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/Score.html" title="class in compbio.data.sequence"><B>Score</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>A value class for AACon annotation results storage.<DT><A HREF="../compbio/data/sequence/Score.html#Score(java.lang.Enum, java.util.ArrayList)"><B>Score(Enum&lt;?&gt;, ArrayList&lt;Float&gt;)</B></A> - \r
  92 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
  93 <DD>Instantiate the Score\r
  94 <DT><A HREF="../compbio/data/sequence/Score.html#Score(java.lang.Enum, java.util.ArrayList, java.util.TreeSet)"><B>Score(Enum&lt;?&gt;, ArrayList&lt;Float&gt;, TreeSet&lt;Range&gt;)</B></A> - \r
  95 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
  96 <DD>&nbsp;\r
  97 <DT><A HREF="../compbio/data/sequence/Score.html#Score(java.lang.Enum, java.util.TreeSet)"><B>Score(Enum&lt;?&gt;, TreeSet&lt;Range&gt;)</B></A> - \r
  98 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
  99 <DD>&nbsp;\r
 100 <DT><A HREF="../compbio/data/sequence/Score.html#Score(java.lang.Enum, float[])"><B>Score(Enum&lt;?&gt;, float[])</B></A> - \r
 101 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
 102 <DD>&nbsp;\r
 103 <DT><A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence"><B>ScoreManager</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>&nbsp;<DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence"><B>ScoreManager.ScoreHolder</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>&nbsp;<DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#scores"><B>scores</B></A> - \r
 104 Variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
 105 <DD>&nbsp;\r
 106 <DT><A HREF="../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa"><B>SequenceAnnotation</B></A>&lt;<A HREF="../compbio/data/msa/SequenceAnnotation.html" title="type parameter in SequenceAnnotation">T</A>&gt; - Interface in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD>Interface for tools that results to one or more annotation to sequence(s)
 107
 108  Single, multiple sequences their groups or alignments can be annotated<DT><A HREF="../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server"><B>SequenceAnnotationService</B></A>&lt;<A HREF="../compbio/ws/server/SequenceAnnotationService.html" title="type parameter in SequenceAnnotationService">T</A>&gt; - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>Common methods for all SequenceAnnotation web services<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/JABAService.html#SERVICE_NAMESPACE"><B>SERVICE_NAMESPACE</B></A> - \r
 109 Static variable in interface compbio.data.msa.<A HREF="../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>\r
 110 <DD>&nbsp;\r
 111 <DT><A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><B>Services</B></A> - Enum in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>List of web services currently supported by JABAWS version 2<DT><A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client"><B>ServicesUtil</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>&nbsp;<DT><A HREF="../compbio/ws/client/ServicesUtil.html#ServicesUtil()"><B>ServicesUtil()</B></A> - \r
 112 Constructor for class compbio.ws.client.<A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</A>\r
 113 <DD>&nbsp;\r
 114 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setActualNumberofSequences(int)"><B>setActualNumberofSequences(int)</B></A> - \r
 115 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
 116 <DD>&nbsp;\r
 117 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTested.html#setArg0(compbio.ws.client.Services)"><B>setArg0(Services)</B></A> - \r
 118 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws">GetLastTested</A>\r
 119 <DD>&nbsp;\r
 120 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html#setArg0(compbio.ws.client.Services)"><B>setArg0(Services)</B></A> - \r
 121 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws">GetLastTestedOn</A>\r
 122 <DD>&nbsp;\r
 123 <DT><A HREF="../compbio/data/msa/jaxws/IsOperating.html#setArg0(compbio.ws.client.Services)"><B>setArg0(Services)</B></A> - \r
 124 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperating.html" title="class in compbio.data.msa.jaxws">IsOperating</A>\r
 125 <DD>&nbsp;\r
 126 <DT><A HREF="../compbio/data/msa/jaxws/TestService.html#setArg0(compbio.ws.client.Services)"><B>setArg0(Services)</B></A> - \r
 127 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestService.html" title="class in compbio.data.msa.jaxws">TestService</A>\r
 128 <DD>&nbsp;\r
 129 <DT><A HREF="../compbio/metadata/Option.html#setDefaultValue(java.lang.String)"><B>setDefaultValue(String)</B></A> - \r
