stemWord(tmp[i]).toLowerCase();
- // select the correct list
- if (word[0] == '-') {
- var toAppend = excluded;
- word = word.substr(1);
- }
- else {
- var toAppend = searchterms;
- hlterms.push(tmp[i].toLowerCase());
- }
- // only add if not already in the list
- if (!$.contains(toAppend, word))
- toAppend.push(word);
- };
- var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
-
- // console.debug('SEARCH: searching for:');
- // console.info('required: ', searchterms);
- // console.info('excluded: ', excluded);
-
- // prepare search
- var filenames = this._index.filenames;
- var titles = this._index.titles;
- var terms = this._index.terms;
- var fileMap = {};
- var files = null;
- // different result priorities
- var importantResults = [];
- var objectResults = [];
- var regularResults = [];
- var unimportantResults = [];
- $('#search-progress').empty();
-
- // lookup as object
- for (var i = 0; i < objectterms.length; i++) {
- var others = [].concat(objectterms.slice(0,i),
- objectterms.slice(i+1, objectterms.length))
- var results = this.performObjectSearch(objectterms[i], others);
- // Assume first word is most likely to be the object,
- // other words more likely to be in description.
- // Therefore put matches for earlier words first.
- // (Results are eventually used in reverse order).
- objectResults = results[0].concat(objectResults);
- importantResults = results[1].concat(importantResults);
- unimportantResults = results[2].concat(unimportantResults);
- }
-
- // perform the search on the required terms
- for (var i = 0; i < searchterms.length; i++) {
- var word = searchterms[i];
- // no match but word was a required one
- if ((files = terms[word]) == null)
- break;
- if (files.length == undefined) {
- files = [files];
- }
- // create the mapping
- for (var j = 0; j < files.length; j++) {
- var file = files[j];
- if (file in fileMap)
- fileMap[file].push(word);
- else
- fileMap[file] = [word];
- }
- }
-
- // now check if the files don't contain excluded terms
- for (var file in fileMap) {
- var valid = true;
-
- // check if all requirements are matched
- if (fileMap[file].length != searchterms.length)
- continue;
-
- // ensure that none of the excluded terms is in the
- // search result.
- for (var i = 0; i < excluded.length; i++) {
- if (terms[excluded[i]] == file ||
- $.contains(terms[excluded[i]] || [], file)) {
- valid = false;
- break;
- }
- }
-
- // if we have still a valid result we can add it
- // to the result list
- if (valid)
- regularResults.push([filenames[file], titles[file], '', null]);
- }
-
- // delete unused variables in order to not waste
- // memory until list is retrieved completely
- delete filenames, titles, terms;
-
- // now sort the regular results descending by title
- regularResults.sort(function(a, b) {
- var left = a[1].toLowerCase();
- var right = b[1].toLowerCase();
- return (left > right) ? -1 : ((left < right) ? 1 : 0);
- });
-
- // combine all results
- var results = unimportantResults.concat(regularResults)
- .concat(objectResults).concat(importantResults);
-
- // print the results
- var resultCount = results.length;
- function displayNextItem() {
- // results left, load the summary and display it
- if (results.length) {
- var item = results.pop();
- var listItem = $('<li style="display:none"></li>');
- if (DOCUMENTATION_OPTIONS.FILE_SUFFIX == '') {
- // dirhtml builder
- var dirname = item[0] + '/';
- if (dirname.match(/\/index\/$/)) {
- dirname = dirname.substring(0, dirname.length-6);
- } else if (dirname == 'index/') {
- dirname = '';
- }
- listItem.append($('<a/>').attr('href',
- DOCUMENTATION_OPTIONS.URL_ROOT + dirname +
- highlightstring + item[2]).html(item[1]));
- } else {
- // normal html builders
- listItem.append($('<a/>').attr('href',
- item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
- highlightstring + item[2]).html(item[1]));
- }
- if (item[3]) {
- listItem.append($('<span> (' + item[3] + ')</span>'));
- Search.output.append(listItem);
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
- $.get(DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' +
- item[0] + '.txt', function(data) {
- if (data != '') {
- listItem.append($.makeSearchSummary(data, searchterms, hlterms));
- Search.output.append(listItem);
- }
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- }, "text");
- } else {
- // no source available, just display title
- Search.output.append(listItem);
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- }
- }
- // search finished, update title and status message
- else {
- Search.stopPulse();
- Search.title.text(_('Search Results'));
- if (!resultCount)
- Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
- else
- Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
- Search.status.fadeIn(500);
- }
- }
- displayNextItem();
- },
-
- performObjectSearch : function(object, otherterms) {
- var filenames = this._index.filenames;
- var objects = this._index.objects;
- var objnames = this._index.objnames;
- var titles = this._index.titles;
-
- var importantResults = [];
- var objectResults = [];
- var unimportantResults = [];
-
- for (var prefix in objects) {
- for (var name in objects[prefix]) {
- var fullname = (prefix ? prefix + '.' : '') + name;
- if (fullname.toLowerCase().indexOf(object) > -1) {
- var match = objects[prefix][name];
- var objname = objnames[match[1]][2];
- var title = titles[match[0]];
- // If more than one term searched for, we require other words to be
- // found in the name/title/description
- if (otherterms.length > 0) {
- var haystack = (prefix + ' ' + name + ' ' +
- objname + ' ' + title).toLowerCase();
- var allfound = true;
- for (var i = 0; i < otherterms.length; i++) {
- if (haystack.indexOf(otherterms[i]) == -1) {
- allfound = false;
- break;
- }
- }
- if (!allfound) {
- continue;
- }
- }
- var descr = objname + _(', in ') + title;
- anchor = match[3];
- if (anchor == '')
- anchor = fullname;
- else if (anchor == '-')
- anchor = objnames[match[1]][1] + '-' + fullname;
- result = [filenames[match[0]], fullname, '#'+anchor, descr];
- switch (match[2]) {
- case 1: objectResults.push(result); break;
- case 0: importantResults.push(result); break;
- case 2: unimportantResults.push(result); break;
- }
- }
- }
- }
-
- // sort results descending
- objectResults.sort(function(a, b) {
- return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
- });
-
- importantResults.sort(function(a, b) {
- return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
- });
-
- unimportantResults.sort(function(a, b) {
- return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
- });
-
- return [importantResults, objectResults, unimportantResults]
- }
-}
-
-$(document).ready(function() {
- Search.init();
-});
\ No newline at end of file
diff --git a/doc/plasmodium_RNA-seq/_static/underscore.js b/doc/plasmodium_RNA-seq/_static/underscore.js
deleted file mode 100644
index 5d89914..0000000
--- a/doc/plasmodium_RNA-seq/_static/underscore.js
+++ /dev/null
@@ -1,23 +0,0 @@
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-// (c) 2009 Jeremy Ashkenas, DocumentCloud Inc.
-// Underscore is freely distributable under the terms of the MIT license.
-// Portions of Underscore are inspired by or borrowed from Prototype.js,
-// Oliver Steele's Functional, and John Resig's Micro-Templating.
-// For all details and documentation:
-// http://documentcloud.github.com/underscore/
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-" ").replace(/'(?=[^%]*%>)/g,"\t").split("'").join("\\'").split("\t").join("'").replace(/<%=(.+?)%>/g,"',$1,'").split("<%").join("');").split("%>").join("p.push('")+"');}return p.join('');");return c?a(c):a};b.forEach=b.each;b.foldl=b.inject=b.reduce;b.foldr=b.reduceRight;b.filter=b.select;b.every=b.all;b.some=b.any;b.head=b.first;b.tail=b.rest;b.methods=b.functions;var l=function(a,c){return c?b(a).chain():a};b.each(b.functions(b),function(a){var c=b[a];i.prototype[a]=function(){var d=b [...]
