1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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5 <!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:51 GMT 2010 -->
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10 <META NAME="date" CONTENT="2010-02-17">
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12 <LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">
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17 <BODY BGCOLOR="white">
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18 <FONT size="+1" CLASS="FrameHeadingFont">
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19 <B>All Classes</B></FONT>
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22 <TABLE BORDER="0" WIDTH="100%" SUMMARY="">
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24 <TD NOWRAP><FONT CLASS="FrameItemFont"><A HREF="compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws" target="classFrame">Align</A>
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26 <A HREF="compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence" target="classFrame">Alignment</A>
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28 <A HREF="compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence" target="classFrame">AlignmentMetadata</A>
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30 <A HREF="compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">AlignResponse</A>
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32 <A HREF="compbio/metadata/Argument.html" title="interface in compbio.metadata" target="classFrame"><I>Argument</I></A>
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34 <A HREF="compbio/engine/AsyncExecutor.html" title="interface in compbio.engine" target="classFrame"><I>AsyncExecutor</I></A>
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36 <A HREF="compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa" target="classFrame">AsyncJobRunner</A>
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38 <A HREF="compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local" target="classFrame">AsyncLocalRunner</A>
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40 <A HREF="compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl" target="classFrame">BlastAll</A>
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42 <A HREF="compbio/runner/_impl/BlastParameters.html" title="class in compbio.runner._impl" target="classFrame">BlastParameters</A>
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44 <A HREF="compbio/pipeline/_jpred/BlastParser.html" title="class in compbio.pipeline._jpred" target="classFrame">BlastParser</A>
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46 <A HREF="compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws" target="classFrame">CancelJob</A>
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48 <A HREF="compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">CancelJobResponse</A>
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50 <A HREF="compbio/metadata/ChunkHolder.html" title="class in compbio.metadata" target="classFrame">ChunkHolder</A>
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52 <A HREF="compbio/engine/Cleaner.html" title="class in compbio.engine" target="classFrame">Cleaner</A>
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54 <A HREF="compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence" target="classFrame">ClustalAlignmentUtil</A>
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56 <A HREF="compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa" target="classFrame">ClustalW</A>
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58 <A HREF="compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server" target="classFrame">ClustalWS</A>
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60 <A HREF="compbio/engine/ClusterJobId.html" title="class in compbio.engine" target="classFrame">ClusterJobId</A>
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62 <A HREF="compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client" target="classFrame"><I>ClusterNativeSpecExecutable</I></A>
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64 <A HREF="compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa" target="classFrame">ClusterSession</A>
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66 <A HREF="compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa" target="classFrame">ClusterUtil</A>
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68 <A HREF="compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client" target="classFrame">CommandBuilder</A>
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70 <A HREF="compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client" target="classFrame">ConfExecutable</A>
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72 <A HREF="compbio/engine/Configurator.html" title="class in compbio.engine" target="classFrame">Configurator</A>
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74 <A HREF="compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client" target="classFrame"><I>ConfiguredExecutable</I></A>
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76 <A HREF="compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws" target="classFrame">CustomAlign</A>
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78 <A HREF="compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">CustomAlignResponse</A>
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80 <A HREF="compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf" target="classFrame">DirectoryManager</A>
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82 <A HREF="compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl" target="classFrame">Disembl</A>
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84 <A HREF="compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl" target="classFrame">Environment</A>
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86 <A HREF="compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client" target="classFrame">EnvVariableProcessor</A>
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88 <A HREF="compbio/engine/client/Executable.html" title="interface in compbio.engine.client" target="classFrame"><I>Executable</I></A>
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90 <A HREF="compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client" target="classFrame">Executable.ExecProvider</A>
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92 <A HREF="compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local" target="classFrame">ExecutableWrapper</A>
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94 <A HREF="compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence" target="classFrame">FastaSequence</A>
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96 <A HREF="compbio/engine/FilePuller.html" title="class in compbio.engine" target="classFrame">FilePuller</A>
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98 <A HREF="compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetJobStatus</A>
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100 <A HREF="compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetJobStatusResponse</A>
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102 <A HREF="compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetLimit</A>
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104 <A HREF="compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetLimitResponse</A>
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106 <A HREF="compbio/data/msa/jaxws/GetLimits.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetLimits</A>
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108 <A HREF="compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetLimitsResponse</A>
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110 <A HREF="compbio/data/msa/jaxws/GetPresets.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetPresets</A>
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112 <A HREF="compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetPresetsResponse</A>