 130 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 131 <DD>Sets one of the values defined in optionList as default.\r
 132 <DT><A HREF="../compbio/metadata/Parameter.html#setDefaultValue(java.lang.String)"><B>setDefaultValue(String)</B></A> - \r
 133 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
 134 <DD>&nbsp;\r
 135 <DT><A HREF="../compbio/metadata/Option.html#setDescription(java.lang.String)"><B>setDescription(String)</B></A> - \r
 136 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 137 <DD>&nbsp;\r
 138 <DT><A HREF="../compbio/metadata/Preset.html#setDescription(java.lang.String)"><B>setDescription(String)</B></A> - \r
 139 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
 140 <DD>&nbsp;\r
 141 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)"><B>setEmail(String)</B></A> - \r
 142 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 143 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 144 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#setError(java.lang.String)"><B>setError(String)</B></A> - \r
 145 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 146 <DD>&nbsp;\r
 147 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)"><B>setError(String)</B></A> - \r
 148 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 149 <DD>&nbsp;\r
 150 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#setExecProvider(compbio.engine.client.Executable.ExecProvider)"><B>setExecProvider(Executable.ExecProvider)</B></A> - \r
 151 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 152 <DD>&nbsp;\r
 153 <DT><A HREF="../compbio/data/msa/jaxws/Align.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List&lt;FastaSequence&gt;)</B></A> - \r
 154 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
 155 <DD>&nbsp;\r
 156 <DT><A HREF="../compbio/data/msa/jaxws/Analize.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List&lt;FastaSequence&gt;)</B></A> - \r
 157 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Analize.html" title="class in compbio.data.msa.jaxws">Analize</A>\r
 158 <DD>&nbsp;\r
 159 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List&lt;FastaSequence&gt;)</B></A> - \r
 160 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
 161 <DD>&nbsp;\r
 162 <DT><A HREF="../compbio/data/msa/jaxws/CustomAnalize.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List&lt;FastaSequence&gt;)</B></A> - \r
 163 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</A>\r
 164 <DD>&nbsp;\r
 165 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List&lt;FastaSequence&gt;)</B></A> - \r
 166 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
 167 <DD>&nbsp;\r
 168 <DT><A HREF="../compbio/data/msa/jaxws/PresetAnalize.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List&lt;FastaSequence&gt;)</B></A> - \r
 169 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</A>\r
 170 <DD>&nbsp;\r
 171 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setFirst(java.lang.String)"><B>setFirst(String)</B></A> - \r
 172 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 173 <DD>&nbsp;\r
 174 <DT><A HREF="../compbio/metadata/Option.html#setFurtherDetails(java.net.URL)"><B>setFurtherDetails(URL)</B></A> - \r
 175 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 176 <DD>&nbsp;\r
 177 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#setInput(java.lang.String)"><B>setInput(String)</B></A> - \r
 178 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 179 <DD>&nbsp;\r
 180 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)"><B>setInput(String)</B></A> - \r
 181 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 182 <DD>&nbsp;\r
 183 <DT><A HREF="../compbio/runner/conservation/AACon.html#setInput(java.lang.String)"><B>setInput(String)</B></A> - \r
 184 Method in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
 185 <DD>&nbsp;\r
 186 <DT><A HREF="../compbio/runner/disorder/Disembl.html#setInput(java.lang.String)"><B>setInput(String)</B></A> - \r
 187 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>\r
 188 <DD>&nbsp;\r
 189 <DT><A HREF="../compbio/runner/disorder/GlobPlot.html#setInput(java.lang.String)"><B>setInput(String)</B></A> - \r
 190 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>\r
 191 <DD>&nbsp;\r
 192 <DT><A HREF="../compbio/runner/disorder/IUPred.html#setInput(java.lang.String)"><B>setInput(String)</B></A> - \r
 193 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>\r
 194 <DD>&nbsp;\r
 195 <DT><A HREF="../compbio/runner/disorder/Jronn.html#setInput(java.lang.String)"><B>setInput(String)</B></A> - \r