-o.call(d,this._wrapped);return l(c.apply(b,d),this._chain)}});b.each(["pop","push","reverse","shift","sort","splice","unshift"],function(a){var c=Array.prototype[a];i.prototype[a]=function(){c.apply(this._wrapped,arguments);return l(this._wrapped,this._chain)}});b.each(["concat","join","slice"],function(a){var c=Array.prototype[a];i.prototype[a]=function(){return l(c.apply(this._wrapped,arguments),this._chain)}});i.prototype.chain=function(){this._chain=true;return this};i.prototype.valu [...]
diff --git a/doc/plasmodium_RNA-seq/_static/up-pressed.png b/doc/plasmodium_RNA-seq/_static/up-pressed.png
deleted file mode 100644
index 8bd587a..0000000
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diff --git a/doc/plasmodium_RNA-seq/_static/up.png b/doc/plasmodium_RNA-seq/_static/up.png
deleted file mode 100644
index b946256..0000000
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diff --git a/doc/plasmodium_RNA-seq/_static/websupport.js b/doc/plasmodium_RNA-seq/_static/websupport.js
deleted file mode 100644
index e9bd1b8..0000000
--- a/doc/plasmodium_RNA-seq/_static/websupport.js
+++ /dev/null
@@ -1,808 +0,0 @@
-/*
- * websupport.js
- * ~~~~~~~~~~~~~
- *
- * sphinx.websupport utilties for all documentation.
- *
- * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
-
-(function($) {
- $.fn.autogrow = function() {
- return this.each(function() {
- var textarea = this;
-
- $.fn.autogrow.resize(textarea);
-
- $(textarea)
- .focus(function() {
- textarea.interval = setInterval(function() {
- $.fn.autogrow.resize(textarea);
- }, 500);
- })
- .blur(function() {
- clearInterval(textarea.interval);
- });
- });
- };
-
- $.fn.autogrow.resize = function(textarea) {
- var lineHeight = parseInt($(textarea).css('line-height'), 10);
- var lines = textarea.value.split('\n');
- var columns = textarea.cols;
- var lineCount = 0;
- $.each(lines, function() {
- lineCount += Math.ceil(this.length / columns) || 1;
- });
- var height = lineHeight * (lineCount + 1);
- $(textarea).css('height', height);
- };
-})(jQuery);
-
-(function($) {
- var comp, by;
-
- function init() {
- initEvents();
- initComparator();
- }
-
- function initEvents() {
- $('a.comment-close').live("click", function(event) {
- event.preventDefault();
- hide($(this).attr('id').substring(2));
- });
- $('a.vote').live("click", function(event) {
- event.preventDefault();
- handleVote($(this));
- });
- $('a.reply').live("click", function(event) {
- event.preventDefault();
- openReply($(this).attr('id').substring(2));
- });
- $('a.close-reply').live("click", function(event) {
- event.preventDefault();
- closeReply($(this).attr('id').substring(2));
- });
- $('a.sort-option').live("click", function(event) {
- event.preventDefault();
- handleReSort($(this));
- });
- $('a.show-proposal').live("click", function(event) {
- event.preventDefault();
- showProposal($(this).attr('id').substring(2));
- });
- $('a.hide-proposal').live("click", function(event) {
- event.preventDefault();
- hideProposal($(this).attr('id').substring(2));
- });
- $('a.show-propose-change').live("click", function(event) {
- event.preventDefault();
- showProposeChange($(this).attr('id').substring(2));
- });
- $('a.hide-propose-change').live("click", function(event) {
- event.preventDefault();
- hideProposeChange($(this).attr('id').substring(2));
- });
- $('a.accept-comment').live("click", function(event) {
- event.preventDefault();
- acceptComment($(this).attr('id').substring(2));
- });
- $('a.delete-comment').live("click", function(event) {
- event.preventDefault();
- deleteComment($(this).attr('id').substring(2));
- });
- $('a.comment-markup').live("click", function(event) {
- event.preventDefault();
- toggleCommentMarkupBox($(this).attr('id').substring(2));
- });
- }
-
- /**
- * Set comp, which is a comparator function used for sorting and
- * inserting comments into the list.
- */
- function setComparator() {
- // If the first three letters are "asc", sort in ascending order
- // and remove the prefix.
- if (by.substring(0,3) == 'asc') {
- var i = by.substring(3);
- comp = function(a, b) { return a[i] - b[i]; };
- } else {
- // Otherwise sort in descending order.
- comp = function(a, b) { return b[by] - a[by]; };
- }
-
- // Reset link styles and format the selected sort option.
- $('a.sel').attr('href', '#').removeClass('sel');
- $('a.by' + by).removeAttr('href').addClass('sel');
- }
-
- /**
- * Create a comp function. If the user has preferences stored in
- * the sortBy cookie, use those, otherwise use the default.
- */
- function initComparator() {
- by = 'rating'; // Default to sort by rating.
- // If the sortBy cookie is set, use that instead.
- if (document.cookie.length > 0) {
- var start = document.cookie.indexOf('sortBy=');
- if (start != -1) {
- start = start + 7;
- var end = document.cookie.indexOf(";", start);
- if (end == -1) {
- end = document.cookie.length;
- by = unescape(document.cookie.substring(start, end));
- }
- }
- }
- setComparator();
- }
-
- /**
- * Show a comment div.
- */
- function show(id) {
- $('#ao' + id).hide();
- $('#ah' + id).show();
- var context = $.extend({id: id}, opts);
- var popup = $(renderTemplate(popupTemplate, context)).hide();
- popup.find('textarea[name="proposal"]').hide();
- popup.find('a.by' + by).addClass('sel');
- var form = popup.find('#cf' + id);
- form.submit(function(event) {
- event.preventDefault();
- addComment(form);
- });
- $('#s' + id).after(popup);
- popup.slideDown('fast', function() {
- getComments(id);
- });
- }
-
- /**
- * Hide a comment div.
- */
- function hide(id) {
- $('#ah' + id).hide();
- $('#ao' + id).show();
- var div = $('#sc' + id);
- div.slideUp('fast', function() {
- div.remove();
- });
- }
-
- /**
- * Perform an ajax request to get comments for a node
- * and insert the comments into the comments tree.
- */
- function getComments(id) {
- $.ajax({
- type: 'GET',
- url: opts.getCommentsURL,
- data: {node: id},
- success: function(data, textStatus, request) {
- var ul = $('#cl' + id);
- var speed = 100;
- $('#cf' + id)
- .find('textarea[name="proposal"]')
- .data('source', data.source);
-
- if (data.comments.length === 0) {
- ul.html('<li>No comments yet.</li>');
- ul.data('empty', true);
- } else {
- // If there are comments, sort them and put them in the list.
- var comments = sortComments(data.comments);
- speed = data.comments.length * 100;
- appendComments(comments, ul);
- ul.data('empty', false);
- }
- $('#cn' + id).slideUp(speed + 200);
- ul.slideDown(speed);
- },
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem retrieving the comments.');
- },
- dataType: 'json'
- });
- }
-
- /**
- * Add a comment via ajax and insert the comment into the comment tree.
- */
- function addComment(form) {
- var node_id = form.find('input[name="node"]').val();
- var parent_id = form.find('input[name="parent"]').val();
- var text = form.find('textarea[name="comment"]').val();
- var proposal = form.find('textarea[name="proposal"]').val();
-
- if (text == '') {
- showError('Please enter a comment.');
- return;
- }
-
- // Disable the form that is being submitted.
- form.find('textarea,input').attr('disabled', 'disabled');
-
- // Send the comment to the server.
- $.ajax({
- type: "POST",
- url: opts.addCommentURL,
- dataType: 'json',
- data: {
- node: node_id,
- parent: parent_id,
- text: text,
- proposal: proposal
- },
- success: function(data, textStatus, error) {
- // Reset the form.
- if (node_id) {
- hideProposeChange(node_id);
- }
- form.find('textarea')
- .val('')
- .add(form.find('input'))
- .removeAttr('disabled');
- var ul = $('#cl' + (node_id || parent_id));
- if (ul.data('empty')) {
- $(ul).empty();
- ul.data('empty', false);
- }
- insertComment(data.comment);
- var ao = $('#ao' + node_id);
- ao.find('img').attr({'src': opts.commentBrightImage});
- if (node_id) {
- // if this was a "root" comment, remove the commenting box
- // (the user can get it back by reopening the comment popup)
- $('#ca' + node_id).slideUp();
- }
- },
- error: function(request, textStatus, error) {
- form.find('textarea,input').removeAttr('disabled');
- showError('Oops, there was a problem adding the comment.');
- }
- });
- }
-
- /**
- * Recursively append comments to the main comment list and children
- * lists, creating the comment tree.
