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75 <h2 class="title">L</h2>
77 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.Parameter.html#LAST">LAST</a></span> - Static variable in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.Parameter.html" title="class in compbio.engine.client">CommandBuilder.Parameter</a></dt>
79 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#lastAccessTime">lastAccessTime</a></span> - Variable in class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
81 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalEngineUtil.html#launderThrowable-java.lang.Throwable-">launderThrowable(Throwable)</a></span> - Static method in class compbio.engine.local.<a href="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</a></dt>
83 <div class="block">Coerce an unchecked Throwable to a RuntimeException or Error</div>
85 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/DirCleaner.html#LifeSpanInHours">LifeSpanInHours</a></span> - Variable in class compbio.stat.collector.<a href="../compbio/stat/collector/DirCleaner.html" title="class in compbio.stat.collector">DirCleaner</a></dt>
87 <dt><a href="../compbio/metadata/Limit.html" title="class in compbio.metadata"><span class="typeNameLink">Limit</span></a><<a href="../compbio/metadata/Limit.html" title="type parameter in Limit">T</a>> - Class in <a href="../compbio/metadata/package-summary.html">compbio.metadata</a></dt>
89 <div class="block">A value object containing a maximum number of sequences and a maximum average
90 sequence length for a preset.</div>
92 <dt><span class="memberNameLink"><a href="../compbio/metadata/Limit.html#Limit--">Limit()</a></span> - Constructor for class compbio.metadata.<a href="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a></dt>
94 <dt><span class="memberNameLink"><a href="../compbio/metadata/Limit.html#Limit-int-int-java.lang.String-">Limit(int, int, String)</a></span> - Constructor for class compbio.metadata.<a href="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a></dt>
96 <div class="block">Instantiate the limit</div>
98 <dt><span class="memberNameLink"><a href="../compbio/metadata/Limit.html#Limit-int-int-java.lang.String-boolean-">Limit(int, int, String, boolean)</a></span> - Constructor for class compbio.metadata.<a href="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a></dt>
100 <dt><span class="memberNameLink"><a href="../compbio/metadata/LimitsManager.html#limit">limit</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a></dt>
102 <dt><a href="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><span class="typeNameLink">LimitExceededException</span></a> - Exception in <a href="../compbio/metadata/package-summary.html">compbio.metadata</a></dt>
104 <div class="block">This exception is thrown if the task larger in size that the limit that
105 applies to the calculation.</div>
107 <dt><span class="memberNameLink"><a href="../compbio/metadata/LimitExceededException.html#LimitExceededException-java.lang.String-">LimitExceededException(String)</a></span> - Constructor for exception compbio.metadata.<a href="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></dt>
109 <dt><a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">LimitExceededExceptionBean</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
111 <div class="block">This class was generated by the JAX-WS RI.</div>
113 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#LimitExceededExceptionBean--">LimitExceededExceptionBean()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</a></dt>
115 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Constraints.html#limitList">limitList</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>
117 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalOWS.html#limitMan">limitMan</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</a></dt>
119 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalWS.html#limitMan">limitMan</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</a></dt>
121 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GenericMetadataService.html#limitMan">limitMan</a></span> - Variable in class compbio.ws.server.<a href="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</a></dt>
123 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GLprobsWS.html#limitMan">limitMan</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/GLprobsWS.html" title="class in compbio.ws.server">GLprobsWS</a></dt>
125 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MafftWS.html#limitMan">limitMan</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</a></dt>
127 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MSAprobsWS.html#limitMan">limitMan</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/MSAprobsWS.html" title="class in compbio.ws.server">MSAprobsWS</a></dt>
129 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MuscleWS.html#limitMan">limitMan</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</a></dt>
131 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ProbconsWS.html#limitMan">limitMan</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</a></dt>
133 <dt><span class="memberNameLink"><a href="../compbio/ws/server/TcoffeeWS.html#limitMan">limitMan</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</a></dt>
