[med-svn] [salmon] 02/04: Imported Upstream version 0.4.2+ds1
Michael Crusoe
misterc-guest at moszumanska.debian.org
Thu Oct 1 07:26:47 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository salmon.
commit a2657b1806e7caacbdbcff45728be39ae60e75bd
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Wed Sep 30 23:06:36 2015 -0700
Imported Upstream version 0.4.2+ds1
---
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-# Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 0e2b30cad323b017c247ad4d9d521088
-tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/doc/build/html/_sources/building.txt b/doc/build/html/_sources/building.txt
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-Requirements
-============
-
-* A C++11 conformant compiler (currently tested with GCC>=4.7 and Clang>=3.4)
-* CMake_. Sailfish uses the CMake build system to check, fetch and install
- dependencies, and to compile and install Sailfish. CMake is available for all
- major platforms (though Sailfish is currently unsupported on Windows.)
-
-Installation
-============
-
-After downloading the Sailfish source distribution and unpacking it, change into the top-level directory:
-
-::
-
- > cd Sailfish
-
-Then, create and out-of-source build directory and change into it:
-
-::
-
- > mkdir build
- > cd build
-
-
-Sailfish makes extensive use of Boost_. We recommend installing the most
-recent version (1.55) systemwide if possible. If Boost is not installed on your
-system, the build process will fetch, compile and install it locally. However,
-if you already have a recent version of Boost available on your system, it make
-sense to tell the build system to use that.
-
-If you have Boost installed you can tell CMake where to look for it. Likewise,
-if you already have `Intel's Threading Building Blocks
-<http://threadingbuildingblocks.org/>`_ library installed, you can tell CMake
-where it is as well. The flags for CMake are as follows:
-
-* -DFETCH_BOOST=TRUE -- If you don't have Boost installed (or have an older
- version of it), you can provide the FETCH_BOOST flag instead of the
- BOOST_ROOT variable, which will cause CMake to fetch and build Boost locally.
-
-* -DBOOST_ROOT=<boostdir> -- Tells CMake where an existing installtion of Boost
- resides, and looks for the appropritate version in <boostdir>. This is the
- top-level directory where Boost is installed (e.g. /opt/local).
-
-* -DTBB_INSTALL_DIR=<tbbroot> -- Tells CMake where an existing installation of
- Intel's TBB is installed (<tbbroot>), and looks for the apropriate headers
- and libraries there. This is the top-level directory where TBB is installed
- (e.g. /opt/local).
-
-* -DCMAKE_INSTALL_PREFIX=<install_dir> -- <install_dir> is the directory to
- which you wish Sailfish to be installed. If you don't specify this option,
- it will be installed locally in the top-level directory (i.e. the directory
- directly above "build").
-
-Setting the appropriate flags, you can then run the CMake configure step as
-follows:
-
-::
-
- > cmake [FLAGS] ..
-
-The above command is the cmake configuration step, which *should* complain if
-anything goes wrong. Next, you have to run the build step. Depending on what
-libraries need to be fetched and installed, this could take a while
-(specifically if the installation needs to install Boost). To start the build,
-just run make.
-
-::
-
- > make
-
-If the build is successful, the appropriate executables and libraries should be
-created. There are two points to note about the build process. First, if the
-build system is downloading and compiling boost, you may see a large number of
-warnings during compilation; these are normal. Second, note that CMake has
-colored output by default, and the steps which create or link libraries are
-printed in red. This is the color chosen by CMake for linking messages, and
-does not denote an error in the build process.
-
-Finally, after everything is built, the libraries and executable can be
-installed with:
-
-::
-
- > make install
-
-To ensure that Sailfish has access to the appropriate libraries you should
-ensure that the PATH variabile contains <install_dir>/bin, and that
-LD_LIBRARY_PATH (or DYLD_FALLBACK_LIBRARY_PATH on OSX) contains
-<install_dir>/lib.
-
-After the paths are set, you can test the installation by running
-
-::
-
- > make test
-
-This should run a simple test and tell you if it succeeded or not.
-
-Running Sailfish
-================
-
-Sailfish is a tool for transcript quantification from RNA-seq data. It
-requires a set of target transcripts (either from a reference or _de-novo_
-assembly) to quantify. All you need to run Sailfish is a fasta file containing
-your reference transcripts and a (set of) fasta/fastq file(s) containing your
-reads. Sailfish runs in two phases; indexing and quantification. The indexing
-step is independent of the reads, and only need to be run one for a particular
-set of reference transcripts and choice of k (the k-mer size). The
-quantification step, obviously, is specific to the set of RNA-seq reads and is
-thus run more frequently. For a more complete description of all available
-options in Sailfish, see the manual.
-
-
-Indexing
---------
-
-To generate the Sailfish index for your reference set of transcripts, you
-should run the following command:
-
-::
- > sailfish index -t <ref_transcripts> -o <out_dir> -k <kmer_len>
-
-
-This will build a Sailfish index for k-mers of length \<kmer_len\> for the
-reference transcripts provided in the file \<ref_transcripts\> and place the
-index under the directory \<out_dir\>. There are additional options that can
-be passed to the Sailfish indexer (e.g. the number of threads to use). These
-can be seen by executing the command "Sailfish index -h".
