website/docs/full_javadoc/compbio/data/sequence/class-use/FastaSequence.html

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   6 <title>Uses of Class compbio.data.sequence.FastaSequence</title>
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  72 <div class="header">
  73 <h2 title="Uses of Class compbio.data.sequence.FastaSequence" class="title">Uses of Class<br>compbio.data.sequence.FastaSequence</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/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</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.data.msa">compbio.data.msa</a></td>
  87 <td class="colLast">
  88 <div class="block">Web Service interfaces for JAva Bioinformatics Analysis Web Services.</div>
  89 </td>
  90 </tr>
  91 <tr class="rowColor">
  92 <td class="colFirst"><a href="#compbio.data.msa.jaxws">compbio.data.msa.jaxws</a></td>
  93 <td class="colLast">&nbsp;</td>
  94 </tr>
  95 <tr class="altColor">
  96 <td class="colFirst"><a href="#compbio.data.sequence">compbio.data.sequence</a></td>
  97 <td class="colLast">
  98 <div class="block">A data model for multiple sequence alignment web services and utility methods
  99  that work on the objects of this model.</div>
 100 </td>
 101 </tr>
 102 <tr class="rowColor">
 103 <td class="colFirst"><a href="#compbio.engine">compbio.engine</a></td>
 104 <td class="colLast">&nbsp;</td>
 105 </tr>
 106 <tr class="altColor">
 107 <td class="colFirst"><a href="#compbio.metadata">compbio.metadata</a></td>
 108 <td class="colLast">
 109 <div class="block">A meta-data model for multiple sequence alignment web services
 110  Classes in this package have no dependencies to other sources in the project.</div>
 111 </td>
 112 </tr>
 113 <tr class="rowColor">
 114 <td class="colFirst"><a href="#compbio.runner">compbio.runner</a></td>
 115 <td class="colLast">
 116 <div class="block">Utilities commonly used by all runners.</div>
 117 </td>
 118 </tr>
 119 <tr class="altColor">
 120 <td class="colFirst"><a href="#compbio.ws.client">compbio.ws.client</a></td>
 121 <td class="colLast">
 122 <div class="block">A command line client and web services testing client for
 123  JAva Bioinformatics Analysis Web Services.</div>
 124 </td>
 125 </tr>
 126 <tr class="rowColor">
 127 <td class="colFirst"><a href="#compbio.ws.server">compbio.ws.server</a></td>
 128 <td class="colLast">&nbsp;</td>
 129 </tr>
 130 </tbody>
 131 </table>
 132 </li>
 133 <li class="blockList">
 134 <ul class="blockList">
 135 <li class="blockList"><a name="compbio.data.msa">
 136 <!--   -->
 137 </a>
 138 <h3>Uses of <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a> in <a href="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</a></h3>
 139 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 140 <caption><span>Method parameters in <a href="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</a> with type arguments of type <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></span><span class="tabEnd">&nbsp;</span></caption>
 141 <tr>
 142 <th class="colFirst" scope="col">Modifier and Type</th>
 143 <th class="colLast" scope="col">Method and Description</th>
 144 </tr>
 145 <tbody>
 146 <tr class="altColor">
 147 <td class="colFirst"><code>java.lang.String</code></td>
 148 <td class="colLast"><span class="typeNameLabel">MsaWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/MsaWS.html#align-java.util.List-">align</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)</code>
 149 <div class="block">Align a list of sequences with default settings.</div>
 150 </td>
 151 </tr>
 152 <tr class="rowColor">
 153 <td class="colFirst"><code>java.lang.String</code></td>
 154 <td class="colLast"><span class="typeNameLabel">SequenceAnnotation.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/SequenceAnnotation.html#analize-java.util.List-">analize</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)</code>
 155 <div class="block">Analyse the sequences.</div>
 156 </td>
 157 </tr>
 158 <tr class="altColor">
 159 <td class="colFirst"><code>java.lang.String</code></td>
 160 <td class="colLast"><span class="typeNameLabel">MsaWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/MsaWS.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,
 161            java.util.List&lt;<a href="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;<a href="../../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</a>&gt;&gt;&nbsp;options)</code>
 162 <div class="block">Align a list of sequences with options.</div>
 163 </td>
 164 </tr>
 165 <tr class="rowColor">
 166 <td class="colFirst"><code>java.lang.String</code></td>
 167 <td class="colLast"><span class="typeNameLabel">SequenceAnnotation.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/SequenceAnnotation.html#customAnalize-java.util.List-java.util.List-">customAnalize</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 168              java.util.List&lt;<a href="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;<a href="../../../../compbio/data/msa/SequenceAnnotation.html" title="type parameter in SequenceAnnotation">T</a>&gt;&gt;&nbsp;options)</code>
 169 <div class="block">Analyse the sequences according to custom settings defined in options
 170  list.</div>
 171 </td>
 172 </tr>
 173 <tr class="altColor">
 174 <td class="colFirst"><code>java.lang.String</code></td>
 175 <td class="colLast"><span class="typeNameLabel">MsaWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/MsaWS.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,
 176            <a href="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</a>&gt;&nbsp;preset)</code>
 177 <div class="block">Align a list of sequences with preset.</div>
 178 </td>
 179 </tr>
 180 <tr class="rowColor">
 181 <td class="colFirst"><code>java.lang.String</code></td>
 182 <td class="colLast"><span class="typeNameLabel">SequenceAnnotation.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/SequenceAnnotation.html#presetAnalize-java.util.List-compbio.metadata.Preset-">presetAnalize</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 183              <a href="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../../compbio/data/msa/SequenceAnnotation.html" title="type parameter in SequenceAnnotation">T</a>&gt;&nbsp;preset)</code>
 184 <div class="block">Analyse the sequences according to the preset settings.</div>
 185 </td>
 186 </tr>
 187 </tbody>
 188 </table>
 189 </li>
 190 <li class="blockList"><a name="compbio.data.msa.jaxws">
 191 <!--   -->
 192 </a>
 193 <h3>Uses of <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a> in <a href="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></h3>
 194 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing fields, and an explanation">
 195 <caption><span>Fields in <a href="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a> with type parameters of type <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></span><span class="tabEnd">&nbsp;</span></caption>
 196 <tr>
 197 <th class="colFirst" scope="col">Modifier and Type</th>
 198 <th class="colLast" scope="col">Field and Description</th>
 199 </tr>
 200 <tbody>
 201 <tr class="altColor">
 202 <td class="colFirst"><code>private java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></td>
 203 <td class="colLast"><span class="typeNameLabel">PresetAnalize.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/PresetAnalize.html#fastaSequences">fastaSequences</a></span></code>&nbsp;</td>