135 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#limits">limits</a></span> - Variable in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
137 <dt><a href="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><span class="typeNameLink">LimitsManager</span></a><<a href="../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</a>> - Class in <a href="../compbio/metadata/package-summary.html">compbio.metadata</a></dt>
139 <div class="block">A collection of Limits</div>
141 <dt><span class="memberNameLink"><a href="../compbio/metadata/LimitsManager.html#LimitsManager--">LimitsManager()</a></span> - Constructor for class compbio.metadata.<a href="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a></dt>
143 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.ServiceInfo.html#line_delimiter">line_delimiter</a></span> - Static variable in class compbio.ws.client.<a href="../compbio/ws/client/Services.ServiceInfo.html" title="class in compbio.ws.client">Services.ServiceInfo</a></dt>
145 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Jws2Client.html#listAllServices-java.lang.String-">listAllServices(String)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</a></dt>
147 <dt><span class="memberNameLink"><a href="../compbio/ws/client/CmdHelper.html#listLimits-java.lang.String:A-">listLimits(String[])</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/CmdHelper.html" title="class in compbio.ws.client">CmdHelper</a></dt>
149 <div class="block">Checks whether limitList parameter is in the command line</div>
151 <dt><span class="memberNameLink"><a href="../compbio/ws/client/CmdHelper.html#listParameters-java.lang.String:A-">listParameters(String[])</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/CmdHelper.html" title="class in compbio.ws.client">CmdHelper</a></dt>
153 <div class="block">Searches the command line keys in the array of parameters</div>
155 <dt><span class="memberNameLink"><a href="../compbio/ws/client/CmdHelper.html#listPresets-java.lang.String:A-">listPresets(String[])</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/CmdHelper.html" title="class in compbio.ws.client">CmdHelper</a></dt>
157 <div class="block">Check whether presetList is set in the command line</div>
159 <dt><span class="memberNameLink"><a href="../compbio/ws/client/CmdHelper.html#listServices-java.lang.String:A-">listServices(String[])</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/CmdHelper.html" title="class in compbio.ws.client">CmdHelper</a></dt>
161 <div class="block">list available services</div>
163 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Constraints.html#listServices">listServices</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>
165 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Constraints.html#listServicesOld">listServicesOld</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>
167 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/DirCleaner.html#livesOverLifeSpan-compbio.stat.collector.JobDirectory-">livesOverLifeSpan(JobDirectory)</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/DirCleaner.html" title="class in compbio.stat.collector">DirCleaner</a></dt>
169 <dt><span class="memberNameLink"><a href="../compbio/engine/client/RunConfiguration.html#load-java.io.InputStream-">load(InputStream)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</a></dt>
171 <dt><span class="memberNameLink"><a href="../compbio/ws/client/WSTester.html#loadAlignment--">loadAlignment()</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</a></dt>
173 <div class="block">Converting input to a form accepted by WS</div>
175 <dt><a href="../compbio/engine/LoadBalancer.html" title="class in compbio.engine"><span class="typeNameLink">LoadBalancer</span></a> - Class in <a href="../compbio/engine/package-summary.html">compbio.engine</a></dt>
177 <div class="block">This class decides where to execute the job.</div>
179 <dt><span class="memberNameLink"><a href="../compbio/engine/LoadBalancer.html#LoadBalancer--">LoadBalancer()</a></span> - Constructor for class compbio.engine.<a href="../compbio/engine/LoadBalancer.html" title="class in compbio.engine">LoadBalancer</a></dt>
181 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EngineUtil.html#loadExecutable-java.lang.String-">loadExecutable(String)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/EngineUtil.html" title="class in compbio.engine.client">EngineUtil</a></dt>
183 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Util.html#loadExecutable-java.lang.String-">loadExecutable(String)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</a></dt>
185 <dt><span class="memberNameLink"><a href="../compbio/ws/client/IOHelper.html#loadParameters-java.io.File-">loadParameters(File)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/IOHelper.html" title="class in compbio.ws.client">IOHelper</a></dt>
187 <div class="block">Load parameters from file</div>
189 <dt><span class="memberNameLink"><a href="../compbio/ws/client/WSTester.html#loadRNAAlignment--">loadRNAAlignment()</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</a></dt>
191 <div class="block">Converting input to a form accepted by WS</div>
193 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#loadRunConfiguration-compbio.engine.client.RunConfiguration-">loadRunConfiguration(RunConfiguration)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
