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  75 <h2 class="title">G</h2>
  76 <dl>
  77 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/AlignmentMetadata.html#gapchar">gapchar</a></span> - Variable in class compbio.data.sequence.<a href="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</a></dt>
  78 <dd>&nbsp;</dd>
  79 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ClustalAlignmentUtil.html#gapchar">gapchar</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>
  80 <dd>
  81 <div class="block">Dash char to be used as gap char in the alignments</div>
  82 </dd>
  83 <dt><a href="../compbio/ws/server/GAUtils.html" title="class in compbio.ws.server"><span class="typeNameLink">GAUtils</span></a> - Class in <a href="../compbio/ws/server/package-summary.html">compbio.ws.server</a></dt>
  84 <dd>&nbsp;</dd>
  85 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GAUtils.html#GAUtils--">GAUtils()</a></span> - Constructor for class compbio.ws.server.<a href="../compbio/ws/server/GAUtils.html" title="class in compbio.ws.server">GAUtils</a></dt>
  86 <dd>&nbsp;</dd>
  87 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/RunnerConfigMarshaller.html#generateSchema-java.lang.String-java.lang.String-">generateSchema(String, String)</a></span> - Method in class compbio.engine.conf.<a href="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</a></dt>
  88 <dd>&nbsp;</dd>
  89 <dt><a href="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server"><span class="typeNameLink">GenericMetadataService</span></a>&lt;<a href="../compbio/ws/server/GenericMetadataService.html" title="type parameter in GenericMetadataService">T</a>&gt; - Class in <a href="../compbio/ws/server/package-summary.html">compbio.ws.server</a></dt>
  90 <dd>&nbsp;</dd>
  91 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GenericMetadataService.html#GenericMetadataService-compbio.engine.client.SkeletalExecutable-org.apache.log4j.Logger-">GenericMetadataService(SkeletalExecutable&lt;T&gt;, Logger)</a></span> - Constructor for class compbio.ws.server.<a href="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</a></dt>
  92 <dd>&nbsp;</dd>
  93 <dt><span class="memberNameLink"><a href="../compbio/engine/PulledFileCache.html#get-java.lang.String-">get(String)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</a></dt>
  94 <dd>&nbsp;</dd>
  95 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/Totals.html#getAbandoned--">getAbandoned()</a></span> - 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>
  96 <dd>&nbsp;</dd>
  97 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatDB.html#getAbandonedCount-java.sql.Timestamp-java.sql.Timestamp-">getAbandonedCount(Timestamp, Timestamp)</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</a></dt>
  98 <dd>&nbsp;</dd>
  99 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatProcessor.html#getAbandonedJobs--">getAbandonedJobs()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</a></dt>
 100 <dd>
 101 <div class="block">Not collected.</div>
 102 </dd>
 103 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getActualNumberofSequences--">getActualNumberofSequences()</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>
 104 <dd>&nbsp;</dd>
 105 <dt><span class="memberNameLink"><a href="../compbio/metadata/LimitExceededException.html#getActualNumberofSequences--">getActualNumberofSequences()</a></span> - Method in exception compbio.metadata.<a href="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></dt>
 106 <dd>&nbsp;</dd>
 107 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomFold.html#getAlignment--">getAlignment()</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>
 108 <dd>&nbsp;</dd>
 109 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/Fold.html#getAlignment--">getAlignment()</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>
 110 <dd>&nbsp;</dd>
 111 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetFold.html#getAlignment--">getAlignment()</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>
 112 <dd>&nbsp;</dd>
 113 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#getAllConstrainedParametersWithBorderValues-boolean-">getAllConstrainedParametersWithBorderValues(boolean)</a></span> - Method in class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
 114 <dd>&nbsp;</dd>
 115 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#getAllConstrainedParametersWithRandomValues--">getAllConstrainedParametersWithRandomValues()</a></span> - Method in class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
 116 <dd>&nbsp;</dd>
 117 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#getAllOptions--">getAllOptions()</a></span> - Method in class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
 118 <dd>&nbsp;</dd>
 119 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#getAllParameters--">getAllParameters()</a></span> - Method in class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
 120 <dd>&nbsp;</dd>
 121 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/StatCollection.html#getAllStat--">getAllStat()</a></span> - Method in class compbio.stat.servlet.util.<a href="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</a></dt>
 122 <dd>&nbsp;</dd>
 123 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#getAllStats--">getAllStats()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 124 <dd>&nbsp;</dd>
 125 <dt><a href="../compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetAnnotation</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 126 <dd>&nbsp;</dd>
 127 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetAnnotation.html#GetAnnotation--">GetAnnotation()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws">GetAnnotation</a></dt>
 128 <dd>&nbsp;</dd>
 129 <dt><span class="memberNameLink"><a href="../compbio/data/msa/SequenceAnnotation.html#getAnnotation-java.lang.String-">getAnnotation(String)</a></span> - Method in interface compbio.data.msa.<a href="../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</a></dt>
 130 <dd>
 131 <div class="block">Return the result of the job.</div>
 132 </dd>
 133 <dt><span class="memberNameLink"><a href="../compbio/ws/server/SequenceAnnotationService.html#getAnnotation-java.lang.String-">getAnnotation(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</a></dt>
 134 <dd>&nbsp;</dd>
 135 <dt><span class="memberNameLink"><a href="../compbio/ws/server/WSUtil.html#getAnnotation-java.lang.String-org.apache.log4j.Logger-">getAnnotation(String, Logger)</a></span> - Static method in class compbio.ws.server.<a href="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</a></dt>
 136 <dd>&nbsp;</dd>
 137 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ScoreManager.html#getAnnotationForSequence-java.lang.String-">getAnnotationForSequence(String)</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></dt>
 138 <dd>&nbsp;</dd>
 139 <dt><a href="../compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetAnnotationResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 140 <dd>&nbsp;</dd>
 141 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetAnnotationResponse.html#GetAnnotationResponse--">GetAnnotationResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws">GetAnnotationResponse</a></dt>
 142 <dd>&nbsp;</dd>
 143 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLastTested.html#getArg0--">getArg0()</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>
 144 <dd>&nbsp;</dd>
 145 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLastTestedOn.html#getArg0--">getArg0()</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>
 146 <dd>&nbsp;</dd>
 147 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetServiceDescription.html#getArg0--">getArg0()</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>
 148 <dd>&nbsp;</dd>
 149 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/IsOperating.html#getArg0--">getArg0()</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>
 150 <dd>&nbsp;</dd>
 151 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/TestService.html#getArg0--">getArg0()</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>
 152 <dd>&nbsp;</dd>
 153 <dt><span class="memberNameLink"><a href="../compbio/metadata/PresetManager.html#getArgument-compbio.metadata.RunnerConfig-java.lang.String-">getArgument(RunnerConfig&lt;T&gt;, String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a></dt>
 154 <dd>&nbsp;</dd>
 155 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#getArgument-java.lang.String-">getArgument(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
 156 <dd>
 157 <div class="block">Returns the argument by its name if found, NULL otherwise.</div>
 158 </dd>
 159 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#getArgumentByOptionName-java.lang.String-">getArgumentByOptionName(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
 160 <dd>
 161 <div class="block">Returns the argument by option name, NULL if the argument is not found</div>
 162 </dd>
 163 <dt><span class="memberNameLink"><a href="../compbio/metadata/Preset.html#getArguments-compbio.metadata.RunnerConfig-">getArguments(RunnerConfig&lt;T&gt;)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a></dt>
 164 <dd>
 165 <div class="block">Converts list of options as String to type Option</div>
 166 </dd>
 167 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#getArguments--">getArguments()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
 168 <dd>
 169 <div class="block">Returns list of <a href="../compbio/metadata/Parameter.html" title="class in compbio.metadata"><code>Parameter</code></a> and <a href="../compbio/metadata/Option.html" title="class in compbio.metadata"><code>Option</code></a> supported by current
 170  runner</div>
 171 </dd>
 172 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#getAsyncEngine-compbio.engine.client.ConfiguredExecutable-compbio.engine.client.Executable.ExecProvider-">getAsyncEngine(ConfiguredExecutable&lt;?&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>
 173 <dd>&nbsp;</dd>
 174 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#getAsyncEngine-compbio.engine.client.ConfiguredExecutable-">getAsyncEngine(ConfiguredExecutable&lt;?&gt;)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></dt>
 175 <dd>&nbsp;</dd>
 176 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#getAsyncEngine-java.lang.String-">getAsyncEngine(String)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></dt>
 177 <dd>&nbsp;</dd>
 178 <dt><span class="memberNameLink"><a href="../compbio/metadata/Limit.html#getAvgSeqLength--">getAvgSeqLength()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a></dt>
 179 <dd>&nbsp;</dd>
 180 <dt><span class="memberNameLink"><a href="../compbio/metadata/Limit.html#getAvgSequenceLength-java.util.List-">getAvgSequenceLength(List&lt;FastaSequence&gt;)</a></span> - Static method in class compbio.metadata.<a href="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a></dt>
 181 <dd>
 182 <div class="block">Calculates an average sequence length of the dataset</div>
 183 </dd>
 184 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#getBasicURL--">getBasicURL()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 185 <dd>&nbsp;</dd>
 186 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/PropertyHelperManager.html#getBooleanProperty-java.lang.String-">getBooleanProperty(String)</a></span> - Static method in class compbio.engine.conf.<a href="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</a></dt>
 187 <dd>&nbsp;</dd>
 188 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/StatisticCollector.html#getBooleanProperty-java.lang.String-">getBooleanProperty(String)</a></span> - Static method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</a></dt>
 189 <dd>&nbsp;</dd>
 190 <dt><span class="memberNameLink"><a href="../compbio/engine/Job.html#getByJobId-java.lang.String-java.util.List-">getByJobId(String, List&lt;Job&gt;)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/Job.html" title="class in compbio.engine">Job</a></dt>
 191 <dd>&nbsp;</dd>
 192 <dt><span class="memberNameLink"><a href="../compbio/engine/Job.html#getByTaskId-java.lang.String-java.util.List-">getByTaskId(String, List&lt;Job&gt;)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/Job.html" title="class in compbio.engine">Job</a></dt>
 193 <dd>&nbsp;</dd>
 194 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#getCalculationTime--">getCalculationTime()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 195 <dd>&nbsp;</dd>
 196 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/Totals.html#getCancelled--">getCancelled()</a></span> - 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>
 197 <dd>&nbsp;</dd>
 198 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatDB.html#getCancelledCount-java.sql.Timestamp-java.sql.Timestamp-">getCancelledCount(Timestamp, Timestamp)</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</a></dt>
 199 <dd>&nbsp;</dd>
 200 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatProcessor.html#getCancelledJobs--">getCancelledJobs()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</a></dt>
 201 <dd>&nbsp;</dd>
 202 <dt><span class="memberNameLink"><a href="../compbio/data/msa/Category.html#getCategories--">getCategories()</a></span> - Static method in class compbio.data.msa.<a href="../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</a></dt>
 203 <dd>&nbsp;</dd>
 204 <dt><span class="memberNameLink"><a href="../compbio/metadata/ChunkHolder.html#getChunk--">getChunk()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</a></dt>
 205 <dd>&nbsp;</dd>
 206 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/DirectoryManager.html#getClass-java.lang.String-">getClass(String)</a></span> - Static method in class compbio.engine.conf.<a href="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</a></dt>
 207 <dd>&nbsp;</dd>
 208 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#getClusterCpuNum-java.lang.Class-">getClusterCpuNum(Class&lt;? extends Executable&lt;?&gt;&gt;)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 209 <dd>&nbsp;</dd>
 210 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/StatisticCollector.html#getClusterJobDir--">getClusterJobDir()</a></span> - Static method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</a></dt>
 211 <dd>&nbsp;</dd>
 212 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MainManager.html#getClusterJobDir--">getClusterJobDir()</a></span> - Static method in class compbio.ws.server.<a href="../compbio/ws/server/MainManager.html" title="class in compbio.ws.server">MainManager</a></dt>
 213 <dd>&nbsp;</dd>
 214 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#getClusterJobId-java.lang.String-">getClusterJobId(String)</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>
 215 <dd>&nbsp;</dd>
 216 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobDirectory.html#getClusterJobID--">getClusterJobID()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobDirectory.html" title="class in compbio.stat.collector">JobDirectory</a></dt>
 217 <dd>&nbsp;</dd>
 218 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#getClusterJobId--">getClusterJobId()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 219 <dd>&nbsp;</dd>
 220 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatProcessor.html#getClusterJobs--">getClusterJobs()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</a></dt>
 221 <dd>&nbsp;</dd>
 222 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getClusterJobSettings--">getClusterJobSettings()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
 223 <dd>&nbsp;</dd>
 224 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Executable.html#getClusterJobSettings--">getClusterJobSettings()</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a></dt>
 225 <dd>&nbsp;</dd>
 226 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#getClusterJobSettings--">getClusterJobSettings()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 227 <dd>&nbsp;</dd>
 228 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/StatisticCollector.html#getClusterJobTimeOut--">getClusterJobTimeOut()</a></span> - Static method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</a></dt>
 229 <dd>&nbsp;</dd>
 230 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/StatCollection.html#getClusterStat--">getClusterStat()</a></span> - Method in class compbio.stat.servlet.util.<a href="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</a></dt>
 231 <dd>&nbsp;</dd>
 232 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getCommand-compbio.engine.client.Executable.ExecProvider-">getCommand(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>
 233 <dd>&nbsp;</dd>
 234 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfiguredExecutable.html#getCommand-compbio.engine.client.Executable.ExecProvider-">getCommand(Executable.ExecProvider)</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a></dt>
 235 <dd>&nbsp;</dd>
 236 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EngineUtil.html#getCommand-compbio.engine.client.Executable.ExecProvider-java.lang.Class-">getCommand(Executable.ExecProvider, Class&lt;?&gt;)</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>
 237 <dd>&nbsp;</dd>
 238 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Util.html#getCommand-compbio.engine.client.Executable.ExecProvider-java.lang.Class-">getCommand(Executable.ExecProvider, Class&lt;?&gt;)</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>
 239 <dd>&nbsp;</dd>