 196 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
 197 <DD>&nbsp;\r
 198 <DT><A HREF="../compbio/runner/msa/ClustalO.html#setInput(java.lang.String)"><B>setInput(String)</B></A> - \r
 199 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>\r
 200 <DD>&nbsp;\r
 201 <DT><A HREF="../compbio/runner/msa/ClustalW.html#setInput(java.lang.String)"><B>setInput(String)</B></A> - \r
 202 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
 203 <DD>&nbsp;\r
 204 <DT><A HREF="../compbio/runner/msa/Mafft.html#setInput(java.lang.String)"><B>setInput(String)</B></A> - \r
 205 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>\r
 206 <DD>&nbsp;\r
 207 <DT><A HREF="../compbio/runner/msa/Muscle.html#setInput(java.lang.String)"><B>setInput(String)</B></A> - \r
 208 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
 209 <DD>&nbsp;\r
 210 <DT><A HREF="../compbio/runner/msa/Probcons.html#setInput(java.lang.String)"><B>setInput(String)</B></A> - \r
 211 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>\r
 212 <DD>&nbsp;\r
 213 <DT><A HREF="../compbio/runner/msa/Tcoffee.html#setInput(java.lang.String)"><B>setInput(String)</B></A> - \r
 214 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
 215 <DD>&nbsp;\r
 216 <DT><A HREF="../compbio/data/msa/jaxws/CancelJob.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> - \r
 217 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
 218 <DD>&nbsp;\r
 219 <DT><A HREF="../compbio/data/msa/jaxws/GetAnnotation.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> - \r
 220 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws">GetAnnotation</A>\r
 221 <DD>&nbsp;\r
 222 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> - \r
 223 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
 224 <DD>&nbsp;\r
 225 <DT><A HREF="../compbio/data/msa/jaxws/GetResult.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> - \r
 226 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
 227 <DD>&nbsp;\r
 228 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> - \r
 229 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
 230 <DD>&nbsp;\r
 231 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setLast(java.lang.String)"><B>setLast(String)</B></A> - \r
 232 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 233 <DD>&nbsp;\r
 234 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setLast(java.lang.String, java.lang.String)"><B>setLast(String, String)</B></A> - \r
 235 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 236 <DD>&nbsp;\r
 237 <DT><A HREF="../compbio/metadata/ValueConstrain.html#setMax(java.lang.String)"><B>setMax(String)</B></A> - \r
 238 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
 239 <DD>&nbsp;\r
 240 <DT><A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> - \r
 241 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
 242 <DD>&nbsp;\r
 243 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> - \r
 244 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
 245 <DD>&nbsp;\r
 246 <DT><A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> - \r
 247 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
 248 <DD>&nbsp;\r
 249 <DT><A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> - \r
 250 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
 251 <DD>&nbsp;\r
 252 <DT><A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> - \r
 253 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
 254 <DD>&nbsp;\r
 255 <DT><A HREF="../compbio/metadata/ValueConstrain.html#setMin(java.lang.String)"><B>setMin(String)</B></A> - \r
 256 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
 257 <DD>&nbsp;\r
 258 <DT><A HREF="../compbio/metadata/Option.html#setName(java.lang.String)"><B>setName(String)</B></A> - \r
 259 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 260 <DD>&nbsp;\r
 261 <DT><A HREF="../compbio/metadata/Preset.html#setName(java.lang.String)"><B>setName(String)</B></A> - \r
 262 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
 263 <DD>&nbsp;\r
 264 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)"><B>setName(String)</B></A> - \r
 265 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 266 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 267 <DT><A HREF="../compbio/runner/conservation/AACon.html#setNCore(int)"><B>setNCore(int)</B></A> - \r
 268 Method in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
 269 <DD>&nbsp;\r
 270 <DT><A HREF="../compbio/runner/disorder/Jronn.html#setNCore(int)"><B>setNCore(int)</B></A> - \r
 271 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
 272 <DD>&nbsp;\r
