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  75 <h2 class="title">R</h2>
  76 <dl>
  77 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#rand">rand</a></span> - Static variable in class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
  78 <dd>&nbsp;</dd>
  79 <dt><a href="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence"><span class="typeNameLink">Range</span></a> - Class in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
  80 <dd>&nbsp;</dd>
  81 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Range.html#Range--">Range()</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a></dt>
  82 <dd>&nbsp;</dd>
  83 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Range.html#Range-int-int-">Range(int, int)</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a></dt>
  84 <dd>&nbsp;</dd>
  85 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Range.html#Range-java.lang.String:A-">Range(String[])</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a></dt>
  86 <dd>&nbsp;</dd>
  87 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Score.html#ranges">ranges</a></span> - Variable in class compbio.data.sequence.<a href="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a></dt>
  88 <dd>&nbsp;</dd>
  89 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#rconfig">rconfig</a></span> - Variable in class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
  90 <dd>&nbsp;</dd>
  91 <dt><span class="memberNameLink"><a href="../compbio/engine/client/RunConfiguration.html#rconfigFile">rconfigFile</a></span> - Static variable in class compbio.engine.client.<a href="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</a></dt>
  92 <dd>&nbsp;</dd>
  93 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/RunnerConfigMarshaller.html#read-java.io.InputStream-java.lang.Class-">read(InputStream, Class&lt;V&gt;)</a></span> - Method in class compbio.engine.conf.<a href="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</a></dt>
  94 <dd>&nbsp;</dd>
  95 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/RunnerConfigMarshaller.html#read-java.io.InputStream-java.lang.Class-java.lang.Class...-">read(InputStream, Class&lt;V&gt;, Class&lt;?&gt;...)</a></span> - Method in class compbio.engine.conf.<a href="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</a></dt>
  96 <dd>&nbsp;</dd>
  97 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#readAAConResults-java.io.InputStream-">readAAConResults(InputStream)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
  98 <dd>
  99 <div class="block">Read AACon result with no alignment files.</div>
 100 </dd>
 101 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/RunnerConfigMarshaller.html#readAndValidate-java.io.InputStream-java.lang.Class-">readAndValidate(InputStream, Class&lt;V&gt;)</a></span> - Method in class compbio.engine.conf.<a href="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</a></dt>
 102 <dd>&nbsp;</dd>
 103 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile-java.io.InputStream-">readClustalFile(InputStream)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</a></dt>
 104 <dd>
 105 <div class="block">Read Clustal formatted alignment.</div>
 106 </dd>
 107 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile-java.io.File-">readClustalFile(File)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</a></dt>
 108 <dd>&nbsp;</dd>
 109 <dt><span class="memberNameLink"><a href="../compbio/runner/RunnerUtil.html#readClustalFile-java.lang.String-java.lang.String-">readClustalFile(String, String)</a></span> - Static method in class compbio.runner.<a href="../compbio/runner/RunnerUtil.html" title="class in compbio.runner">RunnerUtil</a></dt>
 110 <dd>&nbsp;</dd>
 111 <dt><span class="memberNameLink"><a href="../compbio/runner/Util.html#readClustalFile-java.lang.String-java.lang.String-">readClustalFile(String, String)</a></span> - Static method in class compbio.runner.<a href="../compbio/runner/Util.html" title="class in compbio.runner">Util</a></dt>
 112 <dd>&nbsp;</dd>
 113 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatDB.html#readData-java.sql.Timestamp-java.sql.Timestamp-compbio.ws.client.Services-java.lang.Boolean-">readData(Timestamp, Timestamp, Services, Boolean)</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</a></dt>
 114 <dd>&nbsp;</dd>
 115 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#readDisembl-java.io.InputStream-">readDisembl(InputStream)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 116 <dd>
 117 <div class="block">> Foobar_dundeefriends
