website/full_javadoc/index-files/index-18.html

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  82 <A NAME="_S_"><!-- --></A><H2>\r
  83 <B>S</B></H2>\r
  84 <DL>\r
  85 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#saveRunConfiguration()"><B>saveRunConfiguration()</B></A> - \r
  86 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
  87 <DD>&nbsp;\r
  88 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#saveRunConfiguration()"><B>saveRunConfiguration()</B></A> - \r
  89 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
  90 <DD>&nbsp;\r
  91 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>SequenceUtil</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Utility class for operations on sequences<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setActualNumberofSequences(int)"><B>setActualNumberofSequences(int)</B></A> - \r
  92 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
  93 <DD>&nbsp;\r
  94 <DT><A HREF="../compbio/metadata/Option.html#setDefaultValue(java.lang.String)"><B>setDefaultValue(String)</B></A> - \r
  95 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
  96 <DD>Sets one of the values defined in optionList as default.\r
  97 <DT><A HREF="../compbio/metadata/Parameter.html#setDefaultValue(java.lang.String)"><B>setDefaultValue(String)</B></A> - \r
  98 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
  99 <DD>&nbsp;\r
 100 <DT><A HREF="../compbio/metadata/Option.html#setDescription(java.lang.String)"><B>setDescription(String)</B></A> - \r
 101 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 102 <DD>&nbsp;\r
 103 <DT><A HREF="../compbio/metadata/Preset.html#setDescription(java.lang.String)"><B>setDescription(String)</B></A> - \r
 104 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
 105 <DD>&nbsp;\r
 106 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)"><B>setEmail(String)</B></A> - \r
 107 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 108 <DD>&nbsp;\r
 109 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#setError(java.lang.String)"><B>setError(String)</B></A> - \r
 110 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 111 <DD>&nbsp;\r
 112 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)"><B>setError(String)</B></A> - \r
 113 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 114 <DD>&nbsp;\r
 115 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#setExecProvider(compbio.engine.client.Executable.ExecProvider)"><B>setExecProvider(Executable.ExecProvider)</B></A> - \r
 116 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 117 <DD>&nbsp;\r
 118 <DT><A HREF="../compbio/data/msa/jaxws/Align.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List&lt;FastaSequence&gt;)</B></A> - \r
 119 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws">Align</A>\r
 120 <DD>&nbsp;\r
 121 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List&lt;FastaSequence&gt;)</B></A> - \r
 122 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>\r
 123 <DD>&nbsp;\r
 124 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List&lt;FastaSequence&gt;)</B></A> - \r
 125 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>\r
 126 <DD>&nbsp;\r
 127 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setFirst(java.lang.String)"><B>setFirst(String)</B></A> - \r
 128 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 129 <DD>&nbsp;\r
 130 <DT><A HREF="../compbio/metadata/Option.html#setFurtherDetails(java.net.URL)"><B>setFurtherDetails(URL)</B></A> - \r
 131 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 132 <DD>&nbsp;\r
 133 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#setInput(java.lang.String)"><B>setInput(String)</B></A> - \r
 134 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 135 <DD>&nbsp;\r
 136 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)"><B>setInput(String)</B></A> - \r
 137 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 138 <DD>&nbsp;\r
 139 <DT><A HREF="../compbio/runner/msa/ClustalW.html#setInput(java.lang.String)"><B>setInput(String)</B></A> - \r
 140 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
 141 <DD>&nbsp;\r
 142 <DT><A HREF="../compbio/runner/msa/Mafft.html#setInput(java.lang.String)"><B>setInput(String)</B></A> - \r
 143 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>\r
 144 <DD>&nbsp;\r
 145 <DT><A HREF="../compbio/runner/msa/Muscle.html#setInput(java.lang.String)"><B>setInput(String)</B></A> - \r
 146 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
 147 <DD>&nbsp;\r
 148 <DT><A HREF="../compbio/runner/msa/Probcons.html#setInput(java.lang.String)"><B>setInput(String)</B></A> - \r
 149 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>\r
 150 <DD>&nbsp;\r
 151 <DT><A HREF="../compbio/runner/msa/Tcoffee.html#setInput(java.lang.String)"><B>setInput(String)</B></A> - \r
 152 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
 153 <DD>&nbsp;\r
