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  95 <div class="subTitle">compbio.data.sequence</div>
  96 <h2 title="Class Alignment" class="title">Class Alignment</h2>
  97 </div>
  98 <div class="contentContainer">
  99 <ul class="inheritance">
 100 <li>java.lang.Object</li>
 101 <li>
 102 <ul class="inheritance">
 103 <li>compbio.data.sequence.Alignment</li>
 104 </ul>
 105 </li>
 106 </ul>
 107 <div class="description">
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 110 <hr>
 111 <br>
 112 <pre>public class <span class="typeNameLabel">Alignment</span>
 113 extends java.lang.Object</pre>
 114 <div class="block">Multiple sequence alignment.
 115
 116  Does not give any guarantees on the content of individual FastaSequece
 117  records. It does not guarantee neither the uniqueness of the names of
 118  sequences nor it guarantees the uniqueness of the sequences.</div>
 119 <dl>
 120 <dt><span class="simpleTagLabel">Version:</span></dt>
 121 <dd>1.0 September 2009</dd>
 122 <dt><span class="simpleTagLabel">Author:</span></dt>
 123 <dd>pvtroshin</dd>
 124 <dt><span class="seeLabel">See Also:</span></dt>
 125 <dd><a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><code>FastaSequence</code></a>,
 126 <a href="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><code>AlignmentMetadata</code></a></dd>
 127 </dl>
 128 </li>
 129 </ul>
 130 </div>
 131 <div class="summary">
 132 <ul class="blockList">
 133 <li class="blockList">
 134 <!-- =========== FIELD SUMMARY =========== -->
 135 <ul class="blockList">
 136 <li class="blockList"><a name="field.summary">
 137 <!--   -->
 138 </a>
 139 <h3>Field Summary</h3>
 140 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Field Summary table, listing fields, and an explanation">
 141 <caption><span>Fields</span><span class="tabEnd">&nbsp;</span></caption>
 142 <tr>
 143 <th class="colFirst" scope="col">Modifier and Type</th>
 144 <th class="colLast" scope="col">Field and Description</th>
 145 </tr>
 146 <tr class="altColor">
 147 <td class="colFirst"><code>protected <a href="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</a></code></td>
 148 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Alignment.html#metadata">metadata</a></span></code>&nbsp;</td>
 149 </tr>
 150 <tr class="rowColor">
 151 <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>
 152 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Alignment.html#sequences">sequences</a></span></code>&nbsp;</td>
 153 </tr>
 154 </table>
 155 </li>
 156 </ul>
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 165 <tr>
 166 <th class="colFirst" scope="col">Modifier</th>
 167 <th class="colLast" scope="col">Constructor and Description</th>
 168 </tr>
 169 <tr class="altColor">
 170 <td class="colFirst"><code>protected </code></td>
 171 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Alignment.html#Alignment--">Alignment</a></span>()</code>&nbsp;</td>
 172 </tr>
 173 <tr class="rowColor">
 174 <td class="colFirst"><code>&nbsp;</code></td>
 175 <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,
 176          <a href="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</a>&nbsp;metadata)</code>&nbsp;</td>
 177 </tr>
 178 <tr class="altColor">
 179 <td class="colFirst"><code>&nbsp;</code></td>
 180 <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,
 181          <a href="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</a>&nbsp;program,
 182          char&nbsp;gapchar)</code>&nbsp;</td>
 183 </tr>
 184 </table>
 185 </li>
 186 </ul>
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 191 </a>
 192 <h3>Method Summary</h3>
 193 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
 194 <caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
 195 <tr>
 196 <th class="colFirst" scope="col">Modifier and Type</th>
 197 <th class="colLast" scope="col">Method and Description</th>
 198 </tr>
 199 <tr id="i0" class="altColor">
 200 <td class="colFirst"><code>boolean</code></td>
 201 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Alignment.html#equals-java.lang.Object-">equals</a></span>(java.lang.Object&nbsp;obj)</code>
 202 <div class="block">Please note that this implementation does not take the order of sequences
 203  into account!</div>
 204 </td>
 205 </tr>
 206 <tr id="i1" class="rowColor">
 207 <td class="colFirst"><code><a href="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</a></code></td>
 208 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Alignment.html#getMetadata--">getMetadata</a></span>()</code>&nbsp;</td>
 209 </tr>
 210 <tr id="i2" class="altColor">
 211 <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>
 212 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Alignment.html#getSequences--">getSequences</a></span>()</code>&nbsp;</td>
 213 </tr>
 214 <tr id="i3" class="rowColor">
 215 <td class="colFirst"><code>int</code></td>
 216 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Alignment.html#getSize--">getSize</a></span>()</code>&nbsp;</td>
 217 </tr>
 218 <tr id="i4" class="altColor">
 219 <td class="colFirst"><code>int</code></td>
 220 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Alignment.html#hashCode--">hashCode</a></span>()</code>&nbsp;</td>
 221 </tr>
 222 <tr id="i5" class="rowColor">
 223 <td class="colFirst"><code>java.lang.String</code></td>
 224 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Alignment.html#toString--">toString</a></span>()</code>&nbsp;</td>
