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40 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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41 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
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42 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
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43 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
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81 <A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>
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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/msa/Category.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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89 Method in class compbio.data.msa.<A HREF="../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</A>
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91 <DT><A HREF="../compbio/data/sequence/Alignment.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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92 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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93 <DD>Please note that this implementation does not take the order of sequences
95 <DT><A HREF="../compbio/data/sequence/AlignmentMetadata.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/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>
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98 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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99 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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101 <DT><A HREF="../compbio/data/sequence/Range.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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102 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>
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104 <DT><A HREF="../compbio/data/sequence/Score.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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105 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>
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107 <DT><A HREF="../compbio/data/sequence/ScoreManager.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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108 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>
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110 <DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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111 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>
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113 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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114 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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116 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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117 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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119 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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120 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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122 <DT><A HREF="../compbio/engine/ClusterJobId.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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123 Method in class compbio.engine.<A HREF="../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>
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125 <DT><A HREF="../compbio/engine/conf/_Key.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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126 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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127 <DD><B>Deprecated.</B>
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128 <DT><A HREF="../compbio/engine/FilePuller.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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129 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>
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131 <DT><A HREF="../compbio/engine/Job.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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132 Method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>
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134 <DT><A HREF="../compbio/metadata/ChunkHolder.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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135 Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>
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137 <DT><A HREF="../compbio/metadata/Limit.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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138 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>
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140 <DT><A HREF="../compbio/metadata/Option.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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141 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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143 <DT><A HREF="../compbio/metadata/Parameter.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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144 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
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146 <DT><A HREF="../compbio/metadata/Preset.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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147 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>
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149 <DT><A HREF="../compbio/metadata/RunnerConfig.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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150 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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152 <DT><A HREF="../compbio/metadata/ValueConstrain.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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153 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>
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155 <DT><A HREF="../compbio/pipeline/_jpred/Hit.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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156 Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Hit.html" title="class in compbio.pipeline._jpred">Hit</A>
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158 <DT><A HREF="../compbio/pipeline/_jpred/PScore.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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159 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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161 <DT><A HREF="../compbio/stat/collector/JobStat.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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162 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>
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164 <DT><A HREF="../compbio/stat/servlet/ServiceTestResult.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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165 Method in class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</A>
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167 <DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
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168 Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</A>
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170 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#ERROR"><B>ERROR</B></A> -
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171 Static variable in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>
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173 <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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174 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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176 <DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#executeJob()"><B>executeJob()</B></A> -
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177 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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179 <DT><A HREF="../compbio/engine/local/LocalRunner.html#executeJob()"><B>executeJob()</B></A> -
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180 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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182 <DT><A HREF="../compbio/engine/SyncExecutor.html#executeJob()"><B>executeJob()</B></A> -
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183 Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>
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184 <DD>Execute the job
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185 <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
187 Number of successful runs = all runs with no result file
189 Per period of time = limit per file creating time Runtime (avg/max) =
191 started time - finished time
193 Task & result size = result.size
195 Abandoned runs - not collected runs
197 Cancelled runs - cancelled
199 Cluster vs local runs
201 Reasons for failure = look in the err out?
206 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> -
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207 Constructor for class compbio.stat.collector.<A HREF="../compbio/stat/collector/ExecutionStatCollector.html" title="class in compbio.stat.collector">ExecutionStatCollector</A>
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208 <DD>List subdirectories in the job directory
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