 240 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#getCommandList--">getCommandList()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
 241 <dd>&nbsp;</dd>
 242 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#getCommands--">getCommands()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
 243 <dd>&nbsp;</dd>
 244 <dt><span class="memberNameLink"><a href="../compbio/ws/server/WSUtil.html#getCommands-java.util.List-java.lang.String-">getCommands(List&lt;Option&lt;T&gt;&gt;, String)</a></span> - Static method in class compbio.ws.server.<a href="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</a></dt>
 245 <dd>&nbsp;</dd>
 246 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#getCommandString--">getCommandString()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
 247 <dd>&nbsp;</dd>
 248 <dt><span class="memberNameLink"><a href="../compbio/engine/Job.html#getConfExecutable--">getConfExecutable()</a></span> - Method in class compbio.engine.<a href="../compbio/engine/Job.html" title="class in compbio.engine">Job</a></dt>
 249 <dd>&nbsp;</dd>
 250 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#getCPUTimeStat--">getCPUTimeStat()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 251 <dd>&nbsp;</dd>
 252 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#getCPUUsageTime--">getCPUUsageTime()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 253 <dd>&nbsp;</dd>
 254 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getCreatedFiles--">getCreatedFiles()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
 255 <dd>&nbsp;</dd>
 256 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Executable.html#getCreatedFiles--">getCreatedFiles()</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a></dt>
 257 <dd>
 258 <div class="block"><span class="deprecatedLabel">Deprecated.</span></div>
 259 </dd>
 260 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles--">getCreatedFiles()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 261 <dd>
 262 <div class="block">This method cannot really tell whether the files has actually been
 263  created or not.</div>
 264 </dd>
 265 <dt><span class="memberNameLink"><a href="../compbio/runner/conservation/AACon.html#getCreatedFiles--">getCreatedFiles()</a></span> - Method in class compbio.runner.conservation.<a href="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a></dt>
 266 <dd>&nbsp;</dd>
 267 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Jronn.html#getCreatedFiles--">getCreatedFiles()</a></span> - Method in class compbio.runner.disorder.<a href="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</a></dt>
 268 <dd>&nbsp;</dd>
 269 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/ClustalW.html#getCreatedFiles--">getCreatedFiles()</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</a></dt>
 270 <dd>&nbsp;</dd>
 271 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/GLprobs.html#getCreatedFiles--">getCreatedFiles()</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a></dt>
 272 <dd>&nbsp;</dd>
 273 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/MSAprobs.html#getCreatedFiles--">getCreatedFiles()</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a></dt>
 274 <dd>&nbsp;</dd>
 275 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Muscle.html#getCreatedFiles--">getCreatedFiles()</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</a></dt>
 276 <dd>&nbsp;</dd>
 277 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Probcons.html#getCreatedFiles--">getCreatedFiles()</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</a></dt>
 278 <dd>&nbsp;</dd>
 279 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Tcoffee.html#getCreatedFiles--">getCreatedFiles()</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</a></dt>
 280 <dd>&nbsp;</dd>
 281 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructScoreManager.html#getData--">getData()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructScoreManager.html" title="class in compbio.data.sequence">RNAStructScoreManager</a></dt>
 282 <dd>&nbsp;</dd>
 283 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#getDataTransfered--">getDataTransfered()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 284 <dd>&nbsp;</dd>
 285 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatDB.html#getDBConnection--">getDBConnection()</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>
 286 <dd>&nbsp;</dd>
 287 <dt><span class="memberNameLink"><a href="../compbio/metadata/LimitsManager.html#getDefaultLimit--">getDefaultLimit()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a></dt>
 288 <dd>&nbsp;</dd>
 289 <dt><span class="memberNameLink"><a href="../compbio/metadata/Argument.html#getDefaultValue--">getDefaultValue()</a></span> - Method in interface compbio.metadata.<a href="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</a></dt>
 290 <dd>&nbsp;</dd>
 291 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#getDefaultValue--">getDefaultValue()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 292 <dd>
 293 <div class="block">A default value of the option.</div>
 294 </dd>
 295 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#getDelay-java.util.concurrent.TimeUnit-">getDelay(TimeUnit)</a></span> - Method in class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
 296 <dd>&nbsp;</dd>
 297 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#getDelayValue-java.util.concurrent.TimeUnit-">getDelayValue(TimeUnit)</a></span> - Method in class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
 298 <dd>&nbsp;</dd>
 299 <dt><span class="memberNameLink"><a href="../compbio/metadata/Argument.html#getDescription--">getDescription()</a></span> - Method in interface compbio.metadata.<a href="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</a></dt>
 300 <dd>&nbsp;</dd>
 301 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#getDescription--">getDescription()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 302 <dd>
 303 <div class="block">A long description of the Option</div>
 304 </dd>
 305 <dt><span class="memberNameLink"><a href="../compbio/metadata/Preset.html#getDescription--">getDescription()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a></dt>
 306 <dd>&nbsp;</dd>
 307 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/ServiceTestResult.html#getDetails--">getDetails()</a></span> - Method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</a></dt>
 308 <dd>&nbsp;</dd>
 309 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatDB.html#getEarliestRecord--">getEarliestRecord()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</a></dt>
 310 <dd>&nbsp;</dd>
 311 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/ServiceStatus.html#getEndPoints--">getEndPoints()</a></span> - Method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/ServiceStatus.html" title="class in compbio.stat.servlet">ServiceStatus</a></dt>
 312 <dd>&nbsp;</dd>
 313 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#getEndTime--">getEndTime()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 314 <dd>&nbsp;</dd>
 315 <dt><span class="memberNameLink"><a href="../compbio/engine/LoadBalancer.html#getEngine-compbio.engine.client.Executable-">getEngine(Executable&lt;?&gt;)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/LoadBalancer.html" title="class in compbio.engine">LoadBalancer</a></dt>
 316 <dd>&nbsp;</dd>
 317 <dt><span class="memberNameLink"><a href="../compbio/engine/LoadBalancer.html#getEngine-compbio.engine.client.Executable-java.util.List-">getEngine(Executable&lt;V&gt;, List&lt;FastaSequence&gt;)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/LoadBalancer.html" title="class in compbio.engine">LoadBalancer</a></dt>
 318 <dd>&nbsp;</dd>
 319 <dt><span class="memberNameLink"><a href="../compbio/ws/server/WSUtil.html#getEngine-compbio.engine.client.ConfiguredExecutable-">getEngine(ConfiguredExecutable&lt;?&gt;)</a></span> - Static method in class compbio.ws.server.<a href="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</a></dt>
 320 <dd>&nbsp;</dd>
 321 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getEnvironment--">getEnvironment()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
 322 <dd>&nbsp;</dd>
 323 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfiguredExecutable.html#getEnvironment--">getEnvironment()</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a></dt>
 324 <dd>&nbsp;</dd>
 325 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EnvVariableProcessor.html#getEnvVariableList-java.lang.String-">getEnvVariableList(String)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</a></dt>
 326 <dd>&nbsp;</dd>
 327 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EnvVariableProcessor.html#getEnvVariableName-java.lang.String-">getEnvVariableName(String)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</a></dt>
 328 <dd>&nbsp;</dd>
 329 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EnvVariableProcessor.html#getEnvVariables-java.lang.String-java.lang.Class-">getEnvVariables(String, Class&lt;?&gt;)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</a></dt>
 330 <dd>&nbsp;</dd>
 331 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EnvVariableProcessor.html#getEnvVariableValue-java.lang.String-">getEnvVariableValue(String)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</a></dt>
 332 <dd>&nbsp;</dd>
 333 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getError--">getError()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
 334 <dd>&nbsp;</dd>
 335 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Executable.html#getError--">getError()</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a></dt>
 336 <dd>&nbsp;</dd>
 337 <dt><span class="memberNameLink"><a href="../compbio/engine/client/RunConfiguration.html#getError--">getError()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</a></dt>
 338 <dd>&nbsp;</dd>
 339 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#getError--">getError()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 340 <dd>&nbsp;</dd>
 341 <dt><span class="memberNameLink"><a href="../compbio/engine/local/ExecutableWrapper.html#getError--">getError()</a></span> - Method in class compbio.engine.local.<a href="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</a></dt>
 342 <dd>&nbsp;</dd>
 343 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#getEscJobname--">getEscJobname()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 344 <dd>&nbsp;</dd>
 345 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EngineUtil.html#getExecProperty-java.lang.String-compbio.engine.client.Executable-">getExecProperty(String, Executable&lt;?&gt;)</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>
 346 <dd>&nbsp;</dd>
 347 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EngineUtil.html#getExecProperty-java.lang.String-java.lang.Class-">getExecProperty(String, Class&lt;?&gt;)</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>
 348 <dd>&nbsp;</dd>
 349 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Util.html#getExecProperty-java.lang.String-compbio.engine.client.Executable-">getExecProperty(String, Executable&lt;?&gt;)</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>
 350 <dd>&nbsp;</dd>
 351 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Util.html#getExecProperty-java.lang.String-java.lang.Class-">getExecProperty(String, Class&lt;?&gt;)</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>
 352 <dd>&nbsp;</dd>
 353 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getExecProvider--">getExecProvider()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
 354 <dd>&nbsp;</dd>
 355 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfiguredExecutable.html#getExecProvider--">getExecProvider()</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a></dt>
 356 <dd>&nbsp;</dd>
 357 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#getExecProvider-compbio.engine.client.ConfiguredExecutable-java.util.List-">getExecProvider(ConfiguredExecutable&lt;?&gt;, List&lt;FastaSequence&gt;)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></dt>
 358 <dd>
 359 <div class="block">Depending on the values defined in the properties
 360  (engine.cluster.enable=true and engine.local.enable=true) return either
 361  Cluster job submission engine <code>#JobRunner</code> or local job submission
 362  engine <code>#LocalRunner</code> If both engines enabled than ask
 363  <a href="../compbio/engine/LoadBalancer.html" title="class in compbio.engine"><code>LoadBalancer</code></a> for an engine.</div>
 364 </dd>
 365 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getExecutable--">getExecutable()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
 366 <dd>&nbsp;</dd>
 367 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfiguredExecutable.html#getExecutable--">getExecutable()</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a></dt>
 368 <dd>&nbsp;</dd>
 369 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#getExecutionStat--">getExecutionStat()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 370 <dd>&nbsp;</dd>
 371 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalExecutorService.html#getExecutor--">getExecutor()</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>
 372 <dd>
 373 <div class="block">This method returns the single instance of CachedThreadPoolExecutor which
 374  it cashes internally</div>
 375 </dd>
 376 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#getExitStatus--">getExitStatus()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 377 <dd>&nbsp;</dd>
 378 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/Totals.html#getFailed--">getFailed()</a></span> - 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>
 379 <dd>&nbsp;</dd>
 380 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatProcessor.html#getFailedJobs--">getFailedJobs()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</a></dt>
 381 <dd>
 382 <div class="block">Started & finished but did not produce result</div>
 383 </dd>
 384 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/Align.html#getFastaSequences--">getFastaSequences()</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>
 385 <dd>&nbsp;</dd>
 386 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/Analize.html#getFastaSequences--">getFastaSequences()</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>
 387 <dd>&nbsp;</dd>
 388 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAlign.html#getFastaSequences--">getFastaSequences()</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>
 389 <dd>&nbsp;</dd>
 390 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAnalize.html#getFastaSequences--">getFastaSequences()</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>
 391 <dd>&nbsp;</dd>
 392 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetAlign.html#getFastaSequences--">getFastaSequences()</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>
 393 <dd>&nbsp;</dd>
 394 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetAnalize.html#getFastaSequences--">getFastaSequences()</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>
 395 <dd>&nbsp;</dd>
 396 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#getFile--">getFile()</a></span> - Method in class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
 397 <dd>&nbsp;</dd>
 398 <dt><span class="memberNameLink"><a href="../compbio/ws/client/IOHelper.html#getFile-java.lang.String:A-java.lang.String-boolean-">getFile(String[], String, boolean)</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>
 399 <dd>
 400 <div class="block">Checks -i options and return the File if one was provided, null otherwise</div>
 401 </dd>
 402 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#getFinish--">getFinish()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 403 <dd>&nbsp;</dd>
 404 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobDirectory.html#getFinishedTime--">getFinishedTime()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobDirectory.html" title="class in compbio.stat.collector">JobDirectory</a></dt>
 405 <dd>&nbsp;</dd>
 406 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/FastaSequence.html#getFormatedSequence-int-">getFormatedSequence(int)</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></dt>
 407 <dd>
 408 <div class="block">Format sequence per width letter in one string.</div>
 409 </dd>
 410 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/FastaSequence.html#getFormattedFasta--">getFormattedFasta()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></dt>
 411 <dd>&nbsp;</dd>
 412 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getFullPath-java.util.List-">getFullPath(List&lt;String&gt;)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
 413 <dd>&nbsp;</dd>
 414 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EngineUtil.html#getFullPath-java.lang.String-java.lang.String-">getFullPath(String, 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>
 415 <dd>&nbsp;</dd>
 416 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Util.html#getFullPath-java.lang.String-java.lang.String-">getFullPath(String, 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>
 417 <dd>&nbsp;</dd>
 418 <dt><span class="memberNameLink"><a href="../compbio/metadata/Argument.html#getFurtherDetails--">getFurtherDetails()</a></span> - Method in interface compbio.metadata.<a href="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</a></dt>
 419 <dd>&nbsp;</dd>