-
-Quantification
---------------
-
-Now that you have generated the Sailfish index (say that it's the directory
-<index_dir> --- this corresponds to the <out_dir> argument provided in the
-previous step), you can quantify the transcript expression for a given set of
-reads. To perform the quantification, you run a command like the following:
-
-::
-
- > sailfish quant -i <index_dir> -l "<libtype>" {-r <unmated> | -1 <mates1> -2 <mates2>} -o <quant_dir>
-
-Where <index_dir> is, as described above, the location of the sailfish index,
-<libtype> is a string describing the format of the read library (see the
-[library string](#library-string) section below) <unmated> is a list of files
-containing unmated reads, <mates{1,2}> are lists of files containg,
-respectively, the first and second mates of paired-end reads. Finally,
-<quant_dir> is the directory where the output should be written. Just like the
-indexing step, additional options are available, and can be viewed by running
-"sailfish quant -h".
-
-When the quantification step is finished, the directory \<quant_dir\> will
-contain a file named "quant.sf" (and, if bias correction is enabled, an
-additional file names "quant_bias_corrected.sf"). This file contains the
-result of the Sailfish quantification step. This file contains a number of
-columns (which are listed in the last of the header lines beginning with '#').
-Specifically, the columns are (1) Transcript ID, (2) Transcript Length, (3)
-Transcripts per Million (TPM), (4) Reads Per Kilobase per Million mapped reads
-(RPKM), (5) K-mers Per Kilobase per Million mapped k-mers (KPKM), (6) Estimated
-number of k-mers (an estimate of the number of k-mers drawn from this
-transcript given the transcript's relative abundance and length) and (7)
-Estimated number of reads (an estimate of the number of reads drawn from this
-transcript given the transcript's relative abnundance and length). The first
-two columns are self-explanatory, the next four are measures of transcript
-abundance and the final is a commonly used input for differential expression
-tools. The Transcripts per Million quantification number is computed as
-described in [1]_, and is meant as an estimate of the number of transcripts, per
-million observed transcripts, originating from each isoform. Its benefit over
-the K/RPKM measure is that it is independent of the mean expressed transcript
-length (i.e. if the mean expressed transcript length varies between samples,
-for example, this alone can affect differential analysis based on the K/RPKM.)
-The RPKM is a classic measure of relative transcript abundance, and is an
-estimate of the number of reads per kilobase of transcript (per million mapped
-reads) originating from each transcript. The KPKM should closely track the
-RPKM, but is defined for very short features which are larger than the chosen
-k-mer length but may be shorter than the read length. Typically, you should
-prefer the KPKM measure to the RPKM measure, since the k-mer is the most
-natural unit of coverage for Sailfish.
-
-
-License
-=======
-
-This program is free software: you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation, either version 3 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program. If not, see <http://www.gnu.org/licenses/>.
-
-References
-==========
-
-.. [1] Li, Bo, et al. "RNA-Seq gene expression estimation with read mapping uncertainty."
- Bioinformatics 26.4 (2010): 493-500.i
-
-.. _CMake : http://www.cmake.org
-.. _Boost: http://www.boost.org
diff --git a/doc/build/html/_sources/index.txt b/doc/build/html/_sources/index.txt
deleted file mode 100644
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--- a/doc/build/html/_sources/index.txt
+++ /dev/null
@@ -1,22 +0,0 @@
-.. Sailfish documentation master file, created by
- sphinx-quickstart on Tue Jul 15 17:48:43 2014.
- You can adapt this file completely to your liking, but it should at least
- contain the root `toctree` directive.
-
-Welcome to Sailfish's documentation!
-====================================
-
-Contents:
-
-.. toctree::
- :maxdepth: 2
-
- building.rst
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-
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deleted file mode 100644
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-/*
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diff --git a/doc/build/html/_static/doctools.js b/doc/build/html/_static/doctools.js
deleted file mode 100644
index c5455c9..0000000
--- a/doc/build/html/_static/doctools.js
+++ /dev/null
@@ -1,238 +0,0 @@
-/*
- * doctools.js
- * ~~~~~~~~~~~
- *
- * Sphinx JavaScript utilities for all documentation.
- *
- * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
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- */
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-jQuery.getQueryParameters = function(s) {
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- else if (!jQuery(node).is("button, select, textarea")) {
- jQuery.each(node.childNodes, function() {
- highlight(this);
- });
- }
- }
- return this.each(function() {
- highlight(this);
- });
-};
-
-/**
- * Small JavaScript module for the documentation.
- */
-var Documentation = {
-
- init : function() {
- this.fixFirefoxAnchorBug();
- this.highlightSearchWords();
- this.initIndexTable();
- },
-
- /**
- * i18n support
- */
- TRANSLATIONS : {},
- PLURAL_EXPR : function(n) { return n == 1 ? 0 : 1; },
- LOCALE : 'unknown',
-
- // gettext and ngettext don't access this so that the functions
- // can safely bound to a different name (_ = Documentation.gettext)
- gettext : function(string) {
- var translated = Documentation.TRANSLATIONS[string];
- if (typeof translated == 'undefined')
- return string;
- return (typeof translated == 'string') ? translated : translated[0];
- },
-
- ngettext : function(singular, plural, n) {
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- if (typeof translated == 'undefined')
- return (n == 1) ? singular : plural;
- return translated[Documentation.PLURALEXPR(n)];
- },
-
- addTranslations : function(catalog) {
- for (var key in catalog.messages)
- this.TRANSLATIONS[key] = catalog.messages[key];
- this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
- this.LOCALE = catalog.locale;
- },
-
- /**
- * add context elements like header anchor links
- */
- addContextElements : function() {
- $('div[id] > :header:first').each(function() {
- $('<a class="headerlink">\u00B6</a>').
- attr('href', '#' + this.id).
- attr('title', _('Permalink to this headline')).
