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   6 <title>All Classes</title>
   7 <meta name="date" content="2017-04-21">
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  10 </head>
  11 <body>
  12 <h1 class="bar">All&nbsp;Classes</h1>
  13 <div class="indexContainer">
  14 <ul>
  15 <li><a href="compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a></li>
  16 <li><a href="compbio/ws/client/AAConClient.html" title="class in compbio.ws.client">AAConClient</a></li>
  17 <li><a href="compbio/ws/server/AAConWS.html" title="class in compbio.ws.server">AAConWS</a></li>
  18 <li><a href="compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws">Align</a></li>
  19 <li><a href="compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></li>
  20 <li><a href="compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</a></li>
  21 <li><a href="compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws">AlignResponse</a></li>
  22 <li><a href="compbio/data/msa/jaxws/Analize.html" title="class in compbio.data.msa.jaxws">Analize</a></li>
  23 <li><a href="compbio/data/msa/jaxws/AnalizeResponse.html" title="class in compbio.data.msa.jaxws">AnalizeResponse</a></li>
  24 <li><a href="compbio/stat/servlet/AnnualStat.html" title="class in compbio.stat.servlet">AnnualStat</a></li>
  25 <li><a href="compbio/metadata/Argument.html" title="interface in compbio.metadata"><span class="interfaceName">Argument</span></a></li>
  26 <li><a href="compbio/engine/cluster/drmaa/AsyncClusterRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncClusterRunner</a></li>
  27 <li><a href="compbio/engine/AsyncExecutor.html" title="interface in compbio.engine"><span class="interfaceName">AsyncExecutor</span></a></li>
  28 <li><a href="compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</a></li>
  29 <li><a href="compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</a></li>
  30 <li><a href="compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws">CancelJob</a></li>
  31 <li><a href="compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws">CancelJobResponse</a></li>
  32 <li><a href="compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</a></li>
  33 <li><a href="compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</a></li>
  34 <li><a href="compbio/engine/Cleaner.html" title="class in compbio.engine">Cleaner</a></li>
  35 <li><a href="compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</a></li>
  36 <li><a href="compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a></li>
  37 <li><a href="compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</a></li>
  38 <li><a href="compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</a></li>
  39 <li><a href="compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</a></li>
  40 <li><a href="compbio/engine/cluster/drmaa/ClusterEngineUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterEngineUtil</a></li>
  41 <li><a href="compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</a></li>
  42 <li><a href="compbio/engine/cluster/drmaa/ClusterRunner.html" title="class in compbio.engine.cluster.drmaa">ClusterRunner</a></li>
  43 <li><a href="compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</a></li>
  44 <li><a href="compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterUtil</a></li>
  45 <li><a href="compbio/ws/client/CmdHelper.html" title="class in compbio.ws.client">CmdHelper</a></li>
  46 <li><a href="compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></li>
  47 <li><a href="compbio/engine/client/CommandBuilder.Parameter.html" title="class in compbio.engine.client">CommandBuilder.Parameter</a></li>
  48 <li><a href="compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></li>
  49 <li><a href="compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></li>
  50 <li><a href="compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client"><span class="interfaceName">ConfiguredExecutable</span></a></li>
  51 <li><a href="compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence">ConservationMethod</a></li>
  52 <li><a href="compbio/ws/client/Constraints.html" title="class in compbio.ws.client">Constraints</a></li>
  53 <li><a href="compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</a></li>
  54 <li><a href="compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws">CustomAlignResponse</a></li>
  55 <li><a href="compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</a></li>
  56 <li><a href="compbio/data/msa/jaxws/CustomAnalizeResponse.html" title="class in compbio.data.msa.jaxws">CustomAnalizeResponse</a></li>