 420 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#getFurtherDetails--">getFurtherDetails()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 421 <dd>
 422 <div class="block">The URL where further details about the option can be found</div>
 423 </dd>
 424 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalRunner.html#getFuture--">getFuture()</a></span> - Method in class compbio.engine.local.<a href="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</a></dt>
 425 <dd>&nbsp;</dd>
 426 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/AlignmentMetadata.html#getGapchar--">getGapchar()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</a></dt>
 427 <dd>&nbsp;</dd>
 428 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/ServiceTestResult.html#getGroup--">getGroup()</a></span> - Method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</a></dt>
 429 <dd>&nbsp;</dd>
 430 <dt><span class="memberNameLink"><a href="../compbio/ws/client/CmdHelper.html#getHost-java.lang.String:A-">getHost(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>
 431 <dd>
 432 <div class="block">Extracts host name from the command line</div>
 433 </dd>
 434 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/FastaSequence.html#getId--">getId()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></dt>
 435 <dd>
 436 <div class="block">Gets the value of id</div>
 437 </dd>
 438 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/Totals.html#getIncomplete--">getIncomplete()</a></span> - 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>
 439 <dd>&nbsp;</dd>
 440 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatDB.html#getIncompleteCount-java.sql.Timestamp-java.sql.Timestamp-">getIncompleteCount(Timestamp, Timestamp)</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</a></dt>
 441 <dd>&nbsp;</dd>
 442 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatProcessor.html#getIncompleteJobs--">getIncompleteJobs()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</a></dt>
 443 <dd>&nbsp;</dd>
 444 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getInput--">getInput()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
 445 <dd>
 446 <div class="block">Not all input paths are relative! Input path could be absolute!</div>
 447 </dd>
 448 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Executable.html#getInput--">getInput()</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a></dt>
 449 <dd>&nbsp;</dd>
 450 <dt><span class="memberNameLink"><a href="../compbio/engine/client/RunConfiguration.html#getInput--">getInput()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</a></dt>
 451 <dd>&nbsp;</dd>
 452 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#getInput--">getInput()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 453 <dd>&nbsp;</dd>
 454 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobDirectory.html#getInputSize--">getInputSize()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobDirectory.html" title="class in compbio.stat.collector">JobDirectory</a></dt>
 455 <dd>&nbsp;</dd>
 456 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#getInputSize--">getInputSize()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 457 <dd>&nbsp;</dd>
 458 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#getInstance-compbio.engine.client.ConfiguredExecutable-">getInstance(ConfiguredExecutable&lt;?&gt;)</a></span> - Static 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>
 459 <dd>&nbsp;</dd>
 460 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#getInstance--">getInstance()</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>
 461 <dd>&nbsp;</dd>
 462 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#getInstance-compbio.engine.client.ConfiguredExecutable-">getInstance(ConfiguredExecutable&lt;?&gt;)</a></span> - Static 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>
 463 <dd>&nbsp;</dd>
 464 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#getInterface-javax.xml.ws.Service-">getInterface(Service)</a></span> - Method in enum compbio.ws.client.<a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></dt>
 465 <dd>&nbsp;</dd>
 466 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/PropertyHelperManager.html#getIntProperty-java.lang.String-">getIntProperty(String)</a></span> - Static method in class compbio.engine.conf.<a href="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</a></dt>
 467 <dd>&nbsp;</dd>
 468 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/StatisticCollector.html#getIntProperty-java.lang.String-">getIntProperty(String)</a></span> - Static method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</a></dt>
 469 <dd>&nbsp;</dd>
 470 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatDB.html#getIntResult-java.sql.Timestamp-java.sql.Timestamp-java.lang.String-">getIntResult(Timestamp, Timestamp, String)</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</a></dt>
 471 <dd>&nbsp;</dd>
 472 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#getIOWait--">getIOWait()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 473 <dd>&nbsp;</dd>
 474 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#getIsCancelled--">getIsCancelled()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 475 <dd>&nbsp;</dd>
 476 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#getIsCollected--">getIsCollected()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 477 <dd>&nbsp;</dd>
 478 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#getIsFinished--">getIsFinished()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 479 <dd>&nbsp;</dd>
 480 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#getJabawsVersion--">getJabawsVersion()</a></span> - Method in enum compbio.ws.client.<a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></dt>
 481 <dd>&nbsp;</dd>
 482 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EngineUtil.html#getJava--">getJava()</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>
 483 <dd>
 484 <div class="block">Returns the absolute path to the Java executable from JAVA_HOME</div>
 485 </dd>
 486 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Util.html#getJava--">getJava()</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>
 487 <dd>
 488 <div class="block">Returns the absolute path to the Java executable from JAVA_HOME</div>
 489 </dd>
 490 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/StatCollection.html#getJobCounts-java.util.Date-java.util.Date-">getJobCounts(Date, Date)</a></span> - Static method in class compbio.stat.servlet.util.<a href="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</a></dt>
 491 <dd>&nbsp;</dd>
 492 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CancelJob.html#getJobId--">getJobId()</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>
 493 <dd>&nbsp;</dd>
 494 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetAnnotation.html#getJobId--">getJobId()</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>
 495 <dd>&nbsp;</dd>
 496 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetJobStatus.html#getJobId--">getJobId()</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>
 497 <dd>&nbsp;</dd>
 498 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetResult.html#getJobId--">getJobId()</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>
 499 <dd>&nbsp;</dd>
 500 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PullExecStatistics.html#getJobId--">getJobId()</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>
 501 <dd>&nbsp;</dd>
 502 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#getJobId--">getJobId()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 503 <dd>&nbsp;</dd>
 504 <dt><span class="memberNameLink"><a href="../compbio/engine/ClusterJobId.html#getJobId--">getJobId()</a></span> - Method in class compbio.engine.<a href="../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</a></dt>
 505 <dd>&nbsp;</dd>
 506 <dt><span class="memberNameLink"><a href="../compbio/engine/Job.html#getJobId--">getJobId()</a></span> - Method in class compbio.engine.<a href="../compbio/engine/Job.html" title="class in compbio.engine">Job</a></dt>
 507 <dd>&nbsp;</dd>
 508 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#getJobInfo--">getJobInfo()</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>
 509 <dd>
 510 <div class="block">This method will block before the calculation has completed and then
 511  return the object containing a job execution statistics</div>
 512 </dd>
 513 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#getJobInfo--">getJobInfo()</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>
 514 <dd>
 515 <div class="block">This method will block before the calculation has completed and then
 516  return the object containing a job execution statistics</div>
 517 </dd>
 518 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#getJobname--">getJobname()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 519 <dd>&nbsp;</dd>
 520 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatProcessor.html#getJobNumber--">getJobNumber()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</a></dt>
 521 <dd>&nbsp;</dd>
 522 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#getJobPriority--">getJobPriority()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 523 <dd>&nbsp;</dd>
 524 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#getJobReport--">getJobReport()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 525 <dd>&nbsp;</dd>
 526 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#getJobReportTabulated--">getJobReportTabulated()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 527 <dd>
 528 <div class="block">Header Job Started Finished Runtime Input Result</div>
 529 </dd>
 530 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatProcessor.html#getJobs--">getJobs()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</a></dt>
 531 <dd>&nbsp;</dd>
 532 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobDirectory.html#getJobStat--">getJobStat()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobDirectory.html" title="class in compbio.stat.collector">JobDirectory</a></dt>
 533 <dd>&nbsp;</dd>
 534 <dt><a href="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetJobStatus</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 535 <dd>&nbsp;</dd>
 536 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetJobStatus.html#GetJobStatus--">GetJobStatus()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws">GetJobStatus</a></dt>
 537 <dd>&nbsp;</dd>
 538 <dt><span class="memberNameLink"><a href="../compbio/data/msa/JManagement.html#getJobStatus-java.lang.String-">getJobStatus(String)</a></span> - Method in interface compbio.data.msa.<a href="../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</a></dt>
 539 <dd>
 540 <div class="block">Return the status of the job.</div>
 541 </dd>
 542 <dt><span class="memberNameLink"><a href="../compbio/engine/AsyncExecutor.html#getJobStatus-java.lang.String-">getJobStatus(String)</a></span> - Method in interface compbio.engine.<a href="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</a></dt>
 543 <dd>
 544 <div class="block">Query the status of the job</div>
 545 </dd>
 546 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/AsyncClusterRunner.html#getJobStatus-java.lang.String-">getJobStatus(String)</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>
 547 <dd>&nbsp;</dd>
 548 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getJobStatus-java.lang.String-">getJobStatus(String)</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>
 549 <dd>
 550 <div class="block">This will never return clust.engine.JobStatus.CANCELLED as for sun grid
 551  engine cancelled job is the same as failed.</div>
 552 </dd>
 553 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#getJobStatus-java.lang.String-">getJobStatus(String)</a></span> - Static 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>
 554 <dd>
 555 <div class="block">This will never return clust.engine.JobStatus.CANCELLED as for sun grid
 556  engine cancelled job is the same as failed.</div>
 557 </dd>
 558 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#getJobStatus--">getJobStatus()</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>
 559 <dd>&nbsp;</dd>
 560 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#getJobStatus-compbio.engine.ClusterJobId-">getJobStatus(ClusterJobId)</a></span> - 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>
 561 <dd>
 562 <div class="block">Apparently completed jobs cannot be found! If this happened most likely
 563  that the job is not running any more and Most likely it has been
 564  cancelled, finished or failed.</div>
 565 </dd>
 566 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#getJobStatus-int-">getJobStatus(int)</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>
 567 <dd>
 568 <div class="block"><span class="deprecatedLabel">Deprecated.</span></div>
 569 </dd>
 570 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#getJobStatus-java.lang.String-">getJobStatus(String)</a></span> - Static 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>
 571 <dd>
 572 <div class="block">This will never return clust.engine.JobStatus.CANCELLED as for sun grid
 573  engine cancelled job is the same as failed.</div>
 574 </dd>
 575 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#getJobStatus--">getJobStatus()</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>
 576 <dd>&nbsp;</dd>
 577 <dt><span class="memberNameLink"><a href="../compbio/engine/local/AsyncLocalRunner.html#getJobStatus-java.lang.String-">getJobStatus(String)</a></span> - Method in class compbio.engine.local.<a href="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</a></dt>
 578 <dd>&nbsp;</dd>
 579 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalEngineUtil.html#getJobStatus-java.util.concurrent.Future-">getJobStatus(Future&lt;ConfiguredExecutable&lt;?&gt;&gt;)</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>
 580 <dd>&nbsp;</dd>
 581 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalRunner.html#getJobStatus--">getJobStatus()</a></span> - Method in class compbio.engine.local.<a href="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</a></dt>
 582 <dd>&nbsp;</dd>
 583 <dt><span class="memberNameLink"><a href="../compbio/engine/SyncExecutor.html#getJobStatus--">getJobStatus()</a></span> - Method in interface compbio.engine.<a href="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</a></dt>
 584 <dd>
 585 <div class="block">Query the status of the job by its id.</div>
 586 </dd>
 587 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalOWS.html#getJobStatus-java.lang.String-">getJobStatus(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</a></dt>
 588 <dd>&nbsp;</dd>
 589 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalWS.html#getJobStatus-java.lang.String-">getJobStatus(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</a></dt>
 590 <dd>&nbsp;</dd>
 591 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GenericMetadataService.html#getJobStatus-java.lang.String-">getJobStatus(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</a></dt>
 592 <dd>&nbsp;</dd>
 593 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GLprobsWS.html#getJobStatus-java.lang.String-">getJobStatus(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/GLprobsWS.html" title="class in compbio.ws.server">GLprobsWS</a></dt>
 594 <dd>&nbsp;</dd>
 595 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MafftWS.html#getJobStatus-java.lang.String-">getJobStatus(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</a></dt>
 596 <dd>&nbsp;</dd>
 597 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MSAprobsWS.html#getJobStatus-java.lang.String-">getJobStatus(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MSAprobsWS.html" title="class in compbio.ws.server">MSAprobsWS</a></dt>
 598 <dd>&nbsp;</dd>
 599 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MuscleWS.html#getJobStatus-java.lang.String-">getJobStatus(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</a></dt>
 600 <dd>&nbsp;</dd>
 601 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ProbconsWS.html#getJobStatus-java.lang.String-">getJobStatus(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</a></dt>
 602 <dd>&nbsp;</dd>
 603 <dt><span class="memberNameLink"><a href="../compbio/ws/server/TcoffeeWS.html#getJobStatus-java.lang.String-">getJobStatus(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</a></dt>
 604 <dd>&nbsp;</dd>
 605 <dt><span class="memberNameLink"><a href="../compbio/ws/server/WSUtil.html#getJobStatus-java.lang.String-">getJobStatus(String)</a></span> - Static method in class compbio.ws.server.<a href="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</a></dt>
 606 <dd>&nbsp;</dd>
 607 <dt><a href="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetJobStatusResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 608 <dd>&nbsp;</dd>
 609 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetJobStatusResponse.html#GetJobStatusResponse--">GetJobStatusResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws">GetJobStatusResponse</a></dt>
 610 <dd>&nbsp;</dd>
 611 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatProcessor.html#getJobSubset-boolean-">getJobSubset(boolean)</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</a></dt>
 612 <dd>&nbsp;</dd>
 613 <dt><a href="../compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetLastTested</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 614 <dd>&nbsp;</dd>