 273 <DT><A HREF="../compbio/runner/msa/ClustalO.html#setNCore(int)"><B>setNCore(int)</B></A> - \r
 274 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>\r
 275 <DD>&nbsp;\r
 276 <DT><A HREF="../compbio/runner/msa/Tcoffee.html#setNCore(int)"><B>setNCore(int)</B></A> - \r
 277 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
 278 <DD>&nbsp;\r
 279 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setNumberOfSequencesAllowed(int)"><B>setNumberOfSequencesAllowed(int)</B></A> - \r
 280 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
 281 <DD>&nbsp;\r
 282 <DT><A HREF="../compbio/metadata/Parameter.html#setOptionName(java.lang.String)"><B>setOptionName(String)</B></A> - \r
 283 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
 284 <DD>&nbsp;\r
 285 <DT><A HREF="../compbio/metadata/Option.html#setOptionNames(java.util.Set)"><B>setOptionNames(Set&lt;String&gt;)</B></A> - \r
 286 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 287 <DD>&nbsp;\r
 288 <DT><A HREF="../compbio/metadata/Parameter.html#setOptionNames(java.util.Set)"><B>setOptionNames(Set&lt;String&gt;)</B></A> - \r
 289 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
 290 <DD>&nbsp;\r
 291 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#setOptions(java.util.List)"><B>setOptions(List&lt;Option&gt;)</B></A> - \r
 292 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
 293 <DD>&nbsp;\r
 294 <DT><A HREF="../compbio/data/msa/jaxws/CustomAnalize.html#setOptions(java.util.List)"><B>setOptions(List&lt;Option&gt;)</B></A> - \r
 295 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</A>\r
 296 <DD>&nbsp;\r
 297 <DT><A HREF="../compbio/metadata/Preset.html#setOptions(java.util.List)"><B>setOptions(List&lt;String&gt;)</B></A> - \r
 298 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
 299 <DD>&nbsp;\r
 300 <DT><A HREF="../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)"><B>setOptions(List&lt;Option&lt;T&gt;&gt;)</B></A> - \r
 301 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 302 <DD>Adds the list of options or parameters to the internal list of options\r
 303 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> - \r
 304 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 305 <DD>&nbsp;\r
 306 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> - \r
 307 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 308 <DD>&nbsp;\r
 309 <DT><A HREF="../compbio/runner/conservation/AACon.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> - \r
 310 Method in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
 311 <DD>&nbsp;\r
 312 <DT><A HREF="../compbio/runner/disorder/IUPred.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> - \r
 313 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>\r
 314 <DD>&nbsp;\r
 315 <DT><A HREF="../compbio/runner/disorder/Jronn.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> - \r
 316 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
 317 <DD>&nbsp;\r
 318 <DT><A HREF="../compbio/runner/msa/ClustalO.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> - \r
 319 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>\r
 320 <DD>&nbsp;\r
 321 <DT><A HREF="../compbio/runner/msa/ClustalW.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> - \r
 322 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
 323 <DD>&nbsp;\r
 324 <DT><A HREF="../compbio/runner/msa/Muscle.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> - \r
 325 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
 326 <DD>&nbsp;\r
 327 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setParam(java.lang.String)"><B>setParam(String)</B></A> - \r
 328 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 329 <DD>&nbsp;\r
 330 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setParam(java.lang.String, java.lang.String)"><B>setParam(String, String)</B></A> - \r
 331 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 332 <DD>&nbsp;\r
 333 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)"><B>setParameter(String)</B></A> - \r
 334 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 335 <DD>&nbsp;\r
 336 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#setParameters(compbio.engine.client.CommandBuilder)"><B>setParameters(CommandBuilder&lt;?&gt;)</B></A> - \r
 337 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 338 <DD>&nbsp;\r
 339 <DT><A HREF="../compbio/metadata/RunnerConfig.html#setParameters(java.util.List)"><B>setParameters(List&lt;Parameter&lt;T&gt;&gt;)</B></A> - \r
 340 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 341 <DD>Sets the list of parameters as internal list\r