 154 <DT><A HREF="../compbio/data/msa/jaxws/CancelJob.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> - \r
 155 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws">CancelJob</A>\r
 156 <DD>&nbsp;\r
 157 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> - \r
 158 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws">GetJobStatus</A>\r
 159 <DD>&nbsp;\r
 160 <DT><A HREF="../compbio/data/msa/jaxws/GetProgress.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> - \r
 161 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetProgress.html" title="class in compbio.data.msa.jaxws">GetProgress</A>\r
 162 <DD>&nbsp;\r
 163 <DT><A HREF="../compbio/data/msa/jaxws/GetResult.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> - \r
 164 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws">GetResult</A>\r
 165 <DD>&nbsp;\r
 166 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> - \r
 167 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>\r
 168 <DD>&nbsp;\r
 169 <DT><A HREF="../compbio/data/msa/jaxws/PullFile.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> - \r
 170 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullFile.html" title="class in compbio.data.msa.jaxws">PullFile</A>\r
 171 <DD>&nbsp;\r
 172 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setLast(java.lang.String)"><B>setLast(String)</B></A> - \r
 173 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 174 <DD>&nbsp;\r
 175 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setLast(java.lang.String, java.lang.String)"><B>setLast(String, String)</B></A> - \r
 176 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 177 <DD>&nbsp;\r
 178 <DT><A HREF="../compbio/metadata/ValueConstrain.html#setMax(java.lang.String)"><B>setMax(String)</B></A> - \r
 179 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
 180 <DD>&nbsp;\r
 181 <DT><A HREF="../compbio/data/msa/jaxws/JobExecutionExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> - \r
 182 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/JobExecutionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobExecutionExceptionBean</A>\r
 183 <DD>&nbsp;\r
 184 <DT><A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> - \r
 185 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobSubmissionExceptionBean</A>\r
 186 <DD>&nbsp;\r
 187 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> - \r
 188 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
 189 <DD>&nbsp;\r
 190 <DT><A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> - \r
 191 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws">ResultNotAvailableExceptionBean</A>\r
 192 <DD>&nbsp;\r
 193 <DT><A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> - \r
 194 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html" title="class in compbio.data.msa.jaxws">UnsupportedRuntimeExceptionBean</A>\r
 195 <DD>&nbsp;\r
 196 <DT><A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> - \r
 197 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws">WrongParameterExceptionBean</A>\r
 198 <DD>&nbsp;\r
 199 <DT><A HREF="../compbio/metadata/ValueConstrain.html#setMin(java.lang.String)"><B>setMin(String)</B></A> - \r
 200 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
 201 <DD>&nbsp;\r
 202 <DT><A HREF="../compbio/metadata/Option.html#setName(java.lang.String)"><B>setName(String)</B></A> - \r
 203 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 204 <DD>&nbsp;\r
 205 <DT><A HREF="../compbio/metadata/Preset.html#setName(java.lang.String)"><B>setName(String)</B></A> - \r
 206 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
 207 <DD>&nbsp;\r
 208 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)"><B>setName(String)</B></A> - \r
 209 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 210 <DD>&nbsp;\r
 211 <DT><A HREF="../compbio/runner/msa/Tcoffee.html#setNCore(int)"><B>setNCore(int)</B></A> - \r
 212 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
 213 <DD>&nbsp;\r
 214 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setNumberOfSequencesAllowed(int)"><B>setNumberOfSequencesAllowed(int)</B></A> - \r
 215 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
 216 <DD>&nbsp;\r
 217 <DT><A HREF="../compbio/metadata/Parameter.html#setOptionName(java.lang.String)"><B>setOptionName(String)</B></A> - \r
 218 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
 219 <DD>&nbsp;\r
 220 <DT><A HREF="../compbio/metadata/Option.html#setOptionNames(java.util.Set)"><B>setOptionNames(Set&lt;String&gt;)</B></A> - \r
 221 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 222 <DD>&nbsp;\r
 223 <DT><A HREF="../compbio/metadata/Parameter.html#setOptionNames(java.util.Set)"><B>setOptionNames(Set&lt;String&gt;)</B></A> - \r
 224 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
 225 <DD>&nbsp;\r
 226 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#setOptions(java.util.List)"><B>setOptions(List&lt;Option&gt;)</B></A> - \r
 227 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>\r