 615 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLastTested.html#GetLastTested--">GetLastTested()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws">GetLastTested</a></dt>
 616 <dd>&nbsp;</dd>
 617 <dt><span class="memberNameLink"><a href="../compbio/data/msa/RegistryWS.html#getLastTested-compbio.ws.client.Services-">getLastTested(Services)</a></span> - Method in interface compbio.data.msa.<a href="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</a></dt>
 618 <dd>
 619 <div class="block">Number of seconds since the last test.</div>
 620 </dd>
 621 <dt><span class="memberNameLink"><a href="../compbio/ws/server/RegistryWS.html#getLastTested-compbio.ws.client.Services-">getLastTested(Services)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</a></dt>
 622 <dd>&nbsp;</dd>
 623 <dt><a href="../compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetLastTestedOn</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 624 <dd>&nbsp;</dd>
 625 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLastTestedOn.html#GetLastTestedOn--">GetLastTestedOn()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws">GetLastTestedOn</a></dt>
 626 <dd>&nbsp;</dd>
 627 <dt><span class="memberNameLink"><a href="../compbio/data/msa/RegistryWS.html#getLastTestedOn-compbio.ws.client.Services-">getLastTestedOn(Services)</a></span> - Method in interface compbio.data.msa.<a href="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</a></dt>
 628 <dd>
 629 <div class="block">The date and time the service has been verified to work last time</div>
 630 </dd>
 631 <dt><span class="memberNameLink"><a href="../compbio/ws/server/RegistryWS.html#getLastTestedOn-compbio.ws.client.Services-">getLastTestedOn(Services)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</a></dt>
 632 <dd>
 633 <div class="block">Can potentially return null if the service has not been tested yet.</div>
 634 </dd>
 635 <dt><a href="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetLastTestedOnResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 636 <dd>&nbsp;</dd>
 637 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html#GetLastTestedOnResponse--">GetLastTestedOnResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedOnResponse</a></dt>
 638 <dd>&nbsp;</dd>
 639 <dt><a href="../compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetLastTestedResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 640 <dd>&nbsp;</dd>
 641 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLastTestedResponse.html#GetLastTestedResponse--">GetLastTestedResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedResponse</a></dt>
 642 <dd>&nbsp;</dd>
 643 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/FastaSequence.html#getLength--">getLength()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></dt>
 644 <dd>&nbsp;</dd>
 645 <dt><span class="memberNameLink"><a href="../compbio/runner/conservation/AACon.html#getLibPath--">getLibPath()</a></span> - Static method in class compbio.runner.conservation.<a href="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a></dt>
 646 <dd>&nbsp;</dd>
 647 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Jronn.html#getLibPath--">getLibPath()</a></span> - Static method in class compbio.runner.disorder.<a href="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</a></dt>
 648 <dd>&nbsp;</dd>
 649 <dt><a href="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetLimit</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 650 <dd>&nbsp;</dd>
 651 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLimit.html#GetLimit--">GetLimit()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</a></dt>
 652 <dd>&nbsp;</dd>
 653 <dt><span class="memberNameLink"><a href="../compbio/data/msa/Metadata.html#getLimit-java.lang.String-">getLimit(String)</a></span> - Method in interface compbio.data.msa.<a href="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</a></dt>
 654 <dd>
 655 <div class="block">Get a Limit for a preset.</div>
 656 </dd>
 657 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getLimit-java.lang.String-">getLimit(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>
 658 <dd>&nbsp;</dd>
 659 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Executable.html#getLimit-java.lang.String-">getLimit(String)</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a></dt>
 660 <dd>&nbsp;</dd>
 661 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#getLimit-java.lang.String-">getLimit(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>
 662 <dd>&nbsp;</dd>
 663 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalOWS.html#getLimit-java.lang.String-">getLimit(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</a></dt>
 664 <dd>&nbsp;</dd>
 665 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalWS.html#getLimit-java.lang.String-">getLimit(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</a></dt>
 666 <dd>&nbsp;</dd>
 667 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GenericMetadataService.html#getLimit-java.lang.String-">getLimit(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</a></dt>
 668 <dd>&nbsp;</dd>
 669 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GLprobsWS.html#getLimit-java.lang.String-">getLimit(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/GLprobsWS.html" title="class in compbio.ws.server">GLprobsWS</a></dt>
 670 <dd>&nbsp;</dd>
 671 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MafftWS.html#getLimit-java.lang.String-">getLimit(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</a></dt>
 672 <dd>&nbsp;</dd>
 673 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MSAprobsWS.html#getLimit-java.lang.String-">getLimit(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MSAprobsWS.html" title="class in compbio.ws.server">MSAprobsWS</a></dt>
 674 <dd>&nbsp;</dd>
 675 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MuscleWS.html#getLimit-java.lang.String-">getLimit(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</a></dt>
 676 <dd>&nbsp;</dd>
 677 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ProbconsWS.html#getLimit-java.lang.String-">getLimit(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</a></dt>
 678 <dd>&nbsp;</dd>
 679 <dt><span class="memberNameLink"><a href="../compbio/ws/server/TcoffeeWS.html#getLimit-java.lang.String-">getLimit(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</a></dt>
 680 <dd>&nbsp;</dd>
 681 <dt><span class="memberNameLink"><a href="../compbio/metadata/LimitsManager.html#getLimitByName-java.lang.String-">getLimitByName(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a></dt>
 682 <dd>&nbsp;</dd>
 683 <dt><a href="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetLimitResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 684 <dd>&nbsp;</dd>
 685 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLimitResponse.html#GetLimitResponse--">GetLimitResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws">GetLimitResponse</a></dt>
 686 <dd>&nbsp;</dd>
 687 <dt><a href="../compbio/data/msa/jaxws/GetLimits.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetLimits</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 688 <dd>&nbsp;</dd>
 689 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLimits.html#GetLimits--">GetLimits()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetLimits.html" title="class in compbio.data.msa.jaxws">GetLimits</a></dt>
 690 <dd>&nbsp;</dd>
 691 <dt><span class="memberNameLink"><a href="../compbio/data/msa/Metadata.html#getLimits--">getLimits()</a></span> - Method in interface compbio.data.msa.<a href="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</a></dt>
 692 <dd>
 693 <div class="block">List Limits supported by a web service.</div>
 694 </dd>
 695 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getLimits--">getLimits()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
 696 <dd>&nbsp;</dd>
 697 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EngineUtil.html#getLimits-java.lang.Class-">getLimits(Class&lt;T&gt;)</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>
 698 <dd>
 699 <div class="block">For now just assume that all parameters which came in needs setting it
 700  will be a client responsibility to prepare RunnerConfig object then</div>
 701 </dd>
 702 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Executable.html#getLimits--">getLimits()</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a></dt>
 703 <dd>&nbsp;</dd>
 704 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#getLimits--">getLimits()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 705 <dd>&nbsp;</dd>
 706 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Util.html#getLimits-java.lang.Class-">getLimits(Class&lt;T&gt;)</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>
 707 <dd>
 708 <div class="block">For now just assume that all parameters which came in needs setting it
 709  will be a client responsibility to prepare RunnerConfig object then</div>
 710 </dd>
 711 <dt><span class="memberNameLink"><a href="../compbio/metadata/LimitsManager.html#getLimits--">getLimits()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a></dt>
 712 <dd>&nbsp;</dd>
 713 <dt><span class="memberNameLink"><a href="../compbio/ws/client/MetadataHelper.html#getLimits-compbio.data.msa.Metadata-">getLimits(Metadata&lt;T&gt;)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client">MetadataHelper</a></dt>
 714 <dd>
 715 <div class="block">Returns a list of limits supported by web service Each limit correspond
 716  to a particular preset.</div>
 717 </dd>
 718 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalOWS.html#getLimits--">getLimits()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</a></dt>
 719 <dd>&nbsp;</dd>
 720 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalWS.html#getLimits--">getLimits()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</a></dt>
 721 <dd>&nbsp;</dd>
 722 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GenericMetadataService.html#getLimits--">getLimits()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</a></dt>
 723 <dd>&nbsp;</dd>
 724 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GLprobsWS.html#getLimits--">getLimits()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/GLprobsWS.html" title="class in compbio.ws.server">GLprobsWS</a></dt>
 725 <dd>&nbsp;</dd>
 726 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MafftWS.html#getLimits--">getLimits()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</a></dt>
 727 <dd>&nbsp;</dd>
 728 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MSAprobsWS.html#getLimits--">getLimits()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MSAprobsWS.html" title="class in compbio.ws.server">MSAprobsWS</a></dt>
 729 <dd>&nbsp;</dd>
 730 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MuscleWS.html#getLimits--">getLimits()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</a></dt>
 731 <dd>&nbsp;</dd>
 732 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ProbconsWS.html#getLimits--">getLimits()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</a></dt>
 733 <dd>&nbsp;</dd>
 734 <dt><span class="memberNameLink"><a href="../compbio/ws/server/TcoffeeWS.html#getLimits--">getLimits()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</a></dt>
 735 <dd>&nbsp;</dd>
 736 <dt><a href="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetLimitsResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 737 <dd>&nbsp;</dd>
 738 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLimitsResponse.html#GetLimitsResponse--">GetLimitsResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws">GetLimitsResponse</a></dt>
 739 <dd>&nbsp;</dd>
 740 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/StatisticCollector.html#getLocalJobDir--">getLocalJobDir()</a></span> - Static method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</a></dt>
 741 <dd>&nbsp;</dd>
 742 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MainManager.html#getLocalJobDir--">getLocalJobDir()</a></span> - Static method in class compbio.ws.server.<a href="../compbio/ws/server/MainManager.html" title="class in compbio.ws.server">MainManager</a></dt>
 743 <dd>&nbsp;</dd>
 744 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatProcessor.html#getLocalJobs--">getLocalJobs()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</a></dt>
 745 <dd>&nbsp;</dd>
 746 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/StatisticCollector.html#getLocalJobTimeOut--">getLocalJobTimeOut()</a></span> - Static method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</a></dt>
 747 <dd>&nbsp;</dd>
 748 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/PropertyHelperManager.html#getLocalPath--">getLocalPath()</a></span> - Static method in class compbio.engine.conf.<a href="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</a></dt>
 749 <dd>
 750 <div class="block">Method return the absolute path to the project root directory.</div>
 751 </dd>
 752 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/StatCollection.html#getLocalStat--">getLocalStat()</a></span> - Method in class compbio.stat.servlet.util.<a href="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</a></dt>
 753 <dd>&nbsp;</dd>
 754 <dt><span class="memberNameLink"><a href="../compbio/ws/server/RegistryWS.html#getLongestUntestedServiceTime--">getLongestUntestedServiceTime()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</a></dt>
 755 <dd>
 756 <div class="block">Return time in seconds for the test for the oldest unchecked service</div>
 757 </dd>
 758 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#getLowBorderValue-compbio.metadata.Parameter-">getLowBorderValue(Parameter&lt;?&gt;)</a></span> - Method in class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
 759 <dd>&nbsp;</dd>
 760 <dt><span class="memberNameLink"><a href="../compbio/metadata/ValueConstrain.html#getMax--">getMax()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</a></dt>
 761 <dd>&nbsp;</dd>
 762 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#getMaxVMem--">getMaxVMem()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 763 <dd>&nbsp;</dd>
 764 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#getMemoryStat--">getMemoryStat()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 765 <dd>&nbsp;</dd>
 766 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html#getMessage--">getMessage()</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>
 767 <dd>&nbsp;</dd>
 768 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getMessage--">getMessage()</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>
 769 <dd>&nbsp;</dd>
 770 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html#getMessage--">getMessage()</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>
 771 <dd>&nbsp;</dd>
 772 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html#getMessage--">getMessage()</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>
 773 <dd>&nbsp;</dd>
 774 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html#getMessage--">getMessage()</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>
 775 <dd>&nbsp;</dd>
 776 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Alignment.html#getMetadata--">getMetadata()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></dt>
 777 <dd>&nbsp;</dd>
 778 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ConservationMethod.html#getMethod-java.lang.String-">getMethod(String)</a></span> - Static method in enum compbio.data.sequence.<a href="../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence">ConservationMethod</a></dt>
 779 <dd>&nbsp;</dd>
 780 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Score.html#getMethod--">getMethod()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a></dt>
 781 <dd>
 782 <div class="block">Returns the ConservationMethod</div>
 783 </dd>
 784 <dt><span class="memberNameLink"><a href="../compbio/metadata/ValueConstrain.html#getMin--">getMin()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</a></dt>
 785 <dd>&nbsp;</dd>
 786 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#getName-java.lang.String-">getName(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>
 787 <dd>&nbsp;</dd>
 788 <dt><span class="memberNameLink"><a href="../compbio/metadata/Argument.html#getName--">getName()</a></span> - Method in interface compbio.metadata.<a href="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</a></dt>
 789 <dd>&nbsp;</dd>
 790 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#getName--">getName()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 791 <dd>
 792 <div class="block">Human readable name of the option</div>
 793 </dd>
 794 <dt><span class="memberNameLink"><a href="../compbio/metadata/Preset.html#getName--">getName()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a></dt>
 795 <dd>&nbsp;</dd>
 796 <dt><span class="memberNameLink"><a href="../compbio/metadata/Preset.html#getName-java.lang.String-">getName(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a></dt>
 797 <dd>&nbsp;</dd>
 798 <dt><span class="memberNameLink"><a href="../compbio/runner/conservation/AACon.html#getNCore--">getNCore()</a></span> - Method in class compbio.runner.conservation.<a href="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a></dt>
 799 <dd>&nbsp;</dd>
 800 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Jronn.html#getNCore--">getNCore()</a></span> - Method in class compbio.runner.disorder.<a href="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</a></dt>
