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82 <A NAME="_E_"><!-- --></A><H2>
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85 <DT><A HREF="../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl"><B>Environment</B></A> - Class in <A HREF="../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A><DD>This is utility class to encapsulate environmental variables like directory paths<DT><A HREF="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client"><B>EnvVariableProcessor</B></A> - Class in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD> <DT><A HREF="../compbio/engine/client/EnvVariableProcessor.html#EnvVariableProcessor()"><B>EnvVariableProcessor()</B></A> -
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86 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</A>
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88 <DT><A HREF="../compbio/data/sequence/Alignment.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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89 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>
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90 <DD>Please note that this implementation does not take the order of sequences
92 <DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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93 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>
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95 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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96 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>
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98 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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99 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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101 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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102 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>
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104 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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105 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>
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107 <DT><A HREF="../compbio/engine/ClusterJobId.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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108 Method in class compbio.engine.<A HREF="../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>
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110 <DT><A HREF="../compbio/engine/conf/_Key.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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111 Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A>
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113 <DT><A HREF="../compbio/engine/FilePuller.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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114 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>
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116 <DT><A HREF="../compbio/engine/Job.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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117 Method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>
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119 <DT><A HREF="../compbio/metadata/ChunkHolder.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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120 Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>
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122 <DT><A HREF="../compbio/metadata/Limit.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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123 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>
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125 <DT><A HREF="../compbio/metadata/Option.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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126 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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128 <DT><A HREF="../compbio/metadata/Parameter.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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129 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
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131 <DT><A HREF="../compbio/metadata/Preset.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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132 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>
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134 <DT><A HREF="../compbio/metadata/RunnerConfig.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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135 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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137 <DT><A HREF="../compbio/metadata/ValueConstrain.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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138 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>
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140 <DT><A HREF="../compbio/pipeline/_jpred/PScore.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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141 Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred">PScore</A>
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143 <DT><A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client"><B>Executable</B></A><<A HREF="../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>> - Interface in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>Interface to a native executable.<DT><A HREF="../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client"><B>Executable.ExecProvider</B></A> - Enum in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD> <DT><A HREF="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local"><B>ExecutableWrapper</B></A> - Class in <A HREF="../compbio/engine/local/package-summary.html">compbio.engine.local</A><DD> <DT><A HREF="../compbio/engine/local/ExecutableWrapper.html#ExecutableWrapper(compbio.engine.client.ConfiguredExecutable, java.lang.String)"><B>ExecutableWrapper(ConfiguredExecutable<?>, String)</B></A> -
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144 Constructor for class compbio.engine.local.<A HREF="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A>
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146 <DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#execute(java.lang.Runnable)"><B>execute(Runnable)</B></A> -
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147 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>
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149 <DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#executeJob()"><B>executeJob()</B></A> -
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150 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>
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152 <DT><A HREF="../compbio/engine/local/LocalRunner.html#executeJob()"><B>executeJob()</B></A> -
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153 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>
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155 <DT><A HREF="../compbio/engine/SyncExecutor.html#executeJob()"><B>executeJob()</B></A> -
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156 Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>
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157 <DD>Execute the job
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173 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
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