  57 <li><a href="compbio/data/msa/jaxws/CustomFold.html" title="class in compbio.data.msa.jaxws">CustomFold</a></li>
  58 <li><a href="compbio/data/msa/jaxws/CustomFoldResponse.html" title="class in compbio.data.msa.jaxws">CustomFoldResponse</a></li>
  59 <li><a href="compbio/stat/collector/DirCleaner.html" title="class in compbio.stat.collector">DirCleaner</a></li>
  60 <li><a href="compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</a></li>
  61 <li><a href="compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</a></li>
  62 <li><a href="compbio/data/sequence/DisemblResult.html" title="enum in compbio.data.sequence">DisemblResult</a></li>
  63 <li><a href="compbio/ws/server/DisemblWS.html" title="class in compbio.ws.server">DisemblWS</a></li>
  64 <li><a href="compbio/data/sequence/DisorderMethod.html" title="enum in compbio.data.sequence">DisorderMethod</a></li>
  65 <li><a href="compbio/stat/servlet/DisplayStat.html" title="class in compbio.stat.servlet">DisplayStat</a></li>
  66 <li><a href="compbio/stat/servlet/DownloadRedirector.html" title="class in compbio.stat.servlet">DownloadRedirector</a></li>
  67 <li><a href="compbio/engine/client/EngineUtil.html" title="class in compbio.engine.client">EngineUtil</a></li>
  68 <li><a href="compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</a></li>
  69 <li><a href="compbio/engine/client/Executable.html" title="interface in compbio.engine.client"><span class="interfaceName">Executable</span></a></li>
  70 <li><a href="compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</a></li>
  71 <li><a href="compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</a></li>
  72 <li><a href="compbio/stat/collector/ExecutionStatCollector.html" title="class in compbio.stat.collector">ExecutionStatCollector</a></li>
  73 <li><a href="compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</a></li>
  74 <li><a href="compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></li>
  75 <li><a href="compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></li>
  76 <li><a href="compbio/data/msa/jaxws/Fold.html" title="class in compbio.data.msa.jaxws">Fold</a></li>
  77 <li><a href="compbio/data/msa/jaxws/FoldResponse.html" title="class in compbio.data.msa.jaxws">FoldResponse</a></li>
  78 <li><a href="compbio/ws/server/GAUtils.html" title="class in compbio.ws.server">GAUtils</a></li>
  79 <li><a href="compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</a></li>
  80 <li><a href="compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws">GetAnnotation</a></li>
  81 <li><a href="compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws">GetAnnotationResponse</a></li>
  82 <li><a href="compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws">GetJobStatus</a></li>
  83 <li><a href="compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws">GetJobStatusResponse</a></li>
  84 <li><a href="compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws">GetLastTested</a></li>
  85 <li><a href="compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws">GetLastTestedOn</a></li>
  86 <li><a href="compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedOnResponse</a></li>
  87 <li><a href="compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedResponse</a></li>
  88 <li><a href="compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</a></li>
  89 <li><a href="compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws">GetLimitResponse</a></li>
  90 <li><a href="compbio/data/msa/jaxws/GetLimits.html" title="class in compbio.data.msa.jaxws">GetLimits</a></li>
  91 <li><a href="compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws">GetLimitsResponse</a></li>
  92 <li><a href="compbio/data/msa/jaxws/GetNonoperatedServices.html" title="class in compbio.data.msa.jaxws">GetNonoperatedServices</a></li>
  93 <li><a href="compbio/data/msa/jaxws/GetNonoperatedServicesResponse.html" title="class in compbio.data.msa.jaxws">GetNonoperatedServicesResponse</a></li>
  94 <li><a href="compbio/data/msa/jaxws/GetPresets.html" title="class in compbio.data.msa.jaxws">GetPresets</a></li>
  95 <li><a href="compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws">GetPresetsResponse</a></li>
  96 <li><a href="compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws">GetResult</a></li>
  97 <li><a href="compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws">GetResultResponse</a></li>
  98 <li><a href="compbio/data/msa/jaxws/GetRunnerOptions.html" title="class in compbio.data.msa.jaxws">GetRunnerOptions</a></li>
  99 <li><a href="compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws">GetRunnerOptionsResponse</a></li>