 342 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#setParams(java.util.List)"><B>setParams(List&lt;String&gt;)</B></A> - \r
 343 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 344 <DD>&nbsp;\r
 345 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#setPosition(long)"><B>setPosition(long)</B></A> - \r
 346 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
 347 <DD>&nbsp;\r
 348 <DT><A HREF="../compbio/metadata/Parameter.html#setPossibleValues(java.util.Set)"><B>setPossibleValues(Set&lt;String&gt;)</B></A> - \r
 349 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
 350 <DD>&nbsp;\r
 351 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#setPreset(compbio.metadata.Preset)"><B>setPreset(Preset)</B></A> - \r
 352 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
 353 <DD>&nbsp;\r
 354 <DT><A HREF="../compbio/data/msa/jaxws/PresetAnalize.html#setPreset(compbio.metadata.Preset)"><B>setPreset(Preset)</B></A> - \r
 355 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</A>\r
 356 <DD>&nbsp;\r
 357 <DT><A HREF="../compbio/data/msa/jaxws/GetLimit.html#setPresetName(java.lang.String)"><B>setPresetName(String)</B></A> - \r
 358 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
 359 <DD>&nbsp;\r
 360 <DT><A HREF="../compbio/metadata/PresetManager.html#setPresets(java.util.List)"><B>setPresets(List&lt;Preset&lt;T&gt;&gt;)</B></A> - \r
 361 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
 362 <DD>&nbsp;\r
 363 <DT><A HREF="../compbio/metadata/RunnerConfig.html#setPrmSeparator(java.lang.String)"><B>setPrmSeparator(String)</B></A> - \r
 364 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 365 <DD>Sets name value separator character\r
 366 <DT><A HREF="../compbio/runner/_NativeSpecHelper.html#setQueue(java.lang.String)"><B>setQueue(String)</B></A> - \r
 367 Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
 368 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 369 <DT><A HREF="../compbio/data/sequence/Score.html#setRanges(java.util.TreeSet)"><B>setRanges(TreeSet&lt;Range&gt;)</B></A> - \r
 370 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
 371 <DD>&nbsp;\r
 372 <DT><A HREF="../compbio/metadata/Option.html#setRequired(boolean)"><B>setRequired(boolean)</B></A> - \r
 373 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 374 <DD>&nbsp;\r
 375 <DT><A HREF="../compbio/runner/_NativeSpecHelper.html#setRequiredMemory(int)"><B>setRequiredMemory(int)</B></A> - \r
 376 Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
 377 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 378 <DT><A HREF="../compbio/data/msa/jaxws/AlignResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
 379 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
 380 <DD>&nbsp;\r
 381 <DT><A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
 382 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html" title="class in compbio.data.msa.jaxws">AnalizeResponse</A>\r
 383 <DD>&nbsp;\r
 384 <DT><A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html#setReturn(boolean)"><B>setReturn(boolean)</B></A> - \r
 385 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
 386 <DD>&nbsp;\r
 387 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
 388 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
 389 <DD>&nbsp;\r
 390 <DT><A HREF="../compbio/data/msa/jaxws/CustomAnalizeResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
 391 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalizeResponse.html" title="class in compbio.data.msa.jaxws">CustomAnalizeResponse</A>\r
 392 <DD>&nbsp;\r
 393 <DT><A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html#setReturn(compbio.data.sequence.ScoreManager)"><B>setReturn(ScoreManager)</B></A> - \r
 394 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws">GetAnnotationResponse</A>\r
 395 <DD>&nbsp;\r
 396 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html#setReturn(compbio.metadata.JobStatus)"><B>setReturn(JobStatus)</B></A> - \r
 397 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
 398 <DD>&nbsp;\r
 399 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html#setReturn(java.util.Date)"><B>setReturn(Date)</B></A> - \r
 400 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedOnResponse</A>\r
 401 <DD>&nbsp;\r
 402 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html#setReturn(int)"><B>setReturn(int)</B></A> - \r
 403 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedResponse</A>\r
 404 <DD>&nbsp;\r
 405 <DT><A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html#setReturn(compbio.metadata.Limit)"><B>setReturn(Limit)</B></A> - \r
 406 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
