website/docs/full_javadoc/index-files/index-15.html

   1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
   2 <!-- NewPage -->
   3 <html lang="en">
   4 <head>
   5 <!-- Generated by javadoc (1.8.0_121) on Fri Apr 21 15:32:51 BST 2017 -->
   6 <title>O-Index</title>
   7 <meta name="date" content="2017-04-21">
   8 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
   9 <script type="text/javascript" src="../script.js"></script>
  10 </head>
  11 <body>
  12 <script type="text/javascript"><!--
  13     try {
  14         if (location.href.indexOf('is-external=true') == -1) {
  15             parent.document.title="O-Index";
  16         }
  17     }
  18     catch(err) {
  19     }
  20 //-->
  21 </script>
  22 <noscript>
  23 <div>JavaScript is disabled on your browser.</div>
  24 </noscript>
  25 <!-- ========= START OF TOP NAVBAR ======= -->
  26 <div class="topNav"><a name="navbar.top">
  27 <!--   -->
  28 </a>
  29 <div class="skipNav"><a href="#skip.navbar.top" title="Skip navigation links">Skip navigation links</a></div>
  30 <a name="navbar.top.firstrow">
  31 <!--   -->
  32 </a>
  33 <ul class="navList" title="Navigation">
  34 <li><a href="../overview-summary.html">Overview</a></li>
  35 <li>Package</li>
  36 <li>Class</li>
  37 <li>Use</li>
  38 <li><a href="../overview-tree.html">Tree</a></li>
  39 <li><a href="../deprecated-list.html">Deprecated</a></li>
  40 <li class="navBarCell1Rev">Index</li>
  41 <li><a href="../help-doc.html">Help</a></li>
  42 </ul>
  43 </div>
  44 <div class="subNav">
  45 <ul class="navList">
  46 <li><a href="index-14.html">Prev Letter</a></li>
  47 <li><a href="index-16.html">Next Letter</a></li>
  48 </ul>
  49 <ul class="navList">
  50 <li><a href="../index.html?index-files/index-15.html" target="_top">Frames</a></li>
  51 <li><a href="index-15.html" target="_top">No&nbsp;Frames</a></li>
  52 </ul>
  53 <ul class="navList" id="allclasses_navbar_top">
  54 <li><a href="../allclasses-noframe.html">All&nbsp;Classes</a></li>
  55 </ul>
  56 <div>
  57 <script type="text/javascript"><!--
  58   allClassesLink = document.getElementById("allclasses_navbar_top");
  59   if(window==top) {
  60     allClassesLink.style.display = "block";
  61   }
  62   else {
  63     allClassesLink.style.display = "none";
  64   }
  65   //-->
  66 </script>
  67 </div>
  68 <a name="skip.navbar.top">
  69 <!--   -->
  70 </a></div>
  71 <!-- ========= END OF TOP NAVBAR ========= -->
  72 <div class="contentContainer"><a href="index-1.html">A</a>&nbsp;<a href="index-2.html">B</a>&nbsp;<a href="index-3.html">C</a>&nbsp;<a href="index-4.html">D</a>&nbsp;<a href="index-5.html">E</a>&nbsp;<a href="index-6.html">F</a>&nbsp;<a href="index-7.html">G</a>&nbsp;<a href="index-8.html">H</a>&nbsp;<a href="index-9.html">I</a>&nbsp;<a href="index-10.html">J</a>&nbsp;<a href="index-11.html">K</a>&nbsp;<a href="index-12.html">L</a>&nbsp;<a href="index-13.html">M</a>&nbsp;<a href="index-14.html">N</a>&nbsp;<a href="index-15.html">O</a>&nbsp;<a href="index-16.html">P</a>&nbsp;<a href="index-17.html">Q</a>&nbsp;<a href="index-18.html">R</a>&nbsp;<a href="index-19.html">S</a>&nbsp;<a href="index-20.html">T</a>&nbsp;<a href="index-21.html">U</a>&nbsp;<a href="index-22.html">V</a>&nbsp;<a href="index-23.html">W</a>&nbsp;<a href="index-24.html">_</a>&nbsp;<a name="I:O">
  73 <!--   -->
  74 </a>
  75 <h2 class="title">O</h2>
  76 <dl>
  77 <dt><span class="memberNameLink"><a href="../compbio/ws/client/WSTester.html#OK">OK</a></span> - Static variable in class compbio.ws.client.<a href="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</a></dt>
  78 <dd>&nbsp;</dd>
  79 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ClustalAlignmentUtil.html#oneLineAlignmentLength">oneLineAlignmentLength</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</a></dt>
  80 <dd>&nbsp;</dd>