 100 <li><a href="compbio/data/msa/jaxws/GetServiceCategories.html" title="class in compbio.data.msa.jaxws">GetServiceCategories</a></li>
 101 <li><a href="compbio/data/msa/jaxws/GetServiceCategoriesResponse.html" title="class in compbio.data.msa.jaxws">GetServiceCategoriesResponse</a></li>
 102 <li><a href="compbio/data/msa/jaxws/GetServiceDescription.html" title="class in compbio.data.msa.jaxws">GetServiceDescription</a></li>
 103 <li><a href="compbio/data/msa/jaxws/GetServiceDescriptionResponse.html" title="class in compbio.data.msa.jaxws">GetServiceDescriptionResponse</a></li>
 104 <li><a href="compbio/data/msa/jaxws/GetSupportedServices.html" title="class in compbio.data.msa.jaxws">GetSupportedServices</a></li>
 105 <li><a href="compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws">GetSupportedServicesResponse</a></li>
 106 <li><a href="compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</a></li>
 107 <li><a href="compbio/ws/server/GlobPlotWS.html" title="class in compbio.ws.server">GlobPlotWS</a></li>
 108 <li><a href="compbio/data/sequence/GlobProtResult.html" title="enum in compbio.data.sequence">GlobProtResult</a></li>
 109 <li><a href="compbio/runner/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a></li>
 110 <li><a href="compbio/ws/server/GLprobsWS.html" title="class in compbio.ws.server">GLprobsWS</a></li>
 111 <li><a href="compbio/stat/servlet/HttpCodeResponseServiceStatus.html" title="class in compbio.stat.servlet">HttpCodeResponseServiceStatus</a></li>
 112 <li><a href="compbio/stat/collector/InputFilter.html" title="class in compbio.stat.collector">InputFilter</a></li>
 113 <li><a href="compbio/ws/client/IOHelper.html" title="class in compbio.ws.client">IOHelper</a></li>
 114 <li><a href="compbio/data/msa/jaxws/IsOperating.html" title="class in compbio.data.msa.jaxws">IsOperating</a></li>
 115 <li><a href="compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws">IsOperatingResponse</a></li>
 116 <li><a href="compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</a></li>
 117 <li><a href="compbio/data/sequence/IUPredResult.html" title="enum in compbio.data.sequence">IUPredResult</a></li>
 118 <li><a href="compbio/ws/server/IUPredWS.html" title="class in compbio.ws.server">IUPredWS</a></li>
 119 <li><a href="compbio/data/msa/JABAService.html" title="interface in compbio.data.msa"><span class="interfaceName">JABAService</span></a></li>
 120 <li><a href="compbio/data/msa/JManagement.html" title="interface in compbio.data.msa"><span class="interfaceName">JManagement</span></a></li>
 121 <li><a href="compbio/engine/Job.html" title="class in compbio.engine">Job</a></li>
 122 <li><a href="compbio/stat/collector/JobDirectory.html" title="class in compbio.stat.collector">JobDirectory</a></li>
 123 <li><a href="compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</a></li>
 124 <li><a href="compbio/stat/servlet/Joblist.html" title="class in compbio.stat.servlet">Joblist</a></li>
 125 <li><a href="compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</a></li>
 126 <li><a href="compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></li>
 127 <li><a href="compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</a></li>
 128 <li><a href="compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></li>
 129 <li><a href="compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobSubmissionExceptionBean</a></li>
 130 <li><a href="compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</a></li>
 131 <li><a href="compbio/ws/server/JronnWS.html" title="class in compbio.ws.server">JronnWS</a></li>
 132 <li><a href="compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</a></li>
 133 <li><a href="compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a></li>
 134 <li><a href="compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></li>
 135 <li><a href="compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</a></li>
 136 <li><a href="compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a></li>
 137 <li><a href="compbio/engine/LoadBalancer.html" title="class in compbio.engine">LoadBalancer</a></li>
 138 <li><a href="compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</a></li>
 139 <li><a href="compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</a></li>
 140 <li><a href="compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</a></li>
 141 <li><a href="compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a></li>
 142 <li><a href="compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</a></li>
