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  75 <h2 class="title">S</h2>
  76 <dl>
  77 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#s">s</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructReader.html" title="class in compbio.data.sequence">RNAStructReader</a></dt>
  78 <dd>&nbsp;</dd>
  79 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#saveRunConfiguration--">saveRunConfiguration()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
  80 <dd>&nbsp;</dd>
  81 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfiguredExecutable.html#saveRunConfiguration--">saveRunConfiguration()</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a></dt>
  82 <dd>&nbsp;</dd>
  83 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#sContact">sContact</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</a></dt>
  84 <dd>&nbsp;</dd>
  85 <dt><a href="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence"><span class="typeNameLink">Score</span></a> - Class in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
  86 <dd>
  87 <div class="block">A value class for AACon annotation results storage.</div>
  88 </dd>
  89 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Score.html#Score--">Score()</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a></dt>
  90 <dd>&nbsp;</dd>
  91 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Score.html#Score-java.lang.Enum-java.util.ArrayList-">Score(Enum&lt;?&gt;, ArrayList&lt;Float&gt;)</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a></dt>
  92 <dd>
  93 <div class="block">Instantiate the Score</div>
  94 </dd>
  95 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Score.html#Score-java.lang.Enum-java.util.ArrayList-java.util.TreeSet-">Score(Enum&lt;?&gt;, ArrayList&lt;Float&gt;, TreeSet&lt;Range&gt;)</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a></dt>
  96 <dd>&nbsp;</dd>
  97 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Score.html#Score-java.lang.Enum-java.util.TreeSet-">Score(Enum&lt;?&gt;, TreeSet&lt;Range&gt;)</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a></dt>
  98 <dd>&nbsp;</dd>
  99 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Score.html#Score-java.lang.Enum-float:A-">Score(Enum&lt;?&gt;, float[])</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a></dt>
 100 <dd>&nbsp;</dd>
 101 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ScoreManager.ScoreHolder.html#ScoreHolder--">ScoreHolder()</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</a></dt>
 102 <dd>&nbsp;</dd>
 103 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ScoreManager.ScoreHolder.html#ScoreHolder-java.lang.String-java.util.Set-">ScoreHolder(String, Set&lt;Score&gt;)</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</a></dt>
 104 <dd>&nbsp;</dd>
 105 <dt><a href="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence"><span class="typeNameLink">ScoreManager</span></a> - Class in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
 106 <dd>&nbsp;</dd>
 107 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ScoreManager.html#ScoreManager--">ScoreManager()</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></dt>
 108 <dd>&nbsp;</dd>
 109 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ScoreManager.html#ScoreManager-java.lang.String-java.util.Set-">ScoreManager(String, Set&lt;Score&gt;)</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></dt>
 110 <dd>&nbsp;</dd>
 111 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ScoreManager.html#ScoreManager-java.util.Map-">ScoreManager(Map&lt;String, Set&lt;Score&gt;&gt;)</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></dt>
 112 <dd>&nbsp;</dd>
 113 <dt><a href="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence"><span class="typeNameLink">ScoreManager.ScoreHolder</span></a> - Class in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
 114 <dd>&nbsp;</dd>
 115 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Score.html#scores">scores</a></span> - Variable in class compbio.data.sequence.<a href="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a></dt>
 116 <dd>&nbsp;</dd>
 117 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ScoreManager.ScoreHolder.html#scores">scores</a></span> - Variable in class compbio.data.sequence.<a href="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</a></dt>
 118 <dd>&nbsp;</dd>
 119 <dt><span class="memberNameLink"><a href="../compbio/metadata/Limit.html#seqLength">seqLength</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a></dt>
 120 <dd>&nbsp;</dd>
 121 <dt><span class="memberNameLink"><a href="../compbio/metadata/Limit.html#seqNumber">seqNumber</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a></dt>
 122 <dd>&nbsp;</dd>
 123 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#seqP">seqP</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructReader.html" title="class in compbio.data.sequence">RNAStructReader</a></dt>
 124 <dd>&nbsp;</dd>
 125 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ScoreManager.html#seqScores">seqScores</a></span> - Variable in class compbio.data.sequence.<a href="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></dt>
 126 <dd>&nbsp;</dd>
 127 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/FastaSequence.html#sequence">sequence</a></span> - Variable in class compbio.data.sequence.<a href="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></dt>
 128 <dd>
 129 <div class="block">Returns the string representation of sequence</div>
 130 </dd>
 131 <dt><a href="../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa"><span class="typeNameLink">SequenceAnnotation</span></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></dt>
 132 <dd>
 133 <div class="block">Interface for tools that results to one or more annotation to sequence(s)
 134
 135  Single, multiple sequences their groups or alignments can be annotated</div>
 136 </dd>
 137 <dt><a href="../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server"><span class="typeNameLink">SequenceAnnotationService</span></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></dt>
 138 <dd>
 139 <div class="block">Common methods for all SequenceAnnotation web services</div>
 140 </dd>
 141 <dt><span class="memberNameLink"><a href="../compbio/ws/server/SequenceAnnotationService.html#SequenceAnnotationService-compbio.engine.client.SkeletalExecutable-org.apache.log4j.Logger-">SequenceAnnotationService(SkeletalExecutable&lt;T&gt;, Logger)</a></span> - Constructor for class compbio.ws.server.<a href="../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</a></dt>
 142 <dd>&nbsp;</dd>
 143 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#sequenceLenghtActual">sequenceLenghtActual</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</a></dt>
 144 <dd>&nbsp;</dd>
 145 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#sequenceLenghtAllowed">sequenceLenghtAllowed</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</a></dt>
 146 <dd>&nbsp;</dd>
 147 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Alignment.html#sequences">sequences</a></span> - Variable in class compbio.data.sequence.<a href="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></dt>
 148 <dd>&nbsp;</dd>
 149 <dt><a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><span class="typeNameLink">SequenceUtil</span></a> - Class in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
 150 <dd>
 151 <div class="block">Utility class for operations on sequences</div>
 152 </dd>
 153 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#SequenceUtil--">SequenceUtil()</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 154 <dd>&nbsp;</dd>
 155 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/UnknownFileFormatException.html#serialVersionUID">serialVersionUID</a></span> - Static variable in exception compbio.data.sequence.<a href="../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></dt>
 156 <dd>&nbsp;</dd>
 157 <dt><span class="memberNameLink"><a href="../compbio/metadata/JobExecutionException.html#serialVersionUID">serialVersionUID</a></span> - Static variable in exception compbio.metadata.<a href="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</a></dt>
 158 <dd>
 159 <div class="block">Default stable serial for serialization</div>
 160 </dd>
 161 <dt><span class="memberNameLink"><a href="../compbio/metadata/JobSubmissionException.html#serialVersionUID">serialVersionUID</a></span> - Static variable in exception compbio.metadata.<a href="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></dt>
