website/docs/full_javadoc/compbio/data/sequence/SMERFSConstraints.html

   1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
   2 <!-- NewPage -->
   3 <html lang="en">
   4 <head>
   5 <!-- Generated by javadoc (1.8.0_121) on Fri Apr 21 15:32:50 BST 2017 -->
   6 <title>SMERFSConstraints</title>
   7 <meta name="date" content="2017-04-21">
   8 <link rel="stylesheet" type="text/css" href="../../../stylesheet.css" title="Style">
   9 <script type="text/javascript" src="../../../script.js"></script>
  10 </head>
  11 <body>
  12 <script type="text/javascript"><!--
  13     try {
  14         if (location.href.indexOf('is-external=true') == -1) {
  15             parent.document.title="SMERFSConstraints";
  16         }
  17     }
  18     catch(err) {
  19     }
  20 //-->
  21 var methods = {"i0":9,"i1":9,"i2":9};
  22 var tabs = {65535:["t0","All Methods"],1:["t1","Static Methods"],8:["t4","Concrete Methods"]};
  23 var altColor = "altColor";
  24 var rowColor = "rowColor";
  25 var tableTab = "tableTab";
  26 var activeTableTab = "activeTableTab";
  27 </script>
  28 <noscript>
  29 <div>JavaScript is disabled on your browser.</div>
  30 </noscript>
  31 <!-- ========= START OF TOP NAVBAR ======= -->
  32 <div class="topNav"><a name="navbar.top">
  33 <!--   -->
  34 </a>
  35 <div class="skipNav"><a href="#skip.navbar.top" title="Skip navigation links">Skip navigation links</a></div>
  36 <a name="navbar.top.firstrow">
  37 <!--   -->
  38 </a>
  39 <ul class="navList" title="Navigation">
  40 <li><a href="../../../overview-summary.html">Overview</a></li>
  41 <li><a href="package-summary.html">Package</a></li>
  42 <li class="navBarCell1Rev">Class</li>
  43 <li><a href="class-use/SMERFSConstraints.html">Use</a></li>
  44 <li><a href="package-tree.html">Tree</a></li>
  45 <li><a href="../../../deprecated-list.html">Deprecated</a></li>
  46 <li><a href="../../../index-files/index-1.html">Index</a></li>
  47 <li><a href="../../../help-doc.html">Help</a></li>
  48 </ul>
  49 </div>
  50 <div class="subNav">
  51 <ul class="navList">
  52 <li><a href="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><span class="typeNameLink">Prev&nbsp;Class</span></a></li>
  53 <li><a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence"><span class="typeNameLink">Next&nbsp;Class</span></a></li>
  54 </ul>
  55 <ul class="navList">
  56 <li><a href="../../../index.html?compbio/data/sequence/SMERFSConstraints.html" target="_top">Frames</a></li>
  57 <li><a href="SMERFSConstraints.html" target="_top">No&nbsp;Frames</a></li>
  58 </ul>
  59 <ul class="navList" id="allclasses_navbar_top">
  60 <li><a href="../../../allclasses-noframe.html">All&nbsp;Classes</a></li>
  61 </ul>
  62 <div>
  63 <script type="text/javascript"><!--
  64   allClassesLink = document.getElementById("allclasses_navbar_top");
  65   if(window==top) {
  66     allClassesLink.style.display = "block";
  67   }
  68   else {
  69     allClassesLink.style.display = "none";
  70   }
  71   //-->
  72 </script>
  73 </div>
  74 <div>
  75 <ul class="subNavList">
  76 <li>Summary:&nbsp;</li>
  77 <li>Nested&nbsp;|&nbsp;</li>
  78 <li><a href="#enum.constant.summary">Enum Constants</a>&nbsp;|&nbsp;</li>
  79 <li><a href="#field.summary">Field</a>&nbsp;|&nbsp;</li>
  80 <li><a href="#method.summary">Method</a></li>
  81 </ul>
  82 <ul class="subNavList">
  83 <li>Detail:&nbsp;</li>
  84 <li><a href="#enum.constant.detail">Enum Constants</a>&nbsp;|&nbsp;</li>