 204 </tr>
 205 <tr class="rowColor">
 206 <td class="colFirst"><code>private java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></td>
 207 <td class="colLast"><span class="typeNameLabel">PresetAlign.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/PresetAlign.html#fastaSequences">fastaSequences</a></span></code>&nbsp;</td>
 208 </tr>
 209 <tr class="altColor">
 210 <td class="colFirst"><code>private java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></td>
 211 <td class="colLast"><span class="typeNameLabel">CustomAnalize.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/CustomAnalize.html#fastaSequences">fastaSequences</a></span></code>&nbsp;</td>
 212 </tr>
 213 <tr class="rowColor">
 214 <td class="colFirst"><code>private java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></td>
 215 <td class="colLast"><span class="typeNameLabel">CustomAlign.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/CustomAlign.html#fastaSequences">fastaSequences</a></span></code>&nbsp;</td>
 216 </tr>
 217 <tr class="altColor">
 218 <td class="colFirst"><code>private java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></td>
 219 <td class="colLast"><span class="typeNameLabel">Analize.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/Analize.html#fastaSequences">fastaSequences</a></span></code>&nbsp;</td>
 220 </tr>
 221 <tr class="rowColor">
 222 <td class="colFirst"><code>private java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></td>
 223 <td class="colLast"><span class="typeNameLabel">Align.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/Align.html#fastaSequences">fastaSequences</a></span></code>&nbsp;</td>
 224 </tr>
 225 </tbody>
 226 </table>
 227 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 228 <caption><span>Methods in <a href="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a> that return types with arguments of type <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></span><span class="tabEnd">&nbsp;</span></caption>
 229 <tr>
 230 <th class="colFirst" scope="col">Modifier and Type</th>
 231 <th class="colLast" scope="col">Method and Description</th>
 232 </tr>
 233 <tbody>
 234 <tr class="altColor">
 235 <td class="colFirst"><code>java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></td>
 236 <td class="colLast"><span class="typeNameLabel">PresetAnalize.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/PresetAnalize.html#getFastaSequences--">getFastaSequences</a></span>()</code>&nbsp;</td>
 237 </tr>
 238 <tr class="rowColor">
 239 <td class="colFirst"><code>java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></td>
 240 <td class="colLast"><span class="typeNameLabel">PresetAlign.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/PresetAlign.html#getFastaSequences--">getFastaSequences</a></span>()</code>&nbsp;</td>
 241 </tr>
 242 <tr class="altColor">
 243 <td class="colFirst"><code>java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></td>
 244 <td class="colLast"><span class="typeNameLabel">CustomAnalize.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/CustomAnalize.html#getFastaSequences--">getFastaSequences</a></span>()</code>&nbsp;</td>
 245 </tr>
 246 <tr class="rowColor">
 247 <td class="colFirst"><code>java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></td>
 248 <td class="colLast"><span class="typeNameLabel">CustomAlign.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/CustomAlign.html#getFastaSequences--">getFastaSequences</a></span>()</code>&nbsp;</td>
 249 </tr>
 250 <tr class="altColor">
 251 <td class="colFirst"><code>java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></td>
 252 <td class="colLast"><span class="typeNameLabel">Analize.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/Analize.html#getFastaSequences--">getFastaSequences</a></span>()</code>&nbsp;</td>
 253 </tr>
 254 <tr class="rowColor">
 255 <td class="colFirst"><code>java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></td>
 256 <td class="colLast"><span class="typeNameLabel">Align.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/Align.html#getFastaSequences--">getFastaSequences</a></span>()</code>&nbsp;</td>
 257 </tr>
 258 </tbody>
 259 </table>
 260 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 261 <caption><span>Method parameters in <a href="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a> with type arguments of type <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></span><span class="tabEnd">&nbsp;</span></caption>
 262 <tr>
 263 <th class="colFirst" scope="col">Modifier and Type</th>
 264 <th class="colLast" scope="col">Method and Description</th>
 265 </tr>
 266 <tbody>
 267 <tr class="altColor">
 268 <td class="colFirst"><code>void</code></td>
 269 <td class="colLast"><span class="typeNameLabel">PresetAnalize.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/PresetAnalize.html#setFastaSequences-java.util.List-">setFastaSequences</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;fastaSequences)</code>&nbsp;</td>
 270 </tr>
 271 <tr class="rowColor">
 272 <td class="colFirst"><code>void</code></td>
 273 <td class="colLast"><span class="typeNameLabel">PresetAlign.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/PresetAlign.html#setFastaSequences-java.util.List-">setFastaSequences</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;fastaSequences)</code>&nbsp;</td>
 274 </tr>
 275 <tr class="altColor">
 276 <td class="colFirst"><code>void</code></td>
 277 <td class="colLast"><span class="typeNameLabel">CustomAnalize.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/CustomAnalize.html#setFastaSequences-java.util.List-">setFastaSequences</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;fastaSequences)</code>&nbsp;</td>
 278 </tr>
 279 <tr class="rowColor">
 280 <td class="colFirst"><code>void</code></td>
 281 <td class="colLast"><span class="typeNameLabel">CustomAlign.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/CustomAlign.html#setFastaSequences-java.util.List-">setFastaSequences</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;fastaSequences)</code>&nbsp;</td>
 282 </tr>
 283 <tr class="altColor">
 284 <td class="colFirst"><code>void</code></td>
 285 <td class="colLast"><span class="typeNameLabel">Analize.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/Analize.html#setFastaSequences-java.util.List-">setFastaSequences</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;fastaSequences)</code>&nbsp;</td>
 286 </tr>
 287 <tr class="rowColor">
 288 <td class="colFirst"><code>void</code></td>
 289 <td class="colLast"><span class="typeNameLabel">Align.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/Align.html#setFastaSequences-java.util.List-">setFastaSequences</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;fastaSequences)</code>&nbsp;</td>
 290 </tr>
 291 </tbody>
 292 </table>
 293 </li>
 294 <li class="blockList"><a name="compbio.data.sequence">
 295 <!--   -->
 296 </a>
 297 <h3>Uses of <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a> in <a href="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></h3>
 298 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing fields, and an explanation">
 299 <caption><span>Fields in <a href="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a> with type parameters of type <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></span><span class="tabEnd">&nbsp;</span></caption>