 143 <li><a href="compbio/ws/server/MainManager.html" title="class in compbio.ws.server">MainManager</a></li>
 144 <li><a href="compbio/data/msa/Metadata.html" title="interface in compbio.data.msa"><span class="interfaceName">Metadata</span></a></li>
 145 <li><a href="compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client">MetadataHelper</a></li>
 146 <li><a href="compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a></li>
 147 <li><a href="compbio/ws/server/MSAprobsWS.html" title="class in compbio.ws.server">MSAprobsWS</a></li>
 148 <li><a href="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><span class="interfaceName">MsaWS</span></a></li>
 149 <li><a href="compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</a></li>
 150 <li><a href="compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</a></li>
 151 <li><a href="compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></li>
 152 <li><a href="compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></li>
 153 <li><a href="compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</a></li>
 154 <li><a href="compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</a></li>
 155 <li><a href="compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client"><span class="interfaceName">PipedExecutable</span></a></li>
 156 <li><a href="compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a></li>
 157 <li><a href="compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</a></li>
 158 <li><a href="compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws">PresetAlignResponse</a></li>
 159 <li><a href="compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</a></li>
 160 <li><a href="compbio/data/msa/jaxws/PresetAnalizeResponse.html" title="class in compbio.data.msa.jaxws">PresetAnalizeResponse</a></li>
 161 <li><a href="compbio/data/msa/jaxws/PresetFold.html" title="class in compbio.data.msa.jaxws">PresetFold</a></li>
 162 <li><a href="compbio/data/msa/jaxws/PresetFoldResponse.html" title="class in compbio.data.msa.jaxws">PresetFoldResponse</a></li>
 163 <li><a href="compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a></li>
 164 <li><a href="compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</a></li>
 165 <li><a href="compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</a></li>
 166 <li><a href="compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</a></li>
 167 <li><a href="compbio/engine/ProgressGetter.html" title="class in compbio.engine">ProgressGetter</a></li>
 168 <li><a href="compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</a></li>
 169 <li><a href="compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</a></li>
 170 <li><a href="compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</a></li>
 171 <li><a href="compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws">PullExecStatisticsResponse</a></li>
 172 <li><a href="compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a></li>
 173 <li><a href="compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa"><span class="interfaceName">RegistryWS</span></a></li>
 174 <li><a href="compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</a></li>
 175 <li><a href="compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</a></li>
 176 <li><a href="compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws">ResultNotAvailableExceptionBean</a></li>
 177 <li><a href="compbio/runner/structure/RNAalifold.html" title="class in compbio.runner.structure">RNAalifold</a></li>
 178 <li><a href="compbio/ws/server/RNAalifoldWS.html" title="class in compbio.ws.server">RNAalifoldWS</a></li>
 179 <li><a href="compbio/data/sequence/RNAStructReader.html" title="class in compbio.data.sequence">RNAStructReader</a></li>
 180 <li><a href="compbio/data/sequence/RNAStructReader.AlifoldLine.html" title="enum in compbio.data.sequence">RNAStructReader.AlifoldLine</a></li>
 181 <li><a href="compbio/data/sequence/RNAStructReader.AlifoldResult.html" title="enum in compbio.data.sequence">RNAStructReader.AlifoldResult</a></li>
 182 <li><a href="compbio/data/sequence/RNAStructReader.RNAOut.html" title="enum in compbio.data.sequence">RNAStructReader.RNAOut</a></li>
 183 <li><a href="compbio/data/sequence/RNAStructScoreManager.html" title="class in compbio.data.sequence">RNAStructScoreManager</a></li>
 184 <li><a href="compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</a></li>
 185 <li><a href="compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></li>
 186 <li><a href="compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</a></li>