- appendTo(this);
- });
- $('dt[id]').each(function() {
- $('<a class="headerlink">\u00B6</a>').
- attr('href', '#' + this.id).
- attr('title', _('Permalink to this definition')).
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- });
- },
-
- /**
- * workaround a firefox stupidity
- */
- fixFirefoxAnchorBug : function() {
- if (document.location.hash && $.browser.mozilla)
- window.setTimeout(function() {
- document.location.href += '';
- }, 10);
- },
-
- /**
- * highlight the search words provided in the url in the text
- */
- highlightSearchWords : function() {
- var params = $.getQueryParameters();
- var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
- if (terms.length) {
- var body = $('div.body');
- if (!body.length) {
- body = $('body');
- }
- window.setTimeout(function() {
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- body.highlightText(this.toLowerCase(), 'highlighted');
- });
- }, 10);
- $('<p class="highlight-link"><a href="javascript:Documentation.' +
- 'hideSearchWords()">' + _('Hide Search Matches') + '</a></p>')
- .appendTo($('#searchbox'));
- }
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-
- /**
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- initIndexTable : function() {
- var togglers = $('img.toggler').click(function() {
- var src = $(this).attr('src');
- var idnum = $(this).attr('id').substr(7);
- $('tr.cg-' + idnum).toggle();
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- else
- $(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
- }).css('display', '');
- if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {
- togglers.click();
- }
- },
-
- /**
- * helper function to hide the search marks again
- */
- hideSearchWords : function() {
- $('#searchbox .highlight-link').fadeOut(300);
- $('span.highlighted').removeClass('highlighted');
- },
-
- /**
- * make the url absolute
- */
- makeURL : function(relativeURL) {
- return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
- },
-
- /**
- * get the current relative url
- */
- getCurrentURL : function() {
- var path = document.location.pathname;
- var parts = path.split(/\//);
- $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
- if (this == '..')
- parts.pop();
- });
- var url = parts.join('/');
- return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
- }
-};
-
-// quick alias for translations
-_ = Documentation.gettext;
-
-$(document).ready(function() {
- Documentation.init();
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diff --git a/doc/build/html/_static/down-pressed.png b/doc/build/html/_static/down-pressed.png
deleted file mode 100644
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diff --git a/doc/build/html/_static/down.png b/doc/build/html/_static/down.png
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diff --git a/doc/build/html/_static/jquery.js b/doc/build/html/_static/jquery.js
deleted file mode 100644
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diff --git a/doc/build/html/_static/minus.png b/doc/build/html/_static/minus.png
deleted file mode 100644
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diff --git a/doc/build/html/_static/pygments.css b/doc/build/html/_static/pygments.css
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diff --git a/doc/build/html/_static/searchtools.js b/doc/build/html/_static/searchtools.js
deleted file mode 100644
index 6e1f06b..0000000
--- a/doc/build/html/_static/searchtools.js
+++ /dev/null
@@ -1,622 +0,0 @@
-/*
- * searchtools.js_t
- * ~~~~~~~~~~~~~~~~
- *
- * Sphinx JavaScript utilties for the full-text search.
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- *
- */
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-
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-
- var step2list = {
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- tional: 'tion',
- enci: 'ence',
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- bli: 'ble',
- alli: 'al',
- entli: 'ent',
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- 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;
- }
-}
-
-
-
-/**
- * Simple result scoring code.
- */
-var Scorer = {
- // Implement the following function to further tweak the score for each result
- // The function takes a result array [filename, title, anchor, descr, score]
- // and returns the new score.
- /*
- score: function(result) {
- return result[4];
- },
- */
-
- // query matches the full name of an object
- objNameMatch: 11,
- // or matches in the last dotted part of the object name
- objPartialMatch: 6,
- // Additive scores depending on the priority of the object
- objPrio: {0: 15, // used to be importantResults
- 1: 5, // used to be objectResults
- 2: -5}, // used to be unimportantResults
- // Used when the priority is not in the mapping.
- objPrioDefault: 0,
-
- // query found in title
- title: 15,
- // query found in terms
- term: 5
-};
-
-
-/**
- * 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,
- dataType: "script", cache: true,
- complete: function(jqxhr, textstatus) {
- if (textstatus != "success") {
- document.getElementById("searchindexloader").src = url;
- }
- }});
- },
-
- 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() {
- var i;
- Search._pulse_status = (Search._pulse_status + 1) % 4;
- var dotString = '';
- for (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 (or wait until index is loaded)
- */
- 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);
-
- $('#search-progress').text(_('Preparing search...'));
- this.startPulse();
-
- // index already loaded, the browser was quick!