 118
 119  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
 120
 121  # REM465 355-368
 122
 123  # HOTLOOPS 190-204
 124
 125  # RESIDUE COILS REM465 HOTLOOPS
 126
 127  M 0.86010 0.88512 0.37094
 128
 129  T 0.79983 0.85864 0.44331
 130
 131  >Next Sequence name</div>
 132 </dd>
 133 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#readFasta-java.io.InputStream-">readFasta(InputStream)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 134 <dd>
 135 <div class="block">Reads fasta sequences from inStream into the list of FastaSequence
 136  objects</div>
 137 </dd>
 138 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#readGlobPlot-java.io.InputStream-">readGlobPlot(InputStream)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 139 <dd>
 140 <div class="block">> Foobar_dundeefriends
 141
 142  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
 143
 144  # REM465 355-368
 145
 146  # HOTLOOPS 190-204
 147
 148  # RESIDUE COILS REM465 HOTLOOPS
 149
 150  M 0.86010 0.88512 0.37094
 151
 152  T 0.79983 0.85864 0.44331
 153
 154  >Next Sequence name</div>
 155 </dd>
 156 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#readIUPred-java.io.File-">readIUPred(File)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 157 <dd>
 158 <div class="block">Read IUPred output</div>
 159 </dd>
 160 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#readIUPred-java.io.InputStream-compbio.data.sequence.IUPredResult-">readIUPred(InputStream, IUPredResult)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 161 <dd>
 162 <div class="block">## Long Disorder
 163
 164  # P53_HUMAN
 165
 166  1 M 0.9943
 167
 168  2 E 0.9917
 169
 170  3 E 0.9879
 171
 172  (every line)</div>
 173 </dd>
 174 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#readJRonn-java.io.File-">readJRonn(File)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 175 <dd>&nbsp;</dd>
 176 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#readJRonn-java.io.InputStream-">readJRonn(InputStream)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 177 <dd>
 178 <div class="block">Reader for JRonn horizontal file format</div>
 179 </dd>
 180 <dt><span class="memberNameLink"><a href="../compbio/runner/RunnerUtil.html#readJronnFile-java.lang.String-java.lang.String-">readJronnFile(String, String)</a></span> - Static method in class compbio.runner.<a href="../compbio/runner/RunnerUtil.html" title="class in compbio.runner">RunnerUtil</a></dt>
 181 <dd>&nbsp;</dd>
 182 <dt><span class="memberNameLink"><a href="../compbio/runner/Util.html#readJronnFile-java.lang.String-java.lang.String-">readJronnFile(String, String)</a></span> - Static method in class compbio.runner.<a href="../compbio/runner/Util.html" title="class in compbio.runner">Util</a></dt>
 183 <dd>&nbsp;</dd>
 184 <dt><span class="memberNameLink"><a href="../compbio/runner/RunnerUtil.html#readRNAStruct-java.lang.String-java.lang.String-">readRNAStruct(String, String)</a></span> - Static method in class compbio.runner.<a href="../compbio/runner/RunnerUtil.html" title="class in compbio.runner">RunnerUtil</a></dt>
 185 <dd>&nbsp;</dd>
 186 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#readRNAStructStream-java.io.InputStream-">readRNAStructStream(InputStream)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructReader.html" title="class in compbio.data.sequence">RNAStructReader</a></dt>
 187 <dd>&nbsp;</dd>
 188 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#readRNAStructStream-java.io.InputStream-java.io.InputStream-">readRNAStructStream(InputStream, InputStream)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructReader.html" title="class in compbio.data.sequence">RNAStructReader</a></dt>
 189 <dd>&nbsp;</dd>
 190 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/ServiceTestResult.html#reference">reference</a></span> - Variable in class compbio.stat.servlet.<a href="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</a></dt>
 191 <dd>&nbsp;</dd>
 192 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.ServiceInfo.html#reference">reference</a></span> - Variable in class compbio.ws.client.<a href="../compbio/ws/client/Services.ServiceInfo.html" title="class in compbio.ws.client">Services.ServiceInfo</a></dt>
 193 <dd>&nbsp;</dd>
 194 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.AlifoldLine.html#regex">regex</a></span> - Variable in enum compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructReader.AlifoldLine.html" title="enum in compbio.data.sequence">RNAStructReader.AlifoldLine</a></dt>
