bio-samtools 0.6.2 → 2.0.3

data/doc/fonts.css

@@ -0,0 +1,167 @@
+/*
+ * Copyright 2010, 2012 Adobe Systems Incorporated (http://www.adobe.com/),
+ * with Reserved Font Name "Source". All Rights Reserved. Source is a
+ * trademark of Adobe Systems Incorporated in the United States and/or other
+ * countries.
+ *
+ * This Font Software is licensed under the SIL Open Font License, Version
+ * 1.1.
+ *
+ * This license is copied below, and is also available with a FAQ at:
+ * http://scripts.sil.org/OFL
+ */
+
+@font-face {
+  font-family: "Source Code Pro";
+  font-style: normal;
+  font-weight: 400;
+  src: local("Source Code Pro"),
+       local("SourceCodePro-Regular"),
+       url("fonts/SourceCodePro-Regular.ttf") format("truetype");
+}
+
+@font-face {
+  font-family: "Source Code Pro";
+  font-style: normal;
+  font-weight: 700;
+  src: local("Source Code Pro Bold"),
+       local("SourceCodePro-Bold"),
+       url("fonts/SourceCodePro-Bold.ttf") format("truetype");
+}
+
+/*
+ * Copyright (c) 2010, Łukasz Dziedzic (dziedzic@typoland.com),
+ * with Reserved Font Name Lato.
+ *
+ * This Font Software is licensed under the SIL Open Font License, Version
+ * 1.1.
+ *
+ * This license is copied below, and is also available with a FAQ at:
+ * http://scripts.sil.org/OFL
+ */
+
+@font-face {
+  font-family: "Lato";
+  font-style: normal;
+  font-weight: 300;
+  src: local("Lato Light"),
+       local("Lato-Light"),
+       url("fonts/Lato-Light.ttf") format("truetype");
+}
+
+@font-face {
+  font-family: "Lato";
+  font-style: italic;
+  font-weight: 300;
+  src: local("Lato Light Italic"),
+       local("Lato-LightItalic"),
+       url("fonts/Lato-LightItalic.ttf") format("truetype");
+}
+
+@font-face {
+  font-family: "Lato";
+  font-style: normal;
+  font-weight: 700;
+  src: local("Lato Regular"),
+       local("Lato-Regular"),
+       url("fonts/Lato-Regular.ttf") format("truetype");
+}
+
+@font-face {
+  font-family: "Lato";
+  font-style: italic;
+  font-weight: 700;
+  src: local("Lato Italic"),
+       local("Lato-Italic"),
+       url("fonts/Lato-RegularItalic.ttf") format("truetype");
+}
+
+/*
+ * -----------------------------------------------------------
+ * SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007
+ * -----------------------------------------------------------
+ *
+ * PREAMBLE
+ * The goals of the Open Font License (OFL) are to stimulate worldwide
+ * development of collaborative font projects, to support the font creation
+ * efforts of academic and linguistic communities, and to provide a free and
+ * open framework in which fonts may be shared and improved in partnership
+ * with others.
+ *
+ * The OFL allows the licensed fonts to be used, studied, modified and
+ * redistributed freely as long as they are not sold by themselves. The
+ * fonts, including any derivative works, can be bundled, embedded,
+ * redistributed and/or sold with any software provided that any reserved
+ * names are not used by derivative works. The fonts and derivatives,
+ * however, cannot be released under any other type of license. The
+ * requirement for fonts to remain under this license does not apply
+ * to any document created using the fonts or their derivatives.
+ *
+ * DEFINITIONS
+ * "Font Software" refers to the set of files released by the Copyright
+ * Holder(s) under this license and clearly marked as such. This may
+ * include source files, build scripts and documentation.
+ *
+ * "Reserved Font Name" refers to any names specified as such after the
+ * copyright statement(s).
+ *
+ * "Original Version" refers to the collection of Font Software components as
+ * distributed by the Copyright Holder(s).
+ *
+ * "Modified Version" refers to any derivative made by adding to, deleting,
+ * or substituting -- in part or in whole -- any of the components of the
+ * Original Version, by changing formats or by porting the Font Software to a
+ * new environment.
+ *
+ * "Author" refers to any designer, engineer, programmer, technical
+ * writer or other person who contributed to the Font Software.
+ *
+ * PERMISSION & CONDITIONS
+ * Permission is hereby granted, free of charge, to any person obtaining
+ * a copy of the Font Software, to use, study, copy, merge, embed, modify,
+ * redistribute, and sell modified and unmodified copies of the Font
+ * Software, subject to the following conditions:
+ *
+ * 1) Neither the Font Software nor any of its individual components,
+ * in Original or Modified Versions, may be sold by itself.
+ *
+ * 2) Original or Modified Versions of the Font Software may be bundled,
+ * redistributed and/or sold with any software, provided that each copy
+ * contains the above copyright notice and this license. These can be
+ * included either as stand-alone text files, human-readable headers or
+ * in the appropriate machine-readable metadata fields within text or
+ * binary files as long as those fields can be easily viewed by the user.
+ *
+ * 3) No Modified Version of the Font Software may use the Reserved Font
+ * Name(s) unless explicit written permission is granted by the corresponding
+ * Copyright Holder. This restriction only applies to the primary font name as
+ * presented to the users.
+ *
+ * 4) The name(s) of the Copyright Holder(s) or the Author(s) of the Font
+ * Software shall not be used to promote, endorse or advertise any
+ * Modified Version, except to acknowledge the contribution(s) of the
+ * Copyright Holder(s) and the Author(s) or with their explicit written
+ * permission.
+ *
+ * 5) The Font Software, modified or unmodified, in part or in whole,
+ * must be distributed entirely under this license, and must not be
+ * distributed under any other license. The requirement for fonts to
+ * remain under this license does not apply to any document created
+ * using the Font Software.
+ *
+ * TERMINATION
+ * This license becomes null and void if any of the above conditions are
+ * not met.
+ *
+ * DISCLAIMER
+ * THE FONT SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTIES OF
+ * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
+ * OF COPYRIGHT, PATENT, TRADEMARK, OR OTHER RIGHT. IN NO EVENT SHALL THE
+ * COPYRIGHT HOLDER BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * INCLUDING ANY GENERAL, SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL
+ * DAMAGES, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF THE USE OR INABILITY TO USE THE FONT SOFTWARE OR FROM
+ * OTHER DEALINGS IN THE FONT SOFTWARE.
+ */
+

