website/docs/full_javadoc/compbio/data/sequence/class-use/Score.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 15:32:51 BST 2017 -->
   6 <title>Uses of Class compbio.data.sequence.Score</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="Uses of Class compbio.data.sequence.Score";
  16         }
  17     }
  18     catch(err) {
  19     }
  20 //-->
  21 </script>
  22 <noscript>
  23 <div>JavaScript is disabled on your browser.</div>
  24 </noscript>
  25 <!-- ========= START OF TOP NAVBAR ======= -->
  26 <div class="topNav"><a name="navbar.top">
  27 <!--   -->
  28 </a>
  29 <div class="skipNav"><a href="#skip.navbar.top" title="Skip navigation links">Skip navigation links</a></div>
  30 <a name="navbar.top.firstrow">
  31 <!--   -->
  32 </a>
  33 <ul class="navList" title="Navigation">
  34 <li><a href="../../../../overview-summary.html">Overview</a></li>
  35 <li><a href="../package-summary.html">Package</a></li>
  36 <li><a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Class</a></li>
  37 <li class="navBarCell1Rev">Use</li>
  38 <li><a href="../../../../overview-tree.html">Tree</a></li>
  39 <li><a href="../../../../deprecated-list.html">Deprecated</a></li>
  40 <li><a href="../../../../index-files/index-1.html">Index</a></li>
  41 <li><a href="../../../../help-doc.html">Help</a></li>
  42 </ul>
  43 </div>
  44 <div class="subNav">
  45 <ul class="navList">
  46 <li>Prev</li>
  47 <li>Next</li>
  48 </ul>
  49 <ul class="navList">
  50 <li><a href="../../../../index.html?compbio/data/sequence/class-use/Score.html" target="_top">Frames</a></li>
  51 <li><a href="Score.html" target="_top">No&nbsp;Frames</a></li>
  52 </ul>
  53 <ul class="navList" id="allclasses_navbar_top">
  54 <li><a href="../../../../allclasses-noframe.html">All&nbsp;Classes</a></li>
  55 </ul>
  56 <div>
  57 <script type="text/javascript"><!--
  58   allClassesLink = document.getElementById("allclasses_navbar_top");
  59   if(window==top) {
  60     allClassesLink.style.display = "block";
  61   }
  62   else {
  63     allClassesLink.style.display = "none";
  64   }
  65   //-->
  66 </script>
  67 </div>
  68 <a name="skip.navbar.top">
  69 <!--   -->
  70 </a></div>
  71 <!-- ========= END OF TOP NAVBAR ========= -->
  72 <div class="header">
  73 <h2 title="Uses of Class compbio.data.sequence.Score" class="title">Uses of Class<br>compbio.data.sequence.Score</h2>
  74 </div>
  75 <div class="classUseContainer">
  76 <ul class="blockList">
  77 <li class="blockList">
  78 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing packages, and an explanation">
  79 <caption><span>Packages that use <a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</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.sequence">compbio.data.sequence</a></td>
  87 <td class="colLast">
  88 <div class="block">A data model for multiple sequence alignment web services and utility methods
  89  that work on the objects of this model.</div>
  90 </td>
  91 </tr>
  92 <tr class="rowColor">
  93 <td class="colFirst"><a href="#compbio.runner">compbio.runner</a></td>
  94 <td class="colLast">
  95 <div class="block">Utilities commonly used by all runners.</div>
  96 </td>
  97 </tr>
  98 <tr class="altColor">
  99 <td class="colFirst"><a href="#compbio.runner.disorder">compbio.runner.disorder</a></td>
 100 <td class="colLast">&nbsp;</td>
 101 </tr>
 102 </tbody>
 103 </table>
 104 </li>
 105 <li class="blockList">
 106 <ul class="blockList">
 107 <li class="blockList"><a name="compbio.data.sequence">
 108 <!--   -->
 109 </a>
 110 <h3>Uses of <a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a> in <a href="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></h3>
 111 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing fields, and an explanation">
 112 <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/Score.html" title="class in compbio.data.sequence">Score</a></span><span class="tabEnd">&nbsp;</span></caption>
 113 <tr>
 114 <th class="colFirst" scope="col">Modifier and Type</th>
 115 <th class="colLast" scope="col">Field and Description</th>
 116 </tr>
 117 <tbody>
 118 <tr class="altColor">
 119 <td class="colFirst"><code>java.util.TreeSet&lt;<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</code></td>
 120 <td class="colLast"><span class="typeNameLabel">ScoreManager.ScoreHolder.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/ScoreManager.ScoreHolder.html#scores">scores</a></span></code>&nbsp;</td>
 121 </tr>
 122 </tbody>
 123 </table>
 124 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 125 <caption><span>Methods in <a href="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a> that return <a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a></span><span class="tabEnd">&nbsp;</span></caption>
