website/docs/full_javadoc/index-files/index-1.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>A-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="A-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>Prev Letter</li>
  47 <li><a href="index-2.html">Next Letter</a></li>
  48 </ul>
  49 <ul class="navList">
  50 <li><a href="../index.html?index-files/index-1.html" target="_top">Frames</a></li>
  51 <li><a href="index-1.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:A">
  73 <!--   -->
  74 </a>
  75 <h2 class="title">A</h2>
  76 <dl>
  77 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#AA">AA</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
  78 <dd>
  79 <div class="block">Valid Amino acids</div>
  80 </dd>
  81 <dt><a href="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation"><span class="typeNameLink">AACon</span></a> - Class in <a href="../compbio/runner/conservation/package-summary.html">compbio.runner.conservation</a></dt>
  82 <dd>
  83 <div class="block">Command line
  84
  85  java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out</div>
  86 </dd>
  87 <dt><span class="memberNameLink"><a href="../compbio/runner/conservation/AACon.html#AACon--">AACon()</a></span> - Constructor for class compbio.runner.conservation.<a href="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a></dt>
  88 <dd>&nbsp;</dd>
  89 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#AACON_INFO">AACON_INFO</a></span> - Static variable in enum compbio.ws.client.<a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></dt>
  90 <dd>&nbsp;</dd>
  91 <dt><a href="../compbio/ws/client/AAConClient.html" title="class in compbio.ws.client"><span class="typeNameLink">AAConClient</span></a> - Class in <a href="../compbio/ws/client/package-summary.html">compbio.ws.client</a></dt>
  92 <dd>
  93 <div class="block">A command line client for AACon web service</div>
  94 </dd>
  95 <dt><span class="memberNameLink"><a href="../compbio/ws/client/AAConClient.html#AAConClient-java.lang.String:A-">AAConClient(String[])</a></span> - Constructor for class compbio.ws.client.<a href="../compbio/ws/client/AAConClient.html" title="class in compbio.ws.client">AAConClient</a></dt>
  96 <dd>
  97 <div class="block">Connects to the service and do the job as requested, if something goes
  98  wrong reports or/and prints usage help.</div>
  99 </dd>
 100 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GenericMetadataService.html#aaconOptions">aaconOptions</a></span> - Variable in class compbio.ws.server.<a href="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</a></dt>
 101 <dd>&nbsp;</dd>
 102 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GenericMetadataService.html#aaconPresets">aaconPresets</a></span> - Variable in class compbio.ws.server.<a href="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</a></dt>
 103 <dd>&nbsp;</dd>
 104 <dt><a href="../compbio/ws/server/AAConWS.html" title="class in compbio.ws.server"><span class="typeNameLink">AAConWS</span></a> - Class in <a href="../compbio/ws/server/package-summary.html">compbio.ws.server</a></dt>
 105 <dd>&nbsp;</dd>
 106 <dt><span class="memberNameLink"><a href="../compbio/ws/server/AAConWS.html#AAConWS--">AAConWS()</a></span> - Constructor for class compbio.ws.server.<a href="../compbio/ws/server/AAConWS.html" title="class in compbio.ws.server">AAConWS</a></dt>
 107 <dd>&nbsp;</dd>
 108 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/Totals.html#abandoned">abandoned</a></span> - Variable in class compbio.stat.servlet.util.<a href="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</a></dt>
 109 <dd>&nbsp;</dd>
 110 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/InputFilter.html#accept-java.io.File-">accept(File)</a></span> - Static method in class compbio.stat.collector.<a href="../compbio/stat/collector/InputFilter.html" title="class in compbio.stat.collector">InputFilter</a></dt>
 111 <dd>
 112 <div class="block">Accepts input as valid unless it is a test input</div>
 113 </dd>
 114 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#acct_cpu">acct_cpu</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 115 <dd>&nbsp;</dd>
 116 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#acct_io">acct_io</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 117 <dd>&nbsp;</dd>
 118 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#acct_iow">acct_iow</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 119 <dd>&nbsp;</dd>
 120 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#acct_maxvmem">acct_maxvmem</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 121 <dd>&nbsp;</dd>
 122 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#acct_mem">acct_mem</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 123 <dd>&nbsp;</dd>
