RubyGems - fstrozzi-Gmap - Versions diffs - 1.0.0 - Mend

fstrozzi-Gmap 1.0.0

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Files changed (32) hide show

data/README +41 -0
data/doc/classes/Gmap.html +129 -0
data/doc/classes/Gmap/Core.html +252 -0
data/doc/classes/Gmap/Core.src/M000006.html +18 -0
data/doc/classes/Gmap/Core.src/M000007.html +25 -0
data/doc/classes/Gmap/Core.src/M000008.html +18 -0
data/doc/classes/Gmap/Core.src/M000009.html +52 -0
data/doc/classes/Gmap/Result.html +337 -0
data/doc/classes/Gmap/Result.src/M000010.html +18 -0
data/doc/classes/Gmap/Result.src/M000011.html +41 -0
data/doc/classes/Gmap/Result.src/M000012.html +22 -0
data/doc/classes/Gmap/Result.src/M000013.html +22 -0
data/doc/classes/Gmap/Result.src/M000014.html +18 -0
data/doc/classes/GmapTest.html +197 -0
data/doc/classes/GmapTest.src/M000001.html +18 -0
data/doc/classes/GmapTest.src/M000002.html +21 -0
data/doc/classes/GmapTest.src/M000003.html +25 -0
data/doc/classes/GmapTest.src/M000004.html +62 -0
data/doc/classes/GmapTest.src/M000005.html +65 -0
data/doc/created.rid +1 -0
data/doc/files/lib/gmap/core_rb.html +118 -0
data/doc/files/lib/gmap_rb.html +101 -0
data/doc/files/test/unit/gmap_test_rb.html +109 -0
data/doc/fr_class_index.html +30 -0
data/doc/fr_file_index.html +29 -0
data/doc/fr_method_index.html +40 -0
data/doc/index.html +24 -0
data/lib/gmap.rb +1 -0
data/lib/gmap/core.rb +269 -0
data/samples/test.gmap +148 -0
data/test/unit/gmap_test.rb +127 -0
metadata +93 -0

data/doc/classes/Gmap/Core.src/M000008.html ADDED

@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+  <title>close (Gmap::Core)</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+  <pre><span class="ruby-comment cmt"># File lib/gmap/core.rb, line 70</span>
+    <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">close</span>
+      <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">close</span>
+    <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>

data/doc/classes/Gmap/Core.src/M000009.html ADDED

@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+  <title>each_sequence (Gmap::Core)</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+  <pre><span class="ruby-comment cmt"># File lib/gmap/core.rb, line 78</span>
+    <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each_sequence</span>
+      <span class="ruby-identifier">start</span> = <span class="ruby-keyword kw">false</span>
+      <span class="ruby-identifier">res</span> = <span class="ruby-constant">Gmap</span><span class="ruby-operator">::</span><span class="ruby-constant">Result</span>.<span class="ruby-identifier">new</span>
+      <span class="ruby-identifier">all_results</span> = []
+      <span class="ruby-identifier">query</span> = <span class="ruby-keyword kw">nil</span>
+      <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">each_line</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span>
+         <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">l</span><span class="ruby-operator">=~</span><span class="ruby-regexp re">/&gt;(\d+|\w+)\s/</span> <span class="ruby-keyword kw">and</span> <span class="ruby-operator">!</span><span class="ruby-identifier">start</span> <span class="ruby-keyword kw">then</span>
+           <span class="ruby-identifier">start</span> = <span class="ruby-keyword kw">true</span>
+           <span class="ruby-identifier">query</span> = <span class="ruby-node">&quot;#{$1}&quot;</span>
+         <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span><span class="ruby-operator">=~</span><span class="ruby-regexp re">/&gt;(\d+|\w+)\s/</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">start</span> <span class="ruby-keyword kw">then</span>
+           <span class="ruby-identifier">res</span>.<span class="ruby-identifier">query</span> = <span class="ruby-identifier">query</span>
+           <span class="ruby-identifier">all_results</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-identifier">res</span>.<span class="ruby-identifier">dup</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">res</span>.<span class="ruby-identifier">target</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword kw">nil</span>
+           <span class="ruby-identifier">query</span> = <span class="ruby-node">&quot;#{$1}&quot;</span>
+           <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">block_given?</span>
+             <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">all_results</span>
+           <span class="ruby-keyword kw">else</span>
+             <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-value str">&quot;Block needed&quot;</span>
+           <span class="ruby-keyword kw">end</span>
+           <span class="ruby-identifier">all_results</span>.<span class="ruby-identifier">clear</span>
+           <span class="ruby-identifier">res</span>.<span class="ruby-identifier">clear</span>
+         <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span><span class="ruby-operator">=~</span><span class="ruby-regexp re">/Path\s\d+/</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">res</span>.<span class="ruby-identifier">target</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-keyword kw">then</span>
+           <span class="ruby-identifier">res</span>.<span class="ruby-identifier">query</span> = <span class="ruby-identifier">query</span>
+           <span class="ruby-identifier">all_results</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-identifier">res</span>.<span class="ruby-identifier">dup</span>
+           <span class="ruby-identifier">res</span>.<span class="ruby-identifier">clear</span>
+         <span class="ruby-keyword kw">end</span>
+         <span class="ruby-identifier">res</span> = <span class="ruby-identifier">parse_line</span>(<span class="ruby-identifier">res</span>,<span class="ruby-identifier">l</span>)
+      <span class="ruby-keyword kw">end</span>
+      <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">start</span> <span class="ruby-keyword kw">then</span>
+        <span class="ruby-identifier">res</span>.<span class="ruby-identifier">query</span> = <span class="ruby-identifier">query</span>
+        <span class="ruby-identifier">all_results</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-identifier">res</span>.<span class="ruby-identifier">dup</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">res</span>.<span class="ruby-identifier">target</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword kw">nil</span>
+        <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">block_given?</span>
+          <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">all_results</span>
+        <span class="ruby-keyword kw">else</span>
+          <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-value str">&quot;Block needed&quot;</span>
+        <span class="ruby-keyword kw">end</span>
+      <span class="ruby-keyword kw">end</span>
+    <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>