 126 <tr>
 127 <th class="colFirst" scope="col">Modifier and Type</th>
 128 <th class="colLast" scope="col">Method and Description</th>
 129 </tr>
 130 <tbody>
 131 <tr class="altColor">
 132 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a></code></td>
 133 <td class="colLast"><span class="typeNameLabel">ScoreManager.ScoreHolder.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/ScoreManager.ScoreHolder.html#getScoreByMethod-java.lang.Enum-">getScoreByMethod</a></span>(java.lang.Enum&lt;?&gt;&nbsp;method)</code>&nbsp;</td>
 134 </tr>
 135 <tr class="rowColor">
 136 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a></code></td>
 137 <td class="colLast"><span class="typeNameLabel">ScoreManager.ScoreHolder.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/ScoreManager.ScoreHolder.html#getScoreByMethod-java.lang.String-">getScoreByMethod</a></span>(java.lang.String&nbsp;method)</code>&nbsp;</td>
 138 </tr>
 139 </tbody>
 140 </table>
 141 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 142 <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/Score.html" title="class in compbio.data.sequence">Score</a></span><span class="tabEnd">&nbsp;</span></caption>
 143 <tr>
 144 <th class="colFirst" scope="col">Modifier and Type</th>
 145 <th class="colLast" scope="col">Method and Description</th>
 146 </tr>
 147 <tbody>
 148 <tr class="altColor">
 149 <td class="colFirst"><code>java.util.Map&lt;java.lang.String,java.util.TreeSet&lt;<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&gt;</code></td>
 150 <td class="colLast"><span class="typeNameLabel">ScoreManager.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/ScoreManager.html#asMap--">asMap</a></span>()</code>&nbsp;</td>
 151 </tr>
 152 <tr class="rowColor">
 153 <td class="colFirst"><code>java.util.Set&lt;<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</code></td>
 154 <td class="colLast"><span class="typeNameLabel">ScoreManager.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/ScoreManager.html#asSet--">asSet</a></span>()</code>&nbsp;</td>
 155 </tr>
 156 <tr class="altColor">
 157 <td class="colFirst"><code>java.util.List&lt;java.util.TreeSet&lt;<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&gt;</code></td>
 158 <td class="colLast"><span class="typeNameLabel">RNAStructScoreManager.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/RNAStructScoreManager.html#getData--">getData</a></span>()</code>&nbsp;</td>
 159 </tr>
 160 <tr class="rowColor">
 161 <td class="colFirst"><code>static java.util.TreeSet&lt;<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</code></td>
 162 <td class="colLast"><span class="typeNameLabel">RNAStructReader.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/RNAStructReader.html#newEmptyScore-java.lang.Enum-">newEmptyScore</a></span>(java.lang.Enum&lt;?&gt;&nbsp;res)</code>&nbsp;</td>
 163 </tr>
 164 <tr class="altColor">
 165 <td class="colFirst"><code>private static java.util.TreeSet&lt;<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</code></td>
 166 <td class="colLast"><span class="typeNameLabel">RNAStructReader.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/RNAStructReader.html#newSetScore-java.lang.Enum-java.util.List-">newSetScore</a></span>(java.lang.Enum&lt;?&gt;&nbsp;res,
 167            java.util.List&lt;java.lang.Float&gt;&nbsp;scores)</code>&nbsp;</td>
 168 </tr>
 169 <tr class="rowColor">
 170 <td class="colFirst"><code>static java.util.HashSet&lt;<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</code></td>
 171 <td class="colLast"><span class="typeNameLabel">SequenceUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/SequenceUtil.html#readAAConResults-java.io.InputStream-">readAAConResults</a></span>(java.io.InputStream&nbsp;results)</code>
 172 <div class="block">Read AACon result with no alignment files.</div>
 173 </td>
 174 </tr>
 175 <tr class="altColor">
 176 <td class="colFirst"><code>static java.util.HashMap&lt;java.lang.String,java.util.Set&lt;<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&gt;</code></td>
 177 <td class="colLast"><span class="typeNameLabel">SequenceUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/SequenceUtil.html#readDisembl-java.io.InputStream-">readDisembl</a></span>(java.io.InputStream&nbsp;input)</code>
 178 <div class="block">> Foobar_dundeefriends
 179
 180  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
 181
 182  # REM465 355-368
 183
 184  # HOTLOOPS 190-204
 185
 186  # RESIDUE COILS REM465 HOTLOOPS
 187
 188  M 0.86010 0.88512 0.37094
 189
 190  T 0.79983 0.85864 0.44331