 801 <dd>&nbsp;</dd>
 802 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/ClustalO.html#getNCore--">getNCore()</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a></dt>
 803 <dd>&nbsp;</dd>
 804 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Tcoffee.html#getNCore--">getNCore()</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</a></dt>
 805 <dd>&nbsp;</dd>
 806 <dt><span class="memberNameLink"><a href="../compbio/metadata/ChunkHolder.html#getNextPosition--">getNextPosition()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</a></dt>
 807 <dd>&nbsp;</dd>
 808 <dt><a href="../compbio/data/msa/jaxws/GetNonoperatedServices.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetNonoperatedServices</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 809 <dd>&nbsp;</dd>
 810 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetNonoperatedServices.html#GetNonoperatedServices--">GetNonoperatedServices()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetNonoperatedServices.html" title="class in compbio.data.msa.jaxws">GetNonoperatedServices</a></dt>
 811 <dd>&nbsp;</dd>
 812 <dt><a href="../compbio/data/msa/jaxws/GetNonoperatedServicesResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetNonoperatedServicesResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 813 <dd>&nbsp;</dd>
 814 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetNonoperatedServicesResponse.html#GetNonoperatedServicesResponse--">GetNonoperatedServicesResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetNonoperatedServicesResponse.html" title="class in compbio.data.msa.jaxws">GetNonoperatedServicesResponse</a></dt>
 815 <dd>&nbsp;</dd>
 816 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/DirectoryManager.html#getNonRepeatableNumber--">getNonRepeatableNumber()</a></span> - Static method in class compbio.engine.conf.<a href="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</a></dt>
 817 <dd>&nbsp;</dd>
 818 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ScoreManager.ScoreHolder.html#getNumberOfScores--">getNumberOfScores()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</a></dt>
 819 <dd>&nbsp;</dd>
 820 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ScoreManager.html#getNumberOfSeq--">getNumberOfSeq()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></dt>
 821 <dd>&nbsp;</dd>
 822 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getNumberOfSequencesAllowed--">getNumberOfSequencesAllowed()</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>
 823 <dd>&nbsp;</dd>
 824 <dt><span class="memberNameLink"><a href="../compbio/metadata/LimitExceededException.html#getNumberOfSequencesAllowed--">getNumberOfSequencesAllowed()</a></span> - Method in exception compbio.metadata.<a href="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></dt>
 825 <dd>&nbsp;</dd>
 826 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#getNumericalFinish--">getNumericalFinish()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 827 <dd>&nbsp;</dd>
 828 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#getNumericalStart--">getNumericalStart()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 829 <dd>&nbsp;</dd>
 830 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/FastaSequence.html#getOnelineFasta--">getOnelineFasta()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></dt>
 831 <dd>&nbsp;</dd>
 832 <dt><span class="memberNameLink"><a href="../compbio/metadata/Parameter.html#getOptionName--">getOptionName()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</a></dt>
 833 <dd>&nbsp;</dd>
 834 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#getOptionNames--">getOptionNames()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 835 <dd>&nbsp;</dd>
 836 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAlign.html#getOptions--">getOptions()</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>
 837 <dd>&nbsp;</dd>
 838 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAnalize.html#getOptions--">getOptions()</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>
 839 <dd>&nbsp;</dd>
 840 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomFold.html#getOptions--">getOptions()</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>
 841 <dd>&nbsp;</dd>
 842 <dt><span class="memberNameLink"><a href="../compbio/metadata/Preset.html#getOptions--">getOptions()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a></dt>
 843 <dd>&nbsp;</dd>
 844 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#getOptions--">getOptions()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
 845 <dd>
 846 <div class="block">Returns the list of the Options supported by the executable of type T</div>
 847 </dd>
 848 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#getOptionsAtRandom--">getOptionsAtRandom()</a></span> - Method in class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
 849 <dd>&nbsp;</dd>
 850 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getOutput--">getOutput()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
 851 <dd>&nbsp;</dd>
 852 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Executable.html#getOutput--">getOutput()</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a></dt>
 853 <dd>&nbsp;</dd>
 854 <dt><span class="memberNameLink"><a href="../compbio/engine/client/RunConfiguration.html#getOutput--">getOutput()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</a></dt>
 855 <dd>&nbsp;</dd>
 856 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#getOutput--">getOutput()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 857 <dd>&nbsp;</dd>
 858 <dt><span class="memberNameLink"><a href="../compbio/engine/local/ExecutableWrapper.html#getOutput--">getOutput()</a></span> - Method in class compbio.engine.local.<a href="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</a></dt>
 859 <dd>&nbsp;</dd>
 860 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/IUPred.html#getOutput--">getOutput()</a></span> - Method in class compbio.runner.disorder.<a href="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</a></dt>
 861 <dd>&nbsp;</dd>
 862 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getParameters--">getParameters()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
 863 <dd>&nbsp;</dd>
 864 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getParameters-compbio.engine.client.Executable.ExecProvider-">getParameters(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>
 865 <dd>&nbsp;</dd>
 866 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfiguredExecutable.html#getParameters--">getParameters()</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a></dt>
 867 <dd>&nbsp;</dd>
 868 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Executable.html#getParameters-compbio.engine.client.Executable.ExecProvider-">getParameters(Executable.ExecProvider)</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a></dt>
 869 <dd>&nbsp;</dd>
 870 <dt><span class="memberNameLink"><a href="../compbio/engine/client/RunConfiguration.html#getParameters--">getParameters()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</a></dt>
 871 <dd>&nbsp;</dd>
 872 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#getParameters-compbio.engine.client.Executable.ExecProvider-">getParameters(Executable.ExecProvider)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 873 <dd>&nbsp;</dd>
 874 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#getParameters--">getParameters()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
 875 <dd>
 876 <div class="block">Returns the list of parameters supported executable of type T.</div>
 877 </dd>
 878 <dt><span class="memberNameLink"><a href="../compbio/runner/conservation/AACon.html#getParameters-compbio.engine.client.Executable.ExecProvider-">getParameters(Executable.ExecProvider)</a></span> - Method in class compbio.runner.conservation.<a href="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a></dt>
 879 <dd>&nbsp;</dd>
 880 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Jronn.html#getParameters-compbio.engine.client.Executable.ExecProvider-">getParameters(Executable.ExecProvider)</a></span> - Method in class compbio.runner.disorder.<a href="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</a></dt>
 881 <dd>&nbsp;</dd>
 882 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/ClustalO.html#getParameters-compbio.engine.client.Executable.ExecProvider-">getParameters(Executable.ExecProvider)</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a></dt>
 883 <dd>&nbsp;</dd>
 884 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Tcoffee.html#getParameters-compbio.engine.client.Executable.ExecProvider-">getParameters(Executable.ExecProvider)</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</a></dt>
 885 <dd>&nbsp;</dd>
 886 <dt><span class="memberNameLink"><a href="../compbio/ws/client/MetadataHelper.html#getParametersList-compbio.data.msa.Metadata-">getParametersList(Metadata&lt;T&gt;)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client">MetadataHelper</a></dt>
 887 <dd>
 888 <div class="block">Returns a list of options supported by web service</div>
 889 </dd>
 890 <dt><span class="memberNameLink"><a href="../compbio/ws/client/MetadataHelper.html#getParametersList-compbio.data.msa.Metadata-java.lang.String-">getParametersList(Metadata&lt;T&gt;, String)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client">MetadataHelper</a></dt>
 891 <dd>
 892 <div class="block">Returns a list of options supported by web service</div>
 893 </dd>
 894 <dt><span class="memberNameLink"><a href="../compbio/ws/client/MetadataHelper.html#getParamName-java.lang.String-">getParamName(String)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client">MetadataHelper</a></dt>
 895 <dd>&nbsp;</dd>
 896 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#getParamValue-java.lang.String-">getParamValue(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>
 897 <dd>&nbsp;</dd>
 898 <dt><span class="memberNameLink"><a href="../compbio/ws/client/MetadataHelper.html#getParamValue-java.lang.String-">getParamValue(String)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client">MetadataHelper</a></dt>
 899 <dd>&nbsp;</dd>
 900 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PullExecStatistics.html#getPosition--">getPosition()</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>
 901 <dd>&nbsp;</dd>
 902 <dt><span class="memberNameLink"><a href="../compbio/metadata/Argument.html#getPossibleValues--">getPossibleValues()</a></span> - Method in interface compbio.metadata.<a href="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</a></dt>
 903 <dd>&nbsp;</dd>
 904 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#getPossibleValues--">getPossibleValues()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
 905 <dd>
 906 <div class="block">List of possible optionNames</div>
 907 </dd>
 908 <dt><span class="memberNameLink"><a href="../compbio/metadata/Parameter.html#getPossibleValues--">getPossibleValues()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</a></dt>
 909 <dd>
 910 <div class="block">List is more convenient to work with</div>
 911 </dd>
 912 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetAlign.html#getPreset--">getPreset()</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>
 913 <dd>&nbsp;</dd>
 914 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetAnalize.html#getPreset--">getPreset()</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>
 915 <dd>&nbsp;</dd>
 916 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetFold.html#getPreset--">getPreset()</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>
 917 <dd>&nbsp;</dd>
 918 <dt><span class="memberNameLink"><a href="../compbio/metadata/Limit.html#getPreset--">getPreset()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a></dt>
 919 <dd>&nbsp;</dd>
 920 <dt><span class="memberNameLink"><a href="../compbio/ws/client/MetadataHelper.html#getPreset-compbio.data.msa.Metadata-java.lang.String-">getPreset(Metadata&lt;T&gt;, String)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client">MetadataHelper</a></dt>
 921 <dd>
 922 <div class="block">Returns <code>Preset</code> by its name</div>
 923 </dd>
 924 <dt><span class="memberNameLink"><a href="../compbio/metadata/PresetManager.html#getPresetByName-java.lang.String-">getPresetByName(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a></dt>
 925 <dd>&nbsp;</dd>
 926 <dt><span class="memberNameLink"><a href="../compbio/ws/client/MetadataHelper.html#getPresetList-compbio.data.msa.Metadata-">getPresetList(Metadata&lt;T&gt;)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client">MetadataHelper</a></dt>
 927 <dd>
 928 <div class="block">Returns an objects from which the list of presets supported by web
 929  service <T> can be obtained</div>
 930 </dd>
 931 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLimit.html#getPresetName--">getPresetName()</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>
 932 <dd>&nbsp;</dd>
 933 <dt><span class="memberNameLink"><a href="../compbio/ws/client/CmdHelper.html#getPresetName-java.lang.String:A-">getPresetName(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>
 934 <dd>
 935 <div class="block">Extracts preset name from the command line is any</div>
 936 </dd>
 937 <dt><a href="../compbio/data/msa/jaxws/GetPresets.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetPresets</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 938 <dd>&nbsp;</dd>
 939 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetPresets.html#GetPresets--">GetPresets()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetPresets.html" title="class in compbio.data.msa.jaxws">GetPresets</a></dt>
 940 <dd>&nbsp;</dd>
 941 <dt><span class="memberNameLink"><a href="../compbio/data/msa/Metadata.html#getPresets--">getPresets()</a></span> - Method in interface compbio.data.msa.<a href="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</a></dt>
 942 <dd>
 943 <div class="block">Get presets supported by a web service</div>
 944 </dd>
 945 <dt><span class="memberNameLink"><a href="../compbio/metadata/PresetManager.html#getPresets--">getPresets()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a></dt>
 946 <dd>&nbsp;</dd>
 947 <dt><span class="memberNameLink"><a href="../compbio/runner/RunnerUtil.html#getPresets-java.lang.Class-">getPresets(Class&lt;? extends Executable&lt;T&gt;&gt;)</a></span> - Static method in class compbio.runner.<a href="../compbio/runner/RunnerUtil.html" title="class in compbio.runner">RunnerUtil</a></dt>
 948 <dd>&nbsp;</dd>
 949 <dt><span class="memberNameLink"><a href="../compbio/runner/Util.html#getPresets-java.lang.Class-">getPresets(Class&lt;? extends Executable&lt;T&gt;&gt;)</a></span> - Static method in class compbio.runner.<a href="../compbio/runner/Util.html" title="class in compbio.runner">Util</a></dt>
 950 <dd>&nbsp;</dd>
 951 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalOWS.html#getPresets--">getPresets()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</a></dt>
 952 <dd>&nbsp;</dd>
 953 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalWS.html#getPresets--">getPresets()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</a></dt>
 954 <dd>&nbsp;</dd>
 955 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GenericMetadataService.html#getPresets--">getPresets()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</a></dt>
 956 <dd>&nbsp;</dd>
 957 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GLprobsWS.html#getPresets--">getPresets()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/GLprobsWS.html" title="class in compbio.ws.server">GLprobsWS</a></dt>
 958 <dd>&nbsp;</dd>
 959 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MafftWS.html#getPresets--">getPresets()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</a></dt>
 960 <dd>&nbsp;</dd>
 961 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MSAprobsWS.html#getPresets--">getPresets()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MSAprobsWS.html" title="class in compbio.ws.server">MSAprobsWS</a></dt>
 962 <dd>&nbsp;</dd>
 963 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MuscleWS.html#getPresets--">getPresets()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</a></dt>
 964 <dd>&nbsp;</dd>
 965 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ProbconsWS.html#getPresets--">getPresets()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</a></dt>
 966 <dd>&nbsp;</dd>
 967 <dt><span class="memberNameLink"><a href="../compbio/ws/server/TcoffeeWS.html#getPresets--">getPresets()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</a></dt>
 968 <dd>&nbsp;</dd>
 969 <dt><a href="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetPresetsResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 970 <dd>&nbsp;</dd>
 971 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetPresetsResponse.html#GetPresetsResponse--">GetPresetsResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws">GetPresetsResponse</a></dt>
 972 <dd>&nbsp;</dd>
 973 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#getPrmSeparator--">getPrmSeparator()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
 974 <dd>&nbsp;</dd>
 975 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/AlignmentMetadata.html#getProgram--">getProgram()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</a></dt>
 976 <dd>&nbsp;</dd>