 195 <dd>&nbsp;</dd>
 196 <dt><a href="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa"><span class="typeNameLink">RegistryWS</span></a> - Interface in <a href="../compbio/data/msa/package-summary.html">compbio.data.msa</a></dt>
 197 <dd>
 198 <div class="block">JABAWS services registry</div>
 199 </dd>
 200 <dt><a href="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server"><span class="typeNameLink">RegistryWS</span></a> - Class in <a href="../compbio/ws/server/package-summary.html">compbio.ws.server</a></dt>
 201 <dd>
 202 <div class="block">JABAWS services registry</div>
 203 </dd>
 204 <dt><span class="memberNameLink"><a href="../compbio/ws/server/RegistryWS.html#RegistryWS--">RegistryWS()</a></span> - Constructor for class compbio.ws.server.<a href="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</a></dt>
 205 <dd>&nbsp;</dd>
 206 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Disembl.html#REM_EXPECTATION_THRESHOLD">REM_EXPECTATION_THRESHOLD</a></span> - Variable in class compbio.runner.disorder.<a href="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</a></dt>
 207 <dd>&nbsp;</dd>
 208 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/FastaReader.html#remove--">remove()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</a></dt>
 209 <dd>
 210 <div class="block">Not implemented</div>
 211 </dd>
 212 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#removeArgument-java.lang.String-">removeArgument(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
 213 <dd>
 214 <div class="block">Removes the argument <a href="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><code>Argument</code></a> if found.</div>
 215 </dd>
 216 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#removeArgumentByOptionName-java.lang.String-">removeArgumentByOptionName(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
 217 <dd>
 218 <div class="block">Removes the argument which can be a Parameter or an Option instance by
 219  the value in <optionNames> element of the runner configuration
 220  descriptor.</div>
 221 </dd>
 222 <dt><span class="memberNameLink"><a href="../compbio/engine/Cleaner.html#removeFile-java.lang.String-">removeFile(String)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/Cleaner.html" title="class in compbio.engine">Cleaner</a></dt>
 223 <dd>&nbsp;</dd>
 224 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#removeInvalidXMLCharacters-java.lang.String-">removeInvalidXMLCharacters(String)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
 225 <dd>
 226 <div class="block">This method ensures that the output String has only valid XML unicode
 227  characters as specified by the XML 1.0 standard.</div>
 228 </dd>
 229 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#removeJob-java.lang.String-">removeJob(String)</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</a></dt>
 230 <dd>&nbsp;</dd>
 231 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#removeJobFromListbyTaskId-java.lang.String-">removeJobFromListbyTaskId(String)</a></span> - Static method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</a></dt>
 232 <dd>&nbsp;</dd>
 233 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#removeParam-java.lang.String-">removeParam(String)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
 234 <dd>&nbsp;</dd>
 235 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatDB.html#removeRecordedJobs-java.util.Set-">removeRecordedJobs(Set&lt;JobStat&gt;)</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</a></dt>
 236 <dd>
 237 <div class="block">Removes the job if
 238
 239  1) It has already been recorded
 240
 241  2) It has not completed and did not timeout - this is to prevent
 242  recording the information on the incomplete jobs.</div>
 243 </dd>
 244 <dt><span class="memberNameLink"><a href="../compbio/engine/SubmissionManager.html#removeTask-compbio.engine.client.ConfiguredExecutable-">removeTask(ConfiguredExecutable&lt;?&gt;)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</a></dt>
 245 <dd>&nbsp;</dd>
 246 <dt><span class="memberNameLink"><a href="../compbio/engine/SubmissionManager.html#removeTask-java.lang.String-">removeTask(String)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</a></dt>
 247 <dd>&nbsp;</dd>
 248 <dt><span class="memberNameLink"><a href="../compbio/ws/client/WSTester.html#reportException-java.lang.Exception-">reportException(Exception)</a></span> - Method in class compbio.ws.client.<a href="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</a></dt>
 249 <dd>&nbsp;</dd>