 162 <dd>&nbsp;</dd>
 163 <dt><span class="memberNameLink"><a href="../compbio/metadata/LimitExceededException.html#serialVersionUID">serialVersionUID</a></span> - Static variable in exception compbio.metadata.<a href="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></dt>
 164 <dd>&nbsp;</dd>
 165 <dt><span class="memberNameLink"><a href="../compbio/metadata/ResultNotAvailableException.html#serialVersionUID">serialVersionUID</a></span> - Static variable in exception compbio.metadata.<a href="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</a></dt>
 166 <dd>
 167 <div class="block">Default stable serial for serialization</div>
 168 </dd>
 169 <dt><span class="memberNameLink"><a href="../compbio/metadata/UnsupportedRuntimeException.html#serialVersionUID">serialVersionUID</a></span> - Static variable in exception compbio.metadata.<a href="../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</a></dt>
 170 <dd>&nbsp;</dd>
 171 <dt><span class="memberNameLink"><a href="../compbio/metadata/WrongParameterException.html#serialVersionUID">serialVersionUID</a></span> - Static variable in exception compbio.metadata.<a href="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</a></dt>
 172 <dd>
 173 <div class="block">Default stable serial for serialization</div>
 174 </dd>
 175 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GAUtils.html#SERVER_ADDRESS">SERVER_ADDRESS</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/GAUtils.html" title="class in compbio.ws.server">GAUtils</a></dt>
 176 <dd>&nbsp;</dd>
 177 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/ServiceTestResult.html#service">service</a></span> - Variable in class compbio.stat.servlet.<a href="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</a></dt>
 178 <dd>&nbsp;</dd>
 179 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.ServiceInfo.html#service">service</a></span> - Variable in class compbio.ws.client.<a href="../compbio/ws/client/Services.ServiceInfo.html" title="class in compbio.ws.client">Services.ServiceInfo</a></dt>
 180 <dd>&nbsp;</dd>
 181 <dt><span class="memberNameLink"><a href="../compbio/data/msa/JABAService.html#SERVICE_NAMESPACE">SERVICE_NAMESPACE</a></span> - Static variable in interface compbio.data.msa.<a href="../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</a></dt>
 182 <dd>&nbsp;</dd>
 183 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.ServiceInfo.html#ServiceInfo--">ServiceInfo()</a></span> - Constructor for class compbio.ws.client.<a href="../compbio/ws/client/Services.ServiceInfo.html" title="class in compbio.ws.client">Services.ServiceInfo</a></dt>
 184 <dd>&nbsp;</dd>
 185 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.ServiceInfo.html#ServiceInfo-compbio.ws.client.Services-java.lang.String-java.lang.String-java.lang.String-">ServiceInfo(Services, String, String, String)</a></span> - Constructor for class compbio.ws.client.<a href="../compbio/ws/client/Services.ServiceInfo.html" title="class in compbio.ws.client">Services.ServiceInfo</a></dt>
 186 <dd>&nbsp;</dd>
 187 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Constraints.html#servicekey">servicekey</a></span> - Static variable in class compbio.ws.client.<a href="../compbio/ws/client/Constraints.html" title="class in compbio.ws.client">Constraints</a></dt>
 188 <dd>&nbsp;</dd>
 189 <dt><span class="memberNameLink"><a href="../compbio/ws/client/AAConClient.html#serviceName">serviceName</a></span> - Static variable in class compbio.ws.client.<a href="../compbio/ws/client/AAConClient.html" title="class in compbio.ws.client">AAConClient</a></dt>
 190 <dd>
 191 <div class="block">Web service name</div>
 192 </dd>
 193 <dt><span class="memberNameLink"><a href="../compbio/data/msa/Category.html#services">services</a></span> - Variable in class compbio.data.msa.<a href="../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</a></dt>
 194 <dd>&nbsp;</dd>
 195 <dt><a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><span class="typeNameLink">Services</span></a> - Enum in <a href="../compbio/ws/client/package-summary.html">compbio.ws.client</a></dt>
 196 <dd>
 197 <div class="block">List of web services currently supported by JABAWS version 2.1</div>
 198 </dd>
 199 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#Services--">Services()</a></span> - Constructor for enum compbio.ws.client.<a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></dt>
 200 <dd>&nbsp;</dd>
 201 <dt><a href="../compbio/ws/client/Services.ServiceInfo.html" title="class in compbio.ws.client"><span class="typeNameLink">Services.ServiceInfo</span></a> - Class in <a href="../compbio/ws/client/package-summary.html">compbio.ws.client</a></dt>
 202 <dd>&nbsp;</dd>
 203 <dt><a href="../compbio/stat/servlet/ServiceStatus.html" title="class in compbio.stat.servlet"><span class="typeNameLink">ServiceStatus</span></a> - Class in <a href="../compbio/stat/servlet/package-summary.html">compbio.stat.servlet</a></dt>
 204 <dd>
 205 <div class="block">Use cases:
 206
 207  Test web services and display results on the web page
 208  </div>
 209 </dd>
 210 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/ServiceStatus.html#ServiceStatus--">ServiceStatus()</a></span> - Constructor for class compbio.stat.servlet.<a href="../compbio/stat/servlet/ServiceStatus.html" title="class in compbio.stat.servlet">ServiceStatus</a></dt>
 211 <dd>&nbsp;</dd>
 212 <dt><a href="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client"><span class="typeNameLink">ServicesUtil</span></a> - Class in <a href="../compbio/ws/client/package-summary.html">compbio.ws.client</a></dt>
 213 <dd>&nbsp;</dd>
 214 <dt><span class="memberNameLink"><a href="../compbio/ws/client/ServicesUtil.html#ServicesUtil--">ServicesUtil()</a></span> - Constructor for class compbio.ws.client.<a href="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</a></dt>
 215 <dd>&nbsp;</dd>
 216 <dt><a href="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet"><span class="typeNameLink">ServiceTestResult</span></a> - Class in <a href="../compbio/stat/servlet/package-summary.html">compbio.stat.servlet</a></dt>
 217 <dd>
 218 <div class="block">Value class for test results.</div>
 219 </dd>
 220 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/ServiceTestResult.html#ServiceTestResult-compbio.ws.client.Services-">ServiceTestResult(Services)</a></span> - Constructor for class compbio.stat.servlet.<a href="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</a></dt>
 221 <dd>&nbsp;</dd>
 222 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#session">session</a></span> - Static variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterRunner.html" title="class in compbio.engine.cluster.drmaa">ClusterRunner</a></dt>
 223 <dd>&nbsp;</dd>
 224 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#session">session</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</a></dt>
 225 <dd>&nbsp;</dd>
 226 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#session">session</a></span> - Static variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</a></dt>
 227 <dd>&nbsp;</dd>
 228 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setActualNumberofSequences-int-">setActualNumberofSequences(int)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</a></dt>
 229 <dd>&nbsp;</dd>
 230 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomFold.html#setAlignment-compbio.data.sequence.Alignment-">setAlignment(Alignment)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomFold.html" title="class in compbio.data.msa.jaxws">CustomFold</a></dt>
 231 <dd>&nbsp;</dd>
 232 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/Fold.html#setAlignment-compbio.data.sequence.Alignment-">setAlignment(Alignment)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/Fold.html" title="class in compbio.data.msa.jaxws">Fold</a></dt>
 233 <dd>&nbsp;</dd>
 234 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetFold.html#setAlignment-compbio.data.sequence.Alignment-">setAlignment(Alignment)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PresetFold.html" title="class in compbio.data.msa.jaxws">PresetFold</a></dt>
 235 <dd>&nbsp;</dd>
 236 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLastTested.html#setArg0-compbio.ws.client.Services-">setArg0(Services)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws">GetLastTested</a></dt>
 237 <dd>&nbsp;</dd>
 238 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLastTestedOn.html#setArg0-compbio.ws.client.Services-">setArg0(Services)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws">GetLastTestedOn</a></dt>