- */
- function appendComments(comments, ul) {
- $.each(comments, function() {
- var div = createCommentDiv(this);
- ul.append($(document.createElement('li')).html(div));
- appendComments(this.children, div.find('ul.comment-children'));
- // To avoid stagnating data, don't store the comments children in data.
- this.children = null;
- div.data('comment', this);
- });
- }
-
- /**
- * After adding a new comment, it must be inserted in the correct
- * location in the comment tree.
- */
- function insertComment(comment) {
- var div = createCommentDiv(comment);
-
- // To avoid stagnating data, don't store the comments children in data.
- comment.children = null;
- div.data('comment', comment);
-
- var ul = $('#cl' + (comment.node || comment.parent));
- var siblings = getChildren(ul);
-
- var li = $(document.createElement('li'));
- li.hide();
-
- // Determine where in the parents children list to insert this comment.
- for(i=0; i < siblings.length; i++) {
- if (comp(comment, siblings[i]) <= 0) {
- $('#cd' + siblings[i].id)
- .parent()
- .before(li.html(div));
- li.slideDown('fast');
- return;
- }
- }
-
- // If we get here, this comment rates lower than all the others,
- // or it is the only comment in the list.
- ul.append(li.html(div));
- li.slideDown('fast');
- }
-
- function acceptComment(id) {
- $.ajax({
- type: 'POST',
- url: opts.acceptCommentURL,
- data: {id: id},
- success: function(data, textStatus, request) {
- $('#cm' + id).fadeOut('fast');
- $('#cd' + id).removeClass('moderate');
- },
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem accepting the comment.');
- }
- });
- }
-
- function deleteComment(id) {
- $.ajax({
- type: 'POST',
- url: opts.deleteCommentURL,
- data: {id: id},
- success: function(data, textStatus, request) {
- var div = $('#cd' + id);
- if (data == 'delete') {
- // Moderator mode: remove the comment and all children immediately
- div.slideUp('fast', function() {
- div.remove();
- });
- return;
- }
- // User mode: only mark the comment as deleted
- div
- .find('span.user-id:first')
- .text('[deleted]').end()
- .find('div.comment-text:first')
- .text('[deleted]').end()
- .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id +
- ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id)
- .remove();
- var comment = div.data('comment');
- comment.username = '[deleted]';
- comment.text = '[deleted]';
- div.data('comment', comment);
- },
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem deleting the comment.');
- }
- });
- }
-
- function showProposal(id) {
- $('#sp' + id).hide();
- $('#hp' + id).show();
- $('#pr' + id).slideDown('fast');
- }
-
- function hideProposal(id) {
- $('#hp' + id).hide();
- $('#sp' + id).show();
- $('#pr' + id).slideUp('fast');
- }
-
- function showProposeChange(id) {
- $('#pc' + id).hide();
- $('#hc' + id).show();
- var textarea = $('#pt' + id);
- textarea.val(textarea.data('source'));
- $.fn.autogrow.resize(textarea[0]);
- textarea.slideDown('fast');
- }
-
- function hideProposeChange(id) {
- $('#hc' + id).hide();
- $('#pc' + id).show();
- var textarea = $('#pt' + id);
- textarea.val('').removeAttr('disabled');
- textarea.slideUp('fast');
- }
-
- function toggleCommentMarkupBox(id) {
- $('#mb' + id).toggle();
- }
-
- /** Handle when the user clicks on a sort by link. */
- function handleReSort(link) {
- var classes = link.attr('class').split(/\s+/);
- for (var i=0; i<classes.length; i++) {
- if (classes[i] != 'sort-option') {
- by = classes[i].substring(2);
- }
- }
- setComparator();
- // Save/update the sortBy cookie.
- var expiration = new Date();
- expiration.setDate(expiration.getDate() + 365);
- document.cookie= 'sortBy=' + escape(by) +
- ';expires=' + expiration.toUTCString();
- $('ul.comment-ul').each(function(index, ul) {
- var comments = getChildren($(ul), true);
- comments = sortComments(comments);
- appendComments(comments, $(ul).empty());
- });
- }
-
- /**
- * Function to process a vote when a user clicks an arrow.
- */
- function handleVote(link) {
- if (!opts.voting) {
- showError("You'll need to login to vote.");
- return;
- }
-
- var id = link.attr('id');
- if (!id) {
- // Didn't click on one of the voting arrows.
- return;
- }
- // If it is an unvote, the new vote value is 0,
- // Otherwise it's 1 for an upvote, or -1 for a downvote.
- var value = 0;
- if (id.charAt(1) != 'u') {
- value = id.charAt(0) == 'u' ? 1 : -1;
- }
- // The data to be sent to the server.
- var d = {
- comment_id: id.substring(2),
- value: value
- };
-
- // Swap the vote and unvote links.
- link.hide();
- $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id)
- .show();
-
- // The div the comment is displayed in.
- var div = $('div#cd' + d.comment_id);
- var data = div.data('comment');
-
- // If this is not an unvote, and the other vote arrow has
- // already been pressed, unpress it.
- if ((d.value !== 0) && (data.vote === d.value * -1)) {
- $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide();
- $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show();
- }
-
- // Update the comments rating in the local data.
- data.rating += (data.vote === 0) ? d.value : (d.value - data.vote);
- data.vote = d.value;
- div.data('comment', data);
-
- // Change the rating text.
- div.find('.rating:first')
- .text(data.rating + ' point' + (data.rating == 1 ? '' : 's'));
-
- // Send the vote information to the server.
- $.ajax({
- type: "POST",
- url: opts.processVoteURL,
- data: d,
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem casting that vote.');
- }
- });
- }
-
- /**
- * Open a reply form used to reply to an existing comment.
- */
- function openReply(id) {
- // Swap out the reply link for the hide link
- $('#rl' + id).hide();
- $('#cr' + id).show();
-
- // Add the reply li to the children ul.
- var div = $(renderTemplate(replyTemplate, {id: id})).hide();
- $('#cl' + id)
- .prepend(div)
- // Setup the submit handler for the reply form.
- .find('#rf' + id)
- .submit(function(event) {
- event.preventDefault();
- addComment($('#rf' + id));
- closeReply(id);
- })
- .find('input[type=button]')
- .click(function() {
- closeReply(id);
- });
- div.slideDown('fast', function() {
- $('#rf' + id).find('textarea').focus();
- });
- }
-
- /**
- * Close the reply form opened with openReply.
- */
- function closeReply(id) {
- // Remove the reply div from the DOM.
- $('#rd' + id).slideUp('fast', function() {
- $(this).remove();
- });
-
- // Swap out the hide link for the reply link
- $('#cr' + id).hide();
- $('#rl' + id).show();
- }
-
- /**
- * Recursively sort a tree of comments using the comp comparator.
- */
- function sortComments(comments) {
- comments.sort(comp);
- $.each(comments, function() {
- this.children = sortComments(this.children);
- });
- return comments;
- }
-
- /**
- * Get the children comments from a ul. If recursive is true,
- * recursively include childrens' children.
- */
- function getChildren(ul, recursive) {
- var children = [];
- ul.children().children("[id^='cd']")
- .each(function() {
- var comment = $(this).data('comment');
- if (recursive)
- comment.children = getChildren($(this).find('#cl' + comment.id), true);
- children.push(comment);
- });
- return children;
- }
-
- /** Create a div to display a comment in. */
- function createCommentDiv(comment) {
- if (!comment.displayed && !opts.moderator) {
- return $('<div class="moderate">Thank you! Your comment will show up '
- + 'once it is has been approved by a moderator.</div>');
- }
- // Prettify the comment rating.