 300 <tr>
 301 <th class="colFirst" scope="col">Modifier and Type</th>
 302 <th class="colLast" scope="col">Field and Description</th>
 303 </tr>
 304 <tbody>
 305 <tr class="altColor">
 306 <td class="colFirst"><code>protected java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></td>
 307 <td class="colLast"><span class="typeNameLabel">Alignment.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/Alignment.html#sequences">sequences</a></span></code>&nbsp;</td>
 308 </tr>
 309 </tbody>
 310 </table>
 311 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 312 <caption><span>Methods in <a href="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a> that return <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></span><span class="tabEnd">&nbsp;</span></caption>
 313 <tr>
 314 <th class="colFirst" scope="col">Modifier and Type</th>
 315 <th class="colLast" scope="col">Method and Description</th>
 316 </tr>
 317 <tbody>
 318 <tr class="altColor">
 319 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></code></td>
 320 <td class="colLast"><span class="typeNameLabel">FastaReader.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/FastaReader.html#next--">next</a></span>()</code>
 321 <div class="block">Reads the next FastaSequence from the input</div>
 322 </td>
 323 </tr>
 324 <tr class="rowColor">
 325 <td class="colFirst"><code>private static <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></code></td>
 326 <td class="colLast"><span class="typeNameLabel">FastaReader.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/FastaReader.html#toFastaSequence-java.lang.String-">toFastaSequence</a></span>(java.lang.String&nbsp;singleFastaEntry)</code>&nbsp;</td>
 327 </tr>
 328 </tbody>
 329 </table>
 330 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 331 <caption><span>Methods in <a href="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a> that return types with arguments of type <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></span><span class="tabEnd">&nbsp;</span></caption>
 332 <tr>
 333 <th class="colFirst" scope="col">Modifier and Type</th>
 334 <th class="colLast" scope="col">Method and Description</th>
 335 </tr>
 336 <tbody>
 337 <tr class="altColor">
 338 <td class="colFirst"><code>java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></td>
 339 <td class="colLast"><span class="typeNameLabel">Alignment.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/Alignment.html#getSequences--">getSequences</a></span>()</code>&nbsp;</td>
 340 </tr>
 341 <tr class="rowColor">
 342 <td class="colFirst"><code>static java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></td>
 343 <td class="colLast"><span class="typeNameLabel">SequenceUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/SequenceUtil.html#openInputStream-java.lang.String-">openInputStream</a></span>(java.lang.String&nbsp;inFilePath)</code>
 344 <div class="block">Reads and parses Fasta or Clustal formatted file into a list of
 345  FastaSequence objects</div>
 346 </td>
 347 </tr>
 348 <tr class="altColor">
 349 <td class="colFirst"><code>static java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></td>
 350 <td class="colLast"><span class="typeNameLabel">SequenceUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/SequenceUtil.html#readFasta-java.io.InputStream-">readFasta</a></span>(java.io.InputStream&nbsp;inStream)</code>
 351 <div class="block">Reads fasta sequences from inStream into the list of FastaSequence
 352  objects</div>
 353 </td>
 354 </tr>
 355 </tbody>
 356 </table>
 357 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 358 <caption><span>Methods in <a href="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a> with parameters of type <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></span><span class="tabEnd">&nbsp;</span></caption>
 359 <tr>
 360 <th class="colFirst" scope="col">Modifier and Type</th>
 361 <th class="colLast" scope="col">Method and Description</th>
 362 </tr>
 363 <tbody>
 364 <tr class="altColor">
 365 <td class="colFirst"><code>static boolean</code></td>
 366 <td class="colLast"><span class="typeNameLabel">SequenceUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence-compbio.data.sequence.FastaSequence-">isNucleotideSequence</a></span>(<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&nbsp;s)</code>&nbsp;</td>
 367 </tr>
 368 </tbody>
 369 </table>
 370 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 371 <caption><span>Method parameters in <a href="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a> with type arguments of type <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></span><span class="tabEnd">&nbsp;</span></caption>
 372 <tr>
 373 <th class="colFirst" scope="col">Modifier and Type</th>
 374 <th class="colLast" scope="col">Method and Description</th>
 375 </tr>
 376 <tbody>
 377 <tr class="altColor">
 378 <td class="colFirst"><code>static void</code></td>
 379 <td class="colLast"><span class="typeNameLabel">SequenceUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/SequenceUtil.html#writeClustal-java.io.OutputStream-java.util.List-char-">writeClustal</a></span>(java.io.OutputStream&nbsp;outStream,
 380             java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 381             char&nbsp;gapChar)</code>&nbsp;</td>
 382 </tr>
 383 <tr class="rowColor">
 384 <td class="colFirst"><code>static void</code></td>
 385 <td class="colLast"><span class="typeNameLabel">SequenceUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/SequenceUtil.html#writeFasta-java.io.OutputStream-java.util.List-">writeFasta</a></span>(java.io.OutputStream&nbsp;os,
 386           java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)</code>
 387 <div class="block">Writes FastaSequence in the file, each sequence will take one line only</div>
 388 </td>
 389 </tr>
 390 <tr class="altColor">
 391 <td class="colFirst"><code>static void</code></td>
 392 <td class="colLast"><span class="typeNameLabel">SequenceUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/SequenceUtil.html#writeFasta-java.io.OutputStream-java.util.List-int-">writeFasta</a></span>(java.io.OutputStream&nbsp;outstream,
 393           java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 394           int&nbsp;width)</code>
 395 <div class="block">Writes list of FastaSequeces into the outstream formatting the sequence
 396  so that it contains width chars on each line</div>
 397 </td>
 398 </tr>
 399 <tr class="rowColor">
 400 <td class="colFirst"><code>static void</code></td>
 401 <td class="colLast"><span class="typeNameLabel">SequenceUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/SequenceUtil.html#writeFastaKeepTheStream-java.io.OutputStream-java.util.List-int-">writeFastaKeepTheStream</a></span>(java.io.OutputStream&nbsp;outstream,
 402                        java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 403                        int&nbsp;width)</code>&nbsp;</td>
 404 </tr>
 405 </tbody>
 406 </table>
 407 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing constructors, and an explanation">
 408 <caption><span>Constructor parameters in <a href="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a> with type arguments of type <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></span><span class="tabEnd">&nbsp;</span></caption>