 977 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#getProgress--">getProgress()</a></span> - Method in class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
 978 <dd>&nbsp;</dd>
 979 <dt><span class="memberNameLink"><a href="../compbio/engine/ProgressGetter.html#getProgress-java.lang.String-long-java.util.concurrent.TimeUnit-">getProgress(String, long, TimeUnit)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/ProgressGetter.html" title="class in compbio.engine">ProgressGetter</a></dt>
 980 <dd>&nbsp;</dd>
 981 <dt><span class="memberNameLink"><a href="../compbio/engine/ProgressGetter.html#getProgress-java.lang.String-">getProgress(String)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/ProgressGetter.html" title="class in compbio.engine">ProgressGetter</a></dt>
 982 <dd>&nbsp;</dd>
 983 <dt><span class="memberNameLink"><a href="../compbio/ws/server/WSUtil.html#getProgress-java.lang.String-">getProgress(String)</a></span> - Static method in class compbio.ws.server.<a href="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</a></dt>
 984 <dd>&nbsp;</dd>
 985 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/PropertyHelperManager.html#getPropertyHelper--">getPropertyHelper()</a></span> - Static method in class compbio.engine.conf.<a href="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</a></dt>
 986 <dd>
 987 <div class="block">Ways to fix path problem:
 988  1) find a path to WEB-INF directory based on the path to a known class.</div>
 989 </dd>
 990 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#getRandomValue-compbio.metadata.Parameter-">getRandomValue(Parameter&lt;?&gt;)</a></span> - Method in class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
 991 <dd>&nbsp;</dd>
 992 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Score.html#getRanges--">getRanges()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a></dt>
 993 <dd>
 994 <div class="block">Return Ranges if any Collections.EMPTY_SET otherwise</div>
 995 </dd>
 996 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#getRawUsage--">getRawUsage()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 997 <dd>&nbsp;</dd>
 998 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#getRecordedJobStatus-java.lang.String-">getRecordedJobStatus(String)</a></span> - Static 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>
 999 <dd>&nbsp;</dd>
1000 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#getRecordedJobStatus-java.lang.String-">getRecordedJobStatus(String)</a></span> - Static 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>
1001 <dd>&nbsp;</dd>
1002 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalEngineUtil.html#getRecordedJobStatus-java.lang.String-">getRecordedJobStatus(String)</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>
1003 <dd>&nbsp;</dd>
1004 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/ServiceTestResult.html#getReference--">getReference()</a></span> - Method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</a></dt>
1005 <dd>&nbsp;</dd>
1006 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.ServiceInfo.html#getReference--">getReference()</a></span> - Method in class compbio.ws.client.<a href="../compbio/ws/client/Services.ServiceInfo.html" title="class in compbio.ws.client">Services.ServiceInfo</a></dt>
1007 <dd>&nbsp;</dd>
1008 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/PropertyHelperManager.html#getResourceFromClasspath-java.lang.String-">getResourceFromClasspath(String)</a></span> - Static method in class compbio.engine.conf.<a href="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</a></dt>
1009 <dd>&nbsp;</dd>
1010 <dt><a href="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetResult</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
1011 <dd>&nbsp;</dd>
1012 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetResult.html#GetResult--">GetResult()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws">GetResult</a></dt>
1013 <dd>&nbsp;</dd>
1014 <dt><span class="memberNameLink"><a href="../compbio/data/msa/MsaWS.html#getResult-java.lang.String-">getResult(String)</a></span> - Method in interface compbio.data.msa.<a href="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a></dt>
1015 <dd>
1016 <div class="block">Return the result of the job.</div>
1017 </dd>
1018 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalOWS.html#getResult-java.lang.String-">getResult(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</a></dt>
1019 <dd>&nbsp;</dd>
1020 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalWS.html#getResult-java.lang.String-">getResult(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</a></dt>
1021 <dd>&nbsp;</dd>
1022 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GLprobsWS.html#getResult-java.lang.String-">getResult(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/GLprobsWS.html" title="class in compbio.ws.server">GLprobsWS</a></dt>
1023 <dd>&nbsp;</dd>
1024 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MafftWS.html#getResult-java.lang.String-">getResult(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</a></dt>
1025 <dd>&nbsp;</dd>
1026 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MSAprobsWS.html#getResult-java.lang.String-">getResult(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MSAprobsWS.html" title="class in compbio.ws.server">MSAprobsWS</a></dt>
1027 <dd>&nbsp;</dd>
1028 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MuscleWS.html#getResult-java.lang.String-">getResult(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</a></dt>
1029 <dd>&nbsp;</dd>
1030 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ProbconsWS.html#getResult-java.lang.String-">getResult(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</a></dt>
1031 <dd>&nbsp;</dd>
1032 <dt><span class="memberNameLink"><a href="../compbio/ws/server/TcoffeeWS.html#getResult-java.lang.String-">getResult(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</a></dt>
1033 <dd>&nbsp;</dd>
1034 <dt><a href="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetResultResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
1035 <dd>&nbsp;</dd>
1036 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetResultResponse.html#GetResultResponse--">GetResultResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws">GetResultResponse</a></dt>
1037 <dd>&nbsp;</dd>
1038 <dt><span class="memberNameLink"><a href="../compbio/engine/AsyncExecutor.html#getResults-java.lang.String-">getResults(String)</a></span> - Method in interface compbio.engine.<a href="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</a></dt>
1039 <dd>
1040 <div class="block">Retrieve the results of the job.</div>
1041 </dd>
1042 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getResults--">getResults()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
1043 <dd>&nbsp;</dd>
1044 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getResults-java.lang.String-">getResults(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>
1045 <dd>&nbsp;</dd>
1046 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfiguredExecutable.html#getResults--">getResults()</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a></dt>
1047 <dd>&nbsp;</dd>
1048 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Executable.html#getResults-java.lang.String-">getResults(String)</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a></dt>
1049 <dd>&nbsp;</dd>
1050 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/AsyncClusterRunner.html#getResults-java.lang.String-">getResults(String)</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>
1051 <dd>&nbsp;</dd>
1052 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getResults-java.lang.String-">getResults(String)</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>
1053 <dd>&nbsp;</dd>
1054 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#getResults-java.lang.String-">getResults(String)</a></span> - 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>
1055 <dd>&nbsp;</dd>
1056 <dt><span class="memberNameLink"><a href="../compbio/engine/local/AsyncLocalRunner.html#getResults-java.lang.String-">getResults(String)</a></span> - Method in class compbio.engine.local.<a href="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</a></dt>
1057 <dd>&nbsp;</dd>
1058 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalEngineUtil.html#getResults-java.util.concurrent.Future-java.lang.String-">getResults(Future&lt;ConfiguredExecutable&lt;?&gt;&gt;, String)</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>
1059 <dd>&nbsp;</dd>
1060 <dt><span class="memberNameLink"><a href="../compbio/runner/conservation/AACon.html#getResults-java.lang.String-">getResults(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>
1061 <dd>&nbsp;</dd>
1062 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Disembl.html#getResults-java.lang.String-">getResults(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>
1063 <dd>&nbsp;</dd>
1064 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/GlobPlot.html#getResults-java.lang.String-">getResults(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>
1065 <dd>&nbsp;</dd>
1066 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/IUPred.html#getResults-java.lang.String-">getResults(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>
1067 <dd>&nbsp;</dd>
1068 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Jronn.html#getResults-java.lang.String-">getResults(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>
1069 <dd>&nbsp;</dd>
1070 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/ClustalO.html#getResults-java.lang.String-">getResults(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>
1071 <dd>&nbsp;</dd>
1072 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/ClustalW.html#getResults-java.lang.String-">getResults(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>
1073 <dd>&nbsp;</dd>
1074 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/GLprobs.html#getResults-java.lang.String-">getResults(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>
1075 <dd>&nbsp;</dd>
1076 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Mafft.html#getResults-java.lang.String-">getResults(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>
1077 <dd>&nbsp;</dd>
1078 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/MSAprobs.html#getResults-java.lang.String-">getResults(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>
1079 <dd>&nbsp;</dd>
1080 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Muscle.html#getResults-java.lang.String-">getResults(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>
1081 <dd>&nbsp;</dd>
1082 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Probcons.html#getResults-java.lang.String-">getResults(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>
1083 <dd>&nbsp;</dd>
1084 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Tcoffee.html#getResults-java.lang.String-">getResults(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>
1085 <dd>&nbsp;</dd>
1086 <dt><span class="memberNameLink"><a href="../compbio/runner/structure/RNAalifold.html#getResults-java.lang.String-">getResults(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>
1087 <dd>&nbsp;</dd>
1088 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobDirectory.html#getResultSize--">getResultSize()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobDirectory.html" title="class in compbio.stat.collector">JobDirectory</a></dt>
1089 <dd>&nbsp;</dd>
1090 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#getResultSize--">getResultSize()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
1091 <dd>&nbsp;</dd>
1092 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/AlignResponse.html#getReturn--">getReturn()</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>
1093 <dd>&nbsp;</dd>
1094 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/AnalizeResponse.html#getReturn--">getReturn()</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>
1095 <dd>&nbsp;</dd>
1096 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAlignResponse.html#getReturn--">getReturn()</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>
1097 <dd>&nbsp;</dd>
1098 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAnalizeResponse.html#getReturn--">getReturn()</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>
1099 <dd>&nbsp;</dd>
1100 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomFoldResponse.html#getReturn--">getReturn()</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>
1101 <dd>&nbsp;</dd>
1102 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/FoldResponse.html#getReturn--">getReturn()</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>
1103 <dd>&nbsp;</dd>
1104 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetAnnotationResponse.html#getReturn--">getReturn()</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>
1105 <dd>&nbsp;</dd>
1106 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetJobStatusResponse.html#getReturn--">getReturn()</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>
1107 <dd>&nbsp;</dd>
1108 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html#getReturn--">getReturn()</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>
1109 <dd>&nbsp;</dd>
1110 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLastTestedResponse.html#getReturn--">getReturn()</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>
1111 <dd>&nbsp;</dd>
1112 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLimitResponse.html#getReturn--">getReturn()</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>
1113 <dd>&nbsp;</dd>
1114 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLimitsResponse.html#getReturn--">getReturn()</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>
1115 <dd>&nbsp;</dd>
1116 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetNonoperatedServicesResponse.html#getReturn--">getReturn()</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>
1117 <dd>&nbsp;</dd>
1118 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetPresetsResponse.html#getReturn--">getReturn()</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>
1119 <dd>&nbsp;</dd>
1120 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetResultResponse.html#getReturn--">getReturn()</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>
1121 <dd>&nbsp;</dd>
1122 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#getReturn--">getReturn()</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>
1123 <dd>&nbsp;</dd>
1124 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html#getReturn--">getReturn()</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>
1125 <dd>&nbsp;</dd>
1126 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html#getReturn--">getReturn()</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>
1127 <dd>&nbsp;</dd>
1128 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html#getReturn--">getReturn()</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>
1129 <dd>&nbsp;</dd>
1130 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetAlignResponse.html#getReturn--">getReturn()</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>
1131 <dd>&nbsp;</dd>
1132 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetAnalizeResponse.html#getReturn--">getReturn()</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>
1133 <dd>&nbsp;</dd>
1134 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetFoldResponse.html#getReturn--">getReturn()</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>
1135 <dd>&nbsp;</dd>
1136 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#getReturn--">getReturn()</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>
1137 <dd>&nbsp;</dd>
1138 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/TestAllServicesResponse.html#getReturn--">getReturn()</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>
1139 <dd>&nbsp;</dd>
1140 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/TestServiceResponse.html#getReturn--">getReturn()</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>
1141 <dd>&nbsp;</dd>
1142 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getRunConfiguration--">getRunConfiguration()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
1143 <dd>&nbsp;</dd>
1144 <dt><span class="memberNameLink"><a href="../compbio/ws/client/ServicesUtil.html#getRunnerByJobDirectory-java.io.File-">getRunnerByJobDirectory(File)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</a></dt>
1145 <dd>&nbsp;</dd>
1146 <dt><span class="memberNameLink"><a href="../compbio/engine/client/RunConfiguration.html#getRunnerClassName--">getRunnerClassName()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</a></dt>
1147 <dd>&nbsp;</dd>
1148 <dt><span class="memberNameLink"><a href="../compbio/metadata/PresetManager.html#getRunnerClassName--">getRunnerClassName()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a></dt>
1149 <dd>&nbsp;</dd>
1150 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#getRunnerClassName--">getRunnerClassName()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
1151 <dd>&nbsp;</dd>
1152 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getRunnerConfiguration-java.lang.Class-java.lang.Class-java.lang.String-">getRunnerConfiguration(Class&lt;V&gt;, Class&lt;?&gt;, String)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
1153 <dd>&nbsp;</dd>
1154 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getRunnerLimits-java.lang.Class-">getRunnerLimits(Class&lt;V&gt;)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
1155 <dd>