- comment.pretty_rating = comment.rating + ' point' +
- (comment.rating == 1 ? '' : 's');
- // Make a class (for displaying not yet moderated comments differently)
- comment.css_class = comment.displayed ? '' : ' moderate';
- // Create a div for this comment.
- var context = $.extend({}, opts, comment);
- var div = $(renderTemplate(commentTemplate, context));
-
- // If the user has voted on this comment, highlight the correct arrow.
- if (comment.vote) {
- var direction = (comment.vote == 1) ? 'u' : 'd';
- div.find('#' + direction + 'v' + comment.id).hide();
- div.find('#' + direction + 'u' + comment.id).show();
- }
-
- if (opts.moderator || comment.text != '[deleted]') {
- div.find('a.reply').show();
- if (comment.proposal_diff)
- div.find('#sp' + comment.id).show();
- if (opts.moderator && !comment.displayed)
- div.find('#cm' + comment.id).show();
- if (opts.moderator || (opts.username == comment.username))
- div.find('#dc' + comment.id).show();
- }
- return div;
- }
-
- /**
- * A simple template renderer. Placeholders such as <%id%> are replaced
- * by context['id'] with items being escaped. Placeholders such as <#id#>
- * are not escaped.
- */
- function renderTemplate(template, context) {
- var esc = $(document.createElement('div'));
-
- function handle(ph, escape) {
- var cur = context;
- $.each(ph.split('.'), function() {
- cur = cur[this];
- });
- return escape ? esc.text(cur || "").html() : cur;
- }
-
- return template.replace(/<([%#])([\w\.]*)\1>/g, function() {
- return handle(arguments[2], arguments[1] == '%' ? true : false);
- });
- }
-
- /** Flash an error message briefly. */
- function showError(message) {
- $(document.createElement('div')).attr({'class': 'popup-error'})
- .append($(document.createElement('div'))
- .attr({'class': 'error-message'}).text(message))
- .appendTo('body')
- .fadeIn("slow")
- .delay(2000)
- .fadeOut("slow");
- }
-
- /** Add a link the user uses to open the comments popup. */
- $.fn.comment = function() {
- return this.each(function() {
- var id = $(this).attr('id').substring(1);
- var count = COMMENT_METADATA[id];
- var title = count + ' comment' + (count == 1 ? '' : 's');
- var image = count > 0 ? opts.commentBrightImage : opts.commentImage;
- var addcls = count == 0 ? ' nocomment' : '';
- $(this)
- .append(
- $(document.createElement('a')).attr({
- href: '#',
- 'class': 'sphinx-comment-open' + addcls,
- id: 'ao' + id
- })
- .append($(document.createElement('img')).attr({
- src: image,
- alt: 'comment',
- title: title
- }))
- .click(function(event) {
- event.preventDefault();
- show($(this).attr('id').substring(2));
- })
- )
- .append(
- $(document.createElement('a')).attr({
- href: '#',
- 'class': 'sphinx-comment-close hidden',
- id: 'ah' + id
- })
- .append($(document.createElement('img')).attr({
- src: opts.closeCommentImage,
- alt: 'close',
- title: 'close'
- }))
- .click(function(event) {
- event.preventDefault();
- hide($(this).attr('id').substring(2));
- })
- );
- });
- };
-
- var opts = {
- processVoteURL: '/_process_vote',
- addCommentURL: '/_add_comment',
- getCommentsURL: '/_get_comments',
- acceptCommentURL: '/_accept_comment',
- deleteCommentURL: '/_delete_comment',
- commentImage: '/static/_static/comment.png',
- closeCommentImage: '/static/_static/comment-close.png',
- loadingImage: '/static/_static/ajax-loader.gif',
- commentBrightImage: '/static/_static/comment-bright.png',
- upArrow: '/static/_static/up.png',
- downArrow: '/static/_static/down.png',
- upArrowPressed: '/static/_static/up-pressed.png',
- downArrowPressed: '/static/_static/down-pressed.png',
- voting: false,
- moderator: false
- };
-
- if (typeof COMMENT_OPTIONS != "undefined") {
- opts = jQuery.extend(opts, COMMENT_OPTIONS);
- }
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- re2 = new RegExp(s_v);
- if (re2.test(stem)) {
- w = stem;
- re2 = /(at|bl|iz)$/;
- re3 = new RegExp("([^aeiouylsz])\\1$");
- re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
- if (re2.test(w))
- w = w + "e";
- else if (re3.test(w)) {
- re = /.$/;
- w = w.replace(re,"");
- }
- else if (re4.test(w))
- w = w + "e";
- }
- }
-
- // Step 1c
- re = /^(.+?)y$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(s_v);
- if (re.test(stem))
- w = stem + "i";
- }
-
- // Step 2
- re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- suffix = fp[2];
- re = new RegExp(mgr0);
- if (re.test(stem))
- w = stem + step2list[suffix];
- }
-
- // Step 3
- re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- suffix = fp[2];
- re = new RegExp(mgr0);
- if (re.test(stem))
- w = stem + step3list[suffix];
- }
-
- // Step 4
- re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
- re2 = /^(.+?)(s|t)(ion)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(mgr1);
- if (re.test(stem))
- w = stem;
- }
- else if (re2.test(w)) {
- var fp = re2.exec(w);
- stem = fp[1] + fp[2];
- re2 = new RegExp(mgr1);
- if (re2.test(stem))
- w = stem;
- }
-
- // Step 5
- re = /^(.+?)e$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(mgr1);
- re2 = new RegExp(meq1);
- re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
- if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
- w = stem;
- }
- re = /ll$/;
- re2 = new RegExp(mgr1);
- if (re.test(w) && re2.test(w)) {
- re = /.$/;
- w = w.replace(re,"");
- }
-
- // and turn initial Y back to y
- if (firstch == "y")
- w = firstch.toLowerCase() + w.substr(1);
- return w;
- }
-}
-
-
-/**
- * Search Module
- */
-var Search = {
-
- _index : null,
- _queued_query : null,
- _pulse_status : -1,
-
- init : function() {
- var params = $.getQueryParameters();
- if (params.q) {
- var query = params.q[0];
- $('input[name="q"]')[0].value = query;
- this.performSearch(query);
- }
- },
-
- loadIndex : function(url) {
- $.ajax({type: "GET", url: url, data: null, success: null,
- dataType: "script", cache: true});
- },
-
- setIndex : function(index) {
- var q;
- this._index = index;
- if ((q = this._queued_query) !== null) {
- this._queued_query = null;
- Search.query(q);
- }
- },
-
- hasIndex : function() {
- return this._index !== null;
- },
-
- deferQuery : function(query) {
- this._queued_query = query;
- },
-
- stopPulse : function() {
- this._pulse_status = 0;
- },
-
- startPulse : function() {
- if (this._pulse_status >= 0)
- return;
- function pulse() {
- Search._pulse_status = (Search._pulse_status + 1) % 4;
- var dotString = '';
- for (var i = 0; i < Search._pulse_status; i++)
- dotString += '.';
- Search.dots.text(dotString);
- if (Search._pulse_status > -1)
- window.setTimeout(pulse, 500);
- };
- pulse();
- },
-
- /**
- * perform a search for something
- */
- performSearch : function(query) {
- // create the required interface elements
- this.out = $('#search-results');
- this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
- this.dots = $('<span></span>').appendTo(this.title);
- this.status = $('<p style="display: none"></p>').appendTo(this.out);
- this.output = $('<ul class="search"/>').appendTo(this.out);
-
- $('#search-progress').text(_('Preparing search...'));
- this.startPulse();
-
- // index already loaded, the browser was quick!