 409 <tr>
 410 <th class="colOne" scope="col">Constructor and Description</th>
 411 </tr>
 412 <tbody>
 413 <tr class="altColor">
 414 <td class="colLast"><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/Alignment.html#Alignment-java.util.List-compbio.data.sequence.AlignmentMetadata-">Alignment</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 415          <a href="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</a>&nbsp;metadata)</code>&nbsp;</td>
 416 </tr>
 417 <tr class="rowColor">
 418 <td class="colLast"><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/Alignment.html#Alignment-java.util.List-compbio.data.sequence.Program-char-">Alignment</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 419          <a href="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</a>&nbsp;program,
 420          char&nbsp;gapchar)</code>&nbsp;</td>
 421 </tr>
 422 </tbody>
 423 </table>
 424 </li>
 425 <li class="blockList"><a name="compbio.engine">
 426 <!--   -->
 427 </a>
 428 <h3>Uses of <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a> in <a href="../../../../compbio/engine/package-summary.html">compbio.engine</a></h3>
 429 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 430 <caption><span>Method parameters in <a href="../../../../compbio/engine/package-summary.html">compbio.engine</a> with type arguments of type <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></span><span class="tabEnd">&nbsp;</span></caption>
 431 <tr>
 432 <th class="colFirst" scope="col">Modifier and Type</th>
 433 <th class="colLast" scope="col">Method and Description</th>
 434 </tr>
 435 <tbody>
 436 <tr class="altColor">
 437 <td class="colFirst"><code>static &lt;T&gt;&nbsp;<a href="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;T&gt;</code></td>
 438 <td class="colLast"><span class="typeNameLabel">Configurator.</span><code><span class="memberNameLink"><a href="../../../../compbio/engine/Configurator.html#configureExecutable-compbio.engine.client.Executable-java.util.List-">configureExecutable</a></span>(<a href="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a>&lt;T&gt;&nbsp;executable,
 439                    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>
 440 </tr>
 441 <tr class="rowColor">
 442 <td class="colFirst"><code>static &lt;T,V&gt;&nbsp;<a href="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</a></code></td>
 443 <td class="colLast"><span class="typeNameLabel">LoadBalancer.</span><code><span class="memberNameLink"><a href="../../../../compbio/engine/LoadBalancer.html#getEngine-compbio.engine.client.Executable-java.util.List-">getEngine</a></span>(<a href="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a>&lt;V&gt;&nbsp;executable,
 444          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>
 445 </tr>
 446 <tr class="altColor">
 447 <td class="colFirst"><code>(package private) static <a href="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</a></code></td>
 448 <td class="colLast"><span class="typeNameLabel">Configurator.</span><code><span class="memberNameLink"><a href="../../../../compbio/engine/Configurator.html#getExecProvider-compbio.engine.client.ConfiguredExecutable-java.util.List-">getExecProvider</a></span>(<a href="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;?&gt;&nbsp;executable,
 449                java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;dataSet)</code>
 450 <div class="block">Depending on the values defined in the properties
 451  (engine.cluster.enable=true and engine.local.enable=true) return either
 452  Cluster job submission engine <code>#JobRunner</code> or local job submission
 453  engine <code>#LocalRunner</code> If both engines enabled than ask
 454  <a href="../../../../compbio/engine/LoadBalancer.html" title="class in compbio.engine"><code>LoadBalancer</code></a> for an engine.</div>
 455 </td>
 456 </tr>
 457 </tbody>
 458 </table>
 459 </li>
 460 <li class="blockList"><a name="compbio.metadata">
 461 <!--   -->
 462 </a>
 463 <h3>Uses of <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a> in <a href="../../../../compbio/metadata/package-summary.html">compbio.metadata</a></h3>
 464 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 465 <caption><span>Method parameters in <a href="../../../../compbio/metadata/package-summary.html">compbio.metadata</a> with type arguments of type <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></span><span class="tabEnd">&nbsp;</span></caption>
 466 <tr>
 467 <th class="colFirst" scope="col">Modifier and Type</th>
 468 <th class="colLast" scope="col">Method and Description</th>
 469 </tr>
 470 <tbody>
 471 <tr class="altColor">
 472 <td class="colFirst"><code>static int</code></td>
 473 <td class="colLast"><span class="typeNameLabel">Limit.</span><code><span class="memberNameLink"><a href="../../../../compbio/metadata/Limit.html#getAvgSequenceLength-java.util.List-">getAvgSequenceLength</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;data)</code>
 474 <div class="block">Calculates an average sequence length of the dataset</div>
 475 </td>
 476 </tr>
 477 <tr class="rowColor">
 478 <td class="colFirst"><code>boolean</code></td>
 479 <td class="colLast"><span class="typeNameLabel">Limit.</span><code><span class="memberNameLink"><a href="../../../../compbio/metadata/Limit.html#isExceeded-java.util.List-">isExceeded</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;data)</code>
 480 <div class="block">Checks if the number of sequences or their average length in the dataset
 481  exceeds this limit.</div>
 482 </td>
 483 </tr>
 484 <tr class="altColor">
 485 <td class="colFirst"><code>static <a href="../../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></code></td>
 486 <td class="colLast"><span class="typeNameLabel">LimitExceededException.</span><code><span class="memberNameLink"><a href="../../../../compbio/metadata/LimitExceededException.html#newLimitExceeded-compbio.metadata.Limit-java.util.List-">newLimitExceeded</a></span>(<a href="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a>&lt;?&gt;&nbsp;limit,
 487                 java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;seqs)</code>&nbsp;</td>
 488 </tr>
 489 </tbody>
 490 </table>
 491 </li>
 492 <li class="blockList"><a name="compbio.runner">
 493 <!--   -->
 494 </a>
 495 <h3>Uses of <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a> in <a href="../../../../compbio/runner/package-summary.html">compbio.runner</a></h3>
 496 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 497 <caption><span>Method parameters in <a href="../../../../compbio/runner/package-summary.html">compbio.runner</a> with type arguments of type <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></span><span class="tabEnd">&nbsp;</span></caption>
 498 <tr>
 499 <th class="colFirst" scope="col">Modifier and Type</th>
 500 <th class="colLast" scope="col">Method and Description</th>
 501 </tr>
 502 <tbody>
 503 <tr class="altColor">
 504 <td class="colFirst"><code>static void</code></td>
 505 <td class="colLast"><span class="typeNameLabel">RunnerUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/RunnerUtil.html#writeClustalInput-java.util.List-compbio.engine.client.ConfiguredExecutable-char-">writeClustalInput</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 506                  <a href="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;?&gt;&nbsp;exec,