- if (this.hasIndex())
- this.query(query);
- else
- this.deferQuery(query);
- },
-
- /**
- * execute search (requires search index to be loaded)
- */
- query : function(query) {
- var i;
- var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];
-
- // stem the searchterms and add them to the correct list
- var stemmer = new Stemmer();
- var searchterms = [];
- var excluded = [];
- var hlterms = [];
- var tmp = query.split(/\s+/);
- var objectterms = [];
- for (i = 0; i < tmp.length; i++) {
- if (tmp[i] !== "") {
- objectterms.push(tmp[i].toLowerCase());
- }
-
- if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i].match(/^\d+$/) ||
- tmp[i] === "") {
- // skip this "word"
- continue;
- }
- // stem the word
- var word = stemmer.stemWord(tmp[i].toLowerCase());
- var toAppend;
- // select the correct list
- if (word[0] == '-') {
- toAppend = excluded;
- word = word.substr(1);
- }
- else {
- toAppend = searchterms;
- hlterms.push(tmp[i].toLowerCase());
- }
- // only add if not already in the list
- if (!$u.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 terms = this._index.terms;
- var titleterms = this._index.titleterms;
-
- // array of [filename, title, anchor, descr, score]
- var results = [];
- $('#search-progress').empty();
-
- // lookup as object
- for (i = 0; i < objectterms.length; i++) {
- var others = [].concat(objectterms.slice(0, i),
- objectterms.slice(i+1, objectterms.length));
- results = results.concat(this.performObjectSearch(objectterms[i], others));
- }
-
- // lookup as search terms in fulltext
- results = results.concat(this.performTermsSearch(searchterms, excluded, terms, Scorer.term))
- .concat(this.performTermsSearch(searchterms, excluded, titleterms, Scorer.title));
-
- // let the scorer override scores with a custom scoring function
- if (Scorer.score) {
- for (i = 0; i < results.length; i++)
- results[i][4] = Scorer.score(results[i]);
- }
-
- // now sort the results by score (in opposite order of appearance, since the
- // display function below uses pop() to retrieve items) and then
- // alphabetically
- results.sort(function(a, b) {
- var left = a[4];
- var right = b[4];
- if (left > right) {
- return 1;
- } else if (left < right) {
- return -1;
- } else {
- // same score: sort alphabetically
- left = a[1].toLowerCase();
- right = b[1].toLowerCase();
- return (left > right) ? -1 : ((left < right) ? 1 : 0);
- }
- });
-
- // for debugging
- //Search.lastresults = results.slice(); // a copy
- //console.info('search results:', Search.lastresults);
-
- // 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) {
- $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[0] + '.txt',
- dataType: "text",
- complete: function(jqxhr, textstatus) {
- var data = jqxhr.responseText;
- if (data !== '') {
- listItem.append(Search.makeSearchSummary(data, searchterms, hlterms));
- }
- Search.output.append(listItem);
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- }});
- } 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();
- },
-
- /**
- * search for object names
- */
- 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 i;
- var results = [];
-
- for (var prefix in objects) {
- for (var name in objects[prefix]) {
- var fullname = (prefix ? prefix + '.' : '') + name;
- if (fullname.toLowerCase().indexOf(object) > -1) {
- var score = 0;
- var parts = fullname.split('.');
- // check for different match types: exact matches of full name or
- // "last name" (i.e. last dotted part)
- if (fullname == object || parts[parts.length - 1] == object) {
- score += Scorer.objNameMatch;
- // matches in last name
- } else if (parts[parts.length - 1].indexOf(object) > -1) {
- score += Scorer.objPartialMatch;
- }
- 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 (i = 0; i < otherterms.length; i++) {
- if (haystack.indexOf(otherterms[i]) == -1) {
- allfound = false;
- break;
- }
- }
- if (!allfound) {
- continue;
- }
- }
- var descr = objname + _(', in ') + title;
-
- var anchor = match[3];
- if (anchor === '')
- anchor = fullname;
- else if (anchor == '-')
- anchor = objnames[match[1]][1] + '-' + fullname;
- // add custom score for some objects according to scorer
- if (Scorer.objPrio.hasOwnProperty(match[2])) {
- score += Scorer.objPrio[match[2]];
- } else {
- score += Scorer.objPrioDefault;
- }
- results.push([filenames[match[0]], fullname, '#'+anchor, descr, score]);
- }
- }
- }
-
- return results;
- },
-
- /**
- * search for full-text terms in the index
- */
- performTermsSearch : function(searchterms, excluded, terms, score) {
- var filenames = this._index.filenames;
- var titles = this._index.titles;
-
- var i, j, file, files;
- var fileMap = {};
- var results = [];
-
- // perform the search on the required terms
- for (i = 0; i < searchterms.length; i++) {
- var word = searchterms[i];
- // no match but word was a required one
- if ((files = terms[word]) === undefined)
- break;
- if (files.length === undefined) {
- files = [files];
- }
- // create the mapping
- for (j = 0; j < files.length; j++) {
- 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 (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 (i = 0; i < excluded.length; i++) {
- if (terms[excluded[i]] == file ||
- $u.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) {
- results.push([filenames[file], titles[file], '', null, score]);
- }
- }
- return results;
- },
-
- /**
- * helper function to return a node containing the
- * search summary for a given text. keywords is a list
- * of stemmed words, hlwords is the list of normal, unstemmed
- * words. the first one is used to find the occurance, the
- * latter for highlighting it.
- */
- makeSearchSummary : function(text, keywords, hlwords) {
- var textLower = text.toLowerCase();
- var start = 0;
- $.each(keywords, function() {
- var i = textLower.indexOf(this.toLowerCase());
- if (i > -1)
- start = i;
- });
- start = Math.max(start - 120, 0);
- var excerpt = ((start > 0) ? '...' : '') +
- $.trim(text.substr(start, 240)) +
- ((start + 240 - text.length) ? '...' : '');
- var rv = $('<div class="context"></div>').text(excerpt);
- $.each(hlwords, function() {
- rv = rv.highlightText(this, 'highlighted');
- });
- return rv;
- }
-};
-
-$(document).ready(function() {
- Search.init();
-});
\ No newline at end of file
diff --git a/doc/build/html/_static/sidebar.js b/doc/build/html/_static/sidebar.js
deleted file mode 100644
index 4f09a0d..0000000
--- a/doc/build/html/_static/sidebar.js
+++ /dev/null
@@ -1,159 +0,0 @@
-/*
- * sidebar.js
- * ~~~~~~~~~~
- *
- * This script makes the Sphinx sidebar collapsible.
