website/full_javadoc/index-files/index-5.html

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  82 <A NAME="_E_"><!-- --></A><H2>\r
  83 <B>E</B></H2>\r
  84 <DL>\r
  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>&nbsp;<DT><A HREF="../compbio/engine/client/EnvVariableProcessor.html#EnvVariableProcessor()"><B>EnvVariableProcessor()</B></A> - \r
  86 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</A>\r
  87 <DD>&nbsp;\r
  88 <DT><A HREF="../compbio/data/sequence/Alignment.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
  89 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
  90 <DD>Please note that this implementation does not take the order of sequences
  91  into account!\r
  92 <DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
  93 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
  94 <DD>&nbsp;\r
  95 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
  96 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
  97 <DD>&nbsp;\r
  98 <DT><A HREF="../compbio/data/sequence/Range.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
  99 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>\r
 100 <DD>&nbsp;\r
 101 <DT><A HREF="../compbio/data/sequence/Score.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 102 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
 103 <DD>&nbsp;\r
 104 <DT><A HREF="../compbio/data/sequence/ScoreManager.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 105 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
 106 <DD>&nbsp;\r
 107 <DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 108 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
 109 <DD>&nbsp;\r
 110 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 111 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 112 <DD>&nbsp;\r
 113 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 114 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 115 <DD>&nbsp;\r
 116 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 117 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 118 <DD>&nbsp;\r
 119 <DT><A HREF="../compbio/engine/ClusterJobId.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 120 Method in class compbio.engine.<A HREF="../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>\r
 121 <DD>&nbsp;\r
 122 <DT><A HREF="../compbio/engine/conf/_Key.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 123 Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A>\r
 124 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 125 <DT><A HREF="../compbio/engine/FilePuller.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 126 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
 127 <DD>&nbsp;\r
 128 <DT><A HREF="../compbio/engine/Job.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 129 Method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
 130 <DD>&nbsp;\r
 131 <DT><A HREF="../compbio/metadata/ChunkHolder.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 132 Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
 133 <DD>&nbsp;\r
 134 <DT><A HREF="../compbio/metadata/Limit.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 135 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
 136 <DD>&nbsp;\r
 137 <DT><A HREF="../compbio/metadata/Option.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 138 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 139 <DD>&nbsp;\r
 140 <DT><A HREF="../compbio/metadata/Parameter.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 141 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
 142 <DD>&nbsp;\r
 143 <DT><A HREF="../compbio/metadata/Preset.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 144 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
 145 <DD>&nbsp;\r
 146 <DT><A HREF="../compbio/metadata/RunnerConfig.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 147 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 148 <DD>&nbsp;\r
 149 <DT><A HREF="../compbio/metadata/ValueConstrain.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 150 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
 151 <DD>&nbsp;\r
 152 <DT><A HREF="../compbio/pipeline/_jpred/Hit.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 153 Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Hit.html" title="class in compbio.pipeline._jpred">Hit</A>\r
 154 <DD>&nbsp;\r
 155 <DT><A HREF="../compbio/pipeline/_jpred/PScore.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 156 Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred">PScore</A>\r
 157 <DD>&nbsp;\r
 158 <DT><A HREF="../compbio/stat/collector/JobStat.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 159 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
 160 <DD>&nbsp;\r
 161 <DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 162 Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</A>\r
 163 <DD>&nbsp;\r
 164 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#ERROR"><B>ERROR</B></A> - \r
 165 Static variable in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 166 <DD>&nbsp;\r
 167 <DT><A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client"><B>Executable</B></A>&lt;<A HREF="../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt; - 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>&nbsp;<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>&nbsp;<DT><A HREF="../compbio/engine/local/ExecutableWrapper.html#ExecutableWrapper(compbio.engine.client.ConfiguredExecutable, java.lang.String)"><B>ExecutableWrapper(ConfiguredExecutable&lt;?&gt;, String)</B></A> - \r
 168 Constructor for class compbio.engine.local.<A HREF="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A>\r
 169 <DD>&nbsp;\r
 170 <DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#executeJob()"><B>executeJob()</B></A> - \r
 171 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
 172 <DD>&nbsp;\r
 173 <DT><A HREF="../compbio/engine/local/LocalRunner.html#executeJob()"><B>executeJob()</B></A> - \r
 174 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
 175 <DD>&nbsp;\r
 176 <DT><A HREF="../compbio/engine/SyncExecutor.html#executeJob()"><B>executeJob()</B></A> - \r
 177 Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
 178 <DD>Execute the job\r
 179 <DT><A HREF="../compbio/stat/collector/ExecutionStatCollector.html" title="class in compbio.stat.collector"><B>ExecutionStatCollector</B></A> - Class in <A HREF="../compbio/stat/collector/package-summary.html">compbio.stat.collector</A><DD>Number of runs of each WS = number of folders with name
 180
 181  Number of successful runs = all runs with no result file
 182
 183  Per period of time = limit per file creating time Runtime (avg/max) =
 184
 185  started time - finished time
 186
 187  Task & result size = result.size
 188
 189  Abandoned runs - not collected runs
 190
 191  Cancelled runs - cancelled
 192
 193  Cluster vs local runs
 194
 195  Reasons for failure = look in the err out?
 196
 197
 198  Metadata required:
 199
 200  work directory for local and cluster tasks = from Helper or cmd parameter.<DT><A HREF="../compbio/stat/collector/ExecutionStatCollector.html#ExecutionStatCollector(java.lang.String, int)"><B>ExecutionStatCollector(String, int)</B></A> - \r
 201 Constructor for class compbio.stat.collector.<A HREF="../compbio/stat/collector/ExecutionStatCollector.html" title="class in compbio.stat.collector">ExecutionStatCollector</A>\r
 202 <DD>List subdirectories in the job directory\r
 203 </DL>\r
 204 <HR>\r
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