  81 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#open">open</a></span> - Static variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</a></dt>
  82 <dd>&nbsp;</dd>
  83 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#openInputStream-java.lang.String-">openInputStream(String)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
  84 <dd>
  85 <div class="block">Reads and parses Fasta or Clustal formatted file into a list of
  86  FastaSequence objects</div>
  87 </dd>
  88 <dt><span class="memberNameLink"><a href="../compbio/ws/server/RegistryWS.html#operating">operating</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</a></dt>
  89 <dd>
  90 <div class="block">Stores tested and passed (the test) services and their testing time</div>
  91 </dd>
  92 <dt><a href="../compbio/metadata/Option.html" title="class in compbio.metadata"><span class="typeNameLink">Option</span></a>&lt;<a href="../compbio/metadata/Option.html" title="type parameter in Option">T</a>&gt; - Class in <a href="../compbio/metadata/package-summary.html">compbio.metadata</a></dt>
  93 <dd>
  94 <div class="block">Command line option/flag or multiple exclusive options with no value.</div>
  95 </dd>
  96 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#Option--">Option()</a></span> - Constructor for class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
  97 <dd>&nbsp;</dd>
  98 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#Option-java.lang.String-java.lang.String-">Option(String, String)</a></span> - Constructor for class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
  99 <dd>&nbsp;</dd>
 100 <dt><span class="memberNameLink"><a href="../compbio/metadata/Preset.html#option">option</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a></dt>
 101 <dd>&nbsp;</dd>
 102 <dt><a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner"><span class="typeNameLink">OptionCombinator</span></a> - Class in <a href="../compbio/runner/package-summary.html">compbio.runner</a></dt>
 103 <dd>
 104 <div class="block">This class solve the following problems.</div>
 105 </dd>
 106 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#OptionCombinator-compbio.metadata.RunnerConfig-">OptionCombinator(RunnerConfig&lt;? extends Executable&lt;?&gt;&gt;)</a></span> - Constructor for class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
 107 <dd>&nbsp;</dd>
 108 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#optionNames">optionNames</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 109 <dd>&nbsp;</dd>
 110 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAlign.html#options">options</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</a></dt>
 111 <dd>&nbsp;</dd>
 112 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAnalize.html#options">options</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</a></dt>
 113 <dd>&nbsp;</dd>
 114 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomFold.html#options">options</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomFold.html" title="class in compbio.data.msa.jaxws">CustomFold</a></dt>
 115 <dd>&nbsp;</dd>
 116 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#options">options</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
 117 <dd>&nbsp;</dd>
 118 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#optionsToCommandString-java.util.List-">optionsToCommandString(List&lt;Option&lt;?&gt;&gt;)</a></span> - Method in class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
 119 <dd>&nbsp;</dd>
 120 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#optionToCommandString-compbio.metadata.Option-">optionToCommandString(Option&lt;?&gt;)</a></span> - Static method in class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
 121 <dd>&nbsp;</dd>
 122 <dt><span class="memberNameLink"><a href="../compbio/engine/local/StreamGobbler.html#os">os</a></span> - Variable in class compbio.engine.local.<a href="../compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local">StreamGobbler</a></dt>