- if (this.hasIndex())
- this.query(query);
- else
- this.deferQuery(query);
- },
-
- query : function(query) {
- var stopwords = ["and","then","into","it","as","are","in","if","for","no","there","their","was","is","be","to","that","but","they","not","such","with","by","a","on","these","of","will","this","near","the","or","at"];
-
- // Stem the searchterms and add them to the correct list
- var stemmer = new Stemmer();
- var searchterms = [];
- var excluded = [];
- var hlterms = [];
- var tmp = query.split(/\s+/);
- var objectterms = [];
- for (var i = 0; i < tmp.length; i++) {
- if (tmp[i] != "") {
- objectterms.push(tmp[i].toLowerCase());
- }
-
- if ($u.indexOf(stopwords, tmp[i]) != -1 || tmp[i].match(/^\d+$/) ||
- tmp[i] == "") {
- // skip this "word"
- continue;
- }
- // stem the word
- var word = stemmer.stemWord(tmp[i]).toLowerCase();
- // select the correct list
- if (word[0] == '-') {
- var toAppend = excluded;
- word = word.substr(1);
- }
- else {
- var toAppend = searchterms;
- hlterms.push(tmp[i].toLowerCase());
- }
- // only add if not already in the list
- if (!$.contains(toAppend, word))
- toAppend.push(word);
- };
- var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
-
- // console.debug('SEARCH: searching for:');
- // console.info('required: ', searchterms);
- // console.info('excluded: ', excluded);
-
- // prepare search
- var filenames = this._index.filenames;
- var titles = this._index.titles;
- var terms = this._index.terms;
- var fileMap = {};
- var files = null;
- // different result priorities
- var importantResults = [];
- var objectResults = [];
- var regularResults = [];
- var unimportantResults = [];
- $('#search-progress').empty();
-
- // lookup as object
- for (var i = 0; i < objectterms.length; i++) {
- var others = [].concat(objectterms.slice(0,i),
- objectterms.slice(i+1, objectterms.length))
- var results = this.performObjectSearch(objectterms[i], others);
- // Assume first word is most likely to be the object,
- // other words more likely to be in description.
- // Therefore put matches for earlier words first.
- // (Results are eventually used in reverse order).
- objectResults = results[0].concat(objectResults);
- importantResults = results[1].concat(importantResults);
- unimportantResults = results[2].concat(unimportantResults);
- }
-
- // perform the search on the required terms
- for (var i = 0; i < searchterms.length; i++) {
- var word = searchterms[i];
- // no match but word was a required one
- if ((files = terms[word]) == null)
- break;
- if (files.length == undefined) {
- files = [files];
- }
- // create the mapping
- for (var j = 0; j < files.length; j++) {
- var file = files[j];
- if (file in fileMap)
- fileMap[file].push(word);
- else
- fileMap[file] = [word];
- }
- }
-
- // now check if the files don't contain excluded terms
- for (var file in fileMap) {
- var valid = true;
-
- // check if all requirements are matched
- if (fileMap[file].length != searchterms.length)
- continue;
-
- // ensure that none of the excluded terms is in the
- // search result.
- for (var i = 0; i < excluded.length; i++) {
- if (terms[excluded[i]] == file ||
- $.contains(terms[excluded[i]] || [], file)) {
- valid = false;
- break;
- }
- }
-
- // if we have still a valid result we can add it
- // to the result list
- if (valid)
- regularResults.push([filenames[file], titles[file], '', null]);
- }
-
- // delete unused variables in order to not waste
- // memory until list is retrieved completely
- delete filenames, titles, terms;
-
- // now sort the regular results descending by title
- regularResults.sort(function(a, b) {
- var left = a[1].toLowerCase();
- var right = b[1].toLowerCase();
- return (left > right) ? -1 : ((left < right) ? 1 : 0);
- });
-
- // combine all results
- var results = unimportantResults.concat(regularResults)
- .concat(objectResults).concat(importantResults);
-
- // print the results
- var resultCount = results.length;
- function displayNextItem() {
- // results left, load the summary and display it
- if (results.length) {
- var item = results.pop();
- var listItem = $('<li style="display:none"></li>');
- if (DOCUMENTATION_OPTIONS.FILE_SUFFIX == '') {
- // dirhtml builder
- var dirname = item[0] + '/';
- if (dirname.match(/\/index\/$/)) {
- dirname = dirname.substring(0, dirname.length-6);
- } else if (dirname == 'index/') {
- dirname = '';
- }
- listItem.append($('<a/>').attr('href',
- DOCUMENTATION_OPTIONS.URL_ROOT + dirname +
- highlightstring + item[2]).html(item[1]));
- } else {
- // normal html builders
- listItem.append($('<a/>').attr('href',
- item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
- highlightstring + item[2]).html(item[1]));
- }
- if (item[3]) {
- listItem.append($('<span> (' + item[3] + ')</span>'));
- Search.output.append(listItem);
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
- $.get(DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' +
- item[0] + '.txt', function(data) {
- if (data != '') {
- listItem.append($.makeSearchSummary(data, searchterms, hlterms));
- Search.output.append(listItem);
- }
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- }, "text");
- } else {
- // no source available, just display title
- Search.output.append(listItem);
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- }
- }
- // search finished, update title and status message
- else {
- Search.stopPulse();
- Search.title.text(_('Search Results'));
- if (!resultCount)
- Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
- else
- Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
- Search.status.fadeIn(500);
- }
- }
- displayNextItem();
- },
-
- performObjectSearch : function(object, otherterms) {
- var filenames = this._index.filenames;
- var objects = this._index.objects;
- var objnames = this._index.objnames;
- var titles = this._index.titles;
-
- var importantResults = [];
- var objectResults = [];
- var unimportantResults = [];
-
- for (var prefix in objects) {
- for (var name in objects[prefix]) {
- var fullname = (prefix ? prefix + '.' : '') + name;
- if (fullname.toLowerCase().indexOf(object) > -1) {
- var match = objects[prefix][name];
- var objname = objnames[match[1]][2];
- var title = titles[match[0]];
- // If more than one term searched for, we require other words to be
- // found in the name/title/description
- if (otherterms.length > 0) {
- var haystack = (prefix + ' ' + name + ' ' +
- objname + ' ' + title).toLowerCase();
- var allfound = true;
- for (var i = 0; i < otherterms.length; i++) {
- if (haystack.indexOf(otherterms[i]) == -1) {
- allfound = false;
- break;
- }
- }
- if (!allfound) {
- continue;
- }
- }
- var descr = objname + _(', in ') + title;
- anchor = match[3];
- if (anchor == '')
- anchor = fullname;
- else if (anchor == '-')
- anchor = objnames[match[1]][1] + '-' + fullname;
- result = [filenames[match[0]], fullname, '#'+anchor, descr];
- switch (match[2]) {
- case 1: objectResults.push(result); break;
- case 0: importantResults.push(result); break;
- case 2: unimportantResults.push(result); break;
- }
- }
- }
- }
-
- // sort results descending
- objectResults.sort(function(a, b) {
- return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
- });
-
- importantResults.sort(function(a, b) {
- return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
- });
-
- unimportantResults.sort(function(a, b) {
- return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
- });
-
- return [importantResults, objectResults, unimportantResults]
- }
-}
-
-$(document).ready(function() {
- Search.init();
-});
\ No newline at end of file
diff --git a/doc/rna-seq-example/_static/underscore.js b/doc/rna-seq-example/_static/underscore.js
deleted file mode 100644
index 5d89914..0000000
--- a/doc/rna-seq-example/_static/underscore.js
+++ /dev/null
@@ -1,23 +0,0 @@
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-// Underscore is freely distributable under the terms of the MIT license.
-// Portions of Underscore are inspired by or borrowed from Prototype.js,
-// Oliver Steele's Functional, and John Resig's Micro-Templating.
-// For all details and documentation:
-// http://documentcloud.github.com/underscore/
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diff --git a/doc/rna-seq-example/_static/up-pressed.png b/doc/rna-seq-example/_static/up-pressed.png
deleted file mode 100644
index 8bd587a..0000000
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diff --git a/doc/rna-seq-example/_static/up.png b/doc/rna-seq-example/_static/up.png
deleted file mode 100644
index b946256..0000000
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diff --git a/doc/rna-seq-example/_static/websupport.js b/doc/rna-seq-example/_static/websupport.js
deleted file mode 100644
index e9bd1b8..0000000
--- a/doc/rna-seq-example/_static/websupport.js
+++ /dev/null
@@ -1,808 +0,0 @@
-/*
- * websupport.js
- * ~~~~~~~~~~~~~
- *
- * sphinx.websupport utilties for all documentation.