 407 <DD>&nbsp;\r
 408 <DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html#setReturn(compbio.metadata.LimitsManager)"><B>setReturn(LimitsManager)</B></A> - \r
 409 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
 410 <DD>&nbsp;\r
 411 <DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html#setReturn(compbio.metadata.PresetManager)"><B>setReturn(PresetManager)</B></A> - \r
 412 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
 413 <DD>&nbsp;\r
 414 <DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html#setReturn(compbio.data.sequence.Alignment)"><B>setReturn(Alignment)</B></A> - \r
 415 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
 416 <DD>&nbsp;\r
 417 <DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#setReturn(compbio.metadata.RunnerConfig)"><B>setReturn(RunnerConfig)</B></A> - \r
 418 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
 419 <DD>&nbsp;\r
 420 <DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html#setReturn(java.util.Set)"><B>setReturn(Set&lt;Services&gt;)</B></A> - \r
 421 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws">GetSupportedServicesResponse</A>\r
 422 <DD>&nbsp;\r
 423 <DT><A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html#setReturn(boolean)"><B>setReturn(boolean)</B></A> - \r
 424 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws">IsOperatingResponse</A>\r
 425 <DD>&nbsp;\r
 426 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
 427 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
 428 <DD>&nbsp;\r
 429 <DT><A HREF="../compbio/data/msa/jaxws/PresetAnalizeResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
 430 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalizeResponse.html" title="class in compbio.data.msa.jaxws">PresetAnalizeResponse</A>\r
 431 <DD>&nbsp;\r
 432 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#setReturn(compbio.metadata.ChunkHolder)"><B>setReturn(ChunkHolder)</B></A> - \r
 433 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
 434 <DD>&nbsp;\r
 435 <DT><A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
 436 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html" title="class in compbio.data.msa.jaxws">TestAllServicesResponse</A>\r
 437 <DD>&nbsp;\r
 438 <DT><A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
 439 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html" title="class in compbio.data.msa.jaxws">TestServiceResponse</A>\r
 440 <DD>&nbsp;\r
 441 <DT><A HREF="../compbio/metadata/PresetManager.html#setRunnerClassName(java.lang.String)"><B>setRunnerClassName(String)</B></A> - \r
 442 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
 443 <DD>&nbsp;\r
 444 <DT><A HREF="../compbio/metadata/RunnerConfig.html#setRunnerClassName(java.lang.String)"><B>setRunnerClassName(String)</B></A> - \r
 445 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 446 <DD>Set the name of a runner class\r
 447 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setSequenceLenghtActual(int)"><B>setSequenceLenghtActual(int)</B></A> - \r
 448 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
 449 <DD>&nbsp;\r
 450 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setSequenceLenghtAllowed(int)"><B>setSequenceLenghtAllowed(int)</B></A> - \r
 451 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
 452 <DD>&nbsp;\r
 453 <DT><A HREF="../compbio/metadata/ValueConstrain.html#setType(compbio.metadata.ValueConstrain.Type)"><B>setType(ValueConstrain.Type)</B></A> - \r
 454 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
 455 <DD>&nbsp;\r
 456 <DT><A HREF="../compbio/metadata/Parameter.html#setValidValue(compbio.metadata.ValueConstrain)"><B>setValidValue(ValueConstrain)</B></A> - \r
 457 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
 458 <DD>&nbsp;\r
 459 <DT><A HREF="../compbio/metadata/Argument.html#setValue(java.lang.String)"><B>setValue(String)</B></A> - \r
 460 Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
 461 <DD>Set default values for the parameter or an option\r
 462 <DT><A HREF="../compbio/metadata/Option.html#setValue(java.lang.String)"><B>setValue(String)</B></A> - \r
 463 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 464 <DD>&nbsp;\r
 465 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#setWorkDirectory(java.lang.String)"><B>setWorkDirectory(String)</B></A> - \r
 466 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 467 <DD>&nbsp;\r
 468 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#setWorkDirectory(java.lang.String)"><B>setWorkDirectory(String)</B></A> - \r
 469 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
 470 <DD>&nbsp;\r
