website/full_javadoc/index-files/index-17.html

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  82 <A NAME="_R_"><!-- --></A><H2>\r
  83 <B>R</B></H2>\r
  84 <DL>\r
  85 <DT><A HREF="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence"><B>Range</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>&nbsp;<DT><A HREF="../compbio/data/sequence/Range.html#Range(int, int)"><B>Range(int, int)</B></A> - \r
  86 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>\r
  87 <DD>&nbsp;\r
  88 <DT><A HREF="../compbio/data/sequence/Range.html#Range(java.lang.String[])"><B>Range(String[])</B></A> - \r
  89 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>\r
  90 <DD>&nbsp;\r
  91 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#rconfigFile"><B>rconfigFile</B></A> - \r
  92 Static variable in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
  93 <DD>&nbsp;\r
  94 <DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#read(java.io.InputStream, java.lang.Class)"><B>read(InputStream, Class&lt;V&gt;)</B></A> - \r
  95 Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
  96 <DD>&nbsp;\r
  97 <DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#read(java.io.InputStream, java.lang.Class, java.lang.Class...)"><B>read(InputStream, Class&lt;V&gt;, Class&lt;?&gt;...)</B></A> - \r
  98 Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
  99 <DD>&nbsp;\r
 100 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readAAConResults(java.io.InputStream)"><B>readAAConResults(InputStream)</B></A> - \r
 101 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 102 <DD>Read AACon result with no alignment files.\r
 103 <DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#readAndValidate(java.io.InputStream, java.lang.Class)"><B>readAndValidate(InputStream, Class&lt;V&gt;)</B></A> - \r
 104 Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
 105 <DD>&nbsp;\r
 106 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)"><B>readClustalFile(InputStream)</B></A> - \r
 107 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
 108 <DD>Read Clustal formatted alignment.\r
 109 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)"><B>readClustalFile(File)</B></A> - \r
 110 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
 111 <DD>&nbsp;\r
 112 <DT><A HREF="../compbio/runner/Util.html#readClustalFile(java.lang.String, java.lang.String)"><B>readClustalFile(String, String)</B></A> - \r
 113 Static method in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
 114 <DD>&nbsp;\r
 115 <DT><A HREF="../compbio/stat/collector/StatDB.html#readData(java.sql.Timestamp, java.sql.Timestamp, compbio.ws.client.Services, java.lang.Boolean)"><B>readData(Timestamp, Timestamp, Services, Boolean)</B></A> - \r
 116 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
 117 <DD>&nbsp;\r
 118 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readDisembl(java.io.InputStream)"><B>readDisembl(InputStream)</B></A> - \r
 119 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 120 <DD>> Foobar_dundeefriends
 121
 122  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
 123
 124  # REM465 355-368
 125
 126  # HOTLOOPS 190-204
 127
 128  # RESIDUE COILS REM465 HOTLOOPS
 129
 130  M 0.86010 0.88512 0.37094
 131
 132  T 0.79983 0.85864 0.44331
 133
 134  >Next Sequence name\r
 135 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)"><B>readFasta(InputStream)</B></A> - \r
 136 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 137 <DD>Reads fasta sequences from inStream into the list of FastaSequence
 138  objects\r
 139 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readGlobPlot(java.io.InputStream)"><B>readGlobPlot(InputStream)</B></A> - \r
 140 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 141 <DD>> Foobar_dundeefriends
 142
 143  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
 144
 145  # REM465 355-368
 146
 147  # HOTLOOPS 190-204
 148
 149  # RESIDUE COILS REM465 HOTLOOPS
 150
 151  M 0.86010 0.88512 0.37094
 152
 153  T 0.79983 0.85864 0.44331
 154
 155  >Next Sequence name\r
 156 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readIUPred(java.io.File)"><B>readIUPred(File)</B></A> - \r
 157 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 158 <DD>Read IUPred output\r
 159 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.File)"><B>readJRonn(File)</B></A> - \r
 160 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 161 <DD>&nbsp;\r
 162 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.InputStream)"><B>readJRonn(InputStream)</B></A> - \r
 163 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 164 <DD>Reader for JRonn horizontal file format\r
 165 <DT><A HREF="../compbio/runner/Util.html#readJronnFile(java.lang.String, java.lang.String)"><B>readJronnFile(String, String)</B></A> - \r
 166 Static method in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
 167 <DD>&nbsp;\r
 168 <DT><A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa"><B>RegistryWS</B></A> - Interface in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD>JABAWS services registry<DT><A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server"><B>RegistryWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>JABAWS services registry<DT><A HREF="../compbio/ws/server/RegistryWS.html#RegistryWS()"><B>RegistryWS()</B></A> - \r
 169 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>\r
 170 <DD>&nbsp;\r
 171 <DT><A HREF="../compbio/runner/disorder/Disembl.html#REM_EXPECTATION_THRESHOLD"><B>REM_EXPECTATION_THRESHOLD</B></A> - \r
 172 Variable in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>\r
 173 <DD>&nbsp;\r
 174 <DT><A HREF="../compbio/data/sequence/FastaReader.html#remove()"><B>remove()</B></A> - \r
 175 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</A>\r
 176 <DD>Not implemented\r
 177 <DT><A HREF="../compbio/metadata/RunnerConfig.html#removeArgument(java.lang.String)"><B>removeArgument(String)</B></A> - \r
 178 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 179 <DD>Removes the argument <A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> if found.\r
 180 <DT><A HREF="../compbio/metadata/RunnerConfig.html#removeArgumentByOptionName(java.lang.String)"><B>removeArgumentByOptionName(String)</B></A> - \r
 181 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 182 <DD>Removes the argument which can be a Parameter or an Option instance by
 183  the value in <optionNames> element of the runner configuration
 184  descriptor.\r
 185 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#removeJob(java.lang.String)"><B>removeJob(String)</B></A> - \r