 123 <dd>&nbsp;</dd>
 124 <dt><span class="memberNameLink"><a href="../compbio/engine/client/RunConfiguration.html#output">output</a></span> - Variable in class compbio.engine.client.<a href="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</a></dt>
 125 <dd>
 126 <div class="block">Output</div>
 127 </dd>
 128 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#OUTPUT">OUTPUT</a></span> - Static variable in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 129 <dd>&nbsp;</dd>
 130 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#outputFile">outputFile</a></span> - Variable in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 131 <dd>&nbsp;</dd>
 132 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Constraints.html#outputkey">outputkey</a></span> - Static variable in class compbio.ws.client.<a href="../compbio/ws/client/Constraints.html" title="class in compbio.ws.client">Constraints</a></dt>
 133 <dd>&nbsp;</dd>
 134 <dt><span class="memberNameLink"><a href="../compbio/engine/local/StreamGobbler.OutputType.html#OutputType--">OutputType()</a></span> - Constructor for enum compbio.engine.local.<a href="../compbio/engine/local/StreamGobbler.OutputType.html" title="enum in compbio.engine.local">StreamGobbler.OutputType</a></dt>
 135 <dd>&nbsp;</dd>
 136 </dl>
 137 <a href="index-1.html">A</a>&nbsp;<a href="index-2.html">B</a>&nbsp;<a href="index-3.html">C</a>&nbsp;<a href="index-4.html">D</a>&nbsp;<a href="index-5.html">E</a>&nbsp;<a href="index-6.html">F</a>&nbsp;<a href="index-7.html">G</a>&nbsp;<a href="index-8.html">H</a>&nbsp;<a href="index-9.html">I</a>&nbsp;<a href="index-10.html">J</a>&nbsp;<a href="index-11.html">K</a>&nbsp;<a href="index-12.html">L</a>&nbsp;<a href="index-13.html">M</a>&nbsp;<a href="index-14.html">N</a>&nbsp;<a href="index-15.html">O</a>&nbsp;<a href="index-16.html">P</a>&nbsp;<a href="index-17.html">Q</a>&nbsp;<a href="index-18.html">R</a>&nbsp;<a href="index-19.html">S</a>&nbsp;<a href="index-20.html">T</a>&nbsp;<a href="index-21.html">U</a>&nbsp;<a href="index-22.html">V</a>&nbsp;<a href="index-23.html">W</a>&nbsp;<a href="index-24.html">_</a>&nbsp;</div>
 138 <!-- ======= START OF BOTTOM NAVBAR ====== -->
 139 <div class="bottomNav"><a name="navbar.bottom">
 140 <!--   -->
 141 </a>
 142 <div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
 143 <a name="navbar.bottom.firstrow">
 144 <!--   -->
 145 </a>
 146 <ul class="navList" title="Navigation">
 147 <li><a href="../overview-summary.html">Overview</a></li>
 148 <li>Package</li>
 149 <li>Class</li>
 150 <li>Use</li>
 151 <li><a href="../overview-tree.html">Tree</a></li>
 152 <li><a href="../deprecated-list.html">Deprecated</a></li>
 153 <li class="navBarCell1Rev">Index</li>
 154 <li><a href="../help-doc.html">Help</a></li>
 155 </ul>
 156 </div>
 157 <div class="subNav">
 158 <ul class="navList">
 159 <li><a href="index-14.html">Prev Letter</a></li>
 160 <li><a href="index-16.html">Next Letter</a></li>
 161 </ul>
 162 <ul class="navList">
 163 <li><a href="../index.html?index-files/index-15.html" target="_top">Frames</a></li>
 164 <li><a href="index-15.html" target="_top">No&nbsp;Frames</a></li>
 165 </ul>
 166 <ul class="navList" id="allclasses_navbar_bottom">
 167 <li><a href="../allclasses-noframe.html">All&nbsp;Classes</a></li>
 168 </ul>
 169 <div>
 170 <script type="text/javascript"><!--
 171   allClassesLink = document.getElementById("allclasses_navbar_bottom");
 172   if(window==top) {
 173     allClassesLink.style.display = "block";
 174   }
 175   else {
 176     allClassesLink.style.display = "none";
 177   }
 178   //-->
 179 </script>
 180 </div>
 181 <a name="skip.navbar.bottom">
 182 <!--   -->
 183 </a></div>
 184 <!-- ======== END OF BOTTOM NAVBAR ======= -->
 185 </body>
 186 </html>