data/doc/classes/Gmap/Result.html ADDED

@@ -0,0 +1,337 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!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" xml:lang="en" lang="en">
+<head>
+  <title>Class: Gmap::Result</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <meta http-equiv="Content-Script-Type" content="text/javascript" />
+  <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+  <script type="text/javascript">
+  // <![CDATA[
+  function popupCode( url ) {
+    window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
+  }
+  function toggleCode( id ) {
+    if ( document.getElementById )
+      elem = document.getElementById( id );
+    else if ( document.all )
+      elem = eval( "document.all." + id );
+    else
+      return false;
+    elemStyle = elem.style;
+    if ( elemStyle.display != "block" ) {
+      elemStyle.display = "block"
+    } else {
+      elemStyle.display = "none"
+    }
+    return true;
+  }
+  // Make codeblocks hidden by default
+  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
+  // ]]>
+  </script>
+</head>
+<body>
+    <div id="classHeader">
+        <table class="header-table">
+        <tr class="top-aligned-row">
+          <td><strong>Class</strong></td>
+          <td class="class-name-in-header">Gmap::Result</td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>In:</strong></td>
+            <td>
+                <a href="../../files/lib/gmap/core_rb.html">
+                lib/gmap/core.rb
+                </a>
+        <br />
+            </td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>Parent:</strong></td>
+            <td>
+                Object
+            </td>
+        </tr>
+        </table>
+    </div>
+  <!-- banner header -->
+  <div id="bodyContent">
+  <div id="contextContent">
+    <div id="description">
+      <p>
+This class store the informations of a single <a
+href="../Gmap.html">Gmap</a> result
+</p>
+    </div>
+   </div>
+    <div id="method-list">
+      <h3 class="section-bar">Methods</h3>
+      <div class="name-list">
+      <a href="#M000011">clear</a>&nbsp;&nbsp;
+      <a href="#M000014">count</a>&nbsp;&nbsp;
+      <a href="#M000010">new</a>&nbsp;&nbsp;
+      <a href="#M000013">set_save</a>&nbsp;&nbsp;
+      <a href="#M000012">set_search</a>&nbsp;&nbsp;
+      </div>
+    </div>
+  </div>
+    <!-- if includes -->
+    <div id="section">
+    <div id="attribute-list">
+      <h3 class="section-bar">Attributes</h3>
+      <div class="name-list">
+        <table>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">aa_change</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">aln</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">c</td>
+          <td class="context-item-value">&nbsp;[W]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">c</td>
+          <td class="context-item-value">&nbsp;[R]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">coverage</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">end</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">exons</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">gene_end</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">gene_id</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">gene_start</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">indels</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">maps</td>
+          <td class="context-item-value">&nbsp;[W]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">mismatch</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">path</td>
+          <td class="context-item-value">&nbsp;[W]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">perc_identity</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">q_end</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">q_start</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">query</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">save_aln</td>
+          <td class="context-item-value">&nbsp;[R]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">search_aln</td>
+          <td class="context-item-value">&nbsp;[W]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">search_aln</td>
+          <td class="context-item-value">&nbsp;[R]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">start</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">strand</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">target</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        </table>
+      </div>
+    </div>
+    <!-- if method_list -->
+    <div id="methods">
+      <h3 class="section-bar">Public Class methods</h3>
+      <div id="method-M000010" class="method-detail">
+        <a name="M000010"></a>
+        <div class="method-heading">
+          <a href="Result.src/M000010.html" target="Code" class="method-signature"
+            onclick="popupCode('Result.src/M000010.html');return false;">
+          <span class="method-name">new</span><span class="method-args">()</span>
+          </a>
+        </div>
+        <div class="method-description">
+        </div>
+      </div>
+      <h3 class="section-bar">Public Instance methods</h3>
+      <div id="method-M000011" class="method-detail">
+        <a name="M000011"></a>
+        <div class="method-heading">
+          <a href="Result.src/M000011.html" target="Code" class="method-signature"
+            onclick="popupCode('Result.src/M000011.html');return false;">
+          <span class="method-name">clear</span><span class="method-args">()</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p>
+Initializes all the attributes of the result
+</p>
+        </div>
+      </div>
+      <div id="method-M000014" class="method-detail">
+        <a name="M000014"></a>
+        <div class="method-heading">
+          <a href="Result.src/M000014.html" target="Code" class="method-signature"
+            onclick="popupCode('Result.src/M000014.html');return false;">
+          <span class="method-name">count</span><span class="method-args">()</span>
+          </a>
+        </div>
+        <div class="method-description">
+        </div>
+      </div>
+      <div id="method-M000013" class="method-detail">
+        <a name="M000013"></a>
+        <div class="method-heading">
+          <a href="Result.src/M000013.html" target="Code" class="method-signature"
+            onclick="popupCode('Result.src/M000013.html');return false;">
+          <span class="method-name">set_save</span><span class="method-args">()</span>
+          </a>
+        </div>
+        <div class="method-description">
+        </div>
+      </div>
+      <div id="method-M000012" class="method-detail">
+        <a name="M000012"></a>
+        <div class="method-heading">
+          <a href="Result.src/M000012.html" target="Code" class="method-signature"
+            onclick="popupCode('Result.src/M000012.html');return false;">
+          <span class="method-name">set_search</span><span class="method-args">()</span>
+          </a>
+        </div>
+        <div class="method-description">
+        </div>
+      </div>
+    </div>
+  </div>
+<div id="validator-badges">
+  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+</div>
+</body>
+</html>

