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   6 <title>Uses of Class compbio.runner.msa.MSAprobs</title>
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  73 <h2 title="Uses of Class compbio.runner.msa.MSAprobs" class="title">Uses of Class<br>compbio.runner.msa.MSAprobs</h2>
  74 </div>
  75 <div class="classUseContainer">
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  78 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing packages, and an explanation">
  79 <caption><span>Packages that use <a href="../../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a></span><span class="tabEnd">&nbsp;</span></caption>
  80 <tr>
  81 <th class="colFirst" scope="col">Package</th>
  82 <th class="colLast" scope="col">Description</th>
  83 </tr>
  84 <tbody>
  85 <tr class="altColor">
  86 <td class="colFirst"><a href="#compbio.runner.msa">compbio.runner.msa</a></td>
  87 <td class="colLast">
  88 <div class="block">Wrappers for native executables for multiple sequence alignment (msa)</div>
  89 </td>
  90 </tr>
  91 <tr class="rowColor">
  92 <td class="colFirst"><a href="#compbio.ws.server">compbio.ws.server</a></td>
  93 <td class="colLast">&nbsp;</td>
  94 </tr>
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 100 <li class="blockList"><a name="compbio.runner.msa">
 101 <!--   -->
 102 </a>
 103 <h3>Uses of <a href="../../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a> in <a href="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</a></h3>
 104 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 105 <caption><span>Methods in <a href="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</a> that return <a href="../../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a></span><span class="tabEnd">&nbsp;</span></caption>
 106 <tr>
 107 <th class="colFirst" scope="col">Modifier and Type</th>
 108 <th class="colLast" scope="col">Method and Description</th>
 109 </tr>
 110 <tbody>
 111 <tr class="altColor">
 112 <td class="colFirst"><code><a href="../../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a></code></td>
 113 <td class="colLast"><span class="typeNameLabel">MSAprobs.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/msa/MSAprobs.html#setInput-java.lang.String-">setInput</a></span>(java.lang.String&nbsp;inFile)</code>&nbsp;</td>
 114 </tr>
 115 </tbody>
 116 </table>
 117 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 118 <caption><span>Methods in <a href="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</a> that return types with arguments of type <a href="../../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a></span><span class="tabEnd">&nbsp;</span></caption>
 119 <tr>
 120 <th class="colFirst" scope="col">Modifier and Type</th>
 121 <th class="colLast" scope="col">Method and Description</th>
 122 </tr>
 123 <tbody>
 124 <tr class="altColor">
 125 <td class="colFirst"><code>java.lang.Class&lt;<a href="../../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></td>
 126 <td class="colLast"><span class="typeNameLabel">MSAprobs.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/msa/MSAprobs.html#getType--">getType</a></span>()</code>&nbsp;</td>
 127 </tr>
 128 </tbody>
 129 </table>
 130 </li>
 131 <li class="blockList"><a name="compbio.ws.server">
 132 <!--   -->
 133 </a>
 134 <h3>Uses of <a href="../../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a> in <a href="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</a></h3>
 135 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing fields, and an explanation">
 136 <caption><span>Fields in <a href="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</a> with type parameters of type <a href="../../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a></span><span class="tabEnd">&nbsp;</span></caption>
 137 <tr>
 138 <th class="colFirst" scope="col">Modifier and Type</th>
 139 <th class="colLast" scope="col">Field and Description</th>
 140 </tr>
 141 <tbody>
 142 <tr class="altColor">
 143 <td class="colFirst"><code>private static <a href="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a>&lt;<a href="../../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></td>
 144 <td class="colLast"><span class="typeNameLabel">MSAprobsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/MSAprobsWS.html#limitMan">limitMan</a></span></code>&nbsp;</td>
 145 </tr>
 146 <tr class="rowColor">
 147 <td class="colFirst"><code>private static <a href="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a>&lt;<a href="../../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></td>
 148 <td class="colLast"><span class="typeNameLabel">MSAprobsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/MSAprobsWS.html#MSAprobsOptions">MSAprobsOptions</a></span></code>&nbsp;</td>
 149 </tr>
 150 </tbody>
 151 </table>
 152 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 153 <caption><span>Methods in <a href="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</a> that return types with arguments of type <a href="../../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a></span><span class="tabEnd">&nbsp;</span></caption>
 154 <tr>
 155 <th class="colFirst" scope="col">Modifier and Type</th>
 156 <th class="colLast" scope="col">Method and Description</th>
 157 </tr>
 158 <tbody>
 159 <tr class="altColor">
 160 <td class="colFirst"><code><a href="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a>&lt;<a href="../../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></td>
 161 <td class="colLast"><span class="typeNameLabel">MSAprobsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/MSAprobsWS.html#getLimit-java.lang.String-">getLimit</a></span>(java.lang.String&nbsp;presetName)</code>&nbsp;</td>
 162 </tr>
 163 <tr class="rowColor">
 164 <td class="colFirst"><code><a href="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a>&lt;<a href="../../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></td>
 165 <td class="colLast"><span class="typeNameLabel">MSAprobsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/MSAprobsWS.html#getLimits--">getLimits</a></span>()</code>&nbsp;</td>
 166 </tr>
 167 <tr class="altColor">
 168 <td class="colFirst"><code><a href="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a>&lt;<a href="../../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></td>
 169 <td class="colLast"><span class="typeNameLabel">MSAprobsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/MSAprobsWS.html#getPresets--">getPresets</a></span>()</code>&nbsp;</td>
 170 </tr>
 171 <tr class="rowColor">
 172 <td class="colFirst"><code><a href="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a>&lt;<a href="../../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></td>
 173 <td class="colLast"><span class="typeNameLabel">MSAprobsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/MSAprobsWS.html#getRunnerOptions--">getRunnerOptions</a></span>()</code>&nbsp;</td>
 174 </tr>
 175 <tr class="altColor">
 176 <td class="colFirst"><code>(package private) <a href="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;<a href="../../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></td>
 177 <td class="colLast"><span class="typeNameLabel">MSAprobsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/MSAprobsWS.html#init-java.util.List-">init</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;dataSet)</code>&nbsp;</td>
 178 </tr>
 179 </tbody>
 180 </table>
 181 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 182 <caption><span>Method parameters in <a href="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</a> with type arguments of type <a href="../../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a></span><span class="tabEnd">&nbsp;</span></caption>
 183 <tr>
 184 <th class="colFirst" scope="col">Modifier and Type</th>
 185 <th class="colLast" scope="col">Method and Description</th>
 186 </tr>
 187 <tbody>
 188 <tr class="altColor">
 189 <td class="colFirst"><code>java.lang.String</code></td>
 190 <td class="colLast"><span class="typeNameLabel">MSAprobsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/MSAprobsWS.html#customAlign-java.util.List-java.util.List-">customAlign</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 191            java.util.List&lt;<a href="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;<a href="../../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;&gt;&nbsp;options)</code>&nbsp;</td>
 192 </tr>
 193 <tr class="rowColor">
 194 <td class="colFirst"><code>java.lang.String</code></td>
 195 <td class="colLast"><span class="typeNameLabel">MSAprobsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/MSAprobsWS.html#presetAlign-java.util.List-compbio.metadata.Preset-">presetAlign</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 196            <a href="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;&nbsp;preset)</code>&nbsp;</td>
 197 </tr>
 198 </tbody>
 199 </table>
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