 471 <DT><A HREF="../compbio/engine/local/LocalExecutorService.html#shutDown()"><B>shutDown()</B></A> - \r
 472 Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</A>\r
 473 <DD>This stops all executing processes via interruption.\r
 474 <DT><A HREF="../compbio/stat/collector/StatDB.html#shutdownDBServer()"><B>shutdownDBServer()</B></A> - \r
 475 Static method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
 476 <DD>&nbsp;\r
 477 <DT><A HREF="../compbio/ws/server/ShutdownEngines.html" title="class in compbio.ws.server"><B>ShutdownEngines</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>Switch off engines if JABAWS web application is undeployed, or web server is
 478  shutdown<DT><A HREF="../compbio/ws/server/ShutdownEngines.html#ShutdownEngines()"><B>ShutdownEngines()</B></A> - \r
 479 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/ShutdownEngines.html" title="class in compbio.ws.server">ShutdownEngines</A>\r
 480 <DD>&nbsp;\r
 481 <DT><A HREF="../compbio/engine/local/ExecutableWrapper.html#shutdownService()"><B>shutdownService()</B></A> - \r
 482 Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A>\r
 483 <DD>Stops internal executor service which captures streams of native
 484  executables.\r
 485 <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><B>Deprecated.</B>&nbsp;<DT><A HREF="../compbio/ws/server/SimpleWSPublisher.html#SimpleWSPublisher(java.lang.Object, java.lang.String)"><B>SimpleWSPublisher(Object, String)</B></A> - \r
 486 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server">SimpleWSPublisher</A>\r
 487 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 488 <DT><A HREF="../compbio/data/sequence/ScoreManager.html#SINGLE_ENTRY_KEY"><B>SINGLE_ENTRY_KEY</B></A> - \r
 489 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
 490 <DD>&nbsp;\r
 491 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#size()"><B>size()</B></A> - \r
 492 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 493 <DD>&nbsp;\r
 494 <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
 495 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 496 <DD>&nbsp;\r
 497 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#SkeletalExecutable(java.lang.String)"><B>SkeletalExecutable(String)</B></A> - \r
 498 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 499 <DD>&nbsp;\r
 500 <DT><A HREF="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence"><B>SMERFSConstraints</B></A> - Enum in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Enumeration defining two constraints for SMERFS columns score calculation.<DT><A HREF="../compbio/stat/collector/StatProcessor.html#sortByResultSize()"><B>sortByResultSize()</B></A> - \r
 501 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
 502 <DD>&nbsp;\r
 503 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#sortByRuntime()"><B>sortByRuntime()</B></A> - \r
 504 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
 505 <DD>&nbsp;\r
 506 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#sortByStartTime()"><B>sortByStartTime()</B></A> - \r
 507 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
 508 <DD>&nbsp;\r
 509 <DT><A HREF="../compbio/runner/Util.html#SPACE"><B>SPACE</B></A> - \r
 510 Static variable in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
 511 <DD>&nbsp;\r
 512 <DT><A HREF="../compbio/runner/conservation/AACon.html#STAT_FILE"><B>STAT_FILE</B></A> - \r
 513 Static variable in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
 514 <DD>&nbsp;\r
 515 <DT><A HREF="../compbio/runner/disorder/Jronn.html#STAT_FILE"><B>STAT_FILE</B></A> - \r
 516 Static variable in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
 517 <DD>&nbsp;\r
 518 <DT><A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util"><B>StatCollection</B></A> - Class in <A HREF="../compbio/stat/servlet/util/package-summary.html">compbio.stat.servlet.util</A><DD>&nbsp;<DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#StatCollection()"><B>StatCollection()</B></A> - \r
 519 Constructor for class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</A>\r
 520 <DD>&nbsp;\r
 521 <DT><A HREF="../compbio/stat/servlet/util/StatCollection.Stattype.html" title="enum in compbio.stat.servlet.util"><B>StatCollection.Stattype</B></A> - Enum in <A HREF="../compbio/stat/servlet/util/package-summary.html">compbio.stat.servlet.util</A><DD>Total number of requests
 522
 523  incomplete abandoned cancelled<DT><A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector"><B>StatDB</B></A> - Class in <A HREF="../compbio/stat/collector/package-summary.html">compbio.stat.collector</A><DD>The database must be stored in the application root directory and called