 239 <dd>&nbsp;</dd>
 240 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetServiceDescription.html#setArg0-compbio.ws.client.Services-">setArg0(Services)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetServiceDescription.html" title="class in compbio.data.msa.jaxws">GetServiceDescription</a></dt>
 241 <dd>&nbsp;</dd>
 242 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/IsOperating.html#setArg0-compbio.ws.client.Services-">setArg0(Services)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/IsOperating.html" title="class in compbio.data.msa.jaxws">IsOperating</a></dt>
 243 <dd>&nbsp;</dd>
 244 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/TestService.html#setArg0-compbio.ws.client.Services-">setArg0(Services)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/TestService.html" title="class in compbio.data.msa.jaxws">TestService</a></dt>
 245 <dd>&nbsp;</dd>
 246 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.Parameter.html#setAtPosition-int-">setAtPosition(int)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.Parameter.html" title="class in compbio.engine.client">CommandBuilder.Parameter</a></dt>
 247 <dd>&nbsp;</dd>
 248 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#setBasicURL-java.net.URL-">setBasicURL(URL)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 249 <dd>&nbsp;</dd>
 250 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#setDefaultValue-java.lang.String-">setDefaultValue(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 251 <dd>
 252 <div class="block">Sets one of the values defined in optionList as default.</div>
 253 </dd>
 254 <dt><span class="memberNameLink"><a href="../compbio/metadata/Parameter.html#setDefaultValue-java.lang.String-">setDefaultValue(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</a></dt>
 255 <dd>&nbsp;</dd>
 256 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#setDelay-long-java.util.concurrent.TimeUnit-">setDelay(long, TimeUnit)</a></span> - Method in class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
 257 <dd>&nbsp;</dd>
 258 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#setDescription-java.lang.String-">setDescription(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 259 <dd>&nbsp;</dd>
 260 <dt><span class="memberNameLink"><a href="../compbio/metadata/Preset.html#setDescription-java.lang.String-">setDescription(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a></dt>
 261 <dd>&nbsp;</dd>
 262 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#setEmail-java.lang.String-">setEmail(String)</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterRunner.html" title="class in compbio.engine.cluster.drmaa">ClusterRunner</a></dt>
 263 <dd>&nbsp;</dd>
 264 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#setEmail-java.lang.String-">setEmail(String)</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</a></dt>
 265 <dd>&nbsp;</dd>
 266 <dt><span class="memberNameLink"><a href="../compbio/engine/client/RunConfiguration.html#setError-java.lang.String-">setError(String)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</a></dt>
 267 <dd>&nbsp;</dd>
 268 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#setError-java.lang.String-">setError(String)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 269 <dd>&nbsp;</dd>
 270 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#setExecProvider-compbio.engine.client.Executable.ExecProvider-">setExecProvider(Executable.ExecProvider)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
 271 <dd>&nbsp;</dd>
 272 <dt><a href="../compbio/ws/server/SetExecutableFlag.html" title="class in compbio.ws.server"><span class="typeNameLink">SetExecutableFlag</span></a> - Class in <a href="../compbio/ws/server/package-summary.html">compbio.ws.server</a></dt>
 273 <dd>
 274 <div class="block">Run setexecflag.sh script if executable flag is not set</div>
 275 </dd>
 276 <dt><span class="memberNameLink"><a href="../compbio/ws/server/SetExecutableFlag.html#SetExecutableFlag--">SetExecutableFlag()</a></span> - Constructor for class compbio.ws.server.<a href="../compbio/ws/server/SetExecutableFlag.html" title="class in compbio.ws.server">SetExecutableFlag</a></dt>
 277 <dd>&nbsp;</dd>
 278 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/Align.html#setFastaSequences-java.util.List-">setFastaSequences(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws">Align</a></dt>
 279 <dd>&nbsp;</dd>
 280 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/Analize.html#setFastaSequences-java.util.List-">setFastaSequences(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/Analize.html" title="class in compbio.data.msa.jaxws">Analize</a></dt>
 281 <dd>&nbsp;</dd>
 282 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAlign.html#setFastaSequences-java.util.List-">setFastaSequences(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</a></dt>
 283 <dd>&nbsp;</dd>
 284 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAnalize.html#setFastaSequences-java.util.List-">setFastaSequences(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</a></dt>
 285 <dd>&nbsp;</dd>
 286 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetAlign.html#setFastaSequences-java.util.List-">setFastaSequences(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</a></dt>
 287 <dd>&nbsp;</dd>
 288 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetAnalize.html#setFastaSequences-java.util.List-">setFastaSequences(List&lt;FastaSequence&gt;)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</a></dt>
 289 <dd>&nbsp;</dd>
 290 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.Parameter.html#setFirst--">setFirst()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.Parameter.html" title="class in compbio.engine.client">CommandBuilder.Parameter</a></dt>
 291 <dd>&nbsp;</dd>
 292 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#setFirst-java.lang.String-">setFirst(String)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
 293 <dd>&nbsp;</dd>
 294 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#setFurtherDetails-java.lang.String-">setFurtherDetails(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 295 <dd>&nbsp;</dd>
 296 <dt><span class="memberNameLink"><a href="../compbio/engine/client/RunConfiguration.html#setInput-java.lang.String-">setInput(String)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</a></dt>
 297 <dd>&nbsp;</dd>
 298 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#setInput-java.lang.String-">setInput(String)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 299 <dd>&nbsp;</dd>
 300 <dt><span class="memberNameLink"><a href="../compbio/runner/conservation/AACon.html#setInput-java.lang.String-">setInput(String)</a></span> - Method in class compbio.runner.conservation.<a href="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a></dt>
 301 <dd>&nbsp;</dd>
 302 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Disembl.html#setInput-java.lang.String-">setInput(String)</a></span> - Method in class compbio.runner.disorder.<a href="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</a></dt>
 303 <dd>&nbsp;</dd>
 304 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/GlobPlot.html#setInput-java.lang.String-">setInput(String)</a></span> - Method in class compbio.runner.disorder.<a href="../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</a></dt>
 305 <dd>&nbsp;</dd>
 306 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/IUPred.html#setInput-java.lang.String-">setInput(String)</a></span> - Method in class compbio.runner.disorder.<a href="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</a></dt>
 307 <dd>&nbsp;</dd>
 308 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Jronn.html#setInput-java.lang.String-">setInput(String)</a></span> - Method in class compbio.runner.disorder.<a href="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</a></dt>
 309 <dd>&nbsp;</dd>
 310 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/ClustalO.html#setInput-java.lang.String-">setInput(String)</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a></dt>
 311 <dd>&nbsp;</dd>
 312 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/ClustalW.html#setInput-java.lang.String-">setInput(String)</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</a></dt>
 313 <dd>&nbsp;</dd>
 314 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/GLprobs.html#setInput-java.lang.String-">setInput(String)</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a></dt>
 315 <dd>&nbsp;</dd>