- *
- * .sphinxsidebar contains .sphinxsidebarwrapper. This script adds
- * in .sphixsidebar, after .sphinxsidebarwrapper, the #sidebarbutton
- * used to collapse and expand the sidebar.
- *
- * When the sidebar is collapsed the .sphinxsidebarwrapper is hidden
- * and the width of the sidebar and the margin-left of the document
- * are decreased. When the sidebar is expanded the opposite happens.
- * This script saves a per-browser/per-session cookie used to
- * remember the position of the sidebar among the pages.
- * Once the browser is closed the cookie is deleted and the position
- * reset to the default (expanded).
- *
- * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
-
-$(function() {
-
-
-
-
-
-
-
-
- // global elements used by the functions.
- // the 'sidebarbutton' element is defined as global after its
- // creation, in the add_sidebar_button function
- var bodywrapper = $('.bodywrapper');
- var sidebar = $('.sphinxsidebar');
- var sidebarwrapper = $('.sphinxsidebarwrapper');
-
- // for some reason, the document has no sidebar; do not run into errors
- if (!sidebar.length) return;
-
- // original margin-left of the bodywrapper and width of the sidebar
- // with the sidebar expanded
- var bw_margin_expanded = bodywrapper.css('margin-left');
- var ssb_width_expanded = sidebar.width();
-
- // margin-left of the bodywrapper and width of the sidebar
- // with the sidebar collapsed
- var bw_margin_collapsed = '.8em';
- var ssb_width_collapsed = '.8em';
-
- // colors used by the current theme
- var dark_color = $('.related').css('background-color');
- var light_color = $('.document').css('background-color');
-
- function sidebar_is_collapsed() {
- return sidebarwrapper.is(':not(:visible)');
- }
-
- function toggle_sidebar() {
- if (sidebar_is_collapsed())
- expand_sidebar();
- else
- collapse_sidebar();
- }
-
- function collapse_sidebar() {
- sidebarwrapper.hide();
- sidebar.css('width', ssb_width_collapsed);
- bodywrapper.css('margin-left', bw_margin_collapsed);
- sidebarbutton.css({
- 'margin-left': '0',
- 'height': bodywrapper.height()
- });
- sidebarbutton.find('span').text('»');
- sidebarbutton.attr('title', _('Expand sidebar'));
- document.cookie = 'sidebar=collapsed';
- }
-
- function expand_sidebar() {
- bodywrapper.css('margin-left', bw_margin_expanded);
- sidebar.css('width', ssb_width_expanded);
- sidebarwrapper.show();
- sidebarbutton.css({
- 'margin-left': ssb_width_expanded-12,
- 'height': bodywrapper.height()
- });
- sidebarbutton.find('span').text('«');
- sidebarbutton.attr('title', _('Collapse sidebar'));
- document.cookie = 'sidebar=expanded';
- }
-
- function add_sidebar_button() {
- sidebarwrapper.css({
- 'float': 'left',
- 'margin-right': '0',
- 'width': ssb_width_expanded - 28
- });
- // create the button
- sidebar.append(
- '<div id="sidebarbutton"><span>«</span></div>'
- );
- var sidebarbutton = $('#sidebarbutton');
- light_color = sidebarbutton.css('background-color');
- // find the height of the viewport to center the '<<' in the page
- var viewport_height;
- if (window.innerHeight)
- viewport_height = window.innerHeight;
- else
- viewport_height = $(window).height();
- sidebarbutton.find('span').css({
- 'display': 'block',
- 'margin-top': (viewport_height - sidebar.position().top - 20) / 2
- });
-
- sidebarbutton.click(toggle_sidebar);
- sidebarbutton.attr('title', _('Collapse sidebar'));
- sidebarbutton.css({
- 'color': '#FFFFFF',
- 'border-left': '1px solid ' + dark_color,
- 'font-size': '1.2em',
- 'cursor': 'pointer',
- 'height': bodywrapper.height(),
- 'padding-top': '1px',
- 'margin-left': ssb_width_expanded - 12
- });
-
- sidebarbutton.hover(
- function () {
- $(this).css('background-color', dark_color);
- },
- function () {
- $(this).css('background-color', light_color);
- }
- );
- }
-
- function set_position_from_cookie() {
- if (!document.cookie)
- return;
- var items = document.cookie.split(';');
- for(var k=0; k<items.length; k++) {
- var key_val = items[k].split('=');
- var key = key_val[0].replace(/ /, ""); // strip leading spaces
- if (key == 'sidebar') {
- var value = key_val[1];
- if ((value == 'collapsed') && (!sidebar_is_collapsed()))
- collapse_sidebar();
- else if ((value == 'expanded') && (sidebar_is_collapsed()))
- expand_sidebar();
- }
- }
- }
-
- add_sidebar_button();
- var sidebarbutton = $('#sidebarbutton');
- set_position_from_cookie();
-});
\ No newline at end of file
diff --git a/doc/build/html/_static/underscore.js b/doc/build/html/_static/underscore.js
deleted file mode 100644
index 5b55f32..0000000
--- a/doc/build/html/_static/underscore.js
+++ /dev/null
@@ -1,31 +0,0 @@
-// Underscore.js 1.3.1
-// (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.
-// Underscore is freely distributable under the MIT license.
-// Portions of Underscore are inspired or borrowed from Prototype,
-// Oliver Steele's Functional, and John Resig's Micro-Templating.
