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  73 <h2 title="Uses of Class compbio.data.sequence.UnknownFileFormatException" class="title">Uses of Class<br>compbio.data.sequence.UnknownFileFormatException</h2>
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  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/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</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 </tbody>
  99 </table>
 100 </li>
 101 <li class="blockList">
 102 <ul class="blockList">
 103 <li class="blockList"><a name="compbio.data.sequence">
 104 <!--   -->
 105 </a>
 106 <h3>Uses of <a href="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a> in <a href="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></h3>
 107 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 108 <caption><span>Methods in <a href="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a> that throw <a href="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></span><span class="tabEnd">&nbsp;</span></caption>
 109 <tr>
 110 <th class="colFirst" scope="col">Modifier and Type</th>
 111 <th class="colLast" scope="col">Method and Description</th>
 112 </tr>
 113 <tbody>
 114 <tr class="altColor">
 115 <td class="colFirst"><code>private static float[]</code></td>
 116 <td class="colLast"><span class="typeNameLabel">SequenceUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/SequenceUtil.html#convertToNumber-java.lang.String:A-">convertToNumber</a></span>(java.lang.String[]&nbsp;annotValues)</code>&nbsp;</td>
 117 </tr>
 118 <tr class="rowColor">
 119 <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>
 120 <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>
 121 <div class="block">Reads and parses Fasta or Clustal formatted file into a list of
 122  FastaSequence objects</div>
 123 </td>
 124 </tr>
 125 <tr class="altColor">
 126 <td class="colFirst"><code>private static float[]</code></td>
 127 <td class="colLast"><span class="typeNameLabel">SequenceUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/SequenceUtil.html#parseIUPredScores-java.util.Scanner-">parseIUPredScores</a></span>(java.util.Scanner&nbsp;scan)</code>&nbsp;</td>
 128 </tr>
 129 <tr class="rowColor">
 130 <td class="colFirst"><code>static <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 131 <td class="colLast"><span class="typeNameLabel">ClustalAlignmentUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile-java.io.File-">readClustalFile</a></span>(java.io.File&nbsp;file)</code>&nbsp;</td>
 132 </tr>
 133 <tr class="altColor">
 134 <td class="colFirst"><code>static <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 135 <td class="colLast"><span class="typeNameLabel">ClustalAlignmentUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile-java.io.InputStream-">readClustalFile</a></span>(java.io.InputStream&nbsp;instream)</code>
 136 <div class="block">Read Clustal formatted alignment.</div>
 137 </td>
 138 </tr>
 139 <tr class="rowColor">
 140 <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>
 141 <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>
 142 <div class="block">> Foobar_dundeefriends
 143
 144  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
 145
 146  # REM465 355-368
 147
 148  # HOTLOOPS 190-204
 149
 150  # RESIDUE COILS REM465 HOTLOOPS
 151
 152  M 0.86010 0.88512 0.37094
 153
 154  T 0.79983 0.85864 0.44331
 155
 156  >Next Sequence name</div>
 157 </td>
 158 </tr>
 159 <tr class="altColor">
 160 <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>
 161 <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>
 162 <div class="block">> Foobar_dundeefriends
 163
 164  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
 165
 166  # REM465 355-368
 167
 168  # HOTLOOPS 190-204
 169
 170  # RESIDUE COILS REM465 HOTLOOPS
 171
 172  M 0.86010 0.88512 0.37094
 173
 174  T 0.79983 0.85864 0.44331
 175
 176  >Next Sequence name</div>
 177 </td>
 178 </tr>
 179 <tr class="rowColor">
 180 <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>
 181 <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>
 182 <div class="block">Read IUPred output</div>
 183 </td>
 184 </tr>
 185 <tr class="altColor">
 186 <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>
 187 <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,
 188           <a href="../../../../compbio/data/sequence/IUPredResult.html" title="enum in compbio.data.sequence">IUPredResult</a>&nbsp;type)</code>
 189 <div class="block">## Long Disorder
 190
 191  # P53_HUMAN
 192
 193  1 M 0.9943
 194
 195  2 E 0.9917
 196
 197  3 E 0.9879
 198
 199  (every line)</div>
 200 </td>
 201 </tr>
 202 <tr class="rowColor">
 203 <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>
 204 <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>
 205 </tr>
 206 <tr class="altColor">
 207 <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>
 208 <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>
 209 <div class="block">Reader for JRonn horizontal file format</div>
 210 </td>
 211 </tr>
 212 </tbody>
 213 </table>
 214 </li>
 215 <li class="blockList"><a name="compbio.runner">
 216 <!--   -->
 217 </a>
 218 <h3>Uses of <a href="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a> in <a href="../../../../compbio/runner/package-summary.html">compbio.runner</a></h3>
 219 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 220 <caption><span>Methods in <a href="../../../../compbio/runner/package-summary.html">compbio.runner</a> that throw <a href="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></span><span class="tabEnd">&nbsp;</span></caption>
 221 <tr>
 222 <th class="colFirst" scope="col">Modifier and Type</th>
 223 <th class="colLast" scope="col">Method and Description</th>
 224 </tr>
 225 <tbody>
 226 <tr class="altColor">
 227 <td class="colFirst"><code>static <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 228 <td class="colLast"><span class="typeNameLabel">Util.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/Util.html#readClustalFile-java.lang.String-java.lang.String-">readClustalFile</a></span>(java.lang.String&nbsp;workDirectory,
 229                java.lang.String&nbsp;clustFile)</code>&nbsp;</td>
 230 </tr>
 231 <tr class="rowColor">
 232 <td class="colFirst"><code>static <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 233 <td class="colLast"><span class="typeNameLabel">RunnerUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/RunnerUtil.html#readClustalFile-java.lang.String-java.lang.String-">readClustalFile</a></span>(java.lang.String&nbsp;workDirectory,
 234                java.lang.String&nbsp;clustFile)</code>&nbsp;</td>
 235 </tr>
 236 <tr class="altColor">
 237 <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>
 238 <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,
 239              java.lang.String&nbsp;clustFile)</code>&nbsp;</td>
 240 </tr>
 241 <tr class="rowColor">
 242 <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>
 243 <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,
 244              java.lang.String&nbsp;clustFile)</code>&nbsp;</td>
 245 </tr>
 246 </tbody>
 247 </table>
 248 </li>
 249 </ul>
 250 </li>
 251 </ul>
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