 316 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Mafft.html#setInput-java.lang.String-">setInput(String)</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a></dt>
 317 <dd>&nbsp;</dd>
 318 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/MSAprobs.html#setInput-java.lang.String-">setInput(String)</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a></dt>
 319 <dd>&nbsp;</dd>
 320 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Muscle.html#setInput-java.lang.String-">setInput(String)</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</a></dt>
 321 <dd>&nbsp;</dd>
 322 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Probcons.html#setInput-java.lang.String-">setInput(String)</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</a></dt>
 323 <dd>&nbsp;</dd>
 324 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Tcoffee.html#setInput-java.lang.String-">setInput(String)</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</a></dt>
 325 <dd>&nbsp;</dd>
 326 <dt><span class="memberNameLink"><a href="../compbio/runner/structure/RNAalifold.html#setInput-java.lang.String-">setInput(String)</a></span> - Method in class compbio.runner.structure.<a href="../compbio/runner/structure/RNAalifold.html" title="class in compbio.runner.structure">RNAalifold</a></dt>
 327 <dd>&nbsp;</dd>
 328 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#setJobEnvironmentVariables-java.util.Map-">setJobEnvironmentVariables(Map&lt;String, String&gt;)</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterRunner.html" title="class in compbio.engine.cluster.drmaa">ClusterRunner</a></dt>
 329 <dd>&nbsp;</dd>
 330 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#setJobEnvironmentVariables-java.util.Map-">setJobEnvironmentVariables(Map&lt;String, String&gt;)</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</a></dt>
 331 <dd>&nbsp;</dd>
 332 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CancelJob.html#setJobId-java.lang.String-">setJobId(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws">CancelJob</a></dt>
 333 <dd>&nbsp;</dd>
 334 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetAnnotation.html#setJobId-java.lang.String-">setJobId(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws">GetAnnotation</a></dt>
 335 <dd>&nbsp;</dd>
 336 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetJobStatus.html#setJobId-java.lang.String-">setJobId(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws">GetJobStatus</a></dt>
 337 <dd>&nbsp;</dd>
 338 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetResult.html#setJobId-java.lang.String-">setJobId(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws">GetResult</a></dt>
 339 <dd>&nbsp;</dd>
 340 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PullExecStatistics.html#setJobId-java.lang.String-">setJobId(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</a></dt>
 341 <dd>&nbsp;</dd>
 342 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#setJobName-java.lang.String-">setJobName(String)</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterRunner.html" title="class in compbio.engine.cluster.drmaa">ClusterRunner</a></dt>
 343 <dd>&nbsp;</dd>
 344 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#setJobName-java.lang.String-">setJobName(String)</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</a></dt>
 345 <dd>&nbsp;</dd>
 346 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.Parameter.html#setLast--">setLast()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.Parameter.html" title="class in compbio.engine.client">CommandBuilder.Parameter</a></dt>
 347 <dd>&nbsp;</dd>
 348 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#setLast-java.lang.String-">setLast(String)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
 349 <dd>&nbsp;</dd>
 350 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#setLast-java.lang.String-java.lang.String-">setLast(String, String)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
 351 <dd>&nbsp;</dd>
 352 <dt><span class="memberNameLink"><a href="../compbio/metadata/ValueConstrain.html#setMax-java.lang.String-">setMax(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</a></dt>
 353 <dd>&nbsp;</dd>
 354 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html#setMessage-java.lang.String-">setMessage(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobSubmissionExceptionBean</a></dt>
 355 <dd>&nbsp;</dd>
 356 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setMessage-java.lang.String-">setMessage(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</a></dt>
 357 <dd>&nbsp;</dd>
 358 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html#setMessage-java.lang.String-">setMessage(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws">ResultNotAvailableExceptionBean</a></dt>
 359 <dd>&nbsp;</dd>
 360 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html#setMessage-java.lang.String-">setMessage(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html" title="class in compbio.data.msa.jaxws">UnsupportedRuntimeExceptionBean</a></dt>
 361 <dd>&nbsp;</dd>
 362 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html#setMessage-java.lang.String-">setMessage(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws">WrongParameterExceptionBean</a></dt>
 363 <dd>&nbsp;</dd>
 364 <dt><span class="memberNameLink"><a href="../compbio/metadata/ValueConstrain.html#setMin-java.lang.String-">setMin(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</a></dt>
 365 <dd>&nbsp;</dd>
 366 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#setName-java.lang.String-">setName(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 367 <dd>&nbsp;</dd>
 368 <dt><span class="memberNameLink"><a href="../compbio/metadata/Preset.html#setName-java.lang.String-">setName(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a></dt>
 369 <dd>&nbsp;</dd>
 370 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#setNativeSpecs-compbio.engine.client.Executable-">setNativeSpecs(Executable&lt;?&gt;)</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterRunner.html" title="class in compbio.engine.cluster.drmaa">ClusterRunner</a></dt>
 371 <dd>&nbsp;</dd>
 372 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#setNativeSpecs-compbio.engine.client.Executable-">setNativeSpecs(Executable&lt;?&gt;)</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</a></dt>
 373 <dd>&nbsp;</dd>
 374 <dt><span class="memberNameLink"><a href="../compbio/runner/conservation/AACon.html#setNCore-int-">setNCore(int)</a></span> - Method in class compbio.runner.conservation.<a href="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a></dt>
 375 <dd>&nbsp;</dd>
 376 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Jronn.html#setNCore-int-">setNCore(int)</a></span> - Method in class compbio.runner.disorder.<a href="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</a></dt>
 377 <dd>&nbsp;</dd>
 378 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/ClustalO.html#setNCore-int-">setNCore(int)</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a></dt>
 379 <dd>&nbsp;</dd>
 380 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Tcoffee.html#setNCore-int-">setNCore(int)</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</a></dt>
 381 <dd>&nbsp;</dd>
 382 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setNumberOfSequencesAllowed-int-">setNumberOfSequencesAllowed(int)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</a></dt>
 383 <dd>&nbsp;</dd>
 384 <dt><span class="memberNameLink"><a href="../compbio/metadata/Parameter.html#setOptionName-java.lang.String-">setOptionName(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</a></dt>
 385 <dd>&nbsp;</dd>
 386 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#setOptionNames-java.util.Set-">setOptionNames(Set&lt;String&gt;)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 387 <dd>&nbsp;</dd>
 388 <dt><span class="memberNameLink"><a href="../compbio/metadata/Parameter.html#setOptionNames-java.util.Set-">setOptionNames(Set&lt;String&gt;)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</a></dt>
 389 <dd>&nbsp;</dd>
 390 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAlign.html#setOptions-java.util.List-">setOptions(List&lt;Option&gt;)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</a></dt>
 391 <dd>&nbsp;</dd>
 392 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAnalize.html#setOptions-java.util.List-">setOptions(List&lt;Option&gt;)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</a></dt>
 393 <dd>&nbsp;</dd>