 124 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#actualNumberofSequences">actualNumberofSequences</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</a></dt>
 125 <dd>&nbsp;</dd>
 126 <dt><span class="memberNameLink"><a href="../compbio/metadata/LimitExceededException.html#actualNumberofSequences">actualNumberofSequences</a></span> - Variable in exception compbio.metadata.<a href="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></dt>
 127 <dd>&nbsp;</dd>
 128 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#addJob-java.lang.String-compbio.engine.client.ConfiguredExecutable-">addJob(String, ConfiguredExecutable&lt;?&gt;)</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</a></dt>
 129 <dd>&nbsp;</dd>
 130 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#addOption-compbio.metadata.Option-">addOption(Option&lt;T&gt;)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
 131 <dd>
 132 <div class="block">Adds Option to the internal list of options</div>
 133 </dd>
 134 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#addOptionNames-java.lang.String...-">addOptionNames(String...)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 135 <dd>
 136 <div class="block">Adds an option to the optionName list</div>
 137 </dd>
 138 <dt><span class="memberNameLink"><a href="../compbio/metadata/Parameter.html#addOptionNames-java.lang.String...-">addOptionNames(String...)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</a></dt>
 139 <dd>&nbsp;</dd>
 140 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#addParameter-compbio.metadata.Parameter-">addParameter(Parameter&lt;T&gt;)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
 141 <dd>
 142 <div class="block">Adds parameter to the internal parameter list</div>
 143 </dd>
 144 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#addParameters-java.util.List-">addParameters(List&lt;String&gt;)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
 145 <dd>&nbsp;</dd>
 146 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Executable.html#addParameters-java.util.List-">addParameters(List&lt;String&gt;)</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a></dt>
 147 <dd>
 148 <div class="block">Adds parameter to the list of parameters for a native executable</div>
 149 </dd>
 150 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#addParameters-java.util.List-">addParameters(List&lt;String&gt;)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 151 <dd>&nbsp;</dd>
 152 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Mafft.html#addParameters-java.util.List-">addParameters(List&lt;String&gt;)</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a></dt>
 153 <dd>
 154 <div class="block">Mafft input must always be the last parameter!</div>
 155 </dd>
 156 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#addParams-java.util.List-">addParams(List&lt;String&gt;)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
 157 <dd>&nbsp;</dd>
 158 <dt><span class="memberNameLink"><a href="../compbio/metadata/Parameter.html#addPossibleValues-java.lang.String...-">addPossibleValues(String...)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</a></dt>
 159 <dd>&nbsp;</dd>
 160 <dt><span class="memberNameLink"><a href="../compbio/engine/SubmissionManager.html#addTask-compbio.engine.client.ConfiguredExecutable-java.util.concurrent.Future-">addTask(ConfiguredExecutable&lt;?&gt;, Future&lt;ConfiguredExecutable&lt;?&gt;&gt;)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</a></dt>
 161 <dd>&nbsp;</dd>
 162 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalExecutorService.html#afterExecute-java.lang.Runnable-java.lang.Throwable-">afterExecute(Runnable, Throwable)</a></span> - Method in class compbio.engine.local.<a href="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</a></dt>
 163 <dd>&nbsp;</dd>
 164 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.AlifoldLine.html#AlifoldLine-java.lang.String-">AlifoldLine(String)</a></span> - Constructor for enum compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructReader.AlifoldLine.html" title="enum in compbio.data.sequence">RNAStructReader.AlifoldLine</a></dt>
 165 <dd>&nbsp;</dd>
 166 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.AlifoldResult.html#AlifoldResult--">AlifoldResult()</a></span> - Constructor for enum compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructReader.AlifoldResult.html" title="enum in compbio.data.sequence">RNAStructReader.AlifoldResult</a></dt>
 167 <dd>&nbsp;</dd>
 168 <dt><a href="../compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">Align</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 169 <dd>&nbsp;</dd>
 170 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/Align.html#Align--">Align()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws">Align</a></dt>
 171 <dd>&nbsp;</dd>