1156 <div class="block">This method should be executed once and result of its execution reused.</div>
1157 </dd>
1158 <dt><span class="memberNameLink"><a href="../compbio/ws/client/ServicesUtil.html#getRunnerNameByJobDirectory-java.io.File-">getRunnerNameByJobDirectory(File)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</a></dt>
1159 <dd>&nbsp;</dd>
1160 <dt><a href="../compbio/data/msa/jaxws/GetRunnerOptions.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetRunnerOptions</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
1161 <dd>&nbsp;</dd>
1162 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetRunnerOptions.html#GetRunnerOptions--">GetRunnerOptions()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetRunnerOptions.html" title="class in compbio.data.msa.jaxws">GetRunnerOptions</a></dt>
1163 <dd>&nbsp;</dd>
1164 <dt><span class="memberNameLink"><a href="../compbio/data/msa/Metadata.html#getRunnerOptions--">getRunnerOptions()</a></span> - Method in interface compbio.data.msa.<a href="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</a></dt>
1165 <dd>
1166 <div class="block">Get options supported by a web service</div>
1167 </dd>
1168 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getRunnerOptions-java.lang.Class-">getRunnerOptions(Class&lt;? extends Executable&lt;V&gt;&gt;)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
1169 <dd>&nbsp;</dd>
1170 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalOWS.html#getRunnerOptions--">getRunnerOptions()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</a></dt>
1171 <dd>&nbsp;</dd>
1172 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalWS.html#getRunnerOptions--">getRunnerOptions()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</a></dt>
1173 <dd>&nbsp;</dd>
1174 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GenericMetadataService.html#getRunnerOptions--">getRunnerOptions()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</a></dt>
1175 <dd>&nbsp;</dd>
1176 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GLprobsWS.html#getRunnerOptions--">getRunnerOptions()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/GLprobsWS.html" title="class in compbio.ws.server">GLprobsWS</a></dt>
1177 <dd>&nbsp;</dd>
1178 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MafftWS.html#getRunnerOptions--">getRunnerOptions()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</a></dt>
1179 <dd>&nbsp;</dd>
1180 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MSAprobsWS.html#getRunnerOptions--">getRunnerOptions()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MSAprobsWS.html" title="class in compbio.ws.server">MSAprobsWS</a></dt>
1181 <dd>&nbsp;</dd>
1182 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MuscleWS.html#getRunnerOptions--">getRunnerOptions()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</a></dt>
1183 <dd>&nbsp;</dd>
1184 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ProbconsWS.html#getRunnerOptions--">getRunnerOptions()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</a></dt>
1185 <dd>&nbsp;</dd>
1186 <dt><span class="memberNameLink"><a href="../compbio/ws/server/TcoffeeWS.html#getRunnerOptions--">getRunnerOptions()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</a></dt>
1187 <dd>&nbsp;</dd>
1188 <dt><a href="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetRunnerOptionsResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
1189 <dd>&nbsp;</dd>
1190 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#GetRunnerOptionsResponse--">GetRunnerOptionsResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws">GetRunnerOptionsResponse</a></dt>
1191 <dd>&nbsp;</dd>
1192 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getRunnerPresets-java.lang.Class-">getRunnerPresets(Class&lt;? extends Executable&lt;V&gt;&gt;)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
1193 <dd>&nbsp;</dd>
1194 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#getRuntime--">getRuntime()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
1195 <dd>&nbsp;</dd>
1196 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/RunnerConfigMarshaller.html#getSchema-java.lang.String-">getSchema(String)</a></span> - Static method in class compbio.engine.conf.<a href="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</a></dt>
1197 <dd>&nbsp;</dd>
1198 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ScoreManager.ScoreHolder.html#getScoreByMethod-java.lang.Enum-">getScoreByMethod(Enum&lt;?&gt;)</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</a></dt>
1199 <dd>&nbsp;</dd>
1200 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ScoreManager.ScoreHolder.html#getScoreByMethod-java.lang.String-">getScoreByMethod(String)</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</a></dt>
1201 <dd>&nbsp;</dd>
1202 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Score.html#getScores--">getScores()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a></dt>
1203 <dd>
1204 <div class="block">The column scores for the alignment</div>
1205 </dd>
1206 <dt><span class="memberNameLink"><a href="../compbio/metadata/Limit.html#getSeqNumber--">getSeqNumber()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a></dt>
1207 <dd>&nbsp;</dd>
1208 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/FastaSequence.html#getSequence--">getSequence()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></dt>
1209 <dd>
1210 <div class="block">Gets the value of sequence</div>
1211 </dd>
1212 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getSequenceLenghtActual--">getSequenceLenghtActual()</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>
1213 <dd>&nbsp;</dd>
1214 <dt><span class="memberNameLink"><a href="../compbio/metadata/LimitExceededException.html#getSequenceLenghtActual--">getSequenceLenghtActual()</a></span> - Method in exception compbio.metadata.<a href="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></dt>
1215 <dd>&nbsp;</dd>
1216 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getSequenceLenghtAllowed--">getSequenceLenghtAllowed()</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>
1217 <dd>&nbsp;</dd>
1218 <dt><span class="memberNameLink"><a href="../compbio/metadata/LimitExceededException.html#getSequenceLenghtAllowed--">getSequenceLenghtAllowed()</a></span> - Method in exception compbio.metadata.<a href="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></dt>
1219 <dd>&nbsp;</dd>
1220 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Alignment.html#getSequences--">getSequences()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></dt>
1221 <dd>&nbsp;</dd>
1222 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GAUtils.html#getServerIP--">getServerIP()</a></span> - Static method in class compbio.ws.server.<a href="../compbio/ws/server/GAUtils.html" title="class in compbio.ws.server">GAUtils</a></dt>
1223 <dd>&nbsp;</dd>
1224 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobDirectory.html#getService--">getService()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobDirectory.html" title="class in compbio.stat.collector">JobDirectory</a></dt>
1225 <dd>&nbsp;</dd>
1226 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/ServiceTestResult.html#getService--">getService()</a></span> - Method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</a></dt>
1227 <dd>&nbsp;</dd>
1228 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#getService-java.lang.String-">getService(String)</a></span> - Static method in enum compbio.ws.client.<a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></dt>
1229 <dd>&nbsp;</dd>
1230 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#getService-java.net.URL-java.lang.String-">getService(URL, String)</a></span> - Method in enum compbio.ws.client.<a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></dt>
1231 <dd>&nbsp;</dd>
1232 <dt><span class="memberNameLink"><a href="../compbio/ws/client/ServicesUtil.html#getServiceByJobDirectory-java.io.File-">getServiceByJobDirectory(File)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</a></dt>
1233 <dd>&nbsp;</dd>
1234 <dt><span class="memberNameLink"><a href="../compbio/ws/client/ServicesUtil.html#getServiceByRunner-java.lang.Class-">getServiceByRunner(Class&lt;? extends Executable&gt;)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</a></dt>
1235 <dd>&nbsp;</dd>
1236 <dt><span class="memberNameLink"><a href="../compbio/ws/client/ServicesUtil.html#getServiceByRunnerName-java.lang.String-">getServiceByRunnerName(String)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</a></dt>
1237 <dd>&nbsp;</dd>
1238 <dt><a href="../compbio/data/msa/jaxws/GetServiceCategories.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetServiceCategories</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
1239 <dd>&nbsp;</dd>
1240 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetServiceCategories.html#GetServiceCategories--">GetServiceCategories()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetServiceCategories.html" title="class in compbio.data.msa.jaxws">GetServiceCategories</a></dt>
1241 <dd>&nbsp;</dd>
1242 <dt><span class="memberNameLink"><a href="../compbio/data/msa/RegistryWS.html#getServiceCategories--">getServiceCategories()</a></span> - Method in interface compbio.data.msa.<a href="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</a></dt>
1243 <dd>
1244 <div class="block">Gets the list of services per category.</div>
1245 </dd>
1246 <dt><span class="memberNameLink"><a href="../compbio/ws/server/RegistryWS.html#getServiceCategories--">getServiceCategories()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</a></dt>
1247 <dd>&nbsp;</dd>
1248 <dt><a href="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetServiceCategoriesResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
1249 <dd>&nbsp;</dd>
1250 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html#GetServiceCategoriesResponse--">GetServiceCategoriesResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html" title="class in compbio.data.msa.jaxws">GetServiceCategoriesResponse</a></dt>
1251 <dd>&nbsp;</dd>
1252 <dt><a href="../compbio/data/msa/jaxws/GetServiceDescription.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetServiceDescription</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
1253 <dd>&nbsp;</dd>
1254 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetServiceDescription.html#GetServiceDescription--">GetServiceDescription()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetServiceDescription.html" title="class in compbio.data.msa.jaxws">GetServiceDescription</a></dt>
1255 <dd>&nbsp;</dd>
1256 <dt><span class="memberNameLink"><a href="../compbio/data/msa/RegistryWS.html#getServiceDescription-compbio.ws.client.Services-">getServiceDescription(Services)</a></span> - Method in interface compbio.data.msa.<a href="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</a></dt>
1257 <dd>
1258 <div class="block">Gives the description of the service.</div>
1259 </dd>
1260 <dt><span class="memberNameLink"><a href="../compbio/ws/server/RegistryWS.html#getServiceDescription-compbio.ws.client.Services-">getServiceDescription(Services)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</a></dt>
1261 <dd>&nbsp;</dd>
1262 <dt><a href="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetServiceDescriptionResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
1263 <dd>&nbsp;</dd>
1264 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html#GetServiceDescriptionResponse--">GetServiceDescriptionResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html" title="class in compbio.data.msa.jaxws">GetServiceDescriptionResponse</a></dt>
1265 <dd>&nbsp;</dd>
1266 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#getServiceGroup--">getServiceGroup()</a></span> - Method in enum compbio.ws.client.<a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></dt>
1267 <dd>&nbsp;</dd>
1268 <dt><span class="memberNameLink"><a href="../compbio/ws/client/ServicesUtil.html#getServiceImpl-compbio.ws.client.Services-">getServiceImpl(Services)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</a></dt>
1269 <dd>&nbsp;</dd>
1270 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#getServiceInfo--">getServiceInfo()</a></span> - Method in enum compbio.ws.client.<a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></dt>
1271 <dd>&nbsp;</dd>
1272 <dt><span class="memberNameLink"><a href="../compbio/ws/client/CmdHelper.html#getServiceName-java.lang.String:A-">getServiceName(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>
1273 <dd>
1274 <div class="block">Extracts service name from the command line</div>
1275 </dd>
1276 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#getServiceNamespace--">getServiceNamespace()</a></span> - Method in enum compbio.ws.client.<a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></dt>
1277 <dd>&nbsp;</dd>
1278 <dt><span class="memberNameLink"><a href="../compbio/ws/server/RegistryWS.html#getServicePath--">getServicePath()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</a></dt>
1279 <dd>&nbsp;</dd>
1280 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#getServiceReference--">getServiceReference()</a></span> - Method in enum compbio.ws.client.<a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></dt>
1281 <dd>&nbsp;</dd>
1282 <dt><span class="memberNameLink"><a href="../compbio/data/msa/Category.html#getServices--">getServices()</a></span> - Method in class compbio.data.msa.<a href="../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</a></dt>
1283 <dd>&nbsp;</dd>
1284 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#getServiceType--">getServiceType()</a></span> - Method in enum compbio.ws.client.<a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></dt>
1285 <dd>&nbsp;</dd>
1286 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#getServiceVersion--">getServiceVersion()</a></span> - Method in enum compbio.ws.client.<a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></dt>
1287 <dd>&nbsp;</dd>
1288 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#getSession--">getSession()</a></span> - 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>
1289 <dd>&nbsp;</dd>
1290 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatProcessor.html#getSingleWSStat-compbio.ws.client.Services-">getSingleWSStat(Services)</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</a></dt>
1291 <dd>&nbsp;</dd>
1292 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Alignment.html#getSize--">getSize()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></dt>
1293 <dd>&nbsp;</dd>
1294 <dt><span class="memberNameLink"><a href="../compbio/engine/PulledFileCache.html#getSize--">getSize()</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</a></dt>
1295 <dd>&nbsp;</dd>
1296 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SMERFSConstraints.html#getSMERFSColumnScore-java.lang.String-">getSMERFSColumnScore(String)</a></span> - Static method in enum compbio.data.sequence.<a href="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</a></dt>
1297 <dd>&nbsp;</dd>
1298 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#getStart--">getStart()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
1299 <dd>&nbsp;</dd>
1300 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#getStartTime--">getStartTime()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
1301 <dd>&nbsp;</dd>
1302 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobDirectory.html#getStartTime--">getStartTime()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobDirectory.html" title="class in compbio.stat.collector">JobDirectory</a></dt>
1303 <dd>&nbsp;</dd>
1304 <dt><span class="memberNameLink"><a href="../compbio/runner/conservation/AACon.html#getStatFile--">getStatFile()</a></span> - Static method in class compbio.runner.conservation.<a href="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a></dt>
1305 <dd>&nbsp;</dd>
1306 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Jronn.html#getStatFile--">getStatFile()</a></span> - Static method in class compbio.runner.disorder.<a href="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</a></dt>
1307 <dd>&nbsp;</dd>
1308 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/ClustalO.html#getStatFile--">getStatFile()</a></span> - Static method in class compbio.runner.msa.<a href="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a></dt>
1309 <dd>&nbsp;</dd>
1310 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/ClustalW.html#getStatFile--">getStatFile()</a></span> - Static method in class compbio.runner.msa.<a href="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</a></dt>
1311 <dd>&nbsp;</dd>
1312 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Muscle.html#getStatFile--">getStatFile()</a></span> - Static method in class compbio.runner.msa.<a href="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</a></dt>
1313 <dd>&nbsp;</dd>
1314 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#getStatistics-org.ggf.drmaa.JobInfo-">getStatistics(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>
1315 <dd>&nbsp;</dd>
1316 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/ExecutionStatCollector.html#getStats--">getStats()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/ExecutionStatCollector.html" title="class in compbio.stat.collector">ExecutionStatCollector</a></dt>
1317 <dd>&nbsp;</dd>
1318 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/StatCollection.html#getStats-int-">getStats(int)</a></span> - Static method in class compbio.stat.servlet.util.<a href="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</a></dt>
