website/full_javadoc/allclasses-frame.html

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   5 <!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:51 GMT 2010 -->\r
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  10 <META NAME="date" CONTENT="2010-02-17">\r
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  18 <FONT size="+1" CLASS="FrameHeadingFont">\r
  19 <B>All Classes</B></FONT>\r
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  21 \r
  22 <TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
  23 <TR>\r
  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>\r
  25 <BR>\r
  26 <A HREF="compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence" target="classFrame">Alignment</A>\r
  27 <BR>\r
  28 <A HREF="compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence" target="classFrame">AlignmentMetadata</A>\r
  29 <BR>\r
  30 <A HREF="compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">AlignResponse</A>\r
  31 <BR>\r
  32 <A HREF="compbio/metadata/Argument.html" title="interface in compbio.metadata" target="classFrame"><I>Argument</I></A>\r
  33 <BR>\r
  34 <A HREF="compbio/engine/AsyncExecutor.html" title="interface in compbio.engine" target="classFrame"><I>AsyncExecutor</I></A>\r
  35 <BR>\r
  36 <A HREF="compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa" target="classFrame">AsyncJobRunner</A>\r
  37 <BR>\r
  38 <A HREF="compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local" target="classFrame">AsyncLocalRunner</A>\r
  39 <BR>\r
  40 <A HREF="compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl" target="classFrame">BlastAll</A>\r
  41 <BR>\r
  42 <A HREF="compbio/runner/_impl/BlastParameters.html" title="class in compbio.runner._impl" target="classFrame">BlastParameters</A>\r
  43 <BR>\r
  44 <A HREF="compbio/pipeline/_jpred/BlastParser.html" title="class in compbio.pipeline._jpred" target="classFrame">BlastParser</A>\r
  45 <BR>\r
  46 <A HREF="compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws" target="classFrame">CancelJob</A>\r
  47 <BR>\r
  48 <A HREF="compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">CancelJobResponse</A>\r
  49 <BR>\r
  50 <A HREF="compbio/metadata/ChunkHolder.html" title="class in compbio.metadata" target="classFrame">ChunkHolder</A>\r
  51 <BR>\r
  52 <A HREF="compbio/engine/Cleaner.html" title="class in compbio.engine" target="classFrame">Cleaner</A>\r
  53 <BR>\r
  54 <A HREF="compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence" target="classFrame">ClustalAlignmentUtil</A>\r
  55 <BR>\r
  56 <A HREF="compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa" target="classFrame">ClustalW</A>\r
  57 <BR>\r
  58 <A HREF="compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server" target="classFrame">ClustalWS</A>\r
  59 <BR>\r
  60 <A HREF="compbio/engine/ClusterJobId.html" title="class in compbio.engine" target="classFrame">ClusterJobId</A>\r
  61 <BR>\r
  62 <A HREF="compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client" target="classFrame"><I>ClusterNativeSpecExecutable</I></A>\r
  63 <BR>\r
  64 <A HREF="compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa" target="classFrame">ClusterSession</A>\r
  65 <BR>\r
  66 <A HREF="compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa" target="classFrame">ClusterUtil</A>\r
  67 <BR>\r
  68 <A HREF="compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client" target="classFrame">CommandBuilder</A>\r
  69 <BR>\r
  70 <A HREF="compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client" target="classFrame">ConfExecutable</A>\r
  71 <BR>\r
  72 <A HREF="compbio/engine/Configurator.html" title="class in compbio.engine" target="classFrame">Configurator</A>\r
  73 <BR>\r
  74 <A HREF="compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client" target="classFrame"><I>ConfiguredExecutable</I></A>\r
  75 <BR>\r
  76 <A HREF="compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws" target="classFrame">CustomAlign</A>\r
  77 <BR>\r
  78 <A HREF="compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">CustomAlignResponse</A>\r
  79 <BR>\r
  80 <A HREF="compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf" target="classFrame">DirectoryManager</A>\r
  81 <BR>\r
  82 <A HREF="compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl" target="classFrame">Disembl</A>\r
  83 <BR>\r
  84 <A HREF="compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl" target="classFrame">Environment</A>\r
  85 <BR>\r
  86 <A HREF="compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client" target="classFrame">EnvVariableProcessor</A>\r
  87 <BR>\r
  88 <A HREF="compbio/engine/client/Executable.html" title="interface in compbio.engine.client" target="classFrame"><I>Executable</I></A>\r
  89 <BR>\r
  90 <A HREF="compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client" target="classFrame">Executable.ExecProvider</A>\r
  91 <BR>\r
  92 <A HREF="compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local" target="classFrame">ExecutableWrapper</A>\r
  93 <BR>\r
  94 <A HREF="compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence" target="classFrame">FastaSequence</A>\r
  95 <BR>\r
  96 <A HREF="compbio/engine/FilePuller.html" title="class in compbio.engine" target="classFrame">FilePuller</A>\r
  97 <BR>\r
  98 <A HREF="compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetJobStatus</A>\r