 172 <dt><span class="memberNameLink"><a href="../compbio/data/msa/MsaWS.html#align-java.util.List-">align(List&lt;FastaSequence&gt;)</a></span> - Method in interface compbio.data.msa.<a href="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a></dt>
 173 <dd>
 174 <div class="block">Align a list of sequences with default settings.</div>
 175 </dd>
 176 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Jws2Client.html#align-java.io.File-compbio.data.msa.MsaWS-compbio.metadata.Preset-java.util.List-">align(File, MsaWS&lt;T&gt;, Preset&lt;T&gt;, List&lt;Option&lt;T&gt;&gt;)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</a></dt>
 177 <dd>
 178 <div class="block">Align sequences from the file using MsaWS</div>
 179 </dd>
 180 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalOWS.html#align-java.util.List-">align(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</a></dt>
 181 <dd>&nbsp;</dd>
 182 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalWS.html#align-java.util.List-">align(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</a></dt>
 183 <dd>&nbsp;</dd>
 184 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GLprobsWS.html#align-java.util.List-">align(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/GLprobsWS.html" title="class in compbio.ws.server">GLprobsWS</a></dt>
 185 <dd>&nbsp;</dd>
 186 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MafftWS.html#align-java.util.List-">align(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</a></dt>
 187 <dd>&nbsp;</dd>
 188 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MSAprobsWS.html#align-java.util.List-">align(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MSAprobsWS.html" title="class in compbio.ws.server">MSAprobsWS</a></dt>
 189 <dd>&nbsp;</dd>
 190 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MuscleWS.html#align-java.util.List-">align(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</a></dt>
 191 <dd>&nbsp;</dd>
 192 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ProbconsWS.html#align-java.util.List-">align(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</a></dt>
 193 <dd>&nbsp;</dd>
 194 <dt><span class="memberNameLink"><a href="../compbio/ws/server/TcoffeeWS.html#align-java.util.List-">align(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</a></dt>
 195 <dd>&nbsp;</dd>
 196 <dt><span class="memberNameLink"><a href="../compbio/ws/server/WSUtil.html#align-java.util.List-compbio.engine.client.ConfiguredExecutable-org.apache.log4j.Logger-java.lang.String-compbio.metadata.Limit-">align(List&lt;FastaSequence&gt;, ConfiguredExecutable&lt;T&gt;, Logger, String, Limit&lt;T&gt;)</a></span> - Static method in class compbio.ws.server.<a href="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</a></dt>
 197 <dd>&nbsp;</dd>
 198 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomFold.html#alignment">alignment</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>
 199 <dd>&nbsp;</dd>
 200 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/Fold.html#alignment">alignment</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/Fold.html" title="class in compbio.data.msa.jaxws">Fold</a></dt>
 201 <dd>&nbsp;</dd>
 202 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetFold.html#alignment">alignment</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PresetFold.html" title="class in compbio.data.msa.jaxws">PresetFold</a></dt>
 203 <dd>&nbsp;</dd>
 204 <dt><a href="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence"><span class="typeNameLink">Alignment</span></a> - Class in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
 205 <dd>
 206 <div class="block">Multiple sequence alignment.</div>
 207 </dd>
 208 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Alignment.html#Alignment--">Alignment()</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></dt>
 209 <dd>&nbsp;</dd>
 210 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Alignment.html#Alignment-java.util.List-compbio.data.sequence.Program-char-">Alignment(List&lt;FastaSequence&gt;, Program, char)</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></dt>
 211 <dd>&nbsp;</dd>
 212 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Alignment.html#Alignment-java.util.List-compbio.data.sequence.AlignmentMetadata-">Alignment(List&lt;FastaSequence&gt;, AlignmentMetadata)</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></dt>
 213 <dd>&nbsp;</dd>
 214 <dt><a href="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><span class="typeNameLink">AlignmentMetadata</span></a> - Class in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
 215 <dd>
 216 <div class="block">Alignment metadata e.g.</div>
 217 </dd>
 218 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/AlignmentMetadata.html#AlignmentMetadata--">AlignmentMetadata()</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</a></dt>