 507                  char&nbsp;gapChar)</code>&nbsp;</td>
 508 </tr>
 509 <tr class="rowColor">
 510 <td class="colFirst"><code>static void</code></td>
 511 <td class="colLast"><span class="typeNameLabel">Util.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/Util.html#writeInput-java.util.List-compbio.engine.client.ConfiguredExecutable-">writeInput</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 512           <a href="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;?&gt;&nbsp;exec)</code>&nbsp;</td>
 513 </tr>
 514 <tr class="altColor">
 515 <td class="colFirst"><code>static void</code></td>
 516 <td class="colLast"><span class="typeNameLabel">RunnerUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/RunnerUtil.html#writeInput-java.util.List-compbio.engine.client.ConfiguredExecutable-">writeInput</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 517           <a href="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;?&gt;&nbsp;exec)</code>&nbsp;</td>
 518 </tr>
 519 </tbody>
 520 </table>
 521 </li>
 522 <li class="blockList"><a name="compbio.ws.client">
 523 <!--   -->
 524 </a>
 525 <h3>Uses of <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a> in <a href="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</a></h3>
 526 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 527 <caption><span>Methods in <a href="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</a> that return types with arguments of type <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></span><span class="tabEnd">&nbsp;</span></caption>
 528 <tr>
 529 <th class="colFirst" scope="col">Modifier and Type</th>
 530 <th class="colLast" scope="col">Method and Description</th>
 531 </tr>
 532 <tbody>
 533 <tr class="altColor">
 534 <td class="colFirst"><code>private static java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></td>
 535 <td class="colLast"><span class="typeNameLabel">WSTester.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/client/WSTester.html#loadAlignment--">loadAlignment</a></span>()</code>
 536 <div class="block">Converting input to a form accepted by WS</div>
 537 </td>
 538 </tr>
 539 <tr class="rowColor">
 540 <td class="colFirst"><code>private static java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></td>
 541 <td class="colLast"><span class="typeNameLabel">WSTester.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/client/WSTester.html#loadRNAAlignment--">loadRNAAlignment</a></span>()</code>
 542 <div class="block">Converting input to a form accepted by WS</div>
 543 </td>
 544 </tr>
 545 <tr class="altColor">
 546 <td class="colFirst"><code>private static java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></td>
 547 <td class="colLast"><span class="typeNameLabel">WSTester.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/client/WSTester.html#loadSeqs-int-">loadSeqs</a></span>(int&nbsp;nLines)</code>
 548 <div class="block">Converting input to a form accepted by WS</div>
 549 </td>
 550 </tr>
 551 </tbody>
 552 </table>
 553 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 554 <caption><span>Method parameters in <a href="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</a> with type arguments of type <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></span><span class="tabEnd">&nbsp;</span></caption>
 555 <tr>
 556 <th class="colFirst" scope="col">Modifier and Type</th>
 557 <th class="colLast" scope="col">Method and Description</th>
 558 </tr>
 559 <tbody>
 560 <tr class="altColor">
 561 <td class="colFirst"><code>(package private) static &lt;T&gt;&nbsp;<a href="../../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></code></td>
 562 <td class="colLast"><span class="typeNameLabel">Jws2Client.</span><code><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</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;fastalist,
 563        <a href="../../../../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</a>&lt;T&gt;&nbsp;wsproxy,
 564        <a href="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;T&gt;&nbsp;preset,
 565        java.util.List&lt;<a href="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;T&gt;&gt;&nbsp;customOptions)</code>
 566 <div class="block">Calculate conservation for sequences loaded from a FASTA record list structure</div>
 567 </td>
 568 </tr>
 569 <tr class="rowColor">
 570 <td class="colFirst"><code>private &lt;T&gt;&nbsp;boolean</code></td>
 571 <td class="colLast"><span class="typeNameLabel">WSTester.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/client/WSTester.html#testDefaultAnalyse-java.util.List-compbio.data.msa.SequenceAnnotation-compbio.metadata.Preset-java.util.List-">testDefaultAnalyse</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;fastalist,
 572                   <a href="../../../../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</a>&lt;T&gt;&nbsp;wsproxy,
 573                   <a href="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;T&gt;&nbsp;preset,
 574                   java.util.List&lt;<a href="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;T&gt;&gt;&nbsp;customOptions)</code>&nbsp;</td>
 575 </tr>
 576 </tbody>
 577 </table>
 578 </li>
 579 <li class="blockList"><a name="compbio.ws.server">
 580 <!--   -->
 581 </a>
 582 <h3>Uses of <a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a> in <a href="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</a></h3>
 583 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 584 <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/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></span><span class="tabEnd">&nbsp;</span></caption>
 585 <tr>
 586 <th class="colFirst" scope="col">Modifier and Type</th>
 587 <th class="colLast" scope="col">Method and Description</th>
 588 </tr>
 589 <tbody>
 590 <tr class="altColor">
 591 <td class="colFirst"><code>java.lang.String</code></td>
 592 <td class="colLast"><span class="typeNameLabel">GLprobsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/GLprobsWS.html#align-java.util.List-">align</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)</code>&nbsp;</td>
 593 </tr>
 594 <tr class="rowColor">
 595 <td class="colFirst"><code>java.lang.String</code></td>
 596 <td class="colLast"><span class="typeNameLabel">MafftWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/MafftWS.html#align-java.util.List-">align</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)</code>&nbsp;</td>
 597 </tr>
 598 <tr class="altColor">
 599 <td class="colFirst"><code>java.lang.String</code></td>
 600 <td class="colLast"><span class="typeNameLabel">ClustalOWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/ClustalOWS.html#align-java.util.List-">align</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)</code>&nbsp;</td>
 601 </tr>
 602 <tr class="rowColor">
 603 <td class="colFirst"><code>java.lang.String</code></td>
 604 <td class="colLast"><span class="typeNameLabel">MSAprobsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/MSAprobsWS.html#align-java.util.List-">align</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)</code>&nbsp;</td>
 605 </tr>
 606 <tr class="altColor">
 607 <td class="colFirst"><code>java.lang.String</code></td>
 608 <td class="colLast"><span class="typeNameLabel">MuscleWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/MuscleWS.html#align-java.util.List-">align</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)</code>&nbsp;</td>