data/doc/index.html

@@ -2,111 +2,105 @@
 
 <html>
 <head>
-<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
+<meta charset="UTF-8">
 
 <title>Pileup</title>
 
-<link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet">
+<link href="./fonts.css" rel="stylesheet">
+<link href="./rdoc.css" rel="stylesheet">
 
 <script type="text/javascript">
   var rdoc_rel_prefix = "./";
 </script>
 
-<script type="text/javascript" charset="utf-8" src="./js/jquery.js"></script>
-<script type="text/javascript" charset="utf-8" src="./js/navigation.js"></script>
-<script type="text/javascript" charset="utf-8" src="./js/search_index.js"></script>
-<script type="text/javascript" charset="utf-8" src="./js/search.js"></script>
-<script type="text/javascript" charset="utf-8" src="./js/searcher.js"></script>
-<script type="text/javascript" charset="utf-8" src="./js/darkfish.js"></script>
+<script src="./js/jquery.js"></script>
+<script src="./js/navigation.js"></script>
+<script src="./js/search_index.js"></script>
+<script src="./js/search.js"></script>
+<script src="./js/searcher.js"></script>
+<script src="./js/darkfish.js"></script>
 
 
-<body>
-<nav id="metadata">
-  <nav id="home-section" class="section">
-  <h3 class="section-header">
-    <a href="./index.html">Home</a>
+<body id="top" role="document" class="file">
+<nav role="navigation">
+  <div id="project-navigation">
+    <div id="home-section" role="region" title="Quick navigation" class="nav-section">
+  <h2>
+    <a href="./index.html" rel="home">Home</a>
+  </h2>
+
+  <div id="table-of-contents-navigation">
+    <a href="./table_of_contents.html#pages">Pages</a>
     <a href="./table_of_contents.html#classes">Classes</a>
     <a href="./table_of_contents.html#methods">Methods</a>
-  </h3>
-</nav>
+  </div>
+</div>
 