 219 <dd>&nbsp;</dd>
 220 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/AlignmentMetadata.html#AlignmentMetadata-compbio.data.sequence.Program-char-">AlignmentMetadata(Program, char)</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</a></dt>
 221 <dd>&nbsp;</dd>
 222 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#alignmentP">alignmentP</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructReader.html" title="class in compbio.data.sequence">RNAStructReader</a></dt>
 223 <dd>&nbsp;</dd>
 224 <dt><a href="../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">AlignResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 225 <dd>&nbsp;</dd>
 226 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/AlignResponse.html#AlignResponse--">AlignResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws">AlignResponse</a></dt>
 227 <dd>&nbsp;</dd>
 228 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/StatCollection.html#allStat">allStat</a></span> - Variable in class compbio.stat.servlet.util.<a href="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</a></dt>
 229 <dd>&nbsp;</dd>
 230 <dt><span class="memberNameLink"><a href="../compbio/ws/server/RegistryWS.html#allTested">allTested</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>
 231 <dd>
 232 <div class="block">Indicate whether the services were tested at all</div>
 233 </dd>
 234 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_AA">AMBIGUOUS_AA</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 235 <dd>
 236 <div class="block">Same as AA pattern but with two additional letters - XU</div>
 237 </dd>
 238 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_NUCLEOTIDE">AMBIGUOUS_NUCLEOTIDE</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 239 <dd>
 240 <div class="block">Ambiguous nucleotide</div>
 241 </dd>
 242 <dt><a href="../compbio/data/msa/jaxws/Analize.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">Analize</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 243 <dd>&nbsp;</dd>
 244 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/Analize.html#Analize--">Analize()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/Analize.html" title="class in compbio.data.msa.jaxws">Analize</a></dt>
 245 <dd>&nbsp;</dd>
 246 <dt><span class="memberNameLink"><a href="../compbio/data/msa/SequenceAnnotation.html#analize-java.util.List-">analize(List&lt;FastaSequence&gt;)</a></span> - Method in interface compbio.data.msa.<a href="../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</a></dt>
 247 <dd>
 248 <div class="block">Analyse the sequences.</div>
 249 </dd>
 250 <dt><span class="memberNameLink"><a href="../compbio/ws/client/AAConClient.html#analize-java.io.File-compbio.data.msa.SequenceAnnotation-compbio.metadata.Preset-java.util.List-">analize(File, SequenceAnnotation&lt;AAConWS&gt;, Preset&lt;AAConWS&gt;, List&lt;Option&lt;AAConWS&gt;&gt;)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/AAConClient.html" title="class in compbio.ws.client">AAConClient</a></dt>
 251 <dd>
 252 <div class="block">Calculate conservation for sequences loaded from the file</div>
 253 </dd>
 254 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Jws2Client.html#analize-java.util.List-compbio.data.msa.SequenceAnnotation-compbio.metadata.Preset-java.util.List-">analize(List&lt;FastaSequence&gt;, SequenceAnnotation&lt;T&gt;, Preset&lt;T&gt;, List&lt;Option&lt;T&gt;&gt;)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</a></dt>
 255 <dd>
 256 <div class="block">Calculate conservation for sequences loaded from a FASTA record list structure</div>
 257 </dd>
 258 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Jws2Client.html#analize-java.io.File-compbio.data.msa.SequenceAnnotation-compbio.metadata.Preset-java.util.List-">analize(File, SequenceAnnotation&lt;T&gt;, Preset&lt;T&gt;, List&lt;Option&lt;T&gt;&gt;)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</a></dt>
 259 <dd>
 260 <div class="block">Calculate conservation for sequences loaded from the file</div>
 261 </dd>
 262 <dt><span class="memberNameLink"><a href="../compbio/ws/server/AAConWS.html#analize-java.util.List-">analize(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/AAConWS.html" title="class in compbio.ws.server">AAConWS</a></dt>
 263 <dd>&nbsp;</dd>
 264 <dt><span class="memberNameLink"><a href="../compbio/ws/server/RNAalifoldWS.html#analize-java.util.List-">analize(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/RNAalifoldWS.html" title="class in compbio.ws.server">RNAalifoldWS</a></dt>
 265 <dd>&nbsp;</dd>
 266 <dt><span class="memberNameLink"><a href="../compbio/ws/server/SequenceAnnotationService.html#analize-java.util.List-">analize(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</a></dt>
 267 <dd>&nbsp;</dd>