 394 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomFold.html#setOptions-java.util.List-">setOptions(List&lt;Option&gt;)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomFold.html" title="class in compbio.data.msa.jaxws">CustomFold</a></dt>
 395 <dd>&nbsp;</dd>
 396 <dt><span class="memberNameLink"><a href="../compbio/metadata/Preset.html#setOptions-java.util.List-">setOptions(List&lt;String&gt;)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a></dt>
 397 <dd>&nbsp;</dd>
 398 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#setOptions-java.util.List-">setOptions(List&lt;Option&lt;T&gt;&gt;)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
 399 <dd>
 400 <div class="block">Adds the list of options or parameters to the internal list of options</div>
 401 </dd>
 402 <dt><span class="memberNameLink"><a href="../compbio/engine/client/RunConfiguration.html#setOutput-java.lang.String-">setOutput(String)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</a></dt>
 403 <dd>&nbsp;</dd>
 404 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#setOutput-java.lang.String-">setOutput(String)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 405 <dd>&nbsp;</dd>
 406 <dt><span class="memberNameLink"><a href="../compbio/runner/conservation/AACon.html#setOutput-java.lang.String-">setOutput(String)</a></span> - Method in class compbio.runner.conservation.<a href="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a></dt>
 407 <dd>&nbsp;</dd>
 408 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/IUPred.html#setOutput-java.lang.String-">setOutput(String)</a></span> - Method in class compbio.runner.disorder.<a href="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</a></dt>
 409 <dd>&nbsp;</dd>
 410 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Jronn.html#setOutput-java.lang.String-">setOutput(String)</a></span> - Method in class compbio.runner.disorder.<a href="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</a></dt>
 411 <dd>&nbsp;</dd>
 412 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/ClustalO.html#setOutput-java.lang.String-">setOutput(String)</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a></dt>
 413 <dd>&nbsp;</dd>
 414 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/ClustalW.html#setOutput-java.lang.String-">setOutput(String)</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</a></dt>
 415 <dd>&nbsp;</dd>
 416 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Muscle.html#setOutput-java.lang.String-">setOutput(String)</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</a></dt>
 417 <dd>&nbsp;</dd>
 418 <dt><span class="memberNameLink"><a href="../compbio/runner/structure/RNAalifold.html#setOutput-java.lang.String-">setOutput(String)</a></span> - Method in class compbio.runner.structure.<a href="../compbio/runner/structure/RNAalifold.html" title="class in compbio.runner.structure">RNAalifold</a></dt>
 419 <dd>&nbsp;</dd>
 420 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#setParam-java.lang.String-">setParam(String)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
 421 <dd>&nbsp;</dd>
 422 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#setParam-compbio.engine.client.CommandBuilder.Parameter-">setParam(CommandBuilder.Parameter)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
 423 <dd>&nbsp;</dd>
 424 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#setParam-java.lang.String-java.lang.String-">setParam(String, String)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
 425 <dd>&nbsp;</dd>
 426 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#setParameter-java.lang.String-">setParameter(String)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 427 <dd>&nbsp;</dd>
 428 <dt><span class="memberNameLink"><a href="../compbio/engine/client/RunConfiguration.html#setParameters-compbio.engine.client.CommandBuilder-">setParameters(CommandBuilder&lt;?&gt;)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</a></dt>
 429 <dd>&nbsp;</dd>
 430 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#setParameters-java.util.List-">setParameters(List&lt;Parameter&lt;T&gt;&gt;)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
 431 <dd>
 432 <div class="block">Sets the list of parameters as internal list</div>
 433 </dd>
 434 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#setParams-java.util.List-">setParams(List&lt;String&gt;)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
 435 <dd>&nbsp;</dd>
 436 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#setPipes-compbio.engine.client.ConfiguredExecutable-">setPipes(ConfiguredExecutable&lt;?&gt;)</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterRunner.html" title="class in compbio.engine.cluster.drmaa">ClusterRunner</a></dt>
 437 <dd>&nbsp;</dd>
 438 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#setPipes-compbio.engine.client.ConfiguredExecutable-">setPipes(ConfiguredExecutable&lt;?&gt;)</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</a></dt>
 439 <dd>&nbsp;</dd>
 440 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PullExecStatistics.html#setPosition-long-">setPosition(long)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</a></dt>
 441 <dd>&nbsp;</dd>
 442 <dt><span class="memberNameLink"><a href="../compbio/metadata/Parameter.html#setPossibleValues-java.util.Set-">setPossibleValues(Set&lt;String&gt;)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</a></dt>
 443 <dd>&nbsp;</dd>
 444 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetAlign.html#setPreset-compbio.metadata.Preset-">setPreset(Preset)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</a></dt>
 445 <dd>&nbsp;</dd>
 446 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetAnalize.html#setPreset-compbio.metadata.Preset-">setPreset(Preset)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</a></dt>
 447 <dd>&nbsp;</dd>
 448 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetFold.html#setPreset-compbio.metadata.Preset-">setPreset(Preset)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PresetFold.html" title="class in compbio.data.msa.jaxws">PresetFold</a></dt>
 449 <dd>&nbsp;</dd>
 450 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLimit.html#setPresetName-java.lang.String-">setPresetName(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</a></dt>
 451 <dd>&nbsp;</dd>
 452 <dt><span class="memberNameLink"><a href="../compbio/metadata/PresetManager.html#setPresets-java.util.List-">setPresets(List&lt;Preset&lt;T&gt;&gt;)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a></dt>
 453 <dd>&nbsp;</dd>
 454 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#setPrmSeparator-java.lang.String-">setPrmSeparator(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
 455 <dd>
 456 <div class="block">Sets name value separator character</div>
 457 </dd>
 458 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Score.html#setRanges-java.util.TreeSet-">setRanges(TreeSet&lt;Range&gt;)</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a></dt>
 459 <dd>&nbsp;</dd>
 460 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#setRequired-boolean-">setRequired(boolean)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 461 <dd>&nbsp;</dd>
 462 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/AlignResponse.html#setReturn-java.lang.String-">setReturn(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws">AlignResponse</a></dt>
 463 <dd>&nbsp;</dd>
 464 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/AnalizeResponse.html#setReturn-java.lang.String-">setReturn(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/AnalizeResponse.html" title="class in compbio.data.msa.jaxws">AnalizeResponse</a></dt>
 465 <dd>&nbsp;</dd>
 466 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CancelJobResponse.html#setReturn-boolean-">setReturn(boolean)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws">CancelJobResponse</a></dt>
 467 <dd>&nbsp;</dd>
 468 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAlignResponse.html#setReturn-java.lang.String-">setReturn(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws">CustomAlignResponse</a></dt>
 469 <dd>&nbsp;</dd>
 470 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAnalizeResponse.html#setReturn-java.lang.String-">setReturn(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomAnalizeResponse.html" title="class in compbio.data.msa.jaxws">CustomAnalizeResponse</a></dt>
 471 <dd>&nbsp;</dd>
 472 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomFoldResponse.html#setReturn-java.lang.String-">setReturn(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomFoldResponse.html" title="class in compbio.data.msa.jaxws">CustomFoldResponse</a></dt>