 228 <DD>&nbsp;\r
 229 <DT><A HREF="../compbio/metadata/Preset.html#setOptions(java.util.List)"><B>setOptions(List&lt;String&gt;)</B></A> - \r
 230 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
 231 <DD>&nbsp;\r
 232 <DT><A HREF="../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)"><B>setOptions(List&lt;Option&lt;T&gt;&gt;)</B></A> - \r
 233 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 234 <DD>&nbsp;\r
 235 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> - \r
 236 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 237 <DD>&nbsp;\r
 238 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> - \r
 239 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 240 <DD>&nbsp;\r
 241 <DT><A HREF="../compbio/runner/msa/ClustalW.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> - \r
 242 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
 243 <DD>&nbsp;\r
 244 <DT><A HREF="../compbio/runner/msa/Muscle.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> - \r
 245 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
 246 <DD>&nbsp;\r
 247 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setParam(java.lang.String)"><B>setParam(String)</B></A> - \r
 248 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 249 <DD>&nbsp;\r
 250 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setParam(java.lang.String, java.lang.String)"><B>setParam(String, String)</B></A> - \r
 251 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 252 <DD>&nbsp;\r
 253 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)"><B>setParameter(String)</B></A> - \r
 254 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 255 <DD>&nbsp;\r
 256 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#setParameters(compbio.engine.client.CommandBuilder)"><B>setParameters(CommandBuilder&lt;?&gt;)</B></A> - \r
 257 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 258 <DD>&nbsp;\r
 259 <DT><A HREF="../compbio/metadata/RunnerConfig.html#setParameters(java.util.List)"><B>setParameters(List&lt;Parameter&lt;T&gt;&gt;)</B></A> - \r
 260 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 261 <DD>&nbsp;\r
 262 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setParams(java.util.List)"><B>setParams(List&lt;String&gt;)</B></A> - \r
 263 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 264 <DD>&nbsp;\r
 265 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#setPosition(long)"><B>setPosition(long)</B></A> - \r
 266 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>\r
 267 <DD>&nbsp;\r
 268 <DT><A HREF="../compbio/data/msa/jaxws/PullFile.html#setPosition(long)"><B>setPosition(long)</B></A> - \r
 269 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullFile.html" title="class in compbio.data.msa.jaxws">PullFile</A>\r
 270 <DD>&nbsp;\r
 271 <DT><A HREF="../compbio/metadata/Parameter.html#setPossibleValues(java.util.Set)"><B>setPossibleValues(Set&lt;String&gt;)</B></A> - \r
 272 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
 273 <DD>&nbsp;\r
 274 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#setPreset(compbio.metadata.Preset)"><B>setPreset(Preset)</B></A> - \r
 275 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>\r
 276 <DD>&nbsp;\r
 277 <DT><A HREF="../compbio/data/msa/jaxws/GetLimit.html#setPresetName(java.lang.String)"><B>setPresetName(String)</B></A> - \r
 278 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</A>\r
 279 <DD>&nbsp;\r
 280 <DT><A HREF="../compbio/metadata/PresetManager.html#setPresets(java.util.List)"><B>setPresets(List&lt;Preset&lt;T&gt;&gt;)</B></A> - \r
 281 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
 282 <DD>&nbsp;\r
 283 <DT><A HREF="../compbio/metadata/RunnerConfig.html#setPrmSeparator(java.lang.String)"><B>setPrmSeparator(String)</B></A> - \r
 284 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 285 <DD>&nbsp;\r
 286 <DT><A HREF="../compbio/runner/_NativeSpecHelper.html#setQueue(java.lang.String)"><B>setQueue(String)</B></A> - \r
 287 Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
 288 <DD>&nbsp;\r
 289 <DT><A HREF="../compbio/metadata/Option.html#setRequired(boolean)"><B>setRequired(boolean)</B></A> - \r
 290 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 291 <DD>&nbsp;\r
 292 <DT><A HREF="../compbio/runner/_NativeSpecHelper.html#setRequiredMemory(int)"><B>setRequiredMemory(int)</B></A> - \r
 293 Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
 294 <DD>&nbsp;\r
 295 <DT><A HREF="../compbio/data/msa/jaxws/AlignResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
 296 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws">AlignResponse</A>\r
 297 <DD>&nbsp;\r
 298 <DT><A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html#setReturn(boolean)"><B>setReturn(boolean)</B></A> - \r
 299 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws">CancelJobResponse</A>\r
 300 <DD>&nbsp;\r
 301 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