-// For all details and documentation:
-// http://documentcloud.github.com/underscore
-(function(){function q(a,c,d){if(a===c)return a!==0||1/a==1/c;if(a==null||c==null)return a===c;if(a._chain)a=a._wrapped;if(c._chain)c=c._wrapped;if(a.isEqual&&b.isFunction(a.isEqual))return a.isEqual(c);if(c.isEqual&&b.isFunction(c.isEqual))return c.isEqual(a);var e=l.call(a);if(e!=l.call(c))return false;switch(e){case "[object String]":return a==String(c);case "[object Number]":return a!=+a?c!=+c:a==0?1/a==1/c:a==+c;case "[object Date]":case "[object Boolean]":return+a==+c;case "[object [...]
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diff --git a/doc/build/html/_static/up-pressed.png b/doc/build/html/_static/up-pressed.png
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index 8bd587a..0000000
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diff --git a/doc/build/html/_static/up.png b/doc/build/html/_static/up.png
deleted file mode 100644
index b946256..0000000
Binary files a/doc/build/html/_static/up.png and /dev/null differ
diff --git a/doc/build/html/_static/websupport.js b/doc/build/html/_static/websupport.js
deleted file mode 100644
index 71c0a13..0000000
--- a/doc/build/html/_static/websupport.js
+++ /dev/null
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-/*
- * websupport.js
- * ~~~~~~~~~~~~~
- *
- * sphinx.websupport utilties for all documentation.
- *
- * :copyright: Copyright 2007-2014 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) {
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- var columns = textarea.cols;
- var lineCount = 0;
- $.each(lines, function() {
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- });
- var height = lineHeight * (lineCount + 1);
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- };
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-
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- 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));
- });
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- event.preventDefault();
- openReply($(this).attr('id').substring(2));
- });
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- closeReply($(this).attr('id').substring(2));
- });
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- });
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- showProposal($(this).attr('id').substring(2));
- });
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- event.preventDefault();
- hideProposal($(this).attr('id').substring(2));
- });
- $('a.show-propose-change').live("click", function(event) {
- event.preventDefault();
- showProposeChange($(this).attr('id').substring(2));
- });
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- 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();
- }
-
- /**
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- */
- function show(id) {
- $('#ao' + id).hide();
- $('#ah' + id).show();
- var context = $.extend({id: id}, opts);
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- 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);
- });
- }
-
- /**
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- */
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- var div = $('#sc' + id);
- div.slideUp('fast', function() {
- div.remove();
- });
- }
-
- /**
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- * 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) {
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- 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);
- });
- }
-
- /**
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- li.slideDown('fast');
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- function acceptComment(id) {
- $.ajax({
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- 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({
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- url: opts.deleteCommentURL,
- data: {id: id},
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- if (data == 'delete') {
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- div
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- .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.');
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- $('#hc' + id).show();
- var textarea = $('#pt' + id);
- textarea.val(textarea.data('source'));
- $.fn.autogrow.resize(textarea[0]);
- textarea.slideDown('fast');
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-
- function hideProposeChange(id) {
- $('#hc' + id).hide();
- $('#pc' + id).show();
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- textarea.val('').removeAttr('disabled');
- textarea.slideUp('fast');
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- $('#mb' + id).toggle();
- }
-
- /** Handle when the user clicks on a sort by link. */
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- 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());
- });
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- /**
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- */
- 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;
- }
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- var value = 0;
- if (id.charAt(1) != 'u') {
- value = id.charAt(0) == 'u' ? 1 : -1;
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- // The data to be sent to the server.
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- // The div the comment is displayed in.
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-
- // Change the rating text.
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-
- // Send the vote information to the server.
- $.ajax({
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- url: opts.processVoteURL,
- data: d,
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-
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-
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- event.preventDefault();
- addComment($('#rf' + id));
- closeReply(id);
- })
- .find('input[type=button]')
- .click(function() {
- closeReply(id);
- });
- div.slideDown('fast', function() {
- $('#rf' + id).find('textarea').focus();
- });
- }
-
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- */
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- // Remove the reply div from the DOM.
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- $(this).remove();
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-
- // Swap out the hide link for the reply link
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- $('#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;
- }
-
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- */
- 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. */
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- 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;
- }
-
- /**
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- */
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-
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- $.fn.comment = function() {
- return this.each(function() {
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- var count = COMMENT_METADATA[id];
- var title = count + ' comment' + (count == 1 ? '' : 's');
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- alt: 'comment',
- title: title
- }))
- .click(function(event) {
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- id: 'ah' + id
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- .append($(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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- downArrowPressed: '/static/_static/down-pressed.png',
- voting: false,
- moderator: false
- };
-
- if (typeof COMMENT_OPTIONS != "undefined") {
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-
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- <p class="tagline comment">\
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- <form id="rf<%id%>">\
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- <input type="button" value="Cancel" />\
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-
- $(document).ready(function() {
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- var terms = (params.q) ? params.q[0].split(/\s+/) : [];
- var result = $(this);
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- $('#ao' + anchor.substring(9)).click();
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diff --git a/doc/build/html/building.html b/doc/build/html/building.html
deleted file mode 100644
index c611c9e..0000000
--- a/doc/build/html/building.html
+++ /dev/null
@@ -1,284 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
-
-<html xmlns="http://www.w3.org/1999/xhtml">
- <head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Requirements — Sailfish 0.6.4 documentation</title>
-
- <link rel="stylesheet" href="_static/default.css" type="text/css" />
- <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: './',
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- };
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- <script type="text/javascript" src="_static/jquery.js"></script>
- <script type="text/javascript" src="_static/underscore.js"></script>
- <script type="text/javascript" src="_static/doctools.js"></script>
- <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
- <link rel="top" title="Sailfish 0.6.4 documentation" href="index.html" />
- <link rel="prev" title="Welcome to Sailfish’s documentation!" href="index.html" />
- </head>
- <body>
- <div class="related">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="index.html" title="Welcome to Sailfish’s documentation!"