 473 <dd>&nbsp;</dd>
 474 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/FoldResponse.html#setReturn-java.lang.String-">setReturn(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/FoldResponse.html" title="class in compbio.data.msa.jaxws">FoldResponse</a></dt>
 475 <dd>&nbsp;</dd>
 476 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetAnnotationResponse.html#setReturn-compbio.data.sequence.ScoreManager-">setReturn(ScoreManager)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws">GetAnnotationResponse</a></dt>
 477 <dd>&nbsp;</dd>
 478 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetJobStatusResponse.html#setReturn-compbio.metadata.JobStatus-">setReturn(JobStatus)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws">GetJobStatusResponse</a></dt>
 479 <dd>&nbsp;</dd>
 480 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html#setReturn-java.util.Date-">setReturn(Date)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedOnResponse</a></dt>
 481 <dd>&nbsp;</dd>
 482 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLastTestedResponse.html#setReturn-int-">setReturn(int)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedResponse</a></dt>
 483 <dd>&nbsp;</dd>
 484 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLimitResponse.html#setReturn-compbio.metadata.Limit-">setReturn(Limit)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws">GetLimitResponse</a></dt>
 485 <dd>&nbsp;</dd>
 486 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLimitsResponse.html#setReturn-compbio.metadata.LimitsManager-">setReturn(LimitsManager)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws">GetLimitsResponse</a></dt>
 487 <dd>&nbsp;</dd>
 488 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetNonoperatedServicesResponse.html#setReturn-java.util.Set-">setReturn(Set&lt;Services&gt;)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetNonoperatedServicesResponse.html" title="class in compbio.data.msa.jaxws">GetNonoperatedServicesResponse</a></dt>
 489 <dd>&nbsp;</dd>
 490 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetPresetsResponse.html#setReturn-compbio.metadata.PresetManager-">setReturn(PresetManager)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws">GetPresetsResponse</a></dt>
 491 <dd>&nbsp;</dd>
 492 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetResultResponse.html#setReturn-compbio.data.sequence.Alignment-">setReturn(Alignment)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws">GetResultResponse</a></dt>
 493 <dd>&nbsp;</dd>
 494 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#setReturn-compbio.metadata.RunnerConfig-">setReturn(RunnerConfig)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws">GetRunnerOptionsResponse</a></dt>
 495 <dd>&nbsp;</dd>
 496 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html#setReturn-java.util.Set-">setReturn(Set&lt;Category&gt;)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html" title="class in compbio.data.msa.jaxws">GetServiceCategoriesResponse</a></dt>
 497 <dd>&nbsp;</dd>
 498 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html#setReturn-java.lang.String-">setReturn(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html" title="class in compbio.data.msa.jaxws">GetServiceDescriptionResponse</a></dt>
 499 <dd>&nbsp;</dd>
 500 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html#setReturn-java.util.Set-">setReturn(Set&lt;Services&gt;)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws">GetSupportedServicesResponse</a></dt>
 501 <dd>&nbsp;</dd>
 502 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/IsOperatingResponse.html#setReturn-boolean-">setReturn(boolean)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws">IsOperatingResponse</a></dt>
 503 <dd>&nbsp;</dd>
 504 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetAlignResponse.html#setReturn-java.lang.String-">setReturn(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws">PresetAlignResponse</a></dt>
 505 <dd>&nbsp;</dd>
 506 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetAnalizeResponse.html#setReturn-java.lang.String-">setReturn(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PresetAnalizeResponse.html" title="class in compbio.data.msa.jaxws">PresetAnalizeResponse</a></dt>
 507 <dd>&nbsp;</dd>
 508 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetFoldResponse.html#setReturn-java.lang.String-">setReturn(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PresetFoldResponse.html" title="class in compbio.data.msa.jaxws">PresetFoldResponse</a></dt>
 509 <dd>&nbsp;</dd>
 510 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#setReturn-compbio.metadata.ChunkHolder-">setReturn(ChunkHolder)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws">PullExecStatisticsResponse</a></dt>
 511 <dd>&nbsp;</dd>
 512 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/TestAllServicesResponse.html#setReturn-java.lang.String-">setReturn(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/TestAllServicesResponse.html" title="class in compbio.data.msa.jaxws">TestAllServicesResponse</a></dt>
 513 <dd>&nbsp;</dd>
 514 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/TestServiceResponse.html#setReturn-java.lang.String-">setReturn(String)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/TestServiceResponse.html" title="class in compbio.data.msa.jaxws">TestServiceResponse</a></dt>
 515 <dd>&nbsp;</dd>
 516 <dt><span class="memberNameLink"><a href="../compbio/metadata/PresetManager.html#setRunnerClassName-java.lang.String-">setRunnerClassName(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a></dt>
 517 <dd>&nbsp;</dd>
 518 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#setRunnerClassName-java.lang.String-">setRunnerClassName(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
 519 <dd>
 520 <div class="block">Set the name of a runner class</div>
 521 </dd>
 522 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setSequenceLenghtActual-int-">setSequenceLenghtActual(int)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</a></dt>
 523 <dd>&nbsp;</dd>
 524 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setSequenceLenghtAllowed-int-">setSequenceLenghtAllowed(int)</a></span> - Method in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</a></dt>
 525 <dd>&nbsp;</dd>
 526 <dt><span class="memberNameLink"><a href="../compbio/metadata/ValueConstrain.html#setType-compbio.metadata.ValueConstrain.Type-">setType(ValueConstrain.Type)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</a></dt>
 527 <dd>&nbsp;</dd>
 528 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#setupWorkDirectory-compbio.engine.client.ConfExecutable-compbio.engine.client.Executable.ExecProvider-">setupWorkDirectory(ConfExecutable&lt;T&gt;, Executable.ExecProvider)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></dt>
 529 <dd>&nbsp;</dd>
 530 <dt><span class="memberNameLink"><a href="../compbio/metadata/Parameter.html#setValidValue-compbio.metadata.ValueConstrain-">setValidValue(ValueConstrain)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</a></dt>
 531 <dd>&nbsp;</dd>
 532 <dt><span class="memberNameLink"><a href="../compbio/metadata/Argument.html#setValue-java.lang.String-">setValue(String)</a></span> - Method in interface compbio.metadata.<a href="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</a></dt>
 533 <dd>
 534 <div class="block">Set default values for the parameter or an option</div>
 535 </dd>
 536 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#setValue-java.lang.String-">setValue(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 537 <dd>&nbsp;</dd>
 538 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#setWorkDirectory-java.lang.String-">setWorkDirectory(String)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
 539 <dd>&nbsp;</dd>
 540 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfiguredExecutable.html#setWorkDirectory-java.lang.String-">setWorkDirectory(String)</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a></dt>
 541 <dd>&nbsp;</dd>
 542 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/IUPred.html#SHORT_OUTPUT">SHORT_OUTPUT</a></span> - Static variable in class compbio.runner.disorder.<a href="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</a></dt>
 543 <dd>&nbsp;</dd>
 544 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalExecutorService.html#shutDown--">shutDown()</a></span> - Static method in class compbio.engine.local.<a href="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</a></dt>