195 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#loadRunConfiguration-java.io.InputStream-">loadRunConfiguration(InputStream)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
197 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfiguredExecutable.html#loadRunConfiguration-java.io.InputStream-">loadRunConfiguration(InputStream)</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a></dt>
199 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Executable.html#loadRunConfiguration-compbio.engine.client.RunConfiguration-">loadRunConfiguration(RunConfiguration)</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a></dt>
201 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration-compbio.engine.client.RunConfiguration-">loadRunConfiguration(RunConfiguration)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
203 <dt><span class="memberNameLink"><a href="../compbio/ws/client/WSTester.html#loadSeqs-int-">loadSeqs(int)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</a></dt>
205 <div class="block">Converting input to a form accepted by WS</div>
207 <dt><span class="memberNameLink"><a href="../compbio/metadata/PresetManager.html#LOCAL_ENGINE_LIMIT_PRESET">LOCAL_ENGINE_LIMIT_PRESET</a></span> - Static variable in class compbio.metadata.<a href="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a></dt>
209 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#LOCAL_WORK_DIRECTORY">LOCAL_WORK_DIRECTORY</a></span> - Static variable in class compbio.engine.<a href="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></dt>
211 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/StatisticCollector.html#localcf">localcf</a></span> - Variable in class compbio.stat.servlet.<a href="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</a></dt>
213 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MainManager.html#localcl">localcl</a></span> - Variable in class compbio.ws.server.<a href="../compbio/ws/server/MainManager.html" title="class in compbio.ws.server">MainManager</a></dt>
215 <dt><a href="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local"><span class="typeNameLink">LocalEngineUtil</span></a> - Class in <a href="../compbio/engine/local/package-summary.html">compbio.engine.local</a></dt>
217 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalEngineUtil.html#LocalEngineUtil--">LocalEngineUtil()</a></span> - Constructor for class compbio.engine.local.<a href="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</a></dt>
219 <dt><a href="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local"><span class="typeNameLink">LocalExecutorService</span></a> - Class in <a href="../compbio/engine/local/package-summary.html">compbio.engine.local</a></dt>
221 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalExecutorService.html#LocalExecutorService-int-int-long-java.util.concurrent.TimeUnit-java.util.concurrent.BlockingQueue-">LocalExecutorService(int, int, long, TimeUnit, BlockingQueue<Runnable>)</a></span> - Constructor for class compbio.engine.local.<a href="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</a></dt>
223 <dt><a href="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local"><span class="typeNameLink">LocalRunner</span></a> - Class in <a href="../compbio/engine/local/package-summary.html">compbio.engine.local</a></dt>
225 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalRunner.html#LocalRunner-compbio.engine.client.ConfiguredExecutable-">LocalRunner(ConfiguredExecutable<?>)</a></span> - Constructor for class compbio.engine.local.<a href="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</a></dt>
227 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/StatCollection.html#localStat">localStat</a></span> - Variable in class compbio.stat.servlet.util.<a href="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</a></dt>
229 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ClustalAlignmentUtil.html#log">log</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>
231 <dt><span class="memberNameLink"><a href="../compbio/engine/Cleaner.html#log">log</a></span> - Static variable in class compbio.engine.<a href="../compbio/engine/Cleaner.html" title="class in compbio.engine">Cleaner</a></dt>
233 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#log">log</a></span> - Static variable in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
235 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#log">log</a></span> - Static variable in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
237 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EngineUtil.html#log">log</a></span> - Static variable in class compbio.engine.client.<a href="../compbio/engine/client/EngineUtil.html" title="class in compbio.engine.client">EngineUtil</a></dt>
239 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EnvVariableProcessor.html#log">log</a></span> - Static variable in class compbio.engine.client.<a href="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</a></dt>
241 <dt><span class="memberNameLink"><a href="../compbio/engine/client/RunConfiguration.html#log">log</a></span> - Static variable in class compbio.engine.client.<a href="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</a></dt>
243 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#log">log</a></span> - Static variable in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
