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41 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
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82 <A NAME="_R_"><!-- --></A><H2>
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85 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#rconfigFile"><B>rconfigFile</B></A> -
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86 Static variable in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>
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88 <DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#read(java.io.InputStream, java.lang.Class)"><B>read(InputStream, Class<V>)</B></A> -
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89 Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>
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91 <DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#read(java.io.InputStream, java.lang.Class, java.lang.Class...)"><B>read(InputStream, Class<V>, Class<?>...)</B></A> -
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92 Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>
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94 <DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#readAndValidate(java.io.InputStream, java.lang.Class)"><B>readAndValidate(InputStream, Class<V>)</B></A> -
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95 Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>
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97 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)"><B>readClustalFile(InputStream)</B></A> -
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98 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>
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99 <DD>Read Clustal formatted alignment.
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100 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)"><B>readClustalFile(File)</B></A> -
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101 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>
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103 <DT><A HREF="../compbio/runner/Util.html#readClustalFile(java.lang.String, java.lang.String)"><B>readClustalFile(String, String)</B></A> -
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104 Static method in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>
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106 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)"><B>readFasta(InputStream)</B></A> -
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107 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>
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108 <DD>Reads fasta sequences from inStream into the list of FastaSequence
110 <DT><A HREF="../compbio/metadata/RunnerConfig.html#removeArgument(java.lang.String)"><B>removeArgument(String)</B></A> -
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111 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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112 <DD>Removes the argument <A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> if found.
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113 <DT><A HREF="../compbio/metadata/RunnerConfig.html#removeArgumentByOptionName(java.lang.String)"><B>removeArgumentByOptionName(String)</B></A> -
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114 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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115 <DD>Removes the argument
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116 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#removeJob(java.lang.String)"><B>removeJob(String)</B></A> -
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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>
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119 <DT><A HREF="../compbio/runner/_impl/BlastAll.html#removeOutput(java.lang.String)"><B>removeOutput(String)</B></A> -
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120 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>
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122 <DT><A HREF="../compbio/runner/_impl/PSIBlast.html#removeOutput(java.lang.String)"><B>removeOutput(String)</B></A> -
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123 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>
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125 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#removeParam(java.lang.String)"><B>removeParam(String)</B></A> -
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126 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>
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128 <DT><A HREF="../compbio/engine/SubmissionManager.html#removeTask(compbio.engine.client.ConfiguredExecutable)"><B>removeTask(ConfiguredExecutable<?>)</B></A> -
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129 Static method in class compbio.engine.<A HREF="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</A>
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131 <DT><A HREF="../compbio/engine/SubmissionManager.html#removeTask(java.lang.String)"><B>removeTask(String)</B></A> -
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132 Static method in class compbio.engine.<A HREF="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</A>
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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> -
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136 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>
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138 <DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.Throwable)"><B>ResultNotAvailableException(Throwable)</B></A> -
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139 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>
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141 <DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String, java.lang.Throwable)"><B>ResultNotAvailableException(String, Throwable)</B></A> -
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142 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>
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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> -
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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>
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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> <DT><A HREF="../compbio/runner/_impl/Ronn.html#Ronn(java.lang.String)"><B>Ronn(String)</B></A> -
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148 Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>
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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> <DT><A HREF="../compbio/runner/_impl/RPSBlast.html#RPSBlast(java.lang.String)"><B>RPSBlast(String)</B></A> -
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151 Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>
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153 <DT><A HREF="../compbio/engine/local/StreamGobbler.html#run()"><B>run()</B></A> -
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154 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local">StreamGobbler</A>
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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> -
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157 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>
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159 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#RunConfiguration(compbio.engine.client.ConfExecutable)"><B>RunConfiguration(ConfExecutable<?>)</B></A> -
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160 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>
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162 <DT><A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><B>RunnerConfig</B></A><<A HREF="../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> - 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> -
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163 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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165 <DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf"><B>RunnerConfigMarshaller</B></A><<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="type parameter in RunnerConfigMarshaller">T</A>> - Class in <A HREF="../compbio/engine/conf/package-summary.html">compbio.engine.conf</A><DD> <DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#RunnerConfigMarshaller(java.lang.Class)"><B>RunnerConfigMarshaller(Class<?>)</B></A> -
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166 Constructor for class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>
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168 <DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#RunnerConfigMarshaller(java.lang.Class, java.lang.Class...)"><B>RunnerConfigMarshaller(Class<?>, Class<?>...)</B></A> -
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169 Constructor for class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>
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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> <DT><A HREF="../compbio/pipeline/_jpred/Jpred4.html#runPsiBlast()"><B>runPsiBlast()</B></A> -
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172 Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred">Jpred4</A>
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