 250 <dt><span class="memberNameLink"><a href="../compbio/ws/client/WSTester.html#reportResults-compbio.ws.client.Services-boolean-">reportResults(Services, boolean)</a></span> - Method in class compbio.ws.client.<a href="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</a></dt>
 251 <dd>&nbsp;</dd>
 252 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatProcessor.html#reportStat--">reportStat()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</a></dt>
 253 <dd>&nbsp;</dd>
 254 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GAUtils.html#reportUsage-compbio.ws.client.Services-">reportUsage(Services)</a></span> - Static method in class compbio.ws.server.<a href="../compbio/ws/server/GAUtils.html" title="class in compbio.ws.server">GAUtils</a></dt>
 255 <dd>&nbsp;</dd>
 256 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GAUtils.html#reportUsage-compbio.ws.client.Services-java.lang.String-">reportUsage(Services, String)</a></span> - Static method in class compbio.ws.server.<a href="../compbio/ws/server/GAUtils.html" title="class in compbio.ws.server">GAUtils</a></dt>
 257 <dd>&nbsp;</dd>
 258 <dt><span class="memberNameLink"><a href="../compbio/ws/server/WSUtil.html#reportUsage-compbio.engine.client.ConfiguredExecutable-org.apache.log4j.Logger-">reportUsage(ConfiguredExecutable&lt;T&gt;, Logger)</a></span> - Static method in class compbio.ws.server.<a href="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</a></dt>
 259 <dd>&nbsp;</dd>
 260 <dt><a href="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><span class="typeNameLink">ResultNotAvailableException</span></a> - Exception in <a href="../compbio/metadata/package-summary.html">compbio.metadata</a></dt>
 261 <dd>
 262 <div class="block">ResultNotAvailableException is thrown wherever the results of the calculation
 263  cannot be obtained.</div>
 264 </dd>
 265 <dt><span class="memberNameLink"><a href="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException-java.lang.String-">ResultNotAvailableException(String)</a></span> - Constructor for exception compbio.metadata.<a href="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</a></dt>
 266 <dd>&nbsp;</dd>
 267 <dt><span class="memberNameLink"><a href="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException-java.lang.Throwable-">ResultNotAvailableException(Throwable)</a></span> - Constructor for exception compbio.metadata.<a href="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</a></dt>
 268 <dd>&nbsp;</dd>
 269 <dt><span class="memberNameLink"><a href="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException-java.lang.String-java.lang.Throwable-">ResultNotAvailableException(String, Throwable)</a></span> - Constructor for exception compbio.metadata.<a href="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</a></dt>
 270 <dd>&nbsp;</dd>
 271 <dt><a href="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">ResultNotAvailableExceptionBean</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 272 <dd>
 273 <div class="block">This class was generated by the JAX-WS RI.</div>
 274 </dd>
 275 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html#ResultNotAvailableExceptionBean--">ResultNotAvailableExceptionBean()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws">ResultNotAvailableExceptionBean</a></dt>
 276 <dd>&nbsp;</dd>
 277 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#RESULTSIZE">RESULTSIZE</a></span> - Static variable in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 278 <dd>&nbsp;</dd>
 279 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#resultSize">resultSize</a></span> - Variable in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 280 <dd>&nbsp;</dd>
 281 <dt><a href="../compbio/runner/structure/RNAalifold.html" title="class in compbio.runner.structure"><span class="typeNameLink">RNAalifold</span></a> - Class in <a href="../compbio/runner/structure/package-summary.html">compbio.runner.structure</a></dt>
 282 <dd>&nbsp;</dd>
 283 <dt><span class="memberNameLink"><a href="../compbio/runner/structure/RNAalifold.html#RNAalifold--">RNAalifold()</a></span> - Constructor for class compbio.runner.structure.<a href="../compbio/runner/structure/RNAalifold.html" title="class in compbio.runner.structure">RNAalifold</a></dt>
 284 <dd>&nbsp;</dd>
 285 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#RNAALIFOLD_INFO">RNAALIFOLD_INFO</a></span> - Static variable in enum compbio.ws.client.<a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></dt>
 286 <dd>&nbsp;</dd>