245 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Util.html#log">log</a></span> - Static variable in class compbio.engine.client.<a href="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</a></dt>
247 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/AsyncClusterRunner.html#log">log</a></span> - Static variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/AsyncClusterRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncClusterRunner</a></dt>
249 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#log">log</a></span> - Static variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</a></dt>
251 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterEngineUtil.html#log">log</a></span> - Static variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterEngineUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterEngineUtil</a></dt>
253 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#log">log</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>
255 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#log">log</a></span> - Static 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>
257 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterUtil.html#log">log</a></span> - Static variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterUtil</a></dt>
259 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#log">log</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>
261 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/DirectoryManager.html#log">log</a></span> - Static variable in class compbio.engine.conf.<a href="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</a></dt>
263 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/PropertyHelperManager.html#log">log</a></span> - Static variable in class compbio.engine.conf.<a href="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</a></dt>
265 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/RunnerConfigMarshaller.html#log">log</a></span> - Static variable in class compbio.engine.conf.<a href="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</a></dt>
267 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#log">log</a></span> - Static variable in class compbio.engine.<a href="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></dt>
269 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#log">log</a></span> - Static variable in class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
271 <dt><span class="memberNameLink"><a href="../compbio/engine/LoadBalancer.html#log">log</a></span> - Static variable in class compbio.engine.<a href="../compbio/engine/LoadBalancer.html" title="class in compbio.engine">LoadBalancer</a></dt>
273 <dt><span class="memberNameLink"><a href="../compbio/engine/local/AsyncLocalRunner.html#log">log</a></span> - Static variable in class compbio.engine.local.<a href="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</a></dt>
275 <dt><span class="memberNameLink"><a href="../compbio/engine/local/ExecutableWrapper.html#log">log</a></span> - Static variable in class compbio.engine.local.<a href="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</a></dt>
277 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalEngineUtil.html#log">log</a></span> - Static variable in class compbio.engine.local.<a href="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</a></dt>
279 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalExecutorService.html#log">log</a></span> - Static variable in class compbio.engine.local.<a href="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</a></dt>
281 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalRunner.html#log">log</a></span> - Static variable in class compbio.engine.local.<a href="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</a></dt>
283 <dt><span class="memberNameLink"><a href="../compbio/engine/local/StreamGobbler.html#log">log</a></span> - Static variable in class compbio.engine.local.<a href="../compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local">StreamGobbler</a></dt>
285 <dt><span class="memberNameLink"><a href="../compbio/engine/ProgressGetter.html#log">log</a></span> - Static variable in class compbio.engine.<a href="../compbio/engine/ProgressGetter.html" title="class in compbio.engine">ProgressGetter</a></dt>
287 <dt><span class="memberNameLink"><a href="../compbio/engine/PulledFileCache.html#log">log</a></span> - Static variable in class compbio.engine.<a href="../compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</a></dt>
289 <dt><span class="memberNameLink"><a href="../compbio/engine/SubmissionManager.html#log">log</a></span> - Static variable in class compbio.engine.<a href="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</a></dt>
291 <dt><span class="memberNameLink"><a href="../compbio/runner/conservation/AACon.html#log">log</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>
293 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Disembl.html#log">log</a></span> - Static variable in class compbio.runner.disorder.<a href="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</a></dt>
295 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/GlobPlot.html#log">log</a></span> - Static variable in class compbio.runner.disorder.<a href="../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</a></dt>