  99 <BR>\r
 100 <A HREF="compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetJobStatusResponse</A>\r
 101 <BR>\r
 102 <A HREF="compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetLimit</A>\r
 103 <BR>\r
 104 <A HREF="compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetLimitResponse</A>\r
 105 <BR>\r
 106 <A HREF="compbio/data/msa/jaxws/GetLimits.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetLimits</A>\r
 107 <BR>\r
 108 <A HREF="compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetLimitsResponse</A>\r
 109 <BR>\r
 110 <A HREF="compbio/data/msa/jaxws/GetPresets.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetPresets</A>\r
 111 <BR>\r
 112 <A HREF="compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetPresetsResponse</A>\r
 113 <BR>\r
 114 <A HREF="compbio/data/msa/jaxws/GetProgress.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetProgress</A>\r
 115 <BR>\r
 116 <A HREF="compbio/data/msa/jaxws/GetProgressResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetProgressResponse</A>\r
 117 <BR>\r
 118 <A HREF="compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetResult</A>\r
 119 <BR>\r
 120 <A HREF="compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetResultResponse</A>\r
 121 <BR>\r
 122 <A HREF="compbio/data/msa/jaxws/GetRunnerOptions.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetRunnerOptions</A>\r
 123 <BR>\r
 124 <A HREF="compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">GetRunnerOptionsResponse</A>\r
 125 <BR>\r
 126 <A HREF="compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure" target="classFrame">JnetAnnotation</A>\r
 127 <BR>\r
 128 <A HREF="compbio/engine/Job.html" title="class in compbio.engine" target="classFrame">Job</A>\r
 129 <BR>\r
 130 <A HREF="compbio/metadata/JobExecutionException.html" title="class in compbio.metadata" target="classFrame">JobExecutionException</A>\r
 131 <BR>\r
 132 <A HREF="compbio/data/msa/jaxws/JobExecutionExceptionBean.html" title="class in compbio.data.msa.jaxws" target="classFrame">JobExecutionExceptionBean</A>\r
 133 <BR>\r
 134 <A HREF="compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa" target="classFrame">JobRunner</A>\r
 135 <BR>\r
 136 <A HREF="compbio/metadata/JobStatus.html" title="enum in compbio.metadata" target="classFrame">JobStatus</A>\r
 137 <BR>\r
 138 <A HREF="compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata" target="classFrame">JobSubmissionException</A>\r
 139 <BR>\r
 140 <A HREF="compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws" target="classFrame">JobSubmissionExceptionBean</A>\r
 141 <BR>\r
 142 <A HREF="compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred" target="classFrame">Jpred4</A>\r
 143 <BR>\r
 144 <A HREF="compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure" target="classFrame">JpredAnnotation</A>\r
 145 <BR>\r
 146 <A HREF="compbio/data/_structure/JpredResult.html" title="class in compbio.data._structure" target="classFrame">JpredResult</A>\r
 147 <BR>\r
 148 <A HREF="compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client" target="classFrame">Jws2Client</A>\r
 149 <BR>\r
 150 <A HREF="compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client" target="classFrame">Jws2Client.Services</A>\r
 151 <BR>\r
 152 <A HREF="compbio/metadata/Limit.html" title="class in compbio.metadata" target="classFrame">Limit</A>\r
 153 <BR>\r
 154 <A HREF="compbio/metadata/LimitExceededException.html" title="class in compbio.metadata" target="classFrame">LimitExceededException</A>\r
 155 <BR>\r
 156 <A HREF="compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws" target="classFrame">LimitExceededExceptionBean</A>\r
 157 <BR>\r
 158 <A HREF="compbio/metadata/LimitsManager.html" title="class in compbio.metadata" target="classFrame">LimitsManager</A>\r
 159 <BR>\r
 160 <A HREF="compbio/engine/LoadBalancer.html" title="class in compbio.engine" target="classFrame">LoadBalancer</A>\r
 161 <BR>\r
 162 <A HREF="compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local" target="classFrame">LocalEngineUtil</A>\r
 163 <BR>\r
 164 <A HREF="compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local" target="classFrame">LocalExecutorService</A>\r
 165 <BR>\r
 166 <A HREF="compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local" target="classFrame">LocalRunner</A>\r
 167 <BR>\r
 168 <A HREF="compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa" target="classFrame">Mafft</A>\r
 169 <BR>\r
 170 <A HREF="compbio/ws/server/MafftWS.html" title="class in compbio.ws.server" target="classFrame">MafftWS</A>\r
 171 <BR>\r
 172 <A HREF="compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl" target="classFrame">Mcl</A>\r
 173 <BR>\r
 174 <A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa" target="classFrame"><I>MsaWS</I></A>\r
 175 <BR>\r
 176 <A HREF="compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa" target="classFrame">Muscle</A>\r
 177 <BR>\r
 178 <A HREF="compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server" target="classFrame">MuscleWS</A>\r
 179 <BR>\r
 180 <A HREF="compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl" target="classFrame">NetNglyc</A>\r
 181 <BR>\r
 182 <A HREF="compbio/runner/_impl/OB.html" title="class in compbio.runner._impl" target="classFrame">OB</A>\r
 183 <BR>\r