 191
 192  >Next Sequence name</div>
 193 </td>
 194 </tr>
 195 <tr class="rowColor">
 196 <td class="colFirst"><code>static java.util.HashMap&lt;java.lang.String,java.util.Set&lt;<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&gt;</code></td>
 197 <td class="colLast"><span class="typeNameLabel">SequenceUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/SequenceUtil.html#readGlobPlot-java.io.InputStream-">readGlobPlot</a></span>(java.io.InputStream&nbsp;input)</code>
 198 <div class="block">> Foobar_dundeefriends
 199
 200  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
 201
 202  # REM465 355-368
 203
 204  # HOTLOOPS 190-204
 205
 206  # RESIDUE COILS REM465 HOTLOOPS
 207
 208  M 0.86010 0.88512 0.37094
 209
 210  T 0.79983 0.85864 0.44331
 211
 212  >Next Sequence name</div>
 213 </td>
 214 </tr>
 215 <tr class="altColor">
 216 <td class="colFirst"><code>static java.util.Map&lt;java.lang.String,<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</code></td>
 217 <td class="colLast"><span class="typeNameLabel">SequenceUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/SequenceUtil.html#readIUPred-java.io.File-">readIUPred</a></span>(java.io.File&nbsp;result)</code>
 218 <div class="block">Read IUPred output</div>
 219 </td>
 220 </tr>
 221 <tr class="rowColor">
 222 <td class="colFirst"><code>private static java.util.Map&lt;java.lang.String,<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</code></td>
 223 <td class="colLast"><span class="typeNameLabel">SequenceUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/SequenceUtil.html#readIUPred-java.io.InputStream-compbio.data.sequence.IUPredResult-">readIUPred</a></span>(java.io.InputStream&nbsp;input,
 224           <a href="../../../../compbio/data/sequence/IUPredResult.html" title="enum in compbio.data.sequence">IUPredResult</a>&nbsp;type)</code>
 225 <div class="block">## Long Disorder
 226
 227  # P53_HUMAN
 228
 229  1 M 0.9943
 230
 231  2 E 0.9917
 232
 233  3 E 0.9879
 234
 235  (every line)</div>
 236 </td>
 237 </tr>
 238 <tr class="altColor">
 239 <td class="colFirst"><code>static java.util.Map&lt;java.lang.String,<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</code></td>
 240 <td class="colLast"><span class="typeNameLabel">SequenceUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/SequenceUtil.html#readJRonn-java.io.File-">readJRonn</a></span>(java.io.File&nbsp;result)</code>&nbsp;</td>
 241 </tr>
 242 <tr class="rowColor">
 243 <td class="colFirst"><code>static java.util.Map&lt;java.lang.String,<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</code></td>
 244 <td class="colLast"><span class="typeNameLabel">SequenceUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/SequenceUtil.html#readJRonn-java.io.InputStream-">readJRonn</a></span>(java.io.InputStream&nbsp;inStream)</code>
 245 <div class="block">Reader for JRonn horizontal file format</div>
 246 </td>
 247 </tr>
 248 </tbody>
 249 </table>
 250 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 251 <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/Score.html" title="class in compbio.data.sequence">Score</a></span><span class="tabEnd">&nbsp;</span></caption>
 252 <tr>
 253 <th class="colFirst" scope="col">Modifier and Type</th>
 254 <th class="colLast" scope="col">Method and Description</th>
 255 </tr>
 256 <tbody>
 257 <tr class="altColor">
 258 <td class="colFirst"><code>int</code></td>
 259 <td class="colLast"><span class="typeNameLabel">Score.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/Score.html#compareTo-compbio.data.sequence.Score-">compareTo</a></span>(<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&nbsp;o)</code>&nbsp;</td>
 260 </tr>
 261 </tbody>
 262 </table>
 263 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 264 <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/Score.html" title="class in compbio.data.sequence">Score</a></span><span class="tabEnd">&nbsp;</span></caption>
 265 <tr>
 266 <th class="colFirst" scope="col">Modifier and Type</th>
 267 <th class="colLast" scope="col">Method and Description</th>
 268 </tr>
 269 <tbody>
 270 <tr class="altColor">
 271 <td class="colFirst"><code>static <a href="../../../../compbio/data/sequence/RNAStructScoreManager.html" title="class in compbio.data.sequence">RNAStructScoreManager</a></code></td>
 272 <td class="colLast"><span class="typeNameLabel">RNAStructScoreManager.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/RNAStructScoreManager.html#newInstance-java.util.List-java.util.List-">newInstance</a></span>(java.util.List&lt;java.lang.String&gt;&nbsp;structs,
 273            java.util.List&lt;java.util.TreeSet&lt;<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&gt;&nbsp;data)</code>&nbsp;</td>