 609 </tr>
 610 <tr class="rowColor">
 611 <td class="colFirst"><code>java.lang.String</code></td>
 612 <td class="colLast"><span class="typeNameLabel">ClustalWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/ClustalWS.html#align-java.util.List-">align</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)</code>&nbsp;</td>
 613 </tr>
 614 <tr class="altColor">
 615 <td class="colFirst"><code>java.lang.String</code></td>
 616 <td class="colLast"><span class="typeNameLabel">TcoffeeWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/TcoffeeWS.html#align-java.util.List-">align</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)</code>&nbsp;</td>
 617 </tr>
 618 <tr class="rowColor">
 619 <td class="colFirst"><code>java.lang.String</code></td>
 620 <td class="colLast"><span class="typeNameLabel">ProbconsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/ProbconsWS.html#align-java.util.List-">align</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)</code>&nbsp;</td>
 621 </tr>
 622 <tr class="altColor">
 623 <td class="colFirst"><code>static &lt;T&gt;&nbsp;java.lang.String</code></td>
 624 <td class="colLast"><span class="typeNameLabel">WSUtil.</span><code><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</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 625      <a href="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;T&gt;&nbsp;confExec,
 626      org.apache.log4j.Logger&nbsp;logger,
 627      java.lang.String&nbsp;callingMethod,
 628      <a href="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a>&lt;T&gt;&nbsp;limit)</code>&nbsp;</td>
 629 </tr>
 630 <tr class="rowColor">
 631 <td class="colFirst"><code>java.lang.String</code></td>
 632 <td class="colLast"><span class="typeNameLabel">SequenceAnnotationService.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/SequenceAnnotationService.html#analize-java.util.List-">analize</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)</code>&nbsp;</td>
 633 </tr>
 634 <tr class="altColor">
 635 <td class="colFirst"><code>java.lang.String</code></td>
 636 <td class="colLast"><span class="typeNameLabel">AAConWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/AAConWS.html#analize-java.util.List-">analize</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)</code>&nbsp;</td>
 637 </tr>
 638 <tr class="rowColor">
 639 <td class="colFirst"><code>java.lang.String</code></td>
 640 <td class="colLast"><span class="typeNameLabel">RNAalifoldWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/RNAalifoldWS.html#analize-java.util.List-">analize</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)</code>&nbsp;</td>
 641 </tr>
 642 <tr class="altColor">
 643 <td class="colFirst"><code>static &lt;T&gt;&nbsp;java.lang.String</code></td>
 644 <td class="colLast"><span class="typeNameLabel">WSUtil.</span><code><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</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 645        <a href="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;T&gt;&nbsp;confExec,
 646        org.apache.log4j.Logger&nbsp;log,
 647        java.lang.String&nbsp;method,
 648        <a href="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a>&lt;T&gt;&nbsp;limit)</code>&nbsp;</td>
 649 </tr>
 650 <tr class="rowColor">
 651 <td class="colFirst"><code>java.lang.String</code></td>
 652 <td class="colLast"><span class="typeNameLabel">ClustalOWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/ClustalOWS.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,
 653            java.util.List&lt;<a href="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;<a href="../../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;&gt;&nbsp;options)</code>&nbsp;</td>
 654 </tr>
 655 <tr class="altColor">
 656 <td class="colFirst"><code>java.lang.String</code></td>
 657 <td class="colLast"><span class="typeNameLabel">ClustalWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/ClustalWS.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,
 658            java.util.List&lt;<a href="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;<a href="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</a>&gt;&gt;&nbsp;options)</code>&nbsp;</td>
 659 </tr>
 660 <tr class="rowColor">
 661 <td class="colFirst"><code>java.lang.String</code></td>
 662 <td class="colLast"><span class="typeNameLabel">GLprobsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/GLprobsWS.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,
 663            java.util.List&lt;<a href="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;<a href="../../../../compbio/runner/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a>&gt;&gt;&nbsp;options)</code>&nbsp;</td>
 664 </tr>
 665 <tr class="altColor">
 666 <td class="colFirst"><code>java.lang.String</code></td>
 667 <td class="colLast"><span class="typeNameLabel">MafftWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/MafftWS.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,
 668            java.util.List&lt;<a href="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;<a href="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>&gt;&gt;&nbsp;options)</code>&nbsp;</td>
 669 </tr>
 670 <tr class="rowColor">
 671 <td class="colFirst"><code>java.lang.String</code></td>
 672 <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,
 673            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>
 674 </tr>
 675 <tr class="altColor">
 676 <td class="colFirst"><code>java.lang.String</code></td>
 677 <td class="colLast"><span class="typeNameLabel">MuscleWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/MuscleWS.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,
 678            java.util.List&lt;<a href="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;<a href="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</a>&gt;&gt;&nbsp;options)</code>&nbsp;</td>
 679 </tr>
 680 <tr class="rowColor">
 681 <td class="colFirst"><code>java.lang.String</code></td>
 682 <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&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 683            java.util.List&lt;<a href="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;<a href="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</a>&gt;&gt;&nbsp;options)</code>&nbsp;</td>
 684 </tr>
 685 <tr class="altColor">
 686 <td class="colFirst"><code>java.lang.String</code></td>
 687 <td class="colLast"><span class="typeNameLabel">TcoffeeWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/TcoffeeWS.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,
 688            java.util.List&lt;<a href="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;<a href="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</a>&gt;&gt;&nbsp;options)</code>&nbsp;</td>
 689 </tr>
 690 <tr class="rowColor">
 691 <td class="colFirst"><code>java.lang.String</code></td>
 692 <td class="colLast"><span class="typeNameLabel">AAConWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/AAConWS.html#customAnalize-java.util.List-java.util.List-">customAnalize</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 693              java.util.List&lt;<a href="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;<a href="../../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a>&gt;&gt;&nbsp;options)</code>&nbsp;</td>
 694 </tr>
 695 <tr class="altColor">