 302 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws">CustomAlignResponse</A>\r
 303 <DD>&nbsp;\r
 304 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html#setReturn(compbio.metadata.JobStatus)"><B>setReturn(JobStatus)</B></A> - \r
 305 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws">GetJobStatusResponse</A>\r
 306 <DD>&nbsp;\r
 307 <DT><A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html#setReturn(compbio.metadata.Limit)"><B>setReturn(Limit)</B></A> - \r
 308 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws">GetLimitResponse</A>\r
 309 <DD>&nbsp;\r
 310 <DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html#setReturn(compbio.metadata.LimitsManager)"><B>setReturn(LimitsManager)</B></A> - \r
 311 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws">GetLimitsResponse</A>\r
 312 <DD>&nbsp;\r
 313 <DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html#setReturn(compbio.metadata.PresetManager)"><B>setReturn(PresetManager)</B></A> - \r
 314 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws">GetPresetsResponse</A>\r
 315 <DD>&nbsp;\r
 316 <DT><A HREF="../compbio/data/msa/jaxws/GetProgressResponse.html#setReturn(byte)"><B>setReturn(byte)</B></A> - \r
 317 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetProgressResponse.html" title="class in compbio.data.msa.jaxws">GetProgressResponse</A>\r
 318 <DD>&nbsp;\r
 319 <DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html#setReturn(compbio.data.sequence.Alignment)"><B>setReturn(Alignment)</B></A> - \r
 320 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws">GetResultResponse</A>\r
 321 <DD>&nbsp;\r
 322 <DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#setReturn(compbio.metadata.RunnerConfig)"><B>setReturn(RunnerConfig)</B></A> - \r
 323 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws">GetRunnerOptionsResponse</A>\r
 324 <DD>&nbsp;\r
 325 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
 326 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws">PresetAlignResponse</A>\r
 327 <DD>&nbsp;\r
 328 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#setReturn(compbio.metadata.ChunkHolder)"><B>setReturn(ChunkHolder)</B></A> - \r
 329 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws">PullExecStatisticsResponse</A>\r
 330 <DD>&nbsp;\r
 331 <DT><A HREF="../compbio/data/msa/jaxws/PullFileResponse.html#setReturn(compbio.metadata.ChunkHolder)"><B>setReturn(ChunkHolder)</B></A> - \r
 332 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullFileResponse.html" title="class in compbio.data.msa.jaxws">PullFileResponse</A>\r
 333 <DD>&nbsp;\r
 334 <DT><A HREF="../compbio/metadata/PresetManager.html#setRunnerClassName(java.lang.String)"><B>setRunnerClassName(String)</B></A> - \r
 335 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
 336 <DD>&nbsp;\r
 337 <DT><A HREF="../compbio/metadata/RunnerConfig.html#setRunnerClassName(java.lang.String)"><B>setRunnerClassName(String)</B></A> - \r
 338 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 339 <DD>&nbsp;\r
 340 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setSequenceLenghtActual(int)"><B>setSequenceLenghtActual(int)</B></A> - \r
 341 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
 342 <DD>&nbsp;\r
 343 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setSequenceLenghtAllowed(int)"><B>setSequenceLenghtAllowed(int)</B></A> - \r
 344 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
 345 <DD>&nbsp;\r
 346 <DT><A HREF="../compbio/metadata/ValueConstrain.html#setType(compbio.metadata.ValueConstrain.Type)"><B>setType(ValueConstrain.Type)</B></A> - \r
 347 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
 348 <DD>&nbsp;\r
 349 <DT><A HREF="../compbio/metadata/Parameter.html#setValidValue(compbio.metadata.ValueConstrain)"><B>setValidValue(ValueConstrain)</B></A> - \r
 350 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
 351 <DD>&nbsp;\r
 352 <DT><A HREF="../compbio/metadata/Argument.html#setValue(java.lang.String)"><B>setValue(String)</B></A> - \r
 353 Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
 354 <DD>Set default values for the parameter or an option\r
 355 <DT><A HREF="../compbio/metadata/Option.html#setValue(java.lang.String)"><B>setValue(String)</B></A> - \r
 356 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 357 <DD>&nbsp;\r
 358 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#setWorkDirectory(java.lang.String)"><B>setWorkDirectory(String)</B></A> - \r
 359 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 360 <DD>&nbsp;\r
 361 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#setWorkDirectory(java.lang.String)"><B>setWorkDirectory(String)</B></A> - \r
 362 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
 363 <DD>&nbsp;\r
 364 <DT><A HREF="../compbio/engine/cluster/dundee/_QueueConstraints.html#SHORT_TIME_LIMIT"><B>SHORT_TIME_LIMIT</B></A> - \r