 274 </tr>
 275 <tr class="rowColor">
 276 <td class="colFirst"><code>static <a href="../../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></code></td>
 277 <td class="colLast"><span class="typeNameLabel">ScoreManager.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/ScoreManager.html#newInstance-java.util.Map-">newInstance</a></span>(java.util.Map&lt;java.lang.String,java.util.Set&lt;<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&gt;&nbsp;data)</code>&nbsp;</td>
 278 </tr>
 279 <tr class="altColor">
 280 <td class="colFirst"><code>static <a href="../../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></code></td>
 281 <td class="colLast"><span class="typeNameLabel">ScoreManager.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/ScoreManager.html#newInstanceSingleScore-java.util.Map-">newInstanceSingleScore</a></span>(java.util.Map&lt;java.lang.String,<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;seqScoresMap)</code>&nbsp;</td>
 282 </tr>
 283 <tr class="rowColor">
 284 <td class="colFirst"><code>static <a href="../../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></code></td>
 285 <td class="colLast"><span class="typeNameLabel">ScoreManager.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/ScoreManager.html#newInstanceSingleSequence-java.util.Set-">newInstanceSingleSequence</a></span>(java.util.Set&lt;<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;data)</code>&nbsp;</td>
 286 </tr>
 287 <tr class="altColor">
 288 <td class="colFirst"><code>static void</code></td>
 289 <td class="colLast"><span class="typeNameLabel">Score.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/Score.html#write-java.util.TreeSet-java.io.Writer-">write</a></span>(java.util.TreeSet&lt;<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;scores,
 290      java.io.Writer&nbsp;writer)</code>
 291 <div class="block">Outputs the List of Score objects into the Output stream.</div>
 292 </td>
 293 </tr>
 294 </tbody>
 295 </table>
 296 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing constructors, and an explanation">
 297 <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/Score.html" title="class in compbio.data.sequence">Score</a></span><span class="tabEnd">&nbsp;</span></caption>
 298 <tr>
 299 <th class="colOne" scope="col">Constructor and Description</th>
 300 </tr>
 301 <tbody>
 302 <tr class="altColor">
 303 <td class="colLast"><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/RNAStructScoreManager.html#RNAStructScoreManager-java.util.List-java.util.List-">RNAStructScoreManager</a></span>(java.util.List&lt;java.lang.String&gt;&nbsp;structs,
 304                      java.util.List&lt;java.util.TreeSet&lt;<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&gt;&nbsp;data)</code>&nbsp;</td>
 305 </tr>
 306 <tr class="rowColor">
 307 <td class="colLast"><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/ScoreManager.ScoreHolder.html#ScoreHolder-java.lang.String-java.util.Set-">ScoreHolder</a></span>(java.lang.String&nbsp;id,
 308            java.util.Set&lt;<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;scores)</code>&nbsp;</td>
 309 </tr>
 310 <tr class="altColor">
 311 <td class="colLast"><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/ScoreManager.html#ScoreManager-java.util.Map-">ScoreManager</a></span>(java.util.Map&lt;java.lang.String,java.util.Set&lt;<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&gt;&nbsp;data)</code>&nbsp;</td>
 312 </tr>
 313 <tr class="rowColor">
 314 <td class="colLast"><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/ScoreManager.html#ScoreManager-java.lang.String-java.util.Set-">ScoreManager</a></span>(java.lang.String&nbsp;id,
 315             java.util.Set&lt;<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;data)</code>&nbsp;</td>
 316 </tr>
 317 </tbody>
 318 </table>
 319 </li>
 320 <li class="blockList"><a name="compbio.runner">
 321 <!--   -->
 322 </a>
 323 <h3>Uses of <a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a> in <a href="../../../../compbio/runner/package-summary.html">compbio.runner</a></h3>
 324 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 325 <caption><span>Methods in <a href="../../../../compbio/runner/package-summary.html">compbio.runner</a> that return types with arguments of type <a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a></span><span class="tabEnd">&nbsp;</span></caption>
 326 <tr>
 327 <th class="colFirst" scope="col">Modifier and Type</th>
 328 <th class="colLast" scope="col">Method and Description</th>
 329 </tr>
 330 <tbody>
 331 <tr class="altColor">