 268 <dt><span class="memberNameLink"><a href="../compbio/ws/server/WSUtil.html#analize-java.util.List-compbio.engine.client.ConfiguredExecutable-org.apache.log4j.Logger-java.lang.String-compbio.metadata.Limit-">analize(List&lt;FastaSequence&gt;, ConfiguredExecutable&lt;T&gt;, Logger, String, Limit&lt;T&gt;)</a></span> - Static method in class compbio.ws.server.<a href="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</a></dt>
 269 <dd>&nbsp;</dd>
 270 <dt><a href="../compbio/data/msa/jaxws/AnalizeResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">AnalizeResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 271 <dd>&nbsp;</dd>
 272 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/AnalizeResponse.html#AnalizeResponse--">AnalizeResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/AnalizeResponse.html" title="class in compbio.data.msa.jaxws">AnalizeResponse</a></dt>
 273 <dd>&nbsp;</dd>
 274 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/GLprobs.html#ANNOTATION">ANNOTATION</a></span> - Static variable in class compbio.runner.msa.<a href="../compbio/runner/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a></dt>
 275 <dd>&nbsp;</dd>
 276 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/MSAprobs.html#ANNOTATION">ANNOTATION</a></span> - Static variable in class compbio.runner.msa.<a href="../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a></dt>
 277 <dd>&nbsp;</dd>
 278 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Probcons.html#ANNOTATION">ANNOTATION</a></span> - Static variable in class compbio.runner.msa.<a href="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</a></dt>
 279 <dd>&nbsp;</dd>
 280 <dt><a href="../compbio/stat/servlet/AnnualStat.html" title="class in compbio.stat.servlet"><span class="typeNameLink">AnnualStat</span></a> - Class in <a href="../compbio/stat/servlet/package-summary.html">compbio.stat.servlet</a></dt>
 281 <dd>&nbsp;</dd>
 282 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/AnnualStat.html#AnnualStat--">AnnualStat()</a></span> - Constructor for class compbio.stat.servlet.<a href="../compbio/stat/servlet/AnnualStat.html" title="class in compbio.stat.servlet">AnnualStat</a></dt>
 283 <dd>&nbsp;</dd>
 284 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GAUtils.html#anonymizeIP--">anonymizeIP()</a></span> - Static method in class compbio.ws.server.<a href="../compbio/ws/server/GAUtils.html" title="class in compbio.ws.server">GAUtils</a></dt>
 285 <dd>&nbsp;</dd>
 286 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLastTested.html#arg0">arg0</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws">GetLastTested</a></dt>
 287 <dd>&nbsp;</dd>
 288 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLastTestedOn.html#arg0">arg0</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws">GetLastTestedOn</a></dt>
 289 <dd>&nbsp;</dd>
 290 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetServiceDescription.html#arg0">arg0</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetServiceDescription.html" title="class in compbio.data.msa.jaxws">GetServiceDescription</a></dt>
 291 <dd>&nbsp;</dd>
 292 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/IsOperating.html#arg0">arg0</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/IsOperating.html" title="class in compbio.data.msa.jaxws">IsOperating</a></dt>
 293 <dd>&nbsp;</dd>
 294 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/TestService.html#arg0">arg0</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/TestService.html" title="class in compbio.data.msa.jaxws">TestService</a></dt>
 295 <dd>&nbsp;</dd>
 296 <dt><a href="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><span class="typeNameLink">Argument</span></a>&lt;<a href="../compbio/metadata/Argument.html" title="type parameter in Argument">T</a>&gt; - Interface in <a href="../compbio/metadata/package-summary.html">compbio.metadata</a></dt>
 297 <dd>
 298 <div class="block">An unmodifiable view for the options and parameters, with one exception - it
 299  allows to set a value</div>
 300 </dd>
 301 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#arguments">arguments</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
 302 <dd>&nbsp;</dd>
 303 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#argumentsToCommandString-java.util.List-">argumentsToCommandString(List&lt;? extends 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>
 304 <dd>&nbsp;</dd>
 305 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#argumentsToCommandString-java.util.List-compbio.metadata.RunnerConfig-">argumentsToCommandString(List&lt;? extends Option&lt;?&gt;&gt;, RunnerConfig&lt;? extends Executable&lt;?&gt;&gt;)</a></span> - Static method in class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
 306 <dd>&nbsp;</dd>