297 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/IUPred.html#log">log</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>
299 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Jronn.html#log">log</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>
301 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/ClustalO.html#log">log</a></span> - Static variable in class compbio.runner.msa.<a href="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a></dt>
303 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/ClustalW.html#log">log</a></span> - Static variable in class compbio.runner.msa.<a href="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</a></dt>
305 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/GLprobs.html#log">log</a></span> - Static variable in class compbio.runner.msa.<a href="../compbio/runner/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a></dt>
307 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Mafft.html#log">log</a></span> - Static variable in class compbio.runner.msa.<a href="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a></dt>
309 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/MSAprobs.html#log">log</a></span> - Static variable in class compbio.runner.msa.<a href="../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a></dt>
311 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Muscle.html#log">log</a></span> - Static variable in class compbio.runner.msa.<a href="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</a></dt>
313 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Probcons.html#log">log</a></span> - Static variable in class compbio.runner.msa.<a href="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</a></dt>
315 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Tcoffee.html#log">log</a></span> - Static variable in class compbio.runner.msa.<a href="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</a></dt>
317 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#log">log</a></span> - Static variable in class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
319 <dt><span class="memberNameLink"><a href="../compbio/runner/RunnerUtil.html#log">log</a></span> - Static variable in class compbio.runner.<a href="../compbio/runner/RunnerUtil.html" title="class in compbio.runner">RunnerUtil</a></dt>
321 <dt><span class="memberNameLink"><a href="../compbio/runner/structure/RNAalifold.html#log">log</a></span> - Static variable in class compbio.runner.structure.<a href="../compbio/runner/structure/RNAalifold.html" title="class in compbio.runner.structure">RNAalifold</a></dt>
323 <dt><span class="memberNameLink"><a href="../compbio/runner/Util.html#log">log</a></span> - Static variable in class compbio.runner.<a href="../compbio/runner/Util.html" title="class in compbio.runner">Util</a></dt>
325 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/DirCleaner.html#log">log</a></span> - Static variable in class compbio.stat.collector.<a href="../compbio/stat/collector/DirCleaner.html" title="class in compbio.stat.collector">DirCleaner</a></dt>
327 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/ExecutionStatCollector.html#log">log</a></span> - Static variable in class compbio.stat.collector.<a href="../compbio/stat/collector/ExecutionStatCollector.html" title="class in compbio.stat.collector">ExecutionStatCollector</a></dt>
329 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/InputFilter.html#log">log</a></span> - Static variable in class compbio.stat.collector.<a href="../compbio/stat/collector/InputFilter.html" title="class in compbio.stat.collector">InputFilter</a></dt>
331 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobDirectory.html#log">log</a></span> - Static variable in class compbio.stat.collector.<a href="../compbio/stat/collector/JobDirectory.html" title="class in compbio.stat.collector">JobDirectory</a></dt>
333 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatDB.html#log">log</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>
335 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/DisplayStat.html#log">log</a></span> - Static variable in class compbio.stat.servlet.<a href="../compbio/stat/servlet/DisplayStat.html" title="class in compbio.stat.servlet">DisplayStat</a></dt>
337 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/HttpCodeResponseServiceStatus.html#log">log</a></span> - Static variable in class compbio.stat.servlet.<a href="../compbio/stat/servlet/HttpCodeResponseServiceStatus.html" title="class in compbio.stat.servlet">HttpCodeResponseServiceStatus</a></dt>
339 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/ServiceStatus.html#log">log</a></span> - Static variable in class compbio.stat.servlet.<a href="../compbio/stat/servlet/ServiceStatus.html" title="class in compbio.stat.servlet">ServiceStatus</a></dt>
341 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/StatisticCollector.html#log">log</a></span> - Variable in class compbio.stat.servlet.<a href="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</a></dt>
343 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/StatCollection.html#log">log</a></span> - Static variable in class compbio.stat.servlet.util.<a href="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</a></dt>
345 <dt><span class="memberNameLink"><a href="../compbio/ws/client/AAConClient.html#log">log</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>