 
-  <nav id="search-section" class="section project-section" class="initially-hidden">
+    <div id="search-section" role="search" class="project-section initially-hidden">
   <form action="#" method="get" accept-charset="utf-8">
-    <h3 class="section-header">
-      <input type="text" name="search" placeholder="Search" id="search-field"
+    <div id="search-field-wrapper">
+      <input id="search-field" role="combobox" aria-label="Search"
+             aria-autocomplete="list" aria-controls="search-results"
+             type="text" name="search" placeholder="Search" spellcheck="false"
              title="Type to search, Up and Down to navigate, Enter to load">
-    </h3>
-  </form>
+    </div>
 
-  <ul id="search-results" class="initially-hidden"></ul>
-</nav>
+    <ul id="search-results" aria-label="Search Results"
+        aria-busy="false" aria-expanded="false"
+        aria-atomic="false" class="initially-hidden"></ul>
+  </form>
+</div>
 
+  </div>
 
   <div id="project-metadata">
-    <nav id="fileindex-section" class="section project-section">
-  <h3 class="section-header">Pages</h3>
+    <div id="fileindex-section" class="nav-section">
+  <h3>Pages</h3>
 
-  <ul>
+  <ul class="link-list">
   
-    <li class="file"><a href="./LICENSE_txt.html">LICENSE</a>
+    <li><a href="./LICENSE_txt.html">LICENSE</a>
   
   </ul>
-</nav>
+</div>
 
-    <nav id="classindex-section" class="section project-section">
-  <h3 class="section-header">Class and Module Index</h3>
+    <div id="classindex-section" class="nav-section">
+  <h3>Class and Module Index</h3>
 
   <ul class="link-list">
   
     <li><a href="./Bio.html">Bio</a>
   
-    <li><a href="./Bio/DB.html">Bio::DB</a>
-  
     <li><a href="./Bio/DB/Alignment.html">Bio::DB::Alignment</a>
   
     <li><a href="./Bio/DB/Pileup.html">Bio::DB::Pileup</a>
   
-    <li><a href="./Bio/DB/SAM.html">Bio::DB::SAM</a>
-  
     <li><a href="./Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
   
     <li><a href="./Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
   
-    <li><a href="./Bio/DB/SAM/Tools/Bam1CoreT.html">Bio::DB::SAM::Tools::Bam1CoreT</a>
-  
-    <li><a href="./Bio/DB/SAM/Tools/Bam1T.html">Bio::DB::SAM::Tools::Bam1T</a>
-  
-    <li><a href="./Bio/DB/SAM/Tools/BamHeaderT.html">Bio::DB::SAM::Tools::BamHeaderT</a>
-  
-    <li><a href="./Bio/DB/SAM/Tools/BamPileup1T.html">Bio::DB::SAM::Tools::BamPileup1T</a>
-  
-    <li><a href="./Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
-  
-    <li><a href="./Bio/DB/SAM/Tools/SamfileTX.html">Bio::DB::SAM::Tools::SamfileTX</a>
-  
-    <li><a href="./Bio/DB/SAMException.html">Bio::DB::SAMException</a>
-  
     <li><a href="./Bio/DB/Sam.html">Bio::DB::Sam</a>
   
     <li><a href="./Bio/DB/Tag.html">Bio::DB::Tag</a>
   
     <li><a href="./Bio/DB/Vcf.html">Bio::DB::Vcf</a>
   
-    <li><a href="./LibC.html">LibC</a>
-  
   </ul>
-</nav>
+</div>
 
   </div>
 </nav>
 
+<main role="main">
 <p>This is the API documentation for Pileup.
+</main>
+
 
 
-<footer id="validator-badges">
-  <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
-  <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
-  <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
+<footer id="validator-badges" role="contentinfo">
+  <p><a href="http://validator.w3.org/check/referer">Validate</a>
+  <p>Generated by <a href="http://rdoc.rubyforge.org">RDoc</a> 4.1.1.
+  <p>Based on <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish</a> by <a href="http://deveiate.org">Michael Granger</a>.
 </footer>
 

data/doc/js/darkfish.js

@@ -52,20 +52,6 @@ function hookDebuggingToggle() {
   $('#debugging-toggle img').click( toggleDebuggingSection );
 };
 