 696 <td class="colFirst"><code>java.lang.String</code></td>
 697 <td class="colLast"><span class="typeNameLabel">DisemblWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/DisemblWS.html#customAnalize-java.util.List-java.util.List-">customAnalize</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 698              java.util.List&lt;<a href="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;<a href="../../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</a>&gt;&gt;&nbsp;options)</code>&nbsp;</td>
 699 </tr>
 700 <tr class="rowColor">
 701 <td class="colFirst"><code>java.lang.String</code></td>
 702 <td class="colLast"><span class="typeNameLabel">GlobPlotWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/GlobPlotWS.html#customAnalize-java.util.List-java.util.List-">customAnalize</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 703              java.util.List&lt;<a href="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;<a href="../../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</a>&gt;&gt;&nbsp;options)</code>&nbsp;</td>
 704 </tr>
 705 <tr class="altColor">
 706 <td class="colFirst"><code>java.lang.String</code></td>
 707 <td class="colLast"><span class="typeNameLabel">RNAalifoldWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/RNAalifoldWS.html#customAnalize-java.util.List-java.util.List-">customAnalize</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 708              java.util.List&lt;<a href="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;<a href="../../../../compbio/runner/structure/RNAalifold.html" title="class in compbio.runner.structure">RNAalifold</a>&gt;&gt;&nbsp;options)</code>&nbsp;</td>
 709 </tr>
 710 <tr class="rowColor">
 711 <td class="colFirst"><code>java.lang.String</code></td>
 712 <td class="colLast"><span class="typeNameLabel">SequenceAnnotationService.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/SequenceAnnotationService.html#customAnalize-java.util.List-java.util.List-">customAnalize</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 713              java.util.List&lt;<a href="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;<a href="../../../../compbio/ws/server/SequenceAnnotationService.html" title="type parameter in SequenceAnnotationService">T</a>&gt;&gt;&nbsp;options)</code>&nbsp;</td>
 714 </tr>
 715 <tr class="altColor">
 716 <td class="colFirst"><code>static &lt;T&gt;&nbsp;java.lang.String</code></td>
 717 <td class="colLast"><span class="typeNameLabel">WSUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/WSUtil.html#fold-java.util.List-compbio.engine.client.ConfiguredExecutable-org.apache.log4j.Logger-java.lang.String-compbio.metadata.Limit-">fold</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 718     <a href="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;T&gt;&nbsp;confExec,
 719     org.apache.log4j.Logger&nbsp;log,
 720     java.lang.String&nbsp;method,
 721     <a href="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a>&lt;T&gt;&nbsp;limit)</code>&nbsp;</td>
 722 </tr>
 723 <tr class="rowColor">
 724 <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/ws/server/GenericMetadataService.html" title="type parameter in GenericMetadataService">T</a>&gt;</code></td>
 725 <td class="colLast"><span class="typeNameLabel">GenericMetadataService.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/GenericMetadataService.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;sequences)</code>&nbsp;</td>
 726 </tr>
 727 <tr class="altColor">
 728 <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/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a>&gt;</code></td>
 729 <td class="colLast"><span class="typeNameLabel">GLprobsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/GLprobsWS.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>
 730 </tr>
 731 <tr class="rowColor">
 732 <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/Mafft.html" title="class in compbio.runner.msa">Mafft</a>&gt;</code></td>
 733 <td class="colLast"><span class="typeNameLabel">MafftWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/MafftWS.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>
 734 </tr>
 735 <tr class="altColor">
 736 <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/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;</code></td>
 737 <td class="colLast"><span class="typeNameLabel">ClustalOWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/ClustalOWS.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>
 738 </tr>
 739 <tr class="rowColor">
 740 <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>
 741 <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>
 742 </tr>
 743 <tr class="altColor">
 744 <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/Muscle.html" title="class in compbio.runner.msa">Muscle</a>&gt;</code></td>
 745 <td class="colLast"><span class="typeNameLabel">MuscleWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/MuscleWS.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;sequences)</code>&nbsp;</td>
 746 </tr>
 747 <tr class="rowColor">
 748 <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/ClustalW.html" title="class in compbio.runner.msa">ClustalW</a>&gt;</code></td>
 749 <td class="colLast"><span class="typeNameLabel">ClustalWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/ClustalWS.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>
 750 </tr>
 751 <tr class="altColor">
 752 <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/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</a>&gt;</code></td>
 753 <td class="colLast"><span class="typeNameLabel">TcoffeeWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/TcoffeeWS.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;sequences)</code>&nbsp;</td>
 754 </tr>
 755 <tr class="rowColor">
 756 <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/Probcons.html" title="class in compbio.runner.msa">Probcons</a>&gt;</code></td>
 757 <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&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;dataSet)</code>&nbsp;</td>
 758 </tr>
 759 <tr class="altColor">
 760 <td class="colFirst"><code>java.lang.String</code></td>
 761 <td class="colLast"><span class="typeNameLabel">ClustalOWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/ClustalOWS.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,
 762            <a href="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;&nbsp;preset)</code>&nbsp;</td>
 763 </tr>
 764 <tr class="rowColor">
 765 <td class="colFirst"><code>java.lang.String</code></td>
 766 <td class="colLast"><span class="typeNameLabel">ClustalWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/ClustalWS.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,
 767            <a href="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</a>&gt;&nbsp;preset)</code>&nbsp;</td>
 768 </tr>
 769 <tr class="altColor">
 770 <td class="colFirst"><code>java.lang.String</code></td>
 771 <td class="colLast"><span class="typeNameLabel">GLprobsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/GLprobsWS.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,
 772            <a href="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../../compbio/runner/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a>&gt;&nbsp;preset)</code>&nbsp;</td>
 773 </tr>
 774 <tr class="rowColor">