  85 <li><a href="#field.detail">Field</a>&nbsp;|&nbsp;</li>
  86 <li><a href="#method.detail">Method</a></li>
  87 </ul>
  88 </div>
  89 <a name="skip.navbar.top">
  90 <!--   -->
  91 </a></div>
  92 <!-- ========= END OF TOP NAVBAR ========= -->
  93 <!-- ======== START OF CLASS DATA ======== -->
  94 <div class="header">
  95 <div class="subTitle">compbio.data.sequence</div>
  96 <h2 title="Enum SMERFSConstraints" class="title">Enum SMERFSConstraints</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>java.lang.Enum&lt;<a href="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</a>&gt;</li>
 104 <li>
 105 <ul class="inheritance">
 106 <li>compbio.data.sequence.SMERFSConstraints</li>
 107 </ul>
 108 </li>
 109 </ul>
 110 </li>
 111 </ul>
 112 <div class="description">
 113 <ul class="blockList">
 114 <li class="blockList">
 115 <dl>
 116 <dt>All Implemented Interfaces:</dt>
 117 <dd>java.io.Serializable, java.lang.Comparable&lt;<a href="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</a>&gt;</dd>
 118 </dl>
 119 <hr>
 120 <br>
 121 <pre>public enum <span class="typeNameLabel">SMERFSConstraints</span>
 122 extends java.lang.Enum&lt;<a href="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</a>&gt;</pre>
 123 <div class="block">Enumeration defining two constraints for SMERFS columns score calculation.
 124  MAX_SCORE gives the highest core of all the windows the column belongs to.
 125  MID_SCORE gives the window score to the column in the middle.</div>
 126 <dl>
 127 <dt><span class="simpleTagLabel">Author:</span></dt>
 128 <dd>Agnieszka Golicz & Peter Troshin</dd>
 129 </dl>
 130 </li>
 131 </ul>
 132 </div>
 133 <div class="summary">
 134 <ul class="blockList">
 135 <li class="blockList">
 136 <!-- =========== ENUM CONSTANT SUMMARY =========== -->
 137 <ul class="blockList">
 138 <li class="blockList"><a name="enum.constant.summary">
 139 <!--   -->
 140 </a>
 141 <h3>Enum Constant Summary</h3>
 142 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Enum Constant Summary table, listing enum constants, and an explanation">
 143 <caption><span>Enum Constants</span><span class="tabEnd">&nbsp;</span></caption>
 144 <tr>
 145 <th class="colOne" scope="col">Enum Constant and Description</th>
 146 </tr>
 147 <tr class="altColor">
 148 <td class="colOne"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SMERFSConstraints.html#MAX_SCORE">MAX_SCORE</a></span></code>&nbsp;</td>
 149 </tr>
 150 <tr class="rowColor">
 151 <td class="colOne"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SMERFSConstraints.html#MID_SCORE">MID_SCORE</a></span></code>&nbsp;</td>
 152 </tr>
 153 </table>
 154 </li>
 155 </ul>
 156 <!-- =========== FIELD SUMMARY =========== -->
 157 <ul class="blockList">
 158 <li class="blockList"><a name="field.summary">
 159 <!--   -->
 160 </a>
 161 <h3>Field Summary</h3>
 162 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Field Summary table, listing fields, and an explanation">
 163 <caption><span>Fields</span><span class="tabEnd">&nbsp;</span></caption>
 164 <tr>
 165 <th class="colFirst" scope="col">Modifier and Type</th>
 166 <th class="colLast" scope="col">Field and Description</th>
 167 </tr>
 168 <tr class="altColor">
 169 <td class="colFirst"><code>static <a href="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</a></code></td>
 170 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SMERFSConstraints.html#DEFAULT_COLUMN_SCORE">DEFAULT_COLUMN_SCORE</a></span></code>
 171 <div class="block">Default column scoring schema</div>