 186 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
 187 <DD>&nbsp;\r
 188 <DT><A HREF="../compbio/runner/_impl/BlastAll.html#removeOutput(java.lang.String)"><B>removeOutput(String)</B></A> - \r
 189 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>\r
 190 <DD>&nbsp;\r
 191 <DT><A HREF="../compbio/runner/_impl/PSIBlast.html#removeOutput(java.lang.String)"><B>removeOutput(String)</B></A> - \r
 192 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
 193 <DD>&nbsp;\r
 194 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#removeParam(java.lang.String)"><B>removeParam(String)</B></A> - \r
 195 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 196 <DD>&nbsp;\r
 197 <DT><A HREF="../compbio/stat/collector/StatDB.html#removeRecordedJobs(java.util.Set)"><B>removeRecordedJobs(Set&lt;JobStat&gt;)</B></A> - \r
 198 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
 199 <DD>Removes the job if
 200
 201  1) It has already been recorded
 202
 203  2) It has not completed and did not timeout - this is to prevent
 204  recording the information on the incomplete jobs.\r
 205 <DT><A HREF="../compbio/engine/SubmissionManager.html#removeTask(compbio.engine.client.ConfiguredExecutable)"><B>removeTask(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
 206 Static method in class compbio.engine.<A HREF="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</A>\r
 207 <DD>&nbsp;\r
 208 <DT><A HREF="../compbio/engine/SubmissionManager.html#removeTask(java.lang.String)"><B>removeTask(String)</B></A> - \r
 209 Static method in class compbio.engine.<A HREF="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</A>\r
 210 <DD>&nbsp;\r
 211 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#reportStat()"><B>reportStat()</B></A> - \r
 212 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
 213 <DD>&nbsp;\r
 214 <DT><A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>ResultNotAvailableException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>ResultNotAvailableException is thrown wherever the results of the calculation
 215  cannot be obtained.<DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String)"><B>ResultNotAvailableException(String)</B></A> - \r
 216 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
 217 <DD>&nbsp;\r
 218 <DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.Throwable)"><B>ResultNotAvailableException(Throwable)</B></A> - \r
 219 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
 220 <DD>&nbsp;\r
 221 <DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String, java.lang.Throwable)"><B>ResultNotAvailableException(String, Throwable)</B></A> - \r
 222 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
 223 <DD>&nbsp;\r
 224 <DT><A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>ResultNotAvailableExceptionBean</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>This class was generated by the JAX-WS RI.<DT><A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html#ResultNotAvailableExceptionBean()"><B>ResultNotAvailableExceptionBean()</B></A> - \r
 225 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws">ResultNotAvailableExceptionBean</A>\r
 226 <DD>&nbsp;\r
 227 <DT><A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl"><B>Ronn</B></A> - Class in <A HREF="../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A><DD>&nbsp;<DT><A HREF="../compbio/runner/_impl/Ronn.html#Ronn(java.lang.String)"><B>Ronn(String)</B></A> - \r
 228 Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
 229 <DD>&nbsp;\r
 230 <DT><A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl"><B>RPSBlast</B></A> - Class in <A HREF="../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A><DD>&nbsp;<DT><A HREF="../compbio/runner/_impl/RPSBlast.html#RPSBlast(java.lang.String)"><B>RPSBlast(String)</B></A> - \r
 231 Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
 232 <DD>&nbsp;\r
 233 <DT><A HREF="../compbio/engine/local/StreamGobbler.html#run()"><B>run()</B></A> - \r
 234 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local">StreamGobbler</A>\r
 235 <DD>&nbsp;\r
 236 <DT><A HREF="../compbio/stat/collector/ExecutionStatCollector.html#run()"><B>run()</B></A> - \r
 237 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/ExecutionStatCollector.html" title="class in compbio.stat.collector">ExecutionStatCollector</A>\r
 238 <DD>&nbsp;\r
 239 <DT><A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client"><B>RunConfiguration</B></A> - Class in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>Value class for persisting ConfExecutable instances<DT><A HREF="../compbio/engine/client/RunConfiguration.html#RunConfiguration()"><B>RunConfiguration()</B></A> - \r
 240 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 241 <DD>&nbsp;\r
 242 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#RunConfiguration(compbio.engine.client.ConfExecutable)"><B>RunConfiguration(ConfExecutable&lt;?&gt;)</B></A> - \r
 243 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 244 <DD>&nbsp;\r
 245 <DT><A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><B>RunnerConfig</B></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><DD>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.<DT><A HREF="../compbio/metadata/RunnerConfig.html#RunnerConfig()"><B>RunnerConfig()</B></A> - \r
 246 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 247 <DD>&nbsp;\r
 248 <DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf"><B>RunnerConfigMarshaller</B></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><DD>&nbsp;<DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#RunnerConfigMarshaller(java.lang.Class)"><B>RunnerConfigMarshaller(Class&lt;?&gt;)</B></A> - \r
 249 Constructor for class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
 250 <DD>&nbsp;\r
 251 <DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#RunnerConfigMarshaller(java.lang.Class, java.lang.Class...)"><B>RunnerConfigMarshaller(Class&lt;?&gt;, Class&lt;?&gt;...)</B></A> - \r
 252 Constructor for class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
 253 <DD>&nbsp;\r
 254 <DT><A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl"><B>Runners</B></A> - Class in <A HREF="../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A><DD>&nbsp;<DT><A HREF="../compbio/pipeline/_jpred/Jpred4.html#runPsiBlast()"><B>runPsiBlast()</B></A> - \r
 255 Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred">Jpred4</A>\r
 256 <DD>&nbsp;\r
 257 </DL>\r
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