data/doc/classes/Gmap/Result.src/M000010.html ADDED

@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+  <title>new (Gmap::Result)</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+  <pre><span class="ruby-comment cmt"># File lib/gmap/core.rb, line 205</span>
+    <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>
+        <span class="ruby-identifier">clear</span>
+    <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>

data/doc/classes/Gmap/Result.src/M000011.html ADDED

@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+  <title>clear (Gmap::Result)</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+  <pre><span class="ruby-comment cmt"># File lib/gmap/core.rb, line 209</span>
+        <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">clear</span>
+                <span class="ruby-ivar">@query</span> = <span class="ruby-keyword kw">nil</span>
+                <span class="ruby-ivar">@target</span> = <span class="ruby-keyword kw">nil</span>
+                <span class="ruby-ivar">@start</span> = <span class="ruby-keyword kw">nil</span>
+                <span class="ruby-ivar">@end</span> = <span class="ruby-keyword kw">nil</span>
+                <span class="ruby-ivar">@strand</span> = <span class="ruby-keyword kw">nil</span>
+                <span class="ruby-ivar">@exons</span> = <span class="ruby-keyword kw">nil</span>
+                <span class="ruby-ivar">@coverage</span> = <span class="ruby-keyword kw">nil</span>
+                <span class="ruby-ivar">@perc_identity</span> = <span class="ruby-keyword kw">nil</span>
+                <span class="ruby-ivar">@indels</span> = <span class="ruby-keyword kw">nil</span>
+                <span class="ruby-ivar">@mismatch</span> = <span class="ruby-keyword kw">nil</span>
+                <span class="ruby-ivar">@aa_change</span> = <span class="ruby-keyword kw">nil</span>
+                <span class="ruby-ivar">@gene_start</span> = <span class="ruby-keyword kw">nil</span>
+                <span class="ruby-ivar">@gene_end</span> = <span class="ruby-keyword kw">nil</span>
+                <span class="ruby-ivar">@gene_id</span> = <span class="ruby-keyword kw">nil</span>
+                <span class="ruby-ivar">@q_start</span> = <span class="ruby-keyword kw">nil</span>
+                <span class="ruby-ivar">@q_end</span> = <span class="ruby-keyword kw">nil</span>
+                <span class="ruby-ivar">@aln</span> = <span class="ruby-value str">&quot;&quot;</span>
+        <span class="ruby-comment cmt"># Inizalize control attributes</span>
+                <span class="ruby-ivar">@maps</span> = <span class="ruby-keyword kw">false</span>
+                <span class="ruby-ivar">@search_aln</span> = <span class="ruby-keyword kw">false</span>
+                <span class="ruby-ivar">@save_aln</span> = <span class="ruby-keyword kw">false</span>
+                <span class="ruby-ivar">@c</span> = <span class="ruby-value">0</span>
+        <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>