 332 <td class="colFirst"><code>static java.util.Map&lt;java.lang.String,<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</code></td>
 333 <td class="colLast"><span class="typeNameLabel">Util.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/Util.html#readJronnFile-java.lang.String-java.lang.String-">readJronnFile</a></span>(java.lang.String&nbsp;workDirectory,
 334              java.lang.String&nbsp;clustFile)</code>&nbsp;</td>
 335 </tr>
 336 <tr class="rowColor">
 337 <td class="colFirst"><code>static java.util.Map&lt;java.lang.String,<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</code></td>
 338 <td class="colLast"><span class="typeNameLabel">RunnerUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/RunnerUtil.html#readJronnFile-java.lang.String-java.lang.String-">readJronnFile</a></span>(java.lang.String&nbsp;workDirectory,
 339              java.lang.String&nbsp;clustFile)</code>&nbsp;</td>
 340 </tr>
 341 </tbody>
 342 </table>
 343 </li>
 344 <li class="blockList"><a name="compbio.runner.disorder">
 345 <!--   -->
 346 </a>
 347 <h3>Uses of <a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a> in <a href="../../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</a></h3>
 348 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 349 <caption><span>Method parameters in <a href="../../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</a> with type arguments of type <a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a></span><span class="tabEnd">&nbsp;</span></caption>
 350 <tr>
 351 <th class="colFirst" scope="col">Modifier and Type</th>
 352 <th class="colLast" scope="col">Method and Description</th>
 353 </tr>
 354 <tbody>
 355 <tr class="altColor">
 356 <td class="colFirst"><code>(package private) void</code></td>
 357 <td class="colLast"><span class="typeNameLabel">IUPred.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/disorder/IUPred.html#combineScores-java.util.Map-java.util.Map-">combineScores</a></span>(java.util.Map&lt;java.lang.String,java.util.Set&lt;<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&gt;&nbsp;combined,
 358              java.util.Map&lt;java.lang.String,<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;scores)</code>&nbsp;</td>
 359 </tr>
 360 <tr class="rowColor">
 361 <td class="colFirst"><code>(package private) void</code></td>
 362 <td class="colLast"><span class="typeNameLabel">IUPred.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/disorder/IUPred.html#combineScores-java.util.Map-java.util.Map-">combineScores</a></span>(java.util.Map&lt;java.lang.String,java.util.Set&lt;<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&gt;&nbsp;combined,
 363              java.util.Map&lt;java.lang.String,<a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;scores)</code>&nbsp;</td>
 364 </tr>
 365 </tbody>
 366 </table>
 367 </li>
 368 </ul>
 369 </li>
 370 </ul>
 371 </div>
 372 <!-- ======= START OF BOTTOM NAVBAR ====== -->
 373 <div class="bottomNav"><a name="navbar.bottom">
 374 <!--   -->
 375 </a>
 376 <div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
 377 <a name="navbar.bottom.firstrow">
 378 <!--   -->
 379 </a>
 380 <ul class="navList" title="Navigation">
 381 <li><a href="../../../../overview-summary.html">Overview</a></li>
 382 <li><a href="../package-summary.html">Package</a></li>
 383 <li><a href="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Class</a></li>
 384 <li class="navBarCell1Rev">Use</li>
 385 <li><a href="../../../../overview-tree.html">Tree</a></li>
 386 <li><a href="../../../../deprecated-list.html">Deprecated</a></li>
 387 <li><a href="../../../../index-files/index-1.html">Index</a></li>
 388 <li><a href="../../../../help-doc.html">Help</a></li>
 389 </ul>
 390 </div>
 391 <div class="subNav">
 392 <ul class="navList">
 393 <li>Prev</li>
 394 <li>Next</li>
 395 </ul>
 396 <ul class="navList">
 397 <li><a href="../../../../index.html?compbio/data/sequence/class-use/Score.html" target="_top">Frames</a></li>
 398 <li><a href="Score.html" target="_top">No&nbsp;Frames</a></li>
 399 </ul>
 400 <ul class="navList" id="allclasses_navbar_bottom">
 401 <li><a href="../../../../allclasses-noframe.html">All&nbsp;Classes</a></li>
 402 </ul>
 403 <div>
 404 <script type="text/javascript"><!--
 405   allClassesLink = document.getElementById("allclasses_navbar_bottom");
 406   if(window==top) {
 407     allClassesLink.style.display = "block";
 408   }
 409   else {
 410     allClassesLink.style.display = "none";
 411   }
 412   //-->
 413 </script>
 414 </div>
 415 <a name="skip.navbar.bottom">
 416 <!--   -->
 417 </a></div>
 418 <!-- ======== END OF BOTTOM NAVBAR ======= -->
 419 </body>
 420 </html>