 172 </td>
 173 </tr>
 174 <tr class="rowColor">
 175 <td class="colFirst"><code>static double</code></td>
 176 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SMERFSConstraints.html#DEFAULT_GAP_THRESHOLD">DEFAULT_GAP_THRESHOLD</a></span></code>
 177 <div class="block">Default gap threshold value for SMERFS algorithm</div>
 178 </td>
 179 </tr>
 180 <tr class="altColor">
 181 <td class="colFirst"><code>static int</code></td>
 182 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SMERFSConstraints.html#DEFAULT_WINDOW_SIZE">DEFAULT_WINDOW_SIZE</a></span></code>
 183 <div class="block">Default window size value for SMERFS algorithm</div>
 184 </td>
 185 </tr>
 186 </table>
 187 </li>
 188 </ul>
 189 <!-- ========== METHOD SUMMARY =========== -->
 190 <ul class="blockList">
 191 <li class="blockList"><a name="method.summary">
 192 <!--   -->
 193 </a>
 194 <h3>Method Summary</h3>
 195 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
 196 <caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t1" class="tableTab"><span><a href="javascript:show(1);">Static 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>
 197 <tr>
 198 <th class="colFirst" scope="col">Modifier and Type</th>
 199 <th class="colLast" scope="col">Method and Description</th>
 200 </tr>
 201 <tr id="i0" class="altColor">
 202 <td class="colFirst"><code>static <a href="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</a></code></td>
 203 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SMERFSConstraints.html#getSMERFSColumnScore-java.lang.String-">getSMERFSColumnScore</a></span>(java.lang.String&nbsp;score)</code>&nbsp;</td>
 204 </tr>
 205 <tr id="i1" class="rowColor">
 206 <td class="colFirst"><code>static <a href="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</a></code></td>
 207 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SMERFSConstraints.html#valueOf-java.lang.String-">valueOf</a></span>(java.lang.String&nbsp;name)</code>
 208 <div class="block">Returns the enum constant of this type with the specified name.</div>
 209 </td>
 210 </tr>
 211 <tr id="i2" class="altColor">
 212 <td class="colFirst"><code>static <a href="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</a>[]</code></td>
 213 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SMERFSConstraints.html#values--">values</a></span>()</code>
 214 <div class="block">Returns an array containing the constants of this enum type, in
 215 the order they are declared.</div>
 216 </td>
 217 </tr>
 218 </table>
 219 <ul class="blockList">
 220 <li class="blockList"><a name="methods.inherited.from.class.java.lang.Enum">
 221 <!--   -->
 222 </a>
 223 <h3>Methods inherited from class&nbsp;java.lang.Enum</h3>
 224 <code>clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf</code></li>
 225 </ul>
 226 <ul class="blockList">
 227 <li class="blockList"><a name="methods.inherited.from.class.java.lang.Object">
 228 <!--   -->
 229 </a>
 230 <h3>Methods inherited from class&nbsp;java.lang.Object</h3>
 231 <code>getClass, notify, notifyAll, wait, wait, wait</code></li>
 232 </ul>
 233 </li>
 234 </ul>
 235 </li>
 236 </ul>
 237 </div>
 238 <div class="details">
 239 <ul class="blockList">
 240 <li class="blockList">
 241 <!-- ============ ENUM CONSTANT DETAIL =========== -->
 242 <ul class="blockList">
 243 <li class="blockList"><a name="enum.constant.detail">
 244 <!--   -->
 245 </a>
 246 <h3>Enum Constant Detail</h3>
 247 <a name="MAX_SCORE">
 248 <!--   -->