- *
- * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
-
-(function($) {
- $.fn.autogrow = function() {
- return this.each(function() {
- var textarea = this;
-
- $.fn.autogrow.resize(textarea);
-
- $(textarea)
- .focus(function() {
- textarea.interval = setInterval(function() {
- $.fn.autogrow.resize(textarea);
- }, 500);
- })
- .blur(function() {
- clearInterval(textarea.interval);
- });
- });
- };
-
- $.fn.autogrow.resize = function(textarea) {
- var lineHeight = parseInt($(textarea).css('line-height'), 10);
- var lines = textarea.value.split('\n');
- var columns = textarea.cols;
- var lineCount = 0;
- $.each(lines, function() {
- lineCount += Math.ceil(this.length / columns) || 1;
- });
- var height = lineHeight * (lineCount + 1);
- $(textarea).css('height', height);
- };
-})(jQuery);
-
-(function($) {
- var comp, by;
-
- function init() {
- initEvents();
- initComparator();
- }
-
- function initEvents() {
- $('a.comment-close').live("click", function(event) {
- event.preventDefault();
- hide($(this).attr('id').substring(2));
- });
- $('a.vote').live("click", function(event) {
- event.preventDefault();
- handleVote($(this));
- });
- $('a.reply').live("click", function(event) {
- event.preventDefault();
- openReply($(this).attr('id').substring(2));
- });
- $('a.close-reply').live("click", function(event) {
- event.preventDefault();
- closeReply($(this).attr('id').substring(2));
- });
- $('a.sort-option').live("click", function(event) {
- event.preventDefault();
- handleReSort($(this));
- });
- $('a.show-proposal').live("click", function(event) {
- event.preventDefault();
- showProposal($(this).attr('id').substring(2));
- });
- $('a.hide-proposal').live("click", function(event) {
- event.preventDefault();
- hideProposal($(this).attr('id').substring(2));
- });
- $('a.show-propose-change').live("click", function(event) {
- event.preventDefault();
- showProposeChange($(this).attr('id').substring(2));
- });
- $('a.hide-propose-change').live("click", function(event) {
- event.preventDefault();
- hideProposeChange($(this).attr('id').substring(2));
- });
- $('a.accept-comment').live("click", function(event) {
- event.preventDefault();
- acceptComment($(this).attr('id').substring(2));
- });
- $('a.delete-comment').live("click", function(event) {
- event.preventDefault();
- deleteComment($(this).attr('id').substring(2));
- });
- $('a.comment-markup').live("click", function(event) {
- event.preventDefault();
- toggleCommentMarkupBox($(this).attr('id').substring(2));
- });
- }
-
- /**
- * Set comp, which is a comparator function used for sorting and
- * inserting comments into the list.
- */
- function setComparator() {
- // If the first three letters are "asc", sort in ascending order
- // and remove the prefix.
- if (by.substring(0,3) == 'asc') {
- var i = by.substring(3);
- comp = function(a, b) { return a[i] - b[i]; };
- } else {
- // Otherwise sort in descending order.
- comp = function(a, b) { return b[by] - a[by]; };
- }
-
- // Reset link styles and format the selected sort option.
- $('a.sel').attr('href', '#').removeClass('sel');
- $('a.by' + by).removeAttr('href').addClass('sel');
- }
-
- /**
- * Create a comp function. If the user has preferences stored in
- * the sortBy cookie, use those, otherwise use the default.
- */
- function initComparator() {
- by = 'rating'; // Default to sort by rating.
- // If the sortBy cookie is set, use that instead.
- if (document.cookie.length > 0) {
- var start = document.cookie.indexOf('sortBy=');
- if (start != -1) {
- start = start + 7;
- var end = document.cookie.indexOf(";", start);
- if (end == -1) {
- end = document.cookie.length;
- by = unescape(document.cookie.substring(start, end));
- }
- }
- }
- setComparator();
- }
-
- /**
- * Show a comment div.
- */
- function show(id) {
- $('#ao' + id).hide();
- $('#ah' + id).show();
- var context = $.extend({id: id}, opts);
- var popup = $(renderTemplate(popupTemplate, context)).hide();
- popup.find('textarea[name="proposal"]').hide();
- popup.find('a.by' + by).addClass('sel');
- var form = popup.find('#cf' + id);
- form.submit(function(event) {
- event.preventDefault();
- addComment(form);
- });
- $('#s' + id).after(popup);
- popup.slideDown('fast', function() {
- getComments(id);
- });
- }
-
- /**
- * Hide a comment div.
- */
- function hide(id) {
- $('#ah' + id).hide();
- $('#ao' + id).show();
- var div = $('#sc' + id);
- div.slideUp('fast', function() {
- div.remove();
- });
- }
-
- /**
- * Perform an ajax request to get comments for a node
- * and insert the comments into the comments tree.
- */
- function getComments(id) {
- $.ajax({
- type: 'GET',
- url: opts.getCommentsURL,
- data: {node: id},
- success: function(data, textStatus, request) {
- var ul = $('#cl' + id);
- var speed = 100;
- $('#cf' + id)
- .find('textarea[name="proposal"]')
- .data('source', data.source);
-
- if (data.comments.length === 0) {
- ul.html('<li>No comments yet.</li>');
- ul.data('empty', true);
- } else {
- // If there are comments, sort them and put them in the list.
- var comments = sortComments(data.comments);
- speed = data.comments.length * 100;
- appendComments(comments, ul);
- ul.data('empty', false);
- }
- $('#cn' + id).slideUp(speed + 200);
- ul.slideDown(speed);
- },
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem retrieving the comments.');
- },
- dataType: 'json'
- });
- }
-
- /**
- * Add a comment via ajax and insert the comment into the comment tree.
- */
- function addComment(form) {
- var node_id = form.find('input[name="node"]').val();
- var parent_id = form.find('input[name="parent"]').val();
- var text = form.find('textarea[name="comment"]').val();
- var proposal = form.find('textarea[name="proposal"]').val();
-
- if (text == '') {
- showError('Please enter a comment.');
- return;
- }
-
- // Disable the form that is being submitted.
- form.find('textarea,input').attr('disabled', 'disabled');
-
- // Send the comment to the server.
- $.ajax({
- type: "POST",
- url: opts.addCommentURL,
- dataType: 'json',
- data: {
- node: node_id,
- parent: parent_id,
- text: text,
- proposal: proposal
- },
- success: function(data, textStatus, error) {
- // Reset the form.
- if (node_id) {
- hideProposeChange(node_id);
- }
- form.find('textarea')
- .val('')
- .add(form.find('input'))
- .removeAttr('disabled');
- var ul = $('#cl' + (node_id || parent_id));
- if (ul.data('empty')) {
- $(ul).empty();
- ul.data('empty', false);
- }
- insertComment(data.comment);
- var ao = $('#ao' + node_id);
- ao.find('img').attr({'src': opts.commentBrightImage});
- if (node_id) {
- // if this was a "root" comment, remove the commenting box
- // (the user can get it back by reopening the comment popup)
- $('#ca' + node_id).slideUp();
- }
- },
- error: function(request, textStatus, error) {
- form.find('textarea,input').removeAttr('disabled');
- showError('Oops, there was a problem adding the comment.');
- }
- });
- }
-
- /**
- * Recursively append comments to the main comment list and children
- * lists, creating the comment tree.
- */
- function appendComments(comments, ul) {
- $.each(comments, function() {
- var div = createCommentDiv(this);
- ul.append($(document.createElement('li')).html(div));
- appendComments(this.children, div.find('ul.comment-children'));
- // To avoid stagnating data, don't store the comments children in data.
- this.children = null;
- div.data('comment', this);
- });
- }
-
- /**
- * After adding a new comment, it must be inserted in the correct
- * location in the comment tree.
- */
- function insertComment(comment) {
- var div = createCommentDiv(comment);
-
- // To avoid stagnating data, don't store the comments children in data.