 287 <dt><a href="../compbio/ws/server/RNAalifoldWS.html" title="class in compbio.ws.server"><span class="typeNameLink">RNAalifoldWS</span></a> - Class in <a href="../compbio/ws/server/package-summary.html">compbio.ws.server</a></dt>
 288 <dd>&nbsp;</dd>
 289 <dt><span class="memberNameLink"><a href="../compbio/ws/server/RNAalifoldWS.html#RNAalifoldWS--">RNAalifoldWS()</a></span> - Constructor for class compbio.ws.server.<a href="../compbio/ws/server/RNAalifoldWS.html" title="class in compbio.ws.server">RNAalifoldWS</a></dt>
 290 <dd>&nbsp;</dd>
 291 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.RNAOut.html#RNAOut--">RNAOut()</a></span> - Constructor for enum compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructReader.RNAOut.html" title="enum in compbio.data.sequence">RNAStructReader.RNAOut</a></dt>
 292 <dd>&nbsp;</dd>
 293 <dt><a href="../compbio/data/sequence/RNAStructReader.html" title="class in compbio.data.sequence"><span class="typeNameLink">RNAStructReader</span></a> - Class in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
 294 <dd>&nbsp;</dd>
 295 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#RNAStructReader--">RNAStructReader()</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructReader.html" title="class in compbio.data.sequence">RNAStructReader</a></dt>
 296 <dd>&nbsp;</dd>
 297 <dt><a href="../compbio/data/sequence/RNAStructReader.AlifoldLine.html" title="enum in compbio.data.sequence"><span class="typeNameLink">RNAStructReader.AlifoldLine</span></a> - Enum in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
 298 <dd>&nbsp;</dd>
 299 <dt><a href="../compbio/data/sequence/RNAStructReader.AlifoldResult.html" title="enum in compbio.data.sequence"><span class="typeNameLink">RNAStructReader.AlifoldResult</span></a> - Enum in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
 300 <dd>&nbsp;</dd>
 301 <dt><a href="../compbio/data/sequence/RNAStructReader.RNAOut.html" title="enum in compbio.data.sequence"><span class="typeNameLink">RNAStructReader.RNAOut</span></a> - Enum in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
 302 <dd>&nbsp;</dd>
 303 <dt><a href="../compbio/data/sequence/RNAStructScoreManager.html" title="class in compbio.data.sequence"><span class="typeNameLink">RNAStructScoreManager</span></a> - Class in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
 304 <dd>&nbsp;</dd>
 305 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructScoreManager.html#RNAStructScoreManager--">RNAStructScoreManager()</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructScoreManager.html" title="class in compbio.data.sequence">RNAStructScoreManager</a></dt>
 306 <dd>&nbsp;</dd>
 307 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructScoreManager.html#RNAStructScoreManager-java.util.List-java.util.List-">RNAStructScoreManager(List&lt;String&gt;, List&lt;TreeSet&lt;Score&gt;&gt;)</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructScoreManager.html" title="class in compbio.data.sequence">RNAStructScoreManager</a></dt>
 308 <dd>&nbsp;</dd>
 309 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#ru_stime">ru_stime</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 310 <dd>&nbsp;</dd>
 311 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#ru_utime">ru_utime</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 312 <dd>&nbsp;</dd>
 313 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#ru_wallclock">ru_wallclock</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 314 <dd>&nbsp;</dd>
 315 <dt><span class="memberNameLink"><a href="../compbio/engine/local/StreamGobbler.html#run--">run()</a></span> - Method in class compbio.engine.local.<a href="../compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local">StreamGobbler</a></dt>
 316 <dd>&nbsp;</dd>
 317 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/DirCleaner.html#run--">run()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/DirCleaner.html" title="class in compbio.stat.collector">DirCleaner</a></dt>
 318 <dd>&nbsp;</dd>
 319 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/ExecutionStatCollector.html#run--">run()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/ExecutionStatCollector.html" title="class in compbio.stat.collector">ExecutionStatCollector</a></dt>
 320 <dd>&nbsp;</dd>
 321 <dt><a href="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client"><span class="typeNameLink">RunConfiguration</span></a> - Class in <a href="../compbio/engine/client/package-summary.html">compbio.engine.client</a></dt>
 322 <dd>