 225 </tr>
 226 </table>
 227 <ul class="blockList">
 228 <li class="blockList"><a name="methods.inherited.from.class.java.lang.Object">
 229 <!--   -->
 230 </a>
 231 <h3>Methods inherited from class&nbsp;java.lang.Object</h3>
 232 <code>clone, finalize, getClass, notify, notifyAll, wait, wait, wait</code></li>
 233 </ul>
 234 </li>
 235 </ul>
 236 </li>
 237 </ul>
 238 </div>
 239 <div class="details">
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 242 <!-- ============ FIELD DETAIL =========== -->
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 245 <!--   -->
 246 </a>
 247 <h3>Field Detail</h3>
 248 <a name="metadata">
 249 <!--   -->
 250 </a>
 251 <ul class="blockList">
 252 <li class="blockList">
 253 <h4>metadata</h4>
 254 <pre>protected&nbsp;<a href="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</a> metadata</pre>
 255 </li>
 256 </ul>
 257 <a name="sequences">
 258 <!--   -->
 259 </a>
 260 <ul class="blockListLast">
 261 <li class="blockList">
 262 <h4>sequences</h4>
 263 <pre>protected&nbsp;java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt; sequences</pre>
 264 </li>
 265 </ul>
 266 </li>
 267 </ul>
 268 <!-- ========= CONSTRUCTOR DETAIL ======== -->
 269 <ul class="blockList">
 270 <li class="blockList"><a name="constructor.detail">
 271 <!--   -->
 272 </a>
 273 <h3>Constructor Detail</h3>
 274 <a name="Alignment--">
 275 <!--   -->
 276 </a>
 277 <ul class="blockList">
 278 <li class="blockList">
 279 <h4>Alignment</h4>
 280 <pre>protected&nbsp;Alignment()</pre>
 281 </li>
 282 </ul>
 283 <a name="Alignment-java.util.List-compbio.data.sequence.Program-char-">
 284 <!--   -->
 285 </a>
 286 <ul class="blockList">
 287 <li class="blockList">
 288 <h4>Alignment</h4>
 289 <pre>public&nbsp;Alignment(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 290                  <a href="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</a>&nbsp;program,
 291                  char&nbsp;gapchar)</pre>
 292 <dl>
 293 <dt><span class="paramLabel">Parameters:</span></dt>
 294 <dd><code>sequences</code> - </dd>
 295 <dd><code>program</code> - </dd>
 296 <dd><code>gapchar</code> - </dd>
 297 </dl>
 298 </li>
 299 </ul>
 300 <a name="Alignment-java.util.List-compbio.data.sequence.AlignmentMetadata-">
 301 <!--   -->
 302 </a>
 303 <ul class="blockListLast">
 304 <li class="blockList">
 305 <h4>Alignment</h4>
 306 <pre>public&nbsp;Alignment(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 307                  <a href="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</a>&nbsp;metadata)</pre>
 308 <dl>
 309 <dt><span class="paramLabel">Parameters:</span></dt>
 310 <dd><code>sequences</code> - </dd>
 311 <dd><code>metadata</code> - </dd>
 312 </dl>
 313 </li>
 314 </ul>
 315 </li>
 316 </ul>
 317 <!-- ============ METHOD DETAIL ========== -->
 318 <ul class="blockList">
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 320 <!--   -->
 321 </a>
 322 <h3>Method Detail</h3>
 323 <a name="getSequences--">
 324 <!--   -->
 325 </a>
 326 <ul class="blockList">
 327 <li class="blockList">
 328 <h4>getSequences</h4>
 329 <pre>public&nbsp;java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;getSequences()</pre>
 330 <dl>
 331 <dt><span class="returnLabel">Returns:</span></dt>
 332 <dd>list of FastaSequence records</dd>
 333 </dl>
 334 </li>
 335 </ul>
 336 <a name="getSize--">
 337 <!--   -->
 338 </a>
 339 <ul class="blockList">
 340 <li class="blockList">
 341 <h4>getSize</h4>
 342 <pre>public&nbsp;int&nbsp;getSize()</pre>
 343 <dl>
 344 <dt><span class="returnLabel">Returns:</span></dt>
 345 <dd>a number of sequence in the alignment</dd>
 346 </dl>
 347 </li>
 348 </ul>
 349 <a name="getMetadata--">
 350 <!--   -->
 351 </a>
 352 <ul class="blockList">
 353 <li class="blockList">
 354 <h4>getMetadata</h4>
 355 <pre>public&nbsp;<a href="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</a>&nbsp;getMetadata()</pre>
 356 <dl>
 357 <dt><span class="returnLabel">Returns:</span></dt>
 358 <dd>AlignmentMetadata object</dd>
 359 </dl>
 360 </li>
 361 </ul>
 362 <a name="toString--">
 363 <!--   -->
 364 </a>
 365 <ul class="blockList">
 366 <li class="blockList">
 367 <h4>toString</h4>
 368 <pre>public&nbsp;java.lang.String&nbsp;toString()</pre>
 369 <dl>
 370 <dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
 371 <dd><code>toString</code>&nbsp;in class&nbsp;<code>java.lang.Object</code></dd>
 372 </dl>
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 375 <a name="hashCode--">
 376 <!--   -->
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 382 <dl>
 383 <dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
 384 <dd><code>hashCode</code>&nbsp;in class&nbsp;<code>java.lang.Object</code></dd>
 385 </dl>
 386 </li>
 387 </ul>
 388 <a name="equals-java.lang.Object-">
 389 <!--   -->
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 391 <ul class="blockListLast">
 392 <li class="blockList">
 393 <h4>equals</h4>
 394 <pre>public&nbsp;boolean&nbsp;equals(java.lang.Object&nbsp;obj)</pre>
 395 <div class="block">Please note that this implementation does not take the order of sequences
 396  into account!</div>
 397 <dl>
 398 <dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
 399 <dd><code>equals</code>&nbsp;in class&nbsp;<code>java.lang.Object</code></dd>
 400 </dl>
 401 </li>
 402 </ul>
 403 </li>
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