- comment.children = null;
- div.data('comment', comment);
-
- var ul = $('#cl' + (comment.node || comment.parent));
- var siblings = getChildren(ul);
-
- var li = $(document.createElement('li'));
- li.hide();
-
- // Determine where in the parents children list to insert this comment.
- for(i=0; i < siblings.length; i++) {
- if (comp(comment, siblings[i]) <= 0) {
- $('#cd' + siblings[i].id)
- .parent()
- .before(li.html(div));
- li.slideDown('fast');
- return;
- }
- }
-
- // If we get here, this comment rates lower than all the others,
- // or it is the only comment in the list.
- ul.append(li.html(div));
- li.slideDown('fast');
- }
-
- function acceptComment(id) {
- $.ajax({
- type: 'POST',
- url: opts.acceptCommentURL,
- data: {id: id},
- success: function(data, textStatus, request) {
- $('#cm' + id).fadeOut('fast');
- $('#cd' + id).removeClass('moderate');
- },
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem accepting the comment.');
- }
- });
- }
-
- function deleteComment(id) {
- $.ajax({
- type: 'POST',
- url: opts.deleteCommentURL,
- data: {id: id},
- success: function(data, textStatus, request) {
- var div = $('#cd' + id);
- if (data == 'delete') {
- // Moderator mode: remove the comment and all children immediately
- div.slideUp('fast', function() {
- div.remove();
- });
- return;
- }
- // User mode: only mark the comment as deleted
- div
- .find('span.user-id:first')
- .text('[deleted]').end()
- .find('div.comment-text:first')
- .text('[deleted]').end()
- .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id +
- ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id)
- .remove();
- var comment = div.data('comment');
- comment.username = '[deleted]';
- comment.text = '[deleted]';
- div.data('comment', comment);
- },
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem deleting the comment.');
- }
- });
- }
-
- function showProposal(id) {
- $('#sp' + id).hide();
- $('#hp' + id).show();
- $('#pr' + id).slideDown('fast');
- }
-
- function hideProposal(id) {
- $('#hp' + id).hide();
- $('#sp' + id).show();
- $('#pr' + id).slideUp('fast');
- }
-
- function showProposeChange(id) {
- $('#pc' + id).hide();
- $('#hc' + id).show();
- var textarea = $('#pt' + id);
- textarea.val(textarea.data('source'));
- $.fn.autogrow.resize(textarea[0]);
- textarea.slideDown('fast');
- }
-
- function hideProposeChange(id) {
- $('#hc' + id).hide();
- $('#pc' + id).show();
- var textarea = $('#pt' + id);
- textarea.val('').removeAttr('disabled');
- textarea.slideUp('fast');
- }
-
- function toggleCommentMarkupBox(id) {
- $('#mb' + id).toggle();
- }
-
- /** Handle when the user clicks on a sort by link. */
- function handleReSort(link) {
- var classes = link.attr('class').split(/\s+/);
- for (var i=0; i<classes.length; i++) {
- if (classes[i] != 'sort-option') {
- by = classes[i].substring(2);
- }
- }
- setComparator();
- // Save/update the sortBy cookie.
- var expiration = new Date();
- expiration.setDate(expiration.getDate() + 365);
- document.cookie= 'sortBy=' + escape(by) +
- ';expires=' + expiration.toUTCString();
- $('ul.comment-ul').each(function(index, ul) {
- var comments = getChildren($(ul), true);
- comments = sortComments(comments);
- appendComments(comments, $(ul).empty());
- });
- }
-
- /**
- * Function to process a vote when a user clicks an arrow.
- */
- function handleVote(link) {
- if (!opts.voting) {
- showError("You'll need to login to vote.");
- return;
- }
-
- var id = link.attr('id');
- if (!id) {
- // Didn't click on one of the voting arrows.
- return;
- }
- // If it is an unvote, the new vote value is 0,
- // Otherwise it's 1 for an upvote, or -1 for a downvote.
- var value = 0;
- if (id.charAt(1) != 'u') {
- value = id.charAt(0) == 'u' ? 1 : -1;
- }
- // The data to be sent to the server.
- var d = {
- comment_id: id.substring(2),
- value: value
- };
-
- // Swap the vote and unvote links.
- link.hide();
- $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id)
- .show();
-
- // The div the comment is displayed in.
- var div = $('div#cd' + d.comment_id);
- var data = div.data('comment');
-
- // If this is not an unvote, and the other vote arrow has
- // already been pressed, unpress it.
- if ((d.value !== 0) && (data.vote === d.value * -1)) {
- $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide();
- $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show();
- }
-
- // Update the comments rating in the local data.
- data.rating += (data.vote === 0) ? d.value : (d.value - data.vote);
- data.vote = d.value;
- div.data('comment', data);
-
- // Change the rating text.
- div.find('.rating:first')
- .text(data.rating + ' point' + (data.rating == 1 ? '' : 's'));
-
- // Send the vote information to the server.
- $.ajax({
- type: "POST",
- url: opts.processVoteURL,
- data: d,
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem casting that vote.');
- }
- });
- }
-
- /**
- * Open a reply form used to reply to an existing comment.
- */
- function openReply(id) {
- // Swap out the reply link for the hide link
- $('#rl' + id).hide();
- $('#cr' + id).show();
-
- // Add the reply li to the children ul.
- var div = $(renderTemplate(replyTemplate, {id: id})).hide();
- $('#cl' + id)
- .prepend(div)
- // Setup the submit handler for the reply form.
- .find('#rf' + id)
- .submit(function(event) {
- event.preventDefault();
- addComment($('#rf' + id));
- closeReply(id);
- })
- .find('input[type=button]')
- .click(function() {
- closeReply(id);
- });
- div.slideDown('fast', function() {
- $('#rf' + id).find('textarea').focus();
- });
- }
-
- /**
- * Close the reply form opened with openReply.
- */
- function closeReply(id) {
- // Remove the reply div from the DOM.
- $('#rd' + id).slideUp('fast', function() {
- $(this).remove();
- });
-
- // Swap out the hide link for the reply link
- $('#cr' + id).hide();
- $('#rl' + id).show();
- }
-
- /**
- * Recursively sort a tree of comments using the comp comparator.
- */
- function sortComments(comments) {
- comments.sort(comp);
- $.each(comments, function() {
- this.children = sortComments(this.children);
- });
- return comments;
- }
-
- /**
- * Get the children comments from a ul. If recursive is true,
- * recursively include childrens' children.
- */
- function getChildren(ul, recursive) {
- var children = [];
- ul.children().children("[id^='cd']")
- .each(function() {
- var comment = $(this).data('comment');
- if (recursive)
- comment.children = getChildren($(this).find('#cl' + comment.id), true);
- children.push(comment);
- });
- return children;
- }
-
- /** Create a div to display a comment in. */
- function createCommentDiv(comment) {
- if (!comment.displayed && !opts.moderator) {
- return $('<div class="moderate">Thank you! Your comment will show up '
- + 'once it is has been approved by a moderator.</div>');
- }
- // Prettify the comment rating.
- comment.pretty_rating = comment.rating + ' point' +
- (comment.rating == 1 ? '' : 's');
- // Make a class (for displaying not yet moderated comments differently)
- comment.css_class = comment.displayed ? '' : ' moderate';
- // Create a div for this comment.
- var context = $.extend({}, opts, comment);
- var div = $(renderTemplate(commentTemplate, context));
-
- // If the user has voted on this comment, highlight the correct arrow.
- if (comment.vote) {
- var direction = (comment.vote == 1) ? 'u' : 'd';
- div.find('#' + direction + 'v' + comment.id).hide();
- div.find('#' + direction + 'u' + comment.id).show();
- }
-
- if (opts.moderator || comment.text != '[deleted]') {
- div.find('a.reply').show();
- if (comment.proposal_diff)
- div.find('#sp' + comment.id).show();
- if (opts.moderator && !comment.displayed)
- div.find('#cm' + comment.id).show();
- if (opts.moderator || (opts.username == comment.username))
- div.find('#dc' + comment.id).show();
- }
- return div;
- }
-
- /**
- * A simple template renderer. Placeholders such as <%id%> are replaced
- * by context['id'] with items being escaped. Placeholders such as <#id#>
- * are not escaped.