347 <div class="block">Use java.util.Logger instead of log4j logger to reduce the size of the
350 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Jws2Client.html#log">log</a></span> - Static variable in class compbio.ws.client.<a href="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</a></dt>
352 <div class="block">Use java.util.Logger instead of log4j logger to reduce the size of the client package</div>
354 <dt><span class="memberNameLink"><a href="../compbio/ws/server/AAConWS.html#log">log</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/AAConWS.html" title="class in compbio.ws.server">AAConWS</a></dt>
356 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalOWS.html#log">log</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</a></dt>
358 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalWS.html#log">log</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</a></dt>
360 <dt><span class="memberNameLink"><a href="../compbio/ws/server/DisemblWS.html#log">log</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/DisemblWS.html" title="class in compbio.ws.server">DisemblWS</a></dt>
362 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GAUtils.html#log">log</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>
364 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GenericMetadataService.html#log">log</a></span> - Variable in class compbio.ws.server.<a href="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</a></dt>
366 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GlobPlotWS.html#log">log</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/GlobPlotWS.html" title="class in compbio.ws.server">GlobPlotWS</a></dt>
368 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GLprobsWS.html#log">log</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/GLprobsWS.html" title="class in compbio.ws.server">GLprobsWS</a></dt>
370 <dt><span class="memberNameLink"><a href="../compbio/ws/server/IUPredWS.html#log">log</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/IUPredWS.html" title="class in compbio.ws.server">IUPredWS</a></dt>
372 <dt><span class="memberNameLink"><a href="../compbio/ws/server/JronnWS.html#log">log</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/JronnWS.html" title="class in compbio.ws.server">JronnWS</a></dt>
374 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MafftWS.html#log">log</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</a></dt>
376 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MainManager.html#log">log</a></span> - Variable in class compbio.ws.server.<a href="../compbio/ws/server/MainManager.html" title="class in compbio.ws.server">MainManager</a></dt>
378 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MSAprobsWS.html#log">log</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/MSAprobsWS.html" title="class in compbio.ws.server">MSAprobsWS</a></dt>
380 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MuscleWS.html#log">log</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</a></dt>
382 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ProbconsWS.html#log">log</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</a></dt>
384 <dt><span class="memberNameLink"><a href="../compbio/ws/server/RegistryWS.html#log">log</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</a></dt>
386 <dt><span class="memberNameLink"><a href="../compbio/ws/server/RNAalifoldWS.html#log">log</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/RNAalifoldWS.html" title="class in compbio.ws.server">RNAalifoldWS</a></dt>
388 <dt><span class="memberNameLink"><a href="../compbio/ws/server/SetExecutableFlag.html#log">log</a></span> - Variable in class compbio.ws.server.<a href="../compbio/ws/server/SetExecutableFlag.html" title="class in compbio.ws.server">SetExecutableFlag</a></dt>
390 <dt><span class="memberNameLink"><a href="../compbio/ws/server/TcoffeeWS.html#log">log</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</a></dt>
392 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#logStatistics-org.ggf.drmaa.JobInfo-">logStatistics(JobInfo)</a></span> - Static method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</a></dt>
394 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/IUPred.html#LONG_OUTPUT">LONG_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>
396 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Disembl.html#LOOPS_EXPECTATION_THRESHOLD">LOOPS_EXPECTATION_THRESHOLD</a></span> - Variable in class compbio.runner.disorder.<a href="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</a></dt>
399 <a href="index-1.html">A</a> <a href="index-2.html">B</a> <a href="index-3.html">C</a> <a href="index-4.html">D</a> <a href="index-5.html">E</a> <a href="index-6.html">F</a> <a href="index-7.html">G</a> <a href="index-8.html">H</a> <a href="index-9.html">I</a> <a href="index-10.html">J</a> <a href="index-11.html">K</a> <a href="index-12.html">L</a> <a href="index-13.html">M</a> <a href="index-14.html">N</a> <a href="index-15.html">O</a> <a href="index-16.html">P</a> <a href="index-17.html">Q</a> <a href="index-18.html">R</a> <a href="index-19.html">S</a> <a href="index-20.html">T</a> <a href="index-21.html">U</a> <a href="index-22.html">V</a> <a href="index-23.html">W</a> <a href="index-24.html">_</a> </div>
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