- accesskey="P">previous</a> |</li>
- <li><a href="index.html">Sailfish 0.6.4 documentation</a> »</li>
- </ul>
- </div>
-
- <div class="document">
- <div class="documentwrapper">
- <div class="bodywrapper">
- <div class="body">
-
- <div class="section" id="requirements">
-<h1>Requirements<a class="headerlink" href="#requirements" title="Permalink to this headline">¶</a></h1>
-<ul class="simple">
-<li>A C++11 conformant compiler (currently tested with GCC>=4.7 and Clang>=3.4)</li>
-<li><a class="reference external" href="http://www.cmake.org">CMake</a>. Sailfish uses the CMake build system to check, fetch and install
-dependencies, and to compile and install Sailfish. CMake is available for all
-major platforms (though Sailfish is currently unsupported on Windows.)</li>
-</ul>
-</div>
-<div class="section" id="installation">
-<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
-<p>After downloading the Sailfish source distribution and unpacking it, change into the top-level directory:</p>
-<div class="highlight-python"><div class="highlight"><pre>> cd Sailfish
-</pre></div>
-</div>
-<p>Then, create and out-of-source build directory and change into it:</p>
-<div class="highlight-python"><div class="highlight"><pre>> mkdir build
-> cd build
-</pre></div>
-</div>
-<p>Sailfish makes extensive use of <a class="reference external" href="http://www.boost.org">Boost</a>. We recommend installing the most
-recent version (1.55) systemwide if possible. If Boost is not installed on your
-system, the build process will fetch, compile and install it locally. However,
-if you already have a recent version of Boost available on your system, it make
-sense to tell the build system to use that.</p>
-<p>If you have Boost installed you can tell CMake where to look for it. Likewise,
-if you already have <a class="reference external" href="http://threadingbuildingblocks.org/">Intel’s Threading Building Blocks</a> library installed, you can tell CMake
-where it is as well. The flags for CMake are as follows:</p>
-<ul class="simple">
-<li>-DFETCH_BOOST=TRUE – If you don’t have Boost installed (or have an older
-version of it), you can provide the FETCH_BOOST flag instead of the
-BOOST_ROOT variable, which will cause CMake to fetch and build Boost locally.</li>
-<li>-DBOOST_ROOT=<boostdir> – Tells CMake where an existing installtion of Boost
-resides, and looks for the appropritate version in <boostdir>. This is the
-top-level directory where Boost is installed (e.g. /opt/local).</li>
-<li>-DTBB_INSTALL_DIR=<tbbroot> – Tells CMake where an existing installation of
-Intel’s TBB is installed (<tbbroot>), and looks for the apropriate headers
-and libraries there. This is the top-level directory where TBB is installed
-(e.g. /opt/local).</li>
-<li>-DCMAKE_INSTALL_PREFIX=<install_dir> – <install_dir> is the directory to
-which you wish Sailfish to be installed. If you don’t specify this option,
-it will be installed locally in the top-level directory (i.e. the directory
-directly above “build”).</li>
-</ul>
-<p>Setting the appropriate flags, you can then run the CMake configure step as
-follows:</p>
-<div class="highlight-python"><div class="highlight"><pre>> cmake [FLAGS] ..
-</pre></div>
-</div>
-<p>The above command is the cmake configuration step, which <em>should</em> complain if
-anything goes wrong. Next, you have to run the build step. Depending on what
-libraries need to be fetched and installed, this could take a while
-(specifically if the installation needs to install Boost). To start the build,
-just run make.</p>
-<div class="highlight-python"><div class="highlight"><pre>> make
-</pre></div>
-</div>
-<p>If the build is successful, the appropriate executables and libraries should be
-created. There are two points to note about the build process. First, if the
-build system is downloading and compiling boost, you may see a large number of
-warnings during compilation; these are normal. Second, note that CMake has
-colored output by default, and the steps which create or link libraries are
-printed in red. This is the color chosen by CMake for linking messages, and
-does not denote an error in the build process.</p>
-<p>Finally, after everything is built, the libraries and executable can be
-installed with:</p>
-<div class="highlight-python"><div class="highlight"><pre>> make install
-</pre></div>
-</div>
-<p>To ensure that Sailfish has access to the appropriate libraries you should
-ensure that the PATH variabile contains <install_dir>/bin, and that
-LD_LIBRARY_PATH (or DYLD_FALLBACK_LIBRARY_PATH on OSX) contains
-<install_dir>/lib.</p>
-<p>After the paths are set, you can test the installation by running</p>
-<div class="highlight-python"><div class="highlight"><pre>> make test
-</pre></div>
-</div>
-<p>This should run a simple test and tell you if it succeeded or not.</p>
-</div>
-<div class="section" id="running-sailfish">
-<h1>Running Sailfish<a class="headerlink" href="#running-sailfish" title="Permalink to this headline">¶</a></h1>
-<p>Sailfish is a tool for transcript quantification from RNA-seq data. It
-requires a set of target transcripts (either from a reference or _de-<a href="#id3"><span class="problematic" id="id4">novo_</span></a>
-assembly) to quantify. All you need to run Sailfish is a fasta file containing
-your reference transcripts and a (set of) fasta/fastq file(s) containing your
-reads. Sailfish runs in two phases; indexing and quantification. The indexing
-step is independent of the reads, and only need to be run one for a particular
-set of reference transcripts and choice of k (the k-mer size). The
-quantification step, obviously, is specific to the set of RNA-seq reads and is
-thus run more frequently. For a more complete description of all available