- */
- function renderTemplate(template, context) {
- var esc = $(document.createElement('div'));
-
- function handle(ph, escape) {
- var cur = context;
- $.each(ph.split('.'), function() {
- cur = cur[this];
- });
- return escape ? esc.text(cur || "").html() : cur;
- }
-
- return template.replace(/<([%#])([\w\.]*)\1>/g, function() {
- return handle(arguments[2], arguments[1] == '%' ? true : false);
- });
- }
-
- /** Flash an error message briefly. */
- function showError(message) {
- $(document.createElement('div')).attr({'class': 'popup-error'})
- .append($(document.createElement('div'))
- .attr({'class': 'error-message'}).text(message))
- .appendTo('body')
- .fadeIn("slow")
- .delay(2000)
- .fadeOut("slow");
- }
-
- /** Add a link the user uses to open the comments popup. */
- $.fn.comment = function() {
- return this.each(function() {
- var id = $(this).attr('id').substring(1);
- var count = COMMENT_METADATA[id];
- var title = count + ' comment' + (count == 1 ? '' : 's');
- var image = count > 0 ? opts.commentBrightImage : opts.commentImage;
- var addcls = count == 0 ? ' nocomment' : '';
- $(this)
- .append(
- $(document.createElement('a')).attr({
- href: '#',
- 'class': 'sphinx-comment-open' + addcls,
- id: 'ao' + id
- })
- .append($(document.createElement('img')).attr({
- src: image,
- alt: 'comment',
- title: title
- }))
- .click(function(event) {
- event.preventDefault();
- show($(this).attr('id').substring(2));
- })
- )
- .append(
- $(document.createElement('a')).attr({
- href: '#',
- 'class': 'sphinx-comment-close hidden',
- id: 'ah' + id
- })
- .append($(document.createElement('img')).attr({
- src: opts.closeCommentImage,
- alt: 'close',
- title: 'close'
- }))
- .click(function(event) {
- event.preventDefault();
- hide($(this).attr('id').substring(2));
- })
- );
- });
- };
-
- var opts = {
- processVoteURL: '/_process_vote',
- addCommentURL: '/_add_comment',
- getCommentsURL: '/_get_comments',
- acceptCommentURL: '/_accept_comment',
- deleteCommentURL: '/_delete_comment',
- commentImage: '/static/_static/comment.png',
- closeCommentImage: '/static/_static/comment-close.png',
- loadingImage: '/static/_static/ajax-loader.gif',
- commentBrightImage: '/static/_static/comment-bright.png',
- upArrow: '/static/_static/up.png',
- downArrow: '/static/_static/down.png',
- upArrowPressed: '/static/_static/up-pressed.png',
- downArrowPressed: '/static/_static/down-pressed.png',
- voting: false,
- moderator: false
- };
-
- if (typeof COMMENT_OPTIONS != "undefined") {
- opts = jQuery.extend(opts, COMMENT_OPTIONS);
- }
-
- var popupTemplate = '\
- <div class="sphinx-comments" id="sc<%id%>">\
- <p class="sort-options">\
- Sort by:\
- <a href="#" class="sort-option byrating">best rated</a>\
- <a href="#" class="sort-option byascage">newest</a>\
- <a href="#" class="sort-option byage">oldest</a>\
- </p>\
- <div class="comment-header">Comments</div>\
- <div class="comment-loading" id="cn<%id%>">\
- loading comments... <img src="<%loadingImage%>" alt="" /></div>\
- <ul id="cl<%id%>" class="comment-ul"></ul>\
- <div id="ca<%id%>">\
- <p class="add-a-comment">Add a comment\
- (<a href="#" class="comment-markup" id="ab<%id%>">markup</a>):</p>\
- <div class="comment-markup-box" id="mb<%id%>">\
- reStructured text markup: <i>*emph*</i>, <b>**strong**</b>, \
- <tt>``code``</tt>, \
- code blocks: <tt>::</tt> and an indented block after blank line</div>\
- <form method="post" id="cf<%id%>" class="comment-form" action="">\
- <textarea name="comment" cols="80"></textarea>\
- <p class="propose-button">\
- <a href="#" id="pc<%id%>" class="show-propose-change">\
- Propose a change ▹\
- </a>\
- <a href="#" id="hc<%id%>" class="hide-propose-change">\
- Propose a change ▿\
- </a>\
- </p>\
- <textarea name="proposal" id="pt<%id%>" cols="80"\
- spellcheck="false"></textarea>\
- <input type="submit" value="Add comment" />\
- <input type="hidden" name="node" value="<%id%>" />\
- <input type="hidden" name="parent" value="" />\
- </form>\
- </div>\
- </div>';
-
- var commentTemplate = '\
- <div id="cd<%id%>" class="sphinx-comment<%css_class%>">\
- <div class="vote">\
- <div class="arrow">\
- <a href="#" id="uv<%id%>" class="vote" title="vote up">\
- <img src="<%upArrow%>" />\
- </a>\
- <a href="#" id="uu<%id%>" class="un vote" title="vote up">\
- <img src="<%upArrowPressed%>" />\
- </a>\
- </div>\
- <div class="arrow">\
- <a href="#" id="dv<%id%>" class="vote" title="vote down">\
- <img src="<%downArrow%>" id="da<%id%>" />\
- </a>\
- <a href="#" id="du<%id%>" class="un vote" title="vote down">\
- <img src="<%downArrowPressed%>" />\
- </a>\
- </div>\
- </div>\
- <div class="comment-content">\
- <p class="tagline comment">\
- <span class="user-id"><%username%></span>\
- <span class="rating"><%pretty_rating%></span>\
- <span class="delta"><%time.delta%></span>\
- </p>\
- <div class="comment-text comment"><#text#></div>\
- <p class="comment-opts comment">\
- <a href="#" class="reply hidden" id="rl<%id%>">reply ▹</a>\
- <a href="#" class="close-reply" id="cr<%id%>">reply ▿</a>\
- <a href="#" id="sp<%id%>" class="show-proposal">proposal ▹</a>\
- <a href="#" id="hp<%id%>" class="hide-proposal">proposal ▿</a>\
- <a href="#" id="dc<%id%>" class="delete-comment hidden">delete</a>\
- <span id="cm<%id%>" class="moderation hidden">\
- <a href="#" id="ac<%id%>" class="accept-comment">accept</a>\
- </span>\
- </p>\
- <pre class="proposal" id="pr<%id%>">\
-<#proposal_diff#>\
- </pre>\
- <ul class="comment-children" id="cl<%id%>"></ul>\
- </div>\
- <div class="clearleft"></div>\
- </div>\
- </div>';
-
- var replyTemplate = '\
- <li>\
- <div class="reply-div" id="rd<%id%>">\
- <form id="rf<%id%>">\
- <textarea name="comment" cols="80"></textarea>\
- <input type="submit" value="Add reply" />\
- <input type="button" value="Cancel" />\
- <input type="hidden" name="parent" value="<%id%>" />\
- <input type="hidden" name="node" value="" />\
- </form>\
- </div>\
- </li>';
-
- $(document).ready(function() {
- init();
- });
-})(jQuery);
-
-$(document).ready(function() {
- // add comment anchors for all paragraphs that are commentable
- $('.sphinx-has-comment').comment();
-
- // highlight search words in search results
- $("div.context").each(function() {
- var params = $.getQueryParameters();
- var terms = (params.q) ? params.q[0].split(/\s+/) : [];
- var result = $(this);
- $.each(terms, function() {
- result.highlightText(this.toLowerCase(), 'highlighted');
- });
- });
-
- // directly open comment window if requested
- var anchor = document.location.hash;
- if (anchor.substring(0, 9) == '#comment-') {
- $('#ao' + anchor.substring(9)).click();
- document.location.hash = '#s' + anchor.substring(9);
- }
-});
--
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