-function hookTableOfContentsToggle() {
-  $('.indexpage li .toc-toggle').each( function() {
-    $(this).click( function() {
-      $(this).toggleClass('open');
-    });
-
-    var section = $(this).next();
-
-    $(this).click( function() {
-      section.slideToggle();
-    });
-  });
-}
-
 function hookSearch() {
   var input  = $('#search-field').eq(0);
   var result = $('#search-results').eq(0);
@@ -109,13 +95,15 @@ function hookSearch() {
 function highlightTarget( anchor ) {
   console.debug( "Highlighting target '%s'.", anchor );
 
-  $("a[name=" + anchor + "]").each( function() {
-    if ( !$(this).parent().parent().hasClass('target-section') ) {
-      console.debug( "Wrapping the target-section" );
-      $('div.method-detail').unwrap( 'div.target-section' );
-      $(this).parent().wrap( '<div class="target-section"></div>' );
-    } else {
-      console.debug( "Already wrapped." );
+  $("a[name]").each( function() {
+    if ( $(this).attr("name") == anchor ) {
+      if ( !$(this).parent().parent().hasClass('target-section') ) {
+        console.debug( "Wrapping the target-section" );
+        $('div.method-detail').unwrap( 'div.target-section' );
+        $(this).parent().wrap( '<div class="target-section"></div>' );
+      } else {
+        console.debug( "Already wrapped." );
+      }
     }
   });
 };
@@ -147,7 +135,6 @@ $(document).ready( function() {
   hookDebuggingToggle();
   hookSearch();
   highlightLocationTarget();
-  hookTableOfContentsToggle();
 
   $('ul.link-list a').bind( "click", highlightClickTarget );
 });

data/doc/js/search.js

@@ -14,7 +14,12 @@ Search.prototype = $.extend({}, Navigation, new function() {
 
   this.init = function() {
     var _this = this;
-    var observer = function() {
+    var observer = function(e) {
+      switch(e.originalEvent.keyCode) {
+        case 38: // Event.KEY_UP
+        case 40: // Event.KEY_DOWN
+          return;
+      }
       _this.search(_this.$input[0].value);
     };
     this.$input.keyup(observer);
@@ -39,9 +44,12 @@ Search.prototype = $.extend({}, Navigation, new function() {
     if (value == '') {
       this.lastQuery = value;
       this.$result.empty();
+      this.$result.attr('aria-expanded', 'false');
       this.setNavigationActive(false);
     } else if (value != this.lastQuery) {
       this.lastQuery = value;
+      this.$result.attr('aria-busy',     'true');
+      this.$result.attr('aria-expanded', 'true');
       this.firstRun = true;
       this.searcher.find(value);
     }
@@ -55,25 +63,32 @@ Search.prototype = $.extend({}, Navigation, new function() {
     }
 
     for (var i=0, l = results.length; i < l; i++) {
-      target.appendChild(this.renderItem.call(this, results[i]));
+      var item = this.renderItem.call(this, results[i]);
+      item.setAttribute('id', 'search-result-' + target.childElementCount);
+      target.appendChild(item);
     };
 
     if (this.firstRun && results.length > 0) {
       this.firstRun = false;
       this.$current = $(target.firstChild);
-      this.$current.addClass('current');
+      this.$current.addClass('search-selected');
     }
     if (jQuery.browser.msie) this.$element[0].className += '';
+
+    if (isLast) this.$result.attr('aria-busy', 'false');
   }
 
   this.move = function(isDown) {
     if (!this.$current) return;
     var $next = this.$current[isDown ? 'next' : 'prev']();
     if ($next.length) {
-      this.$current.removeClass('current');
-      $next.addClass('current');
+      this.$current.removeClass('search-selected');
+      $next.addClass('search-selected');
+      this.$input.attr('aria-activedescendant', $next.attr('id'));
       this.scrollIntoView($next[0], this.$view[0]);
       this.$current = $next;
+      this.$input.val($next[0].firstChild.firstChild.text);
+      this.$input.select();
     }
     return true;
   }