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114 <A HREF="compbio/data/msa/jaxws/GetProgress.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetProgress</A>
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116 <A HREF="compbio/data/msa/jaxws/GetProgressResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetProgressResponse</A>
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118 <A HREF="compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetResult</A>
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120 <A HREF="compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetResultResponse</A>
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122 <A HREF="compbio/data/msa/jaxws/GetRunnerOptions.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetRunnerOptions</A>
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124 <A HREF="compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetRunnerOptionsResponse</A>
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126 <A HREF="compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure" target="classFrame">JnetAnnotation</A>
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128 <A HREF="compbio/engine/Job.html" title="class in compbio.engine" target="classFrame">Job</A>
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130 <A HREF="compbio/metadata/JobExecutionException.html" title="class in compbio.metadata" target="classFrame">JobExecutionException</A>
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132 <A HREF="compbio/data/msa/jaxws/JobExecutionExceptionBean.html" title="class in compbio.data.msa.jaxws" target="classFrame">JobExecutionExceptionBean</A>
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134 <A HREF="compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa" target="classFrame">JobRunner</A>
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136 <A HREF="compbio/metadata/JobStatus.html" title="enum in compbio.metadata" target="classFrame">JobStatus</A>
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138 <A HREF="compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata" target="classFrame">JobSubmissionException</A>
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140 <A HREF="compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws" target="classFrame">JobSubmissionExceptionBean</A>
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142 <A HREF="compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred" target="classFrame">Jpred4</A>
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144 <A HREF="compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure" target="classFrame">JpredAnnotation</A>
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146 <A HREF="compbio/data/_structure/JpredResult.html" title="class in compbio.data._structure" target="classFrame">JpredResult</A>
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148 <A HREF="compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client" target="classFrame">Jws2Client</A>
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150 <A HREF="compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client" target="classFrame">Jws2Client.Services</A>
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152 <A HREF="compbio/metadata/Limit.html" title="class in compbio.metadata" target="classFrame">Limit</A>
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154 <A HREF="compbio/metadata/LimitExceededException.html" title="class in compbio.metadata" target="classFrame">LimitExceededException</A>
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156 <A HREF="compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws" target="classFrame">LimitExceededExceptionBean</A>
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158 <A HREF="compbio/metadata/LimitsManager.html" title="class in compbio.metadata" target="classFrame">LimitsManager</A>
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160 <A HREF="compbio/engine/LoadBalancer.html" title="class in compbio.engine" target="classFrame">LoadBalancer</A>
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162 <A HREF="compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local" target="classFrame">LocalEngineUtil</A>
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164 <A HREF="compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local" target="classFrame">LocalExecutorService</A>
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166 <A HREF="compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local" target="classFrame">LocalRunner</A>
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168 <A HREF="compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa" target="classFrame">Mafft</A>
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170 <A HREF="compbio/ws/server/MafftWS.html" title="class in compbio.ws.server" target="classFrame">MafftWS</A>
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172 <A HREF="compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl" target="classFrame">Mcl</A>
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174 <A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa" target="classFrame"><I>MsaWS</I></A>
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176 <A HREF="compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa" target="classFrame">Muscle</A>
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178 <A HREF="compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server" target="classFrame">MuscleWS</A>
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180 <A HREF="compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl" target="classFrame">NetNglyc</A>
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182 <A HREF="compbio/runner/_impl/OB.html" title="class in compbio.runner._impl" target="classFrame">OB</A>
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184 <A HREF="compbio/metadata/Option.html" title="class in compbio.metadata" target="classFrame">Option</A>
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186 <A HREF="compbio/runner/OptionCombinator.html" title="class in compbio.runner" target="classFrame">OptionCombinator</A>
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188 <A HREF="compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred" target="classFrame">Pairwise</A>
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190 <A HREF="compbio/metadata/Parameter.html" title="class in compbio.metadata" target="classFrame">Parameter</A>
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192 <A HREF="compbio/engine/client/PathValidator.html" title="class in compbio.engine.client" target="classFrame">PathValidator</A>
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194 <A HREF="compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client" target="classFrame"><I>PipedExecutable</I></A>
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196 <A HREF="compbio/metadata/Preset.html" title="class in compbio.metadata" target="classFrame">Preset</A>
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198 <A HREF="compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws" target="classFrame">PresetAlign</A>
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200 <A HREF="compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">PresetAlignResponse</A>
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202 <A HREF="compbio/metadata/PresetManager.html" title="class in compbio.metadata" target="classFrame">PresetManager</A>
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204 <A HREF="compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa" target="classFrame">Probcons</A>
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206 <A HREF="compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server" target="classFrame">ProbconsWS</A>
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208 <A HREF="compbio/data/sequence/Program.html" title="enum in compbio.data.sequence" target="classFrame">Program</A>