 184 <A HREF="compbio/metadata/Option.html" title="class in compbio.metadata" target="classFrame">Option</A>\r
 185 <BR>\r
 186 <A HREF="compbio/runner/OptionCombinator.html" title="class in compbio.runner" target="classFrame">OptionCombinator</A>\r
 187 <BR>\r
 188 <A HREF="compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred" target="classFrame">Pairwise</A>\r
 189 <BR>\r
 190 <A HREF="compbio/metadata/Parameter.html" title="class in compbio.metadata" target="classFrame">Parameter</A>\r
 191 <BR>\r
 192 <A HREF="compbio/engine/client/PathValidator.html" title="class in compbio.engine.client" target="classFrame">PathValidator</A>\r
 193 <BR>\r
 194 <A HREF="compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client" target="classFrame"><I>PipedExecutable</I></A>\r
 195 <BR>\r
 196 <A HREF="compbio/metadata/Preset.html" title="class in compbio.metadata" target="classFrame">Preset</A>\r
 197 <BR>\r
 198 <A HREF="compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws" target="classFrame">PresetAlign</A>\r
 199 <BR>\r
 200 <A HREF="compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">PresetAlignResponse</A>\r
 201 <BR>\r
 202 <A HREF="compbio/metadata/PresetManager.html" title="class in compbio.metadata" target="classFrame">PresetManager</A>\r
 203 <BR>\r
 204 <A HREF="compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa" target="classFrame">Probcons</A>\r
 205 <BR>\r
 206 <A HREF="compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server" target="classFrame">ProbconsWS</A>\r
 207 <BR>\r
 208 <A HREF="compbio/data/sequence/Program.html" title="enum in compbio.data.sequence" target="classFrame">Program</A>\r
 209 <BR>\r
 210 <A HREF="compbio/engine/ProgressGetter.html" title="class in compbio.engine" target="classFrame">ProgressGetter</A>\r
 211 <BR>\r
 212 <A HREF="compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf" target="classFrame">PropertyHelperManager</A>\r
 213 <BR>\r
 214 <A HREF="compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred" target="classFrame">PScore</A>\r
 215 <BR>\r
 216 <A HREF="compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl" target="classFrame">PSIBlast</A>\r
 217 <BR>\r
 218 <A HREF="compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast" target="classFrame">PsiBlast</A>\r
 219 <BR>\r
 220 <A HREF="compbio/engine/PulledFileCache.html" title="class in compbio.engine" target="classFrame">PulledFileCache</A>\r
 221 <BR>\r
 222 <A HREF="compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws" target="classFrame">PullExecStatistics</A>\r
 223 <BR>\r
 224 <A HREF="compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws" target="classFrame">PullExecStatisticsResponse</A>\r
 225 <BR>\r
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 227 <BR>\r
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 229 <BR>\r
 230 <A HREF="compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata" target="classFrame">ResultNotAvailableException</A>\r
 231 <BR>\r
 232 <A HREF="compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws" target="classFrame">ResultNotAvailableExceptionBean</A>\r
 233 <BR>\r
 234 <A HREF="compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl" target="classFrame">Ronn</A>\r
 235 <BR>\r
 236 <A HREF="compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl" target="classFrame">RPSBlast</A>\r
 237 <BR>\r
 238 <A HREF="compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client" target="classFrame">RunConfiguration</A>\r
 239 <BR>\r
 240 <A HREF="compbio/metadata/RunnerConfig.html" title="class in compbio.metadata" target="classFrame">RunnerConfig</A>\r
 241 <BR>\r
 242 <A HREF="compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf" target="classFrame">RunnerConfigMarshaller</A>\r
 243 <BR>\r
 244 <A HREF="compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl" target="classFrame">Runners</A>\r
 245 <BR>\r
 246 <A HREF="compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence" target="classFrame">SequenceUtil</A>\r
 247 <BR>\r
 248 <A HREF="compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server" target="classFrame">SimpleWSPublisher</A>\r
 249 <BR>\r
 250 <A HREF="compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client" target="classFrame">SkeletalExecutable</A>\r
 251 <BR>\r
 252 <A HREF="compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa" target="classFrame">StatisticManager</A>\r
 253 <BR>\r
 254 <A HREF="compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local" target="classFrame">StreamGobbler</A>\r
 255 <BR>\r
 256 <A HREF="compbio/engine/SubmissionManager.html" title="class in compbio.engine" target="classFrame">SubmissionManager</A>\r
 257 <BR>\r
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 263 <BR>\r
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 267 <BR>\r
 268 <A HREF="compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html" title="class in compbio.data.msa.jaxws" target="classFrame">UnsupportedRuntimeExceptionBean</A>\r
 269 <BR>\r
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 271 <BR>\r
 272 <A HREF="compbio/runner/Util.html" title="class in compbio.runner" target="classFrame">Util</A>\r
 273 <BR>\r
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 281 <BR>\r
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 283 <BR>\r
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 285 <BR>\r
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