 775 <td class="colFirst"><code>java.lang.String</code></td>
 776 <td class="colLast"><span class="typeNameLabel">MafftWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/MafftWS.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,
 777            <a href="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>&gt;&nbsp;preset)</code>&nbsp;</td>
 778 </tr>
 779 <tr class="altColor">
 780 <td class="colFirst"><code>java.lang.String</code></td>
 781 <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,
 782            <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>
 783 </tr>
 784 <tr class="rowColor">
 785 <td class="colFirst"><code>java.lang.String</code></td>
 786 <td class="colLast"><span class="typeNameLabel">MuscleWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/MuscleWS.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,
 787            <a href="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</a>&gt;&nbsp;preset)</code>&nbsp;</td>
 788 </tr>
 789 <tr class="altColor">
 790 <td class="colFirst"><code>java.lang.String</code></td>
 791 <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&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 792            <a href="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</a>&gt;&nbsp;preset)</code>&nbsp;</td>
 793 </tr>
 794 <tr class="rowColor">
 795 <td class="colFirst"><code>java.lang.String</code></td>
 796 <td class="colLast"><span class="typeNameLabel">TcoffeeWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/TcoffeeWS.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,
 797            <a href="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</a>&gt;&nbsp;preset)</code>&nbsp;</td>
 798 </tr>
 799 <tr class="altColor">
 800 <td class="colFirst"><code>java.lang.String</code></td>
 801 <td class="colLast"><span class="typeNameLabel">AAConWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/AAConWS.html#presetAnalize-java.util.List-compbio.metadata.Preset-">presetAnalize</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 802              <a href="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a>&gt;&nbsp;preset)</code>&nbsp;</td>
 803 </tr>
 804 <tr class="rowColor">
 805 <td class="colFirst"><code>java.lang.String</code></td>
 806 <td class="colLast"><span class="typeNameLabel">DisemblWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/DisemblWS.html#presetAnalize-java.util.List-compbio.metadata.Preset-">presetAnalize</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 807              <a href="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</a>&gt;&nbsp;preset)</code>&nbsp;</td>
 808 </tr>
 809 <tr class="altColor">
 810 <td class="colFirst"><code>java.lang.String</code></td>
 811 <td class="colLast"><span class="typeNameLabel">GlobPlotWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/GlobPlotWS.html#presetAnalize-java.util.List-compbio.metadata.Preset-">presetAnalize</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 812              <a href="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</a>&gt;&nbsp;preset)</code>&nbsp;</td>
 813 </tr>
 814 <tr class="rowColor">
 815 <td class="colFirst"><code>java.lang.String</code></td>
 816 <td class="colLast"><span class="typeNameLabel">IUPredWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/IUPredWS.html#presetAnalize-java.util.List-compbio.metadata.Preset-">presetAnalize</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 817              <a href="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</a>&gt;&nbsp;preset)</code>&nbsp;</td>
 818 </tr>
 819 <tr class="altColor">
 820 <td class="colFirst"><code>java.lang.String</code></td>
 821 <td class="colLast"><span class="typeNameLabel">RNAalifoldWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/RNAalifoldWS.html#presetAnalize-java.util.List-compbio.metadata.Preset-">presetAnalize</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 822              <a href="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../../compbio/runner/structure/RNAalifold.html" title="class in compbio.runner.structure">RNAalifold</a>&gt;&nbsp;preset)</code>&nbsp;</td>
 823 </tr>
 824 <tr class="rowColor">
 825 <td class="colFirst"><code>java.lang.String</code></td>
 826 <td class="colLast"><span class="typeNameLabel">SequenceAnnotationService.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/SequenceAnnotationService.html#presetAnalize-java.util.List-compbio.metadata.Preset-">presetAnalize</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 827              <a href="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../../compbio/ws/server/SequenceAnnotationService.html" title="type parameter in SequenceAnnotationService">T</a>&gt;&nbsp;preset)</code>&nbsp;</td>
 828 </tr>
 829 <tr class="altColor">
 830 <td class="colFirst"><code>static void</code></td>
 831 <td class="colLast"><span class="typeNameLabel">WSUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/WSUtil.html#validateAAConInput-java.util.List-">validateAAConInput</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)</code>&nbsp;</td>
 832 </tr>
 833 <tr class="rowColor">
 834 <td class="colFirst"><code>static void</code></td>
 835 <td class="colLast"><span class="typeNameLabel">WSUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/WSUtil.html#validateFastaInput-java.util.List-">validateFastaInput</a></span>(java.util.List&lt;<a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)</code>&nbsp;</td>
 836 </tr>
 837 </tbody>
 838 </table>
 839 </li>
 840 </ul>
 841 </li>
 842 </ul>
 843 </div>
 844 <!-- ======= START OF BOTTOM NAVBAR ====== -->
 845 <div class="bottomNav"><a name="navbar.bottom">
 846 <!--   -->
 847 </a>
 848 <div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
 849 <a name="navbar.bottom.firstrow">
 850 <!--   -->
 851 </a>
 852 <ul class="navList" title="Navigation">
 853 <li><a href="../../../../overview-summary.html">Overview</a></li>
 854 <li><a href="../package-summary.html">Package</a></li>
 855 <li><a href="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">Class</a></li>
 856 <li class="navBarCell1Rev">Use</li>
 857 <li><a href="../../../../overview-tree.html">Tree</a></li>
 858 <li><a href="../../../../deprecated-list.html">Deprecated</a></li>
 859 <li><a href="../../../../index-files/index-1.html">Index</a></li>
 860 <li><a href="../../../../help-doc.html">Help</a></li>
 861 </ul>
 862 </div>
 863 <div class="subNav">
 864 <ul class="navList">
 865 <li>Prev</li>
 866 <li>Next</li>
 867 </ul>
 868 <ul class="navList">
 869 <li><a href="../../../../index.html?compbio/data/sequence/class-use/FastaSequence.html" target="_top">Frames</a></li>
 870 <li><a href="FastaSequence.html" target="_top">No&nbsp;Frames</a></li>
 871 </ul>
 872 <ul class="navList" id="allclasses_navbar_bottom">
 873 <li><a href="../../../../allclasses-noframe.html">All&nbsp;Classes</a></li>
 874 </ul>
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 876 <script type="text/javascript"><!--
 877   allClassesLink = document.getElementById("allclasses_navbar_bottom");
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 879     allClassesLink.style.display = "block";
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 882     allClassesLink.style.display = "none";
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 887 <a name="skip.navbar.bottom">
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