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