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210 <A HREF="compbio/engine/ProgressGetter.html" title="class in compbio.engine" target="classFrame">ProgressGetter</A>
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212 <A HREF="compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf" target="classFrame">PropertyHelperManager</A>
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214 <A HREF="compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred" target="classFrame">PScore</A>
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216 <A HREF="compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl" target="classFrame">PSIBlast</A>
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218 <A HREF="compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast" target="classFrame">PsiBlast</A>
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220 <A HREF="compbio/engine/PulledFileCache.html" title="class in compbio.engine" target="classFrame">PulledFileCache</A>
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222 <A HREF="compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws" target="classFrame">PullExecStatistics</A>
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224 <A HREF="compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">PullExecStatisticsResponse</A>
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226 <A HREF="compbio/data/msa/jaxws/PullFile.html" title="class in compbio.data.msa.jaxws" target="classFrame">PullFile</A>
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228 <A HREF="compbio/data/msa/jaxws/PullFileResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">PullFileResponse</A>
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230 <A HREF="compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata" target="classFrame">ResultNotAvailableException</A>
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232 <A HREF="compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws" target="classFrame">ResultNotAvailableExceptionBean</A>
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234 <A HREF="compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl" target="classFrame">Ronn</A>
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236 <A HREF="compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl" target="classFrame">RPSBlast</A>
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238 <A HREF="compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client" target="classFrame">RunConfiguration</A>
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240 <A HREF="compbio/metadata/RunnerConfig.html" title="class in compbio.metadata" target="classFrame">RunnerConfig</A>
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242 <A HREF="compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf" target="classFrame">RunnerConfigMarshaller</A>
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244 <A HREF="compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl" target="classFrame">Runners</A>
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246 <A HREF="compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence" target="classFrame">SequenceUtil</A>
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248 <A HREF="compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server" target="classFrame">SimpleWSPublisher</A>
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250 <A HREF="compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client" target="classFrame">SkeletalExecutable</A>
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252 <A HREF="compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa" target="classFrame">StatisticManager</A>
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254 <A HREF="compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local" target="classFrame">StreamGobbler</A>
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256 <A HREF="compbio/engine/SubmissionManager.html" title="class in compbio.engine" target="classFrame">SubmissionManager</A>
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258 <A HREF="compbio/engine/SyncExecutor.html" title="interface in compbio.engine" target="classFrame"><I>SyncExecutor</I></A>
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260 <A HREF="compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa" target="classFrame">Tcoffee</A>
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262 <A HREF="compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server" target="classFrame">TcoffeeWS</A>
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264 <A HREF="compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence" target="classFrame">UnknownFileFormatException</A>
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266 <A HREF="compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata" target="classFrame">UnsupportedRuntimeException</A>
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268 <A HREF="compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html" title="class in compbio.data.msa.jaxws" target="classFrame">UnsupportedRuntimeExceptionBean</A>
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270 <A HREF="compbio/engine/client/Util.html" title="class in compbio.engine.client" target="classFrame">Util</A>
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272 <A HREF="compbio/runner/Util.html" title="class in compbio.runner" target="classFrame">Util</A>
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274 <A HREF="compbio/metadata/ValueConstrain.html" title="class in compbio.metadata" target="classFrame">ValueConstrain</A>
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276 <A HREF="compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata" target="classFrame">ValueConstrain.Type</A>
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278 <A HREF="compbio/metadata/WrongParameterException.html" title="class in compbio.metadata" target="classFrame">WrongParameterException</A>
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280 <A HREF="compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws" target="classFrame">WrongParameterExceptionBean</A>
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282 <A HREF="compbio/ws/client/WSTester.html" title="class in compbio.ws.client" target="classFrame">WSTester</A>
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284 <A HREF="compbio/ws/server/WSUtil.html" title="class in compbio.ws.server" target="classFrame">WSUtil</A>
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286 <A HREF="compbio/engine/cluster/drmaa/_DrmaaExample.html" title="class in compbio.engine.cluster.drmaa" target="classFrame">_DrmaaExample</A>
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288 <A HREF="compbio/engine/cluster/drmaa/_JobStatus.html" title="class in compbio.engine.cluster.drmaa" target="classFrame">_JobStatus</A>
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290 <A HREF="compbio/runner/_jpred/_Jpred.html" title="class in compbio.runner._jpred" target="classFrame">_Jpred</A>
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292 <A HREF="compbio/engine/conf/_Key.html" title="class in compbio.engine.conf" target="classFrame">_Key</A>
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294 <A HREF="compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner" target="classFrame">_NativeSpecHelper</A>
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296 <A HREF="compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee" target="classFrame">_Queue</A>
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298 <A HREF="compbio/engine/cluster/dundee/_QueueConstraints.html" title="class in compbio.engine.cluster.dundee" target="classFrame">_QueueConstraints</A>
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300 <A HREF="compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner" target="classFrame">_SkeletalCommandBuilder</A>
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302 <A HREF="compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local" target="classFrame">_TrackingExecutor</A>
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