 545 <dd>
 546 <div class="block">This stops all executing processes via interruption.</div>
 547 </dd>
 548 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatDB.html#shutdownDBServer--">shutdownDBServer()</a></span> - Static method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</a></dt>
 549 <dd>&nbsp;</dd>
 550 <dt><span class="memberNameLink"><a href="../compbio/engine/local/ExecutableWrapper.html#shutdownService--">shutdownService()</a></span> - Static method in class compbio.engine.local.<a href="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</a></dt>
 551 <dd>
 552 <div class="block">Stops internal executor service which captures streams of native
 553  executables.</div>
 554 </dd>
 555 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#signal">signal</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 556 <dd>
 557 <div class="block">see man 5 accounting on sun grid engine installed workstation see also
 558  man 2 getrusage</div>
 559 </dd>
 560 <dt><a href="../compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server"><span class="typeNameLink">SimpleWSPublisher</span></a> - Class in <a href="../compbio/ws/server/package-summary.html">compbio.ws.server</a></dt>
 561 <dd>
 562 <div class="block"><span class="deprecatedLabel">Deprecated.</span></div>
 563 </dd>
 564 <dt><span class="memberNameLink"><a href="../compbio/ws/server/SimpleWSPublisher.html#SimpleWSPublisher-java.lang.Object-java.lang.String-">SimpleWSPublisher(Object, String)</a></span> - Constructor for class compbio.ws.server.<a href="../compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server">SimpleWSPublisher</a></dt>
 565 <dd>
 566 <div class="block"><span class="deprecatedLabel">Deprecated.</span></div>
 567 &nbsp;</dd>
 568 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ScoreManager.html#SINGLE_ENTRY_KEY">SINGLE_ENTRY_KEY</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></dt>
 569 <dd>&nbsp;</dd>
 570 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#size--">size()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
 571 <dd>&nbsp;</dd>
 572 <dt><a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client"><span class="typeNameLink">SkeletalExecutable</span></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></dt>
 573 <dd>&nbsp;</dd>
 574 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#SkeletalExecutable--">SkeletalExecutable()</a></span> - Constructor for class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 575 <dd>&nbsp;</dd>
 576 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#SkeletalExecutable-java.lang.String-">SkeletalExecutable(String)</a></span> - Constructor for class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 577 <dd>&nbsp;</dd>
 578 <dt><a href="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence"><span class="typeNameLink">SMERFSConstraints</span></a> - Enum in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
 579 <dd>
 580 <div class="block">Enumeration defining two constraints for SMERFS columns score calculation.</div>
 581 </dd>
 582 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SMERFSConstraints.html#SMERFSConstraints--">SMERFSConstraints()</a></span> - Constructor for enum compbio.data.sequence.<a href="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</a></dt>
 583 <dd>&nbsp;</dd>
 584 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/RunnerConfigMarshaller.MySchemaOutputResolver.html#sname">sname</a></span> - Variable in class compbio.engine.conf.<a href="../compbio/engine/conf/RunnerConfigMarshaller.MySchemaOutputResolver.html" title="class in compbio.engine.conf">RunnerConfigMarshaller.MySchemaOutputResolver</a></dt>
 585 <dd>&nbsp;</dd>
 586 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatProcessor.html#sortByResultSize--">sortByResultSize()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</a></dt>
 587 <dd>&nbsp;</dd>
 588 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatProcessor.html#sortByRuntime--">sortByRuntime()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</a></dt>
 589 <dd>&nbsp;</dd>
 590 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatProcessor.html#sortByStartTime--">sortByStartTime()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</a></dt>
 591 <dd>&nbsp;</dd>
 592 <dt><span class="memberNameLink"><a href="../compbio/metadata/Preset.html#SPACE">SPACE</a></span> - Static variable in class compbio.metadata.<a href="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a></dt>
 593 <dd>&nbsp;</dd>
 594 <dt><span class="memberNameLink"><a href="../compbio/runner/Util.html#SPACE">SPACE</a></span> - Static variable in class compbio.runner.<a href="../compbio/runner/Util.html" title="class in compbio.runner">Util</a></dt>
 595 <dd>&nbsp;</dd>
 596 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ClustalAlignmentUtil.html#spacer">spacer</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</a></dt>
 597 <dd>&nbsp;</dd>
 598 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#start">start</a></span> - Variable in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 599 <dd>&nbsp;</dd>
 600 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#start_time">start_time</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 601 <dd>&nbsp;</dd>
 602 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalExecutorService.html#startTime">startTime</a></span> - Variable in class compbio.engine.local.<a href="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</a></dt>
 603 <dd>&nbsp;</dd>
 604 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#STARTTIME">STARTTIME</a></span> - Static variable in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 605 <dd>&nbsp;</dd>
 606 <dt><span class="memberNameLink"><a href="../compbio/runner/conservation/AACon.html#STAT_FILE">STAT_FILE</a></span> - Static variable in class compbio.runner.conservation.<a href="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a></dt>
 607 <dd>&nbsp;</dd>
 608 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Jronn.html#STAT_FILE">STAT_FILE</a></span> - Static variable in class compbio.runner.disorder.<a href="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</a></dt>
 609 <dd>&nbsp;</dd>
 610 <dt><a href="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util"><span class="typeNameLink">StatCollection</span></a> - Class in <a href="../compbio/stat/servlet/util/package-summary.html">compbio.stat.servlet.util</a></dt>
 611 <dd>&nbsp;</dd>
 612 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/StatCollection.html#StatCollection--">StatCollection()</a></span> - Constructor for class compbio.stat.servlet.util.<a href="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</a></dt>
 613 <dd>&nbsp;</dd>
 614 <dt><a href="../compbio/stat/servlet/util/StatCollection.Stattype.html" title="enum in compbio.stat.servlet.util"><span class="typeNameLink">StatCollection.Stattype</span></a> - Enum in <a href="../compbio/stat/servlet/util/package-summary.html">compbio.stat.servlet.util</a></dt>
 615 <dd>
 616 <div class="block">Total number of requests
 617
 618  incomplete abandoned cancelled</div>
 619 </dd>
 620 <dt><a href="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector"><span class="typeNameLink">StatDB</span></a> - Class in <a href="../compbio/stat/collector/package-summary.html">compbio.stat.collector</a></dt>
 621 <dd>
 622 <div class="block">The database must be stored in the application root directory and called
 623  "ExecutionStatistic"</div>
 624 </dd>
 625 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatDB.html#StatDB--">StatDB()</a></span> - Constructor for class compbio.stat.collector.<a href="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</a></dt>
 626 <dd>&nbsp;</dd>
 627 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatDB.html#StatDB-boolean-">StatDB(boolean)</a></span> - Constructor for class compbio.stat.collector.<a href="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</a></dt>
 628 <dd>
 629 <div class="block">Connect to test database</div>
 630 </dd>
 631 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatDB.html#statDBName">statDBName</a></span> - Static variable in class compbio.stat.collector.<a href="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</a></dt>
 632 <dd>&nbsp;</dd>
 633 <dt><a href="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet"><span class="typeNameLink">StatisticCollector</span></a> - Class in <a href="../compbio/stat/servlet/package-summary.html">compbio.stat.servlet</a></dt>