 365 Static variable in class compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_QueueConstraints.html" title="class in compbio.engine.cluster.dundee">_QueueConstraints</A>\r
 366 <DD>&nbsp;\r
 367 <DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#shutdown()"><B>shutdown()</B></A> - \r
 368 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
 369 <DD>&nbsp;\r
 370 <DT><A HREF="../compbio/engine/local/LocalExecutorService.html#shutDown()"><B>shutDown()</B></A> - \r
 371 Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</A>\r
 372 <DD>This stops all executing processes via interruption.\r
 373 <DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#shutdownNow()"><B>shutdownNow()</B></A> - \r
 374 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
 375 <DD>&nbsp;\r
 376 <DT><A HREF="../compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server"><B>SimpleWSPublisher</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>This class publish a web service.<DT><A HREF="../compbio/ws/server/SimpleWSPublisher.html#SimpleWSPublisher(java.lang.Object, java.lang.String)"><B>SimpleWSPublisher(Object, String)</B></A> - \r
 377 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server">SimpleWSPublisher</A>\r
 378 <DD>&nbsp;\r
 379 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#size()"><B>size()</B></A> - \r
 380 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 381 <DD>&nbsp;\r
 382 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client"><B>SkeletalExecutable</B></A>&lt;<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt; - Class in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>&nbsp;<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#SkeletalExecutable()"><B>SkeletalExecutable()</B></A> - \r
 383 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 384 <DD>&nbsp;\r
 385 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#SkeletalExecutable(java.lang.String)"><B>SkeletalExecutable(String)</B></A> - \r
 386 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 387 <DD>&nbsp;\r
 388 <DT><A HREF="../compbio/runner/Util.html#SPACE"><B>SPACE</B></A> - \r
 389 Static variable in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
 390 <DD>&nbsp;\r
 391 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa"><B>StatisticManager</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD>&nbsp;<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#StatisticManager(org.ggf.drmaa.JobInfo)"><B>StatisticManager(JobInfo)</B></A> - \r
 392 Constructor for class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 393 <DD>&nbsp;\r
 394 <DT><A HREF="../compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local"><B>StreamGobbler</B></A> - Class in <A HREF="../compbio/engine/local/package-summary.html">compbio.engine.local</A><DD>&nbsp;<DT><A HREF="../compbio/engine/SubmissionManager.html" title="class in compbio.engine"><B>SubmissionManager</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>Submit jobs for execution<DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#submit(java.util.concurrent.Callable)"><B>submit(Callable&lt;T&gt;)</B></A> - \r
 395 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
 396 <DD>&nbsp;\r
 397 <DT><A HREF="../compbio/engine/AsyncExecutor.html#submitJob(compbio.engine.client.ConfiguredExecutable)"><B>submitJob(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
 398 Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
 399 <DD>Submits job for the execution
 400  Immediate execution is not guaranteed, this method puts the job in the queue.\r
 401 <DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)"><B>submitJob(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
 402 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
 403 <DD>&nbsp;\r
 404 <DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)"><B>submitJob(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
 405 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
 406 <DD>&nbsp;\r
 407 <DT><A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine"><B>SyncExecutor</B></A> - Interface in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>Synchronous executor, is an engine to run the Executable synchronously.</DL>\r
 408 <HR>\r
 409 \r
 410 \r
 411 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 412 <A NAME="navbar_bottom"><!-- --></A>\r
 413 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 414 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 415 <TR>\r
 416 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 417 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 418 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 419   <TR ALIGN="center" VALIGN="top">\r
 420   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 421   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
 422   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
 423   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
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