 249 </a>
 250 <ul class="blockList">
 251 <li class="blockList">
 252 <h4>MAX_SCORE</h4>
 253 <pre>public static final&nbsp;<a href="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</a> MAX_SCORE</pre>
 254 </li>
 255 </ul>
 256 <a name="MID_SCORE">
 257 <!--   -->
 258 </a>
 259 <ul class="blockListLast">
 260 <li class="blockList">
 261 <h4>MID_SCORE</h4>
 262 <pre>public static final&nbsp;<a href="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</a> MID_SCORE</pre>
 263 </li>
 264 </ul>
 265 </li>
 266 </ul>
 267 <!-- ============ FIELD DETAIL =========== -->
 268 <ul class="blockList">
 269 <li class="blockList"><a name="field.detail">
 270 <!--   -->
 271 </a>
 272 <h3>Field Detail</h3>
 273 <a name="DEFAULT_COLUMN_SCORE">
 274 <!--   -->
 275 </a>
 276 <ul class="blockList">
 277 <li class="blockList">
 278 <h4>DEFAULT_COLUMN_SCORE</h4>
 279 <pre>public static final&nbsp;<a href="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</a> DEFAULT_COLUMN_SCORE</pre>
 280 <div class="block">Default column scoring schema</div>
 281 </li>
 282 </ul>
 283 <a name="DEFAULT_WINDOW_SIZE">
 284 <!--   -->
 285 </a>
 286 <ul class="blockList">
 287 <li class="blockList">
 288 <h4>DEFAULT_WINDOW_SIZE</h4>
 289 <pre>public static final&nbsp;int DEFAULT_WINDOW_SIZE</pre>
 290 <div class="block">Default window size value for SMERFS algorithm</div>
 291 <dl>
 292 <dt><span class="seeLabel">See Also:</span></dt>
 293 <dd><a href="../../../constant-values.html#compbio.data.sequence.SMERFSConstraints.DEFAULT_WINDOW_SIZE">Constant Field Values</a></dd>
 294 </dl>
 295 </li>
 296 </ul>
 297 <a name="DEFAULT_GAP_THRESHOLD">
 298 <!--   -->
 299 </a>
 300 <ul class="blockListLast">
 301 <li class="blockList">
 302 <h4>DEFAULT_GAP_THRESHOLD</h4>
 303 <pre>public static final&nbsp;double DEFAULT_GAP_THRESHOLD</pre>
 304 <div class="block">Default gap threshold value for SMERFS algorithm</div>
 305 <dl>
 306 <dt><span class="seeLabel">See Also:</span></dt>
 307 <dd><a href="../../../constant-values.html#compbio.data.sequence.SMERFSConstraints.DEFAULT_GAP_THRESHOLD">Constant Field Values</a></dd>
 308 </dl>
 309 </li>
 310 </ul>
 311 </li>
 312 </ul>
 313 <!-- ============ METHOD DETAIL ========== -->
 314 <ul class="blockList">
 315 <li class="blockList"><a name="method.detail">
 316 <!--   -->
 317 </a>
 318 <h3>Method Detail</h3>
 319 <a name="values--">
 320 <!--   -->
 321 </a>
 322 <ul class="blockList">
 323 <li class="blockList">
 324 <h4>values</h4>
 325 <pre>public static&nbsp;<a href="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</a>[]&nbsp;values()</pre>
 326 <div class="block">Returns an array containing the constants of this enum type, in
 327 the order they are declared.  This method may be used to iterate
 328 over the constants as follows:
 329 <pre>
 330 for (SMERFSConstraints c : SMERFSConstraints.values())
 331 &nbsp;   System.out.println(c);
 332 </pre></div>
 333 <dl>
 334 <dt><span class="returnLabel">Returns:</span></dt>
 335 <dd>an array containing the constants of this enum type, in the order they are declared</dd>
 336 </dl>
 337 </li>
 338 </ul>
 339 <a name="valueOf-java.lang.String-">
 340 <!--   -->
 341 </a>
 342 <ul class="blockList">
 343 <li class="blockList">
 344 <h4>valueOf</h4>
 345 <pre>public static&nbsp;<a href="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</a>&nbsp;valueOf(java.lang.String&nbsp;name)</pre>
 346 <div class="block">Returns the enum constant of this type with the specified name.