 634 <dd>&nbsp;</dd>
 635 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/StatisticCollector.html#StatisticCollector--">StatisticCollector()</a></span> - Constructor for class compbio.stat.servlet.<a href="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</a></dt>
 636 <dd>&nbsp;</dd>
 637 <dt><a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa"><span class="typeNameLink">StatisticManager</span></a> - Class in <a href="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</a></dt>
 638 <dd>&nbsp;</dd>
 639 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#StatisticManager-org.ggf.drmaa.JobInfo-">StatisticManager(JobInfo)</a></span> - Constructor for class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 640 <dd>&nbsp;</dd>
 641 <dt><a href="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector"><span class="typeNameLink">StatProcessor</span></a> - Class in <a href="../compbio/stat/collector/package-summary.html">compbio.stat.collector</a></dt>
 642 <dd>&nbsp;</dd>
 643 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatProcessor.html#StatProcessor-java.util.List-">StatProcessor(List&lt;JobStat&gt;)</a></span> - Constructor for class compbio.stat.collector.<a href="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</a></dt>
 644 <dd>&nbsp;</dd>
 645 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/ExecutionStatCollector.html#stats">stats</a></span> - Variable in class compbio.stat.collector.<a href="../compbio/stat/collector/ExecutionStatCollector.html" title="class in compbio.stat.collector">ExecutionStatCollector</a></dt>
 646 <dd>&nbsp;</dd>
 647 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatProcessor.html#stats">stats</a></span> - Variable in class compbio.stat.collector.<a href="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</a></dt>
 648 <dd>&nbsp;</dd>
 649 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/StatCollection.Stattype.html#Stattype--">Stattype()</a></span> - Constructor for enum compbio.stat.servlet.util.<a href="../compbio/stat/servlet/util/StatCollection.Stattype.html" title="enum in compbio.stat.servlet.util">StatCollection.Stattype</a></dt>
 650 <dd>&nbsp;</dd>
 651 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#stochBTStructP">stochBTStructP</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructReader.html" title="class in compbio.data.sequence">RNAStructReader</a></dt>
 652 <dd>&nbsp;</dd>
 653 <dt><a href="../compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local"><span class="typeNameLink">StreamGobbler</span></a> - Class in <a href="../compbio/engine/local/package-summary.html">compbio.engine.local</a></dt>
 654 <dd>&nbsp;</dd>
 655 <dt><span class="memberNameLink"><a href="../compbio/engine/local/StreamGobbler.html#StreamGobbler-java.io.InputStream-java.io.OutputStream-compbio.engine.local.StreamGobbler.OutputType-">StreamGobbler(InputStream, OutputStream, StreamGobbler.OutputType)</a></span> - Constructor for class compbio.engine.local.<a href="../compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local">StreamGobbler</a></dt>
 656 <dd>&nbsp;</dd>
 657 <dt><a href="../compbio/engine/local/StreamGobbler.OutputType.html" title="enum in compbio.engine.local"><span class="typeNameLink">StreamGobbler.OutputType</span></a> - Enum in <a href="../compbio/engine/local/package-summary.html">compbio.engine.local</a></dt>
 658 <dd>&nbsp;</dd>
 659 <dt><span class="memberNameLink"><a href="../compbio/engine/client/RunConfiguration.html#strEquals-java.lang.String-java.lang.String-">strEquals(String, String)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</a></dt>
 660 <dd>&nbsp;</dd>
 661 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#structP">structP</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructReader.html" title="class in compbio.data.sequence">RNAStructReader</a></dt>
 662 <dd>&nbsp;</dd>
 663 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#submission_time">submission_time</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 664 <dd>&nbsp;</dd>
 665 <dt><a href="../compbio/engine/SubmissionManager.html" title="class in compbio.engine"><span class="typeNameLink">SubmissionManager</span></a> - Class in <a href="../compbio/engine/package-summary.html">compbio.engine</a></dt>
 666 <dd>
 667 <div class="block">Submit jobs for execution</div>
 668 </dd>
 669 <dt><span class="memberNameLink"><a href="../compbio/engine/SubmissionManager.html#SubmissionManager--">SubmissionManager()</a></span> - Constructor for class compbio.engine.<a href="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</a></dt>
 670 <dd>&nbsp;</dd>
 671 <dt><span class="memberNameLink"><a href="../compbio/engine/AsyncExecutor.html#submitJob-compbio.engine.client.ConfiguredExecutable-">submitJob(ConfiguredExecutable&lt;?&gt;)</a></span> - Method in interface compbio.engine.<a href="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</a></dt>
 672 <dd>
 673 <div class="block">Submits job for the execution
 674  Immediate execution is not guaranteed, this method puts the job in the queue.</div>
 675 </dd>
 676 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/AsyncClusterRunner.html#submitJob-compbio.engine.client.ConfiguredExecutable-">submitJob(ConfiguredExecutable&lt;?&gt;)</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/AsyncClusterRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncClusterRunner</a></dt>
 677 <dd>&nbsp;</dd>
 678 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#submitJob-compbio.engine.client.ConfiguredExecutable-">submitJob(ConfiguredExecutable&lt;?&gt;)</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</a></dt>
 679 <dd>&nbsp;</dd>
 680 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#submitJob--">submitJob()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterRunner.html" title="class in compbio.engine.cluster.drmaa">ClusterRunner</a></dt>
 681 <dd>&nbsp;</dd>
 682 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#submitJob--">submitJob()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</a></dt>
 683 <dd>&nbsp;</dd>
 684 <dt><span class="memberNameLink"><a href="../compbio/engine/local/AsyncLocalRunner.html#submitJob-compbio.engine.client.ConfiguredExecutable-">submitJob(ConfiguredExecutable&lt;?&gt;)</a></span> - Method in class compbio.engine.local.<a href="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</a></dt>
 685 <dd>&nbsp;</dd>
 686 <dt><span class="memberNameLink"><a href="../compbio/engine/SubmissionManager.html#submittedTasks">submittedTasks</a></span> - Static variable in class compbio.engine.<a href="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</a></dt>
 687 <dd>&nbsp;</dd>
 688 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/Totals.html#sumOfTotals-java.util.Map-">sumOfTotals(Map&lt;Date, Totals&gt;)</a></span> - 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></dt>
 689 <dd>&nbsp;</dd>
 690 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/Totals.html#sumStats-java.util.Map-">sumStats(Map&lt;Services, StatProcessor&gt;)</a></span> - 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></dt>
 691 <dd>&nbsp;</dd>
 692 <dt><span class="memberNameLink"><a href="../compbio/engine/PulledFileCache.html#sweep--">sweep()</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</a></dt>
 693 <dd>&nbsp;</dd>
 694 <dt><a href="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine"><span class="typeNameLink">SyncExecutor</span></a> - Interface in <a href="../compbio/engine/package-summary.html">compbio.engine</a></dt>
 695 <dd>
 696 <div class="block">Synchronous executor, is an engine to run the Executable synchronously.</div>
 697 </dd>
 698 </dl>
 699 <a href="index-1.html">A</a>&nbsp;<a href="index-2.html">B</a>&nbsp;<a href="index-3.html">C</a>&nbsp;<a href="index-4.html">D</a>&nbsp;<a href="index-5.html">E</a>&nbsp;<a href="index-6.html">F</a>&nbsp;<a href="index-7.html">G</a>&nbsp;<a href="index-8.html">H</a>&nbsp;<a href="index-9.html">I</a>&nbsp;<a href="index-10.html">J</a>&nbsp;<a href="index-11.html">K</a>&nbsp;<a href="index-12.html">L</a>&nbsp;<a href="index-13.html">M</a>&nbsp;<a href="index-14.html">N</a>&nbsp;<a href="index-15.html">O</a>&nbsp;<a href="index-16.html">P</a>&nbsp;<a href="index-17.html">Q</a>&nbsp;<a href="index-18.html">R</a>&nbsp;<a href="index-19.html">S</a>&nbsp;<a href="index-20.html">T</a>&nbsp;<a href="index-21.html">U</a>&nbsp;<a href="index-22.html">V</a>&nbsp;<a href="index-23.html">W</a>&nbsp;<a href="index-24.html">_</a>&nbsp;</div>
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