 524  "ExecutionStatistic"<DT><A HREF="../compbio/stat/collector/StatDB.html#StatDB()"><B>StatDB()</B></A> - \r
 525 Constructor for class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
 526 <DD>&nbsp;\r
 527 <DT><A HREF="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet"><B>StatisticCollector</B></A> - Class in <A HREF="../compbio/stat/servlet/package-summary.html">compbio.stat.servlet</A><DD>&nbsp;<DT><A HREF="../compbio/stat/servlet/StatisticCollector.html#StatisticCollector()"><B>StatisticCollector()</B></A> - \r
 528 Constructor for class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</A>\r
 529 <DD>&nbsp;\r
 530 <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
 531 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
 532 <DD>&nbsp;\r
 533 <DT><A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector"><B>StatProcessor</B></A> - Class in <A HREF="../compbio/stat/collector/package-summary.html">compbio.stat.collector</A><DD>&nbsp;<DT><A HREF="../compbio/stat/collector/StatProcessor.html#StatProcessor(java.util.List)"><B>StatProcessor(List&lt;JobStat&gt;)</B></A> - \r
 534 Constructor for class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
 535 <DD>&nbsp;\r
 536 <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/AsyncExecutor.html#submitJob(compbio.engine.client.ConfiguredExecutable)"><B>submitJob(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
 537 Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
 538 <DD>Submits job for the execution
 539  Immediate execution is not guaranteed, this method puts the job in the queue.\r
 540 <DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)"><B>submitJob(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
 541 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
 542 <DD>&nbsp;\r
 543 <DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)"><B>submitJob(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
 544 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
 545 <DD>&nbsp;\r
 546 <DT><A HREF="../compbio/stat/servlet/util/Totals.html#sumOfTotals(java.util.Map)"><B>sumOfTotals(Map&lt;Date, Totals&gt;)</B></A> - \r
 547 Static method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>\r
 548 <DD>&nbsp;\r
 549 <DT><A HREF="../compbio/stat/servlet/util/Totals.html#sumStats(java.util.Map)"><B>sumStats(Map&lt;Services, StatProcessor&gt;)</B></A> - \r
 550 Static method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>\r
 551 <DD>&nbsp;\r
 552 <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
 553 <HR>\r
 554 \r
 555 \r
 556 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 557 <A NAME="navbar_bottom"><!-- --></A>\r
 558 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 559 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 560 <TR>\r
 561 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 562 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 563 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 564   <TR ALIGN="center" VALIGN="top">\r
 565   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 566   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
 567   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
 568   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
 569   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 570   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 571   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
 572   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 573   </TR>\r
 574 </TABLE>\r
 575 </TD>\r
 576 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 577 </EM>\r
 578 </TD>\r
 579 </TR>\r
 580 \r
 581 <TR>\r
 582 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 583 &nbsp;<A HREF="index-17.html"><B>PREV LETTER</B></A>&nbsp;\r
 584 &nbsp;<A HREF="index-19.html"><B>NEXT LETTER</B></A></FONT></TD>\r
 585 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 586   <A HREF="../index.html?index-filesindex-18.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 587 &nbsp;<A HREF="index-18.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 588 &nbsp;<SCRIPT type="text/javascript">\r
 589   <!--\r
 590   if(window==top) {\r
 591     document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
 592   }\r
 593   //-->\r
 594 </SCRIPT>\r
 595 <NOSCRIPT>\r
 596   <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
 597 </NOSCRIPT>\r
 598 \r
 599 \r
 600 </FONT></TD>\r
 601 </TR>\r
 602 </TABLE>\r
 603 <A NAME="skip-navbar_bottom"></A>\r
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