-options in Sailfish, see the manual.</p>
-<div class="section" id="indexing">
-<h2>Indexing<a class="headerlink" href="#indexing" title="Permalink to this headline">¶</a></h2>
-<p>To generate the Sailfish index for your reference set of transcripts, you
-should run the following command:</p>
-<dl class="docutils">
-<dt>::</dt>
-<dd>> sailfish index -t <ref_transcripts> -o <out_dir> -k <kmer_len></dd>
-</dl>
-<p>This will build a Sailfish index for k-mers of length <kmer_len> for the
-reference transcripts provided in the file <ref_transcripts> and place the
-index under the directory <out_dir>. There are additional options that can
-be passed to the Sailfish indexer (e.g. the number of threads to use). These
-can be seen by executing the command “Sailfish index -h”.</p>
-</div>
-<div class="section" id="quantification">
-<h2>Quantification<a class="headerlink" href="#quantification" title="Permalink to this headline">¶</a></h2>
-<p>Now that you have generated the Sailfish index (say that it’s the directory
-<index_dir> — this corresponds to the <out_dir> argument provided in the
-previous step), you can quantify the transcript expression for a given set of
-reads. To perform the quantification, you run a command like the following:</p>
-<div class="highlight-python"><div class="highlight"><pre>> sailfish quant -i <index_dir> -l "<libtype>" {-r <unmated> | -1 <mates1> -2 <mates2>} -o <quant_dir>
-</pre></div>
-</div>
-<p>Where <index_dir> is, as described above, the location of the sailfish index,
-<libtype> is a string describing the format of the read library (see the
-[library string](#library-string) section below) <unmated> is a list of files
-containing unmated reads, <mates{1,2}> are lists of files containg,
-respectively, the first and second mates of paired-end reads. Finally,
-<quant_dir> is the directory where the output should be written. Just like the
-indexing step, additional options are available, and can be viewed by running
-“sailfish quant -h”.</p>
-<p>When the quantification step is finished, the directory <quant_dir> will
-contain a file named “quant.sf” (and, if bias correction is enabled, an
-additional file names “quant_bias_corrected.sf”). This file contains the
-result of the Sailfish quantification step. This file contains a number of
-columns (which are listed in the last of the header lines beginning with ‘#’).
-Specifically, the columns are (1) Transcript ID, (2) Transcript Length, (3)
-Transcripts per Million (TPM), (4) Reads Per Kilobase per Million mapped reads
-(RPKM), (5) K-mers Per Kilobase per Million mapped k-mers (KPKM), (6) Estimated
-number of k-mers (an estimate of the number of k-mers drawn from this
-transcript given the transcript’s relative abundance and length) and (7)
-Estimated number of reads (an estimate of the number of reads drawn from this
-transcript given the transcript’s relative abnundance and length). The first
-two columns are self-explanatory, the next four are measures of transcript
-abundance and the final is a commonly used input for differential expression
-tools. The Transcripts per Million quantification number is computed as
-described in <a class="footnote-reference" href="#id2" id="id1">[1]</a>, and is meant as an estimate of the number of transcripts, per
-million observed transcripts, originating from each isoform. Its benefit over
-the K/RPKM measure is that it is independent of the mean expressed transcript
-length (i.e. if the mean expressed transcript length varies between samples,
-for example, this alone can affect differential analysis based on the K/RPKM.)
-The RPKM is a classic measure of relative transcript abundance, and is an
-estimate of the number of reads per kilobase of transcript (per million mapped
-reads) originating from each transcript. The KPKM should closely track the
-RPKM, but is defined for very short features which are larger than the chosen
-k-mer length but may be shorter than the read length. Typically, you should
-prefer the KPKM measure to the RPKM measure, since the k-mer is the most
-natural unit of coverage for Sailfish.</p>
-</div>
-</div>
-<div class="section" id="license">
-<h1>License<a class="headerlink" href="#license" title="Permalink to this headline">¶</a></h1>
-<p>This program is free software: you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation, either version 3 of the License, or (at your option) any later
-version.</p>
-<p>This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.</p>
-<p>You should have received a copy of the GNU General Public License along with
-this program. If not, see <<a class="reference external" href="http://www.gnu.org/licenses/">http://www.gnu.org/licenses/</a>>.</p>
-</div>
-<div class="section" id="references">
-<h1>References<a class="headerlink" href="#references" title="Permalink to this headline">¶</a></h1>
-<table class="docutils footnote" frame="void" id="id2" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id1">[1]</a></td><td>Li, Bo, et al. “RNA-Seq gene expression estimation with read mapping uncertainty.”
-Bioinformatics 26.4 (2010): 493-500.i</td></tr>
-</tbody>
-</table>
-</div>
-
-
- </div>
- </div>
- </div>
- <div class="sphinxsidebar">
- <div class="sphinxsidebarwrapper">
- <h3><a href="index.html">Table Of Contents</a></h3>
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-<li><a class="reference internal" href="#running-sailfish">Running Sailfish</a><ul>
-<li><a class="reference internal" href="#indexing">Indexing</a></li>
-<li><a class="reference internal" href="#quantification">Quantification</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#license">License</a></li>
-<li><a class="reference internal" href="#references">References</a></li>
-</ul>
-
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