 323 <div class="block">Value class for persisting ConfExecutable instances</div>
 324 </dd>
 325 <dt><span class="memberNameLink"><a href="../compbio/engine/client/RunConfiguration.html#RunConfiguration--">RunConfiguration()</a></span> - Constructor for class compbio.engine.client.<a href="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</a></dt>
 326 <dd>&nbsp;</dd>
 327 <dt><span class="memberNameLink"><a href="../compbio/engine/client/RunConfiguration.html#RunConfiguration-compbio.engine.client.ConfExecutable-">RunConfiguration(ConfExecutable&lt;?&gt;)</a></span> - Constructor for class compbio.engine.client.<a href="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</a></dt>
 328 <dd>&nbsp;</dd>
 329 <dt><span class="memberNameLink"><a href="../compbio/engine/client/RunConfiguration.html#runnerClassName">runnerClassName</a></span> - Variable in class compbio.engine.client.<a href="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</a></dt>
 330 <dd>
 331 <div class="block">Runner class name</div>
 332 </dd>
 333 <dt><span class="memberNameLink"><a href="../compbio/metadata/LimitsManager.html#runnerClassName">runnerClassName</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a></dt>
 334 <dd>&nbsp;</dd>
 335 <dt><span class="memberNameLink"><a href="../compbio/metadata/PresetManager.html#runnerClassName">runnerClassName</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a></dt>
 336 <dd>&nbsp;</dd>
 337 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#runnerClassName">runnerClassName</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
 338 <dd>
 339 <div class="block">The class name of a runnable e.g.</div>
 340 </dd>
 341 <dt><a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><span class="typeNameLink">RunnerConfig</span></a>&lt;<a href="../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</a>&gt; - Class in <a href="../compbio/metadata/package-summary.html">compbio.metadata</a></dt>
 342 <dd>
 343 <div class="block">The list of <a href="../compbio/metadata/Parameter.html" title="class in compbio.metadata"><code>Parameter</code></a>s and <a href="../compbio/metadata/Option.html" title="class in compbio.metadata"><code>Option</code></a>s supported by executable.</div>
 344 </dd>
 345 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#RunnerConfig--">RunnerConfig()</a></span> - Constructor for class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
 346 <dd>&nbsp;</dd>
 347 <dt><a href="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf"><span class="typeNameLink">RunnerConfigMarshaller</span></a>&lt;<a href="../compbio/engine/conf/RunnerConfigMarshaller.html" title="type parameter in RunnerConfigMarshaller">T</a>&gt; - Class in <a href="../compbio/engine/conf/package-summary.html">compbio.engine.conf</a></dt>
 348 <dd>&nbsp;</dd>
 349 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/RunnerConfigMarshaller.html#RunnerConfigMarshaller-java.lang.Class-">RunnerConfigMarshaller(Class&lt;?&gt;)</a></span> - Constructor for class compbio.engine.conf.<a href="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</a></dt>
 350 <dd>&nbsp;</dd>
 351 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/RunnerConfigMarshaller.html#RunnerConfigMarshaller-java.lang.Class-java.lang.Class...-">RunnerConfigMarshaller(Class&lt;?&gt;, Class&lt;?&gt;...)</a></span> - Constructor for class compbio.engine.conf.<a href="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</a></dt>
 352 <dd>&nbsp;</dd>
 353 <dt><a href="../compbio/engine/conf/RunnerConfigMarshaller.MySchemaOutputResolver.html" title="class in compbio.engine.conf"><span class="typeNameLink">RunnerConfigMarshaller.MySchemaOutputResolver</span></a> - Class in <a href="../compbio/engine/conf/package-summary.html">compbio.engine.conf</a></dt>
 354 <dd>&nbsp;</dd>
 355 <dt><a href="../compbio/runner/RunnerUtil.html" title="class in compbio.runner"><span class="typeNameLink">RunnerUtil</span></a> - Class in <a href="../compbio/runner/package-summary.html">compbio.runner</a></dt>
 356 <dd>&nbsp;</dd>
 357 <dt><span class="memberNameLink"><a href="../compbio/runner/RunnerUtil.html#RunnerUtil--">RunnerUtil()</a></span> - Constructor for class compbio.runner.<a href="../compbio/runner/RunnerUtil.html" title="class in compbio.runner">RunnerUtil</a></dt>
 358 <dd>&nbsp;</dd>
 359 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#RUNTIME">RUNTIME</a></span> - Static variable in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 360 <dd>&nbsp;</dd>
 361 </dl>
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