 187 <li><a href="compbio/engine/conf/RunnerConfigMarshaller.MySchemaOutputResolver.html" title="class in compbio.engine.conf">RunnerConfigMarshaller.MySchemaOutputResolver</a></li>
 188 <li><a href="compbio/runner/RunnerUtil.html" title="class in compbio.runner">RunnerUtil</a></li>
 189 <li><a href="compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a></li>
 190 <li><a href="compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></li>
 191 <li><a href="compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</a></li>
 192 <li><a href="compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa"><span class="interfaceName">SequenceAnnotation</span></a></li>
 193 <li><a href="compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</a></li>
 194 <li><a href="compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></li>
 195 <li><a href="compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></li>
 196 <li><a href="compbio/ws/client/Services.ServiceInfo.html" title="class in compbio.ws.client">Services.ServiceInfo</a></li>
 197 <li><a href="compbio/stat/servlet/ServiceStatus.html" title="class in compbio.stat.servlet">ServiceStatus</a></li>
 198 <li><a href="compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</a></li>
 199 <li><a href="compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</a></li>
 200 <li><a href="compbio/ws/server/SetExecutableFlag.html" title="class in compbio.ws.server">SetExecutableFlag</a></li>
 201 <li><a href="compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server">SimpleWSPublisher</a></li>
 202 <li><a href="compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></li>
 203 <li><a href="compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</a></li>
 204 <li><a href="compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</a></li>
 205 <li><a href="compbio/stat/servlet/util/StatCollection.Stattype.html" title="enum in compbio.stat.servlet.util">StatCollection.Stattype</a></li>
 206 <li><a href="compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</a></li>
 207 <li><a href="compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</a></li>
 208 <li><a href="compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></li>
 209 <li><a href="compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</a></li>
 210 <li><a href="compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local">StreamGobbler</a></li>
 211 <li><a href="compbio/engine/local/StreamGobbler.OutputType.html" title="enum in compbio.engine.local">StreamGobbler.OutputType</a></li>
 212 <li><a href="compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</a></li>
 213 <li><a href="compbio/engine/SyncExecutor.html" title="interface in compbio.engine"><span class="interfaceName">SyncExecutor</span></a></li>
 214 <li><a href="compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</a></li>
 215 <li><a href="compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</a></li>
 216 <li><a href="compbio/data/msa/jaxws/TestAllServices.html" title="class in compbio.data.msa.jaxws">TestAllServices</a></li>
 217 <li><a href="compbio/data/msa/jaxws/TestAllServicesResponse.html" title="class in compbio.data.msa.jaxws">TestAllServicesResponse</a></li>
 218 <li><a href="compbio/data/msa/jaxws/TestService.html" title="class in compbio.data.msa.jaxws">TestService</a></li>
 219 <li><a href="compbio/data/msa/jaxws/TestServiceResponse.html" title="class in compbio.data.msa.jaxws">TestServiceResponse</a></li>
 220 <li><a href="compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</a></li>
 221 <li><a href="compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></li>
 222 <li><a href="compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</a></li>
 223 <li><a href="compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html" title="class in compbio.data.msa.jaxws">UnsupportedRuntimeExceptionBean</a></li>
 224 <li><a href="compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</a></li>
 225 <li><a href="compbio/runner/Util.html" title="class in compbio.runner">Util</a></li>
 226 <li><a href="compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</a></li>
 227 <li><a href="compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</a></li>
 228 <li><a href="compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</a></li>
 229 <li><a href="compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws">WrongParameterExceptionBean</a></li>
 230 <li><a href="compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</a></li>
 231 <li><a href="compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</a></li>
 232 </ul>
 233 </div>
 234 </body>
 235 </html>