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/engine/client/RunConfiguration.html#rconfigFile"><B>rconfigFile</B></A> - \r
  86 Static variable in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
  87 <DD>&nbsp;\r
  88 <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
  89 Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
  90 <DD>&nbsp;\r
  91 <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
  92 Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
  93 <DD>&nbsp;\r
  94 <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
  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/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)"><B>readClustalFile(InputStream)</B></A> - \r
  98 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
  99 <DD>Read Clustal formatted alignment.\r
 100 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)"><B>readClustalFile(File)</B></A> - \r
 101 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
 102 <DD>&nbsp;\r
 103 <DT><A HREF="../compbio/runner/Util.html#readClustalFile(java.lang.String, java.lang.String)"><B>readClustalFile(String, String)</B></A> - \r
 104 Static method in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
 105 <DD>&nbsp;\r
 106 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)"><B>readFasta(InputStream)</B></A> - \r
 107 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 108 <DD>Reads fasta sequences from inStream into the list of FastaSequence
 109  objects\r
 110 <DT><A HREF="../compbio/metadata/RunnerConfig.html#removeArgument(java.lang.String)"><B>removeArgument(String)</B></A> - \r
 111 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 112 <DD>Removes the argument <A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> if found.\r
 113 <DT><A HREF="../compbio/metadata/RunnerConfig.html#removeArgumentByOptionName(java.lang.String)"><B>removeArgumentByOptionName(String)</B></A> - \r
 114 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 115 <DD>Removes the argument\r
 116 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#removeJob(java.lang.String)"><B>removeJob(String)</B></A> - \r
 117 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
 118 <DD>&nbsp;\r
 119 <DT><A HREF="../compbio/runner/_impl/BlastAll.html#removeOutput(java.lang.String)"><B>removeOutput(String)</B></A> - \r
 120 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>\r
 121 <DD>&nbsp;\r
 122 <DT><A HREF="../compbio/runner/_impl/PSIBlast.html#removeOutput(java.lang.String)"><B>removeOutput(String)</B></A> - \r
 123 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
 124 <DD>&nbsp;\r
 125 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#removeParam(java.lang.String)"><B>removeParam(String)</B></A> - \r
 126 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 127 <DD>&nbsp;\r
 128 <DT><A HREF="../compbio/engine/SubmissionManager.html#removeTask(compbio.engine.client.ConfiguredExecutable)"><B>removeTask(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
 129 Static method in class compbio.engine.<A HREF="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</A>\r
 130 <DD>&nbsp;\r
 131 <DT><A HREF="../compbio/engine/SubmissionManager.html#removeTask(java.lang.String)"><B>removeTask(String)</B></A> - \r
 132 Static method in class compbio.engine.<A HREF="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</A>\r
 133 <DD>&nbsp;\r
 134 <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
 135  cannot be obtained.<DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String)"><B>ResultNotAvailableException(String)</B></A> - \r
 136 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
 137 <DD>&nbsp;\r
 138 <DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.Throwable)"><B>ResultNotAvailableException(Throwable)</B></A> - \r
 139 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
 140 <DD>&nbsp;\r
 141 <DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String, java.lang.Throwable)"><B>ResultNotAvailableException(String, Throwable)</B></A> - \r
 142 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
 143 <DD>&nbsp;\r
 144 <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
 145 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
 146 <DD>&nbsp;\r
 147 <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
 148 Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
 149 <DD>&nbsp;\r
 150 <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
 151 Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
 152 <DD>&nbsp;\r
 153 <DT><A HREF="../compbio/engine/local/StreamGobbler.html#run()"><B>run()</B></A> - \r
 154 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local">StreamGobbler</A>\r
 155 <DD>&nbsp;\r
 156 <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
 157 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 158 <DD>&nbsp;\r
 159 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#RunConfiguration(compbio.engine.client.ConfExecutable)"><B>RunConfiguration(ConfExecutable&lt;?&gt;)</B></A> - \r
 160 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 161 <DD>&nbsp;\r
 162 <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
 163 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 164 <DD>&nbsp;\r
 165 <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
 166 Constructor for class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
 167 <DD>&nbsp;\r
 168 <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
 169 Constructor for class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
 170 <DD>&nbsp;\r
 171 <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
 172 Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred">Jpred4</A>\r
 173 <DD>&nbsp;\r
 174 </DL>\r
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