 307 <dt><span class="memberNameLink"><a href="../compbio/metadata/LimitExceededException.html#aSequenceLenghtActual">aSequenceLenghtActual</a></span> - Variable in exception compbio.metadata.<a href="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></dt>
 308 <dd>&nbsp;</dd>
 309 <dt><span class="memberNameLink"><a href="../compbio/metadata/LimitExceededException.html#aSequenceLenghtAllowed">aSequenceLenghtAllowed</a></span> - Variable in exception compbio.metadata.<a href="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></dt>
 310 <dd>&nbsp;</dd>
 311 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ScoreManager.html#asMap--">asMap()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></dt>
 312 <dd>&nbsp;</dd>
 313 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ScoreManager.html#asSet--">asSet()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></dt>
 314 <dd>&nbsp;</dd>
 315 <dt><a href="../compbio/engine/cluster/drmaa/AsyncClusterRunner.html" title="class in compbio.engine.cluster.drmaa"><span class="typeNameLink">AsyncClusterRunner</span></a> - Class in <a href="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</a></dt>
 316 <dd>
 317 <div class="block">Single cluster job runner class</div>
 318 </dd>
 319 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/AsyncClusterRunner.html#AsyncClusterRunner--">AsyncClusterRunner()</a></span> - Constructor for class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/AsyncClusterRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncClusterRunner</a></dt>
 320 <dd>&nbsp;</dd>
 321 <dt><a href="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine"><span class="typeNameLink">AsyncExecutor</span></a> - Interface in <a href="../compbio/engine/package-summary.html">compbio.engine</a></dt>
 322 <dd>
 323 <div class="block">An asynchronous executor engine, capable of running, cancelling,
 324  obtaining results calculated by a native executable wrapper in Executable interface.</div>
 325 </dd>
 326 <dt><a href="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa"><span class="typeNameLink">AsyncJobRunner</span></a> - Class in <a href="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</a></dt>
 327 <dd>
 328 <div class="block">Single cluster job runner class</div>
 329 </dd>
 330 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#AsyncJobRunner--">AsyncJobRunner()</a></span> - Constructor for class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</a></dt>
 331 <dd>&nbsp;</dd>
 332 <dt><a href="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local"><span class="typeNameLink">AsyncLocalRunner</span></a> - Class in <a href="../compbio/engine/local/package-summary.html">compbio.engine.local</a></dt>
 333 <dd>&nbsp;</dd>
 334 <dt><span class="memberNameLink"><a href="../compbio/engine/local/AsyncLocalRunner.html#AsyncLocalRunner--">AsyncLocalRunner()</a></span> - Constructor for class compbio.engine.local.<a href="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</a></dt>
 335 <dd>&nbsp;</dd>
 336 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Mafft.html#autoOption">autoOption</a></span> - Static variable in class compbio.runner.msa.<a href="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a></dt>
 337 <dd>&nbsp;</dd>
 338 </dl>
 339 <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>
 340 <!-- ======= START OF BOTTOM NAVBAR ====== -->
 341 <div class="bottomNav"><a name="navbar.bottom">
 342 <!--   -->
 343 </a>
 344 <div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
 345 <a name="navbar.bottom.firstrow">
 346 <!--   -->
 347 </a>
 348 <ul class="navList" title="Navigation">
 349 <li><a href="../overview-summary.html">Overview</a></li>
 350 <li>Package</li>
 351 <li>Class</li>
 352 <li>Use</li>
 353 <li><a href="../overview-tree.html">Tree</a></li>
 354 <li><a href="../deprecated-list.html">Deprecated</a></li>
 355 <li class="navBarCell1Rev">Index</li>
 356 <li><a href="../help-doc.html">Help</a></li>
 357 </ul>
 358 </div>
 359 <div class="subNav">
 360 <ul class="navList">
 361 <li>Prev Letter</li>
 362 <li><a href="index-2.html">Next Letter</a></li>
 363 </ul>
 364 <ul class="navList">
 365 <li><a href="../index.html?index-files/index-1.html" target="_top">Frames</a></li>
 366 <li><a href="index-1.html" target="_top">No&nbsp;Frames</a></li>
 367 </ul>
 368 <ul class="navList" id="allclasses_navbar_bottom">
 369 <li><a href="../allclasses-noframe.html">All&nbsp;Classes</a></li>
 370 </ul>
 371 <div>
 372 <script type="text/javascript"><!--
 373   allClassesLink = document.getElementById("allclasses_navbar_bottom");
 374   if(window==top) {
 375     allClassesLink.style.display = "block";
 376   }
 377   else {
 378     allClassesLink.style.display = "none";
 379   }
 380   //-->
 381 </script>
 382 </div>
 383 <a name="skip.navbar.bottom">
 384 <!--   -->
 385 </a></div>
 386 <!-- ======== END OF BOTTOM NAVBAR ======= -->
 387 </body>
 388 </html>