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6 <title>Uses of Class compbio.runner.msa.Probcons</title>
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73 <h2 title="Uses of Class compbio.runner.msa.Probcons" class="title">Uses of Class<br>compbio.runner.msa.Probcons</h2>
75 <div class="classUseContainer">
76 <ul class="blockList">
77 <li class="blockList">
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/Probcons.html" title="class in compbio.runner.msa">Probcons</a></span><span class="tabEnd"> </span></caption>
81 <th class="colFirst" scope="col">Package</th>
82 <th class="colLast" scope="col">Description</th>
86 <td class="colFirst"><a href="#compbio.runner.msa">compbio.runner.msa</a></td>
88 <div class="block">Wrappers for native executables for multiple sequence alignment (msa)</div>
92 <td class="colFirst"><a href="#compbio.ws.server">compbio.ws.server</a></td>
93 <td class="colLast"> </td>
98 <li class="blockList">
99 <ul class="blockList">
100 <li class="blockList"><a name="compbio.runner.msa">
103 <h3>Uses of <a href="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</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/Probcons.html" title="class in compbio.runner.msa">Probcons</a></span><span class="tabEnd"> </span></caption>
107 <th class="colFirst" scope="col">Modifier and Type</th>
108 <th class="colLast" scope="col">Method and Description</th>
111 <tr class="altColor">
112 <td class="colFirst"><code><a href="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</a></code></td>
113 <td class="colLast"><span class="typeNameLabel">Probcons.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/msa/Probcons.html#setInput-java.lang.String-">setInput</a></span>(java.lang.String inFile)</code> </td>
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/Probcons.html" title="class in compbio.runner.msa">Probcons</a></span><span class="tabEnd"> </span></caption>
120 <th class="colFirst" scope="col">Modifier and Type</th>
121 <th class="colLast" scope="col">Method and Description</th>
124 <tr class="altColor">
125 <td class="colFirst"><code>java.lang.Class<<a href="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</a>></code></td>
126 <td class="colLast"><span class="typeNameLabel">Probcons.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/msa/Probcons.html#getType--">getType</a></span>()</code> </td>
131 <li class="blockList"><a name="compbio.ws.server">
134 <h3>Uses of <a href="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</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/Probcons.html" title="class in compbio.runner.msa">Probcons</a></span><span class="tabEnd"> </span></caption>
138 <th class="colFirst" scope="col">Modifier and Type</th>
139 <th class="colLast" scope="col">Field and Description</th>
142 <tr class="altColor">
143 <td class="colFirst"><code>private static <a href="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a><<a href="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</a>></code></td>
144 <td class="colLast"><span class="typeNameLabel">ProbconsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/ProbconsWS.html#limitMan">limitMan</a></span></code> </td>
146 <tr class="rowColor">
147 <td class="colFirst"><code>private static <a href="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a><<a href="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</a>></code></td>
148 <td class="colLast"><span class="typeNameLabel">ProbconsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/ProbconsWS.html#probconsOptions">probconsOptions</a></span></code> </td>
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/Probcons.html" title="class in compbio.runner.msa">Probcons</a></span><span class="tabEnd"> </span></caption>
155 <th class="colFirst" scope="col">Modifier and Type</th>
156 <th class="colLast" scope="col">Method and Description</th>
159 <tr class="altColor">
160 <td class="colFirst"><code><a href="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a><<a href="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</a>></code></td>
161 <td class="colLast"><span class="typeNameLabel">ProbconsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/ProbconsWS.html#getLimit-java.lang.String-">getLimit</a></span>(java.lang.String presetName)</code> </td>
163 <tr class="rowColor">
164 <td class="colFirst"><code><a href="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a><<a href="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</a>></code></td>
165 <td class="colLast"><span class="typeNameLabel">ProbconsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/ProbconsWS.html#getLimits--">getLimits</a></span>()</code> </td>
167 <tr class="altColor">
168 <td class="colFirst"><code><a href="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a><<a href="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</a>></code></td>
169 <td class="colLast"><span class="typeNameLabel">ProbconsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/ProbconsWS.html#getPresets--">getPresets</a></span>()</code> </td>
171 <tr class="rowColor">
172 <td class="colFirst"><code><a href="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a><<a href="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</a>></code></td>
173 <td class="colLast"><span class="typeNameLabel">ProbconsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/ProbconsWS.html#getRunnerOptions--">getRunnerOptions</a></span>()</code> </td>
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><<a href="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</a>></code></td>
177 <td class="colLast"><span class="typeNameLabel">ProbconsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/ProbconsWS.html#init-java.util.List-">init</a></span>(java.util.List<<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> dataSet)</code> </td>
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/Probcons.html" title="class in compbio.runner.msa">Probcons</a></span><span class="tabEnd"> </span></caption>
184 <th class="colFirst" scope="col">Modifier and Type</th>
185 <th class="colLast" scope="col">Method and Description</th>
188 <tr class="altColor">
189 <td class="colFirst"><code>java.lang.String</code></td>
190 <td class="colLast"><span class="typeNameLabel">ProbconsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/ProbconsWS.html#customAlign-java.util.List-java.util.List-">customAlign</a></span>(java.util.List<<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> sequences,
191 java.util.List<<a href="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a><<a href="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</a>>> options)</code> </td>
193 <tr class="rowColor">
194 <td class="colFirst"><code>java.lang.String</code></td>
195 <td class="colLast"><span class="typeNameLabel">ProbconsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/ProbconsWS.html#presetAlign-java.util.List-compbio.metadata.Preset-">presetAlign</a></span>(java.util.List<<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> sequences,
196 <a href="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a><<a href="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</a>> preset)</code> </td>
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