 347 The string must match <i>exactly</i> an identifier used to declare an
 348 enum constant in this type.  (Extraneous whitespace characters are
 349 not permitted.)</div>
 350 <dl>
 351 <dt><span class="paramLabel">Parameters:</span></dt>
 352 <dd><code>name</code> - the name of the enum constant to be returned.</dd>
 353 <dt><span class="returnLabel">Returns:</span></dt>
 354 <dd>the enum constant with the specified name</dd>
 355 <dt><span class="throwsLabel">Throws:</span></dt>
 356 <dd><code>java.lang.IllegalArgumentException</code> - if this enum type has no constant with the specified name</dd>
 357 <dd><code>java.lang.NullPointerException</code> - if the argument is null</dd>
 358 </dl>
 359 </li>
 360 </ul>
 361 <a name="getSMERFSColumnScore-java.lang.String-">
 362 <!--   -->
 363 </a>
 364 <ul class="blockListLast">
 365 <li class="blockList">
 366 <h4>getSMERFSColumnScore</h4>
 367 <pre>public static&nbsp;<a href="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</a>&nbsp;getSMERFSColumnScore(java.lang.String&nbsp;score)</pre>
 368 </li>
 369 </ul>
 370 </li>
 371 </ul>
 372 </li>
 373 </ul>
 374 </div>
 375 </div>
 376 <!-- ========= END OF CLASS DATA ========= -->
 377 <!-- ======= START OF BOTTOM NAVBAR ====== -->
 378 <div class="bottomNav"><a name="navbar.bottom">
 379 <!--   -->
 380 </a>
 381 <div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
 382 <a name="navbar.bottom.firstrow">
 383 <!--   -->
 384 </a>
 385 <ul class="navList" title="Navigation">
 386 <li><a href="../../../overview-summary.html">Overview</a></li>
 387 <li><a href="package-summary.html">Package</a></li>
 388 <li class="navBarCell1Rev">Class</li>
 389 <li><a href="class-use/SMERFSConstraints.html">Use</a></li>
 390 <li><a href="package-tree.html">Tree</a></li>
 391 <li><a href="../../../deprecated-list.html">Deprecated</a></li>
 392 <li><a href="../../../index-files/index-1.html">Index</a></li>
 393 <li><a href="../../../help-doc.html">Help</a></li>
 394 </ul>
 395 </div>
 396 <div class="subNav">
 397 <ul class="navList">
 398 <li><a href="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><span class="typeNameLink">Prev&nbsp;Class</span></a></li>
 399 <li><a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence"><span class="typeNameLink">Next&nbsp;Class</span></a></li>
 400 </ul>
 401 <ul class="navList">
 402 <li><a href="../../../index.html?compbio/data/sequence/SMERFSConstraints.html" target="_top">Frames</a></li>
 403 <li><a href="SMERFSConstraints.html" target="_top">No&nbsp;Frames</a></li>
 404 </ul>
 405 <ul class="navList" id="allclasses_navbar_bottom">
 406 <li><a href="../../../allclasses-noframe.html">All&nbsp;Classes</a></li>
 407 </ul>
 408 <div>
 409 <script type="text/javascript"><!--
 410   allClassesLink = document.getElementById("allclasses_navbar_bottom");
 411   if(window==top) {
 412     allClassesLink.style.display = "block";
 413   }
 414   else {
 415     allClassesLink.style.display = "none";
 416   }
 417   //-->
 418 </script>
 419 </div>
 420 <div>
 421 <ul class="subNavList">
 422 <li>Summary:&nbsp;</li>
 423 <li>Nested&nbsp;|&nbsp;</li>
 424 <li><a href="#enum.constant.summary">Enum Constants</a>&nbsp;|&nbsp;</li>
 425 <li><a href="#field.summary">Field</a>&nbsp;|&nbsp;</li>
 426 <li><a href="#method.summary">Method</a></li>
 427 </ul>
 428 <ul class="subNavList">
 429 <li>Detail:&nbsp;</li>
 430 <li><a href="#enum.constant.detail">Enum Constants</a>&nbsp;|&nbsp;</li>
 431 <li><a href="#field.detail">Field</a>&nbsp;|&nbsp;</li>
 432 <li><a href="#method.detail">Method</a></li>
 433 </ul>
 434 </div>
 435 <a name="skip.navbar.bottom">
 436 <!--   -->
 437 </a></div>
 438 <!-- ======== END OF BOTTOM NAVBAR ======= -->
 439 </body>
 440 </html>