1319 <dd>&nbsp;</dd>
1320 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/StatCollection.html#getStats-java.util.Date-">getStats(Date)</a></span> - Static method in class compbio.stat.servlet.util.<a href="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</a></dt>
1321 <dd>&nbsp;</dd>
1322 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/ServiceTestResult.html#getStatus--">getStatus()</a></span> - Method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</a></dt>
1323 <dd>&nbsp;</dd>
1324 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/StatisticCollector.html#getStringProperty-java.lang.String-">getStringProperty(String)</a></span> - Static method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</a></dt>
1325 <dd>&nbsp;</dd>
1326 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructScoreManager.html#getStructs--">getStructs()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructScoreManager.html" title="class in compbio.data.sequence">RNAStructScoreManager</a></dt>
1327 <dd>&nbsp;</dd>
1328 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#getSubmissionTime--">getSubmissionTime()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
1329 <dd>&nbsp;</dd>
1330 <dt><span class="memberNameLink"><a href="../compbio/runner/RunnerUtil.html#getSupportedOptions-java.lang.Class-">getSupportedOptions(Class&lt;? extends Executable&lt;T&gt;&gt;)</a></span> - Static method in class compbio.runner.<a href="../compbio/runner/RunnerUtil.html" title="class in compbio.runner">RunnerUtil</a></dt>
1331 <dd>&nbsp;</dd>
1332 <dt><span class="memberNameLink"><a href="../compbio/runner/Util.html#getSupportedOptions-java.lang.Class-">getSupportedOptions(Class&lt;? extends Executable&lt;T&gt;&gt;)</a></span> - Static method in class compbio.runner.<a href="../compbio/runner/Util.html" title="class in compbio.runner">Util</a></dt>
1333 <dd>&nbsp;</dd>
1334 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getSupportedRuntimes--">getSupportedRuntimes()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
1335 <dd>&nbsp;</dd>
1336 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfiguredExecutable.html#getSupportedRuntimes--">getSupportedRuntimes()</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a></dt>
1337 <dd>&nbsp;</dd>
1338 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EngineUtil.html#getSupportedRuntimes-java.lang.Class-">getSupportedRuntimes(Class&lt;?&gt;)</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>
1339 <dd>&nbsp;</dd>
1340 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Util.html#getSupportedRuntimes-java.lang.Class-">getSupportedRuntimes(Class&lt;?&gt;)</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>
1341 <dd>&nbsp;</dd>
1342 <dt><a href="../compbio/data/msa/jaxws/GetSupportedServices.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetSupportedServices</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
1343 <dd>&nbsp;</dd>
1344 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetSupportedServices.html#GetSupportedServices--">GetSupportedServices()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetSupportedServices.html" title="class in compbio.data.msa.jaxws">GetSupportedServices</a></dt>
1345 <dd>&nbsp;</dd>
1346 <dt><span class="memberNameLink"><a href="../compbio/data/msa/RegistryWS.html#getSupportedServices--">getSupportedServices()</a></span> - Method in interface compbio.data.msa.<a href="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</a></dt>
1347 <dd>
1348 <div class="block">List of services that are functioning on the server.</div>
1349 </dd>
1350 <dt><span class="memberNameLink"><a href="../compbio/ws/server/RegistryWS.html#getSupportedServices--">getSupportedServices()</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</a></dt>
1351 <dd>&nbsp;</dd>
1352 <dt><a href="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">GetSupportedServicesResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
1353 <dd>&nbsp;</dd>
1354 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html#GetSupportedServicesResponse--">GetSupportedServicesResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws">GetSupportedServicesResponse</a></dt>
1355 <dd>&nbsp;</dd>
1356 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#getSyncEngine-compbio.engine.client.ConfiguredExecutable-compbio.engine.client.Executable.ExecProvider-">getSyncEngine(ConfiguredExecutable&lt;?&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>
1357 <dd>&nbsp;</dd>
1358 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#getSyncEngine-compbio.engine.client.ConfiguredExecutable-">getSyncEngine(ConfiguredExecutable&lt;?&gt;)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></dt>
1359 <dd>&nbsp;</dd>
1360 <dt><span class="memberNameLink"><a href="../compbio/engine/SubmissionManager.html#getTask-java.lang.String-">getTask(String)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</a></dt>
1361 <dd>&nbsp;</dd>
1362 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/DirectoryManager.html#getTaskDirectory-java.lang.Class-">getTaskDirectory(Class&lt;?&gt;)</a></span> - Static method in class compbio.engine.conf.<a href="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</a></dt>
1363 <dd>&nbsp;</dd>
1364 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getTaskId--">getTaskId()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
1365 <dd>&nbsp;</dd>
1366 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfiguredExecutable.html#getTaskId--">getTaskId()</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a></dt>
1367 <dd>&nbsp;</dd>
1368 <dt><span class="memberNameLink"><a href="../compbio/engine/Job.html#getTaskId--">getTaskId()</a></span> - Method in class compbio.engine.<a href="../compbio/engine/Job.html" title="class in compbio.engine">Job</a></dt>
1369 <dd>&nbsp;</dd>
1370 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatDB.html#getTestDBConnection--">getTestDBConnection()</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>
1371 <dd>&nbsp;</dd>
1372 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#getTimeStat--">getTimeStat()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
1373 <dd>&nbsp;</dd>
1374 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/Totals.html#getTotal--">getTotal()</a></span> - 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>
1375 <dd>&nbsp;</dd>
1376 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatDB.html#getTotalJobsCount-java.sql.Timestamp-java.sql.Timestamp-">getTotalJobsCount(Timestamp, Timestamp)</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</a></dt>
1377 <dd>&nbsp;</dd>
1378 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatProcessor.html#getTotalRuntime--">getTotalRuntime()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</a></dt>
1379 <dd>&nbsp;</dd>
1380 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/IUPredResult.html#getType-java.io.File-">getType(File)</a></span> - Static method in enum compbio.data.sequence.<a href="../compbio/data/sequence/IUPredResult.html" title="enum in compbio.data.sequence">IUPredResult</a></dt>
1381 <dd>&nbsp;</dd>
1382 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#getType--">getType()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
1383 <dd>&nbsp;</dd>
1384 <dt><span class="memberNameLink"><a href="../compbio/metadata/ValueConstrain.html#getType--">getType()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</a></dt>
1385 <dd>&nbsp;</dd>
1386 <dt><span class="memberNameLink"><a href="../compbio/runner/conservation/AACon.html#getType--">getType()</a></span> - Method in class compbio.runner.conservation.<a href="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a></dt>
1387 <dd>&nbsp;</dd>
1388 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Disembl.html#getType--">getType()</a></span> - Method in class compbio.runner.disorder.<a href="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</a></dt>
1389 <dd>&nbsp;</dd>
1390 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/GlobPlot.html#getType--">getType()</a></span> - Method in class compbio.runner.disorder.<a href="../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</a></dt>
1391 <dd>&nbsp;</dd>
1392 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/IUPred.html#getType--">getType()</a></span> - Method in class compbio.runner.disorder.<a href="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</a></dt>
1393 <dd>&nbsp;</dd>
1394 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Jronn.html#getType--">getType()</a></span> - Method in class compbio.runner.disorder.<a href="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</a></dt>
1395 <dd>&nbsp;</dd>
1396 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/ClustalO.html#getType--">getType()</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a></dt>
1397 <dd>&nbsp;</dd>
1398 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/ClustalW.html#getType--">getType()</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</a></dt>
1399 <dd>&nbsp;</dd>
1400 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/GLprobs.html#getType--">getType()</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a></dt>
1401 <dd>&nbsp;</dd>
1402 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Mafft.html#getType--">getType()</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a></dt>
1403 <dd>&nbsp;</dd>
1404 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/MSAprobs.html#getType--">getType()</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a></dt>
1405 <dd>&nbsp;</dd>
1406 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Muscle.html#getType--">getType()</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</a></dt>
1407 <dd>&nbsp;</dd>
1408 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Probcons.html#getType--">getType()</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</a></dt>
1409 <dd>&nbsp;</dd>
1410 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Tcoffee.html#getType--">getType()</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</a></dt>
1411 <dd>&nbsp;</dd>
1412 <dt><span class="memberNameLink"><a href="../compbio/runner/structure/RNAalifold.html#getType--">getType()</a></span> - Method in class compbio.runner.structure.<a href="../compbio/runner/structure/RNAalifold.html" title="class in compbio.runner.structure">RNAalifold</a></dt>
1413 <dd>&nbsp;</dd>
1414 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#getUpperBorderValue-compbio.metadata.Parameter-">getUpperBorderValue(Parameter&lt;?&gt;)</a></span> - Method in class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
1415 <dd>&nbsp;</dd>
1416 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#getUsedSysTime--">getUsedSysTime()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
1417 <dd>&nbsp;</dd>
1418 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#getUsedUserTime--">getUsedUserTime()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
1419 <dd>&nbsp;</dd>
1420 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/RunnerConfigMarshaller.html#getValidator-java.lang.String-">getValidator(String)</a></span> - Static method in class compbio.engine.conf.<a href="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</a></dt>
1421 <dd>&nbsp;</dd>
1422 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/RunnerConfigMarshaller.html#getValidator-javax.xml.validation.Schema-">getValidator(Schema)</a></span> - Static method in class compbio.engine.conf.<a href="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</a></dt>
1423 <dd>&nbsp;</dd>
1424 <dt><span class="memberNameLink"><a href="../compbio/metadata/Parameter.html#getValidValue--">getValidValue()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</a></dt>
1425 <dd>&nbsp;</dd>
1426 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#getValue-java.lang.String-">getValue(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>
1427 <dd>&nbsp;</dd>
1428 <dt><span class="memberNameLink"><a href="../compbio/metadata/Parameter.html#getValue--">getValue()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</a></dt>
1429 <dd>&nbsp;</dd>
1430 <dt><span class="memberNameLink"><a href="../compbio/metadata/Preset.html#getValue-java.lang.String-">getValue(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a></dt>
1431 <dd>&nbsp;</dd>
1432 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#getValue-compbio.metadata.Parameter-">getValue(Parameter&lt;?&gt;)</a></span> - Static method in class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
1433 <dd>&nbsp;</dd>
1434 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/ServiceTestResult.html#getVersion--">getVersion()</a></span> - Method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</a></dt>
1435 <dd>&nbsp;</dd>
1436 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.ServiceInfo.html#getVersion--">getVersion()</a></span> - Method in class compbio.ws.client.<a href="../compbio/ws/client/Services.ServiceInfo.html" title="class in compbio.ws.client">Services.ServiceInfo</a></dt>
1437 <dd>&nbsp;</dd>
1438 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#getVMem--">getVMem()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
1439 <dd>&nbsp;</dd>
1440 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#getWebService--">getWebService()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
1441 <dd>&nbsp;</dd>
1442 <dt><span class="memberNameLink"><a href="../compbio/engine/AsyncExecutor.html#getWorkDirectory-java.lang.String-">getWorkDirectory(String)</a></span> - Method in interface compbio.engine.<a href="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</a></dt>
1443 <dd>&nbsp;</dd>
1444 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#getWorkDirectory--">getWorkDirectory()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
1445 <dd>&nbsp;</dd>
1446 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfiguredExecutable.html#getWorkDirectory--">getWorkDirectory()</a></span> - Method in interface compbio.engine.client.<a href="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a></dt>
1447 <dd>&nbsp;</dd>
1448 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/AsyncClusterRunner.html#getWorkDirectory-java.lang.String-">getWorkDirectory(String)</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>
1449 <dd>&nbsp;</dd>
1450 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getWorkDirectory-java.lang.String-">getWorkDirectory(String)</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>
1451 <dd>&nbsp;</dd>
1452 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#getWorkDirectory--">getWorkDirectory()</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>
1453 <dd>&nbsp;</dd>
1454 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#getWorkDirectory--">getWorkDirectory()</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>
1455 <dd>&nbsp;</dd>
1456 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#getWorkDirectory-java.lang.String-">getWorkDirectory(String)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></dt>
1457 <dd>&nbsp;</dd>
1458 <dt><span class="memberNameLink"><a href="../compbio/engine/local/AsyncLocalRunner.html#getWorkDirectory-java.lang.String-">getWorkDirectory(String)</a></span> - Method in class compbio.engine.local.<a href="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</a></dt>
1459 <dd>&nbsp;</dd>
1460 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalRunner.html#getWorkDirectory--">getWorkDirectory()</a></span> - Method in class compbio.engine.local.<a href="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</a></dt>
1461 <dd>&nbsp;</dd>
1462 <dt><span class="memberNameLink"><a href="../compbio/engine/SyncExecutor.html#getWorkDirectory--">getWorkDirectory()</a></span> - Method in interface compbio.engine.<a href="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</a></dt>
1463 <dd>&nbsp;</dd>
1464 <dt><span class="memberNameLink"><a href="../compbio/ws/client/IOHelper.html#getWriter-java.io.File-">getWriter(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>
1465 <dd>&nbsp;</dd>
1466 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/IUPred.html#GLOB_OUTPUT">GLOB_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>
1467 <dd>&nbsp;</dd>
1468 <dt><a href="../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder"><span class="typeNameLink">GlobPlot</span></a> - Class in <a href="../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</a></dt>
1469 <dd>
1470 <div class="block">./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame
1471
1472  FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file'
1473  Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file'
1474
1475  Hard-coded values are 10 15 74 4 5.</div>
1476 </dd>
1477 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/GlobPlot.html#GlobPlot--">GlobPlot()</a></span> - Constructor for class compbio.runner.disorder.<a href="../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</a></dt>
1478 <dd>&nbsp;</dd>
1479 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#GLOBPLOT_INFO">GLOBPLOT_INFO</a></span> - Static variable in enum compbio.ws.client.<a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></dt>
1480 <dd>&nbsp;</dd>
1481 <dt><a href="../compbio/ws/server/GlobPlotWS.html" title="class in compbio.ws.server"><span class="typeNameLink">GlobPlotWS</span></a> - Class in <a href="../compbio/ws/server/package-summary.html">compbio.ws.server</a></dt>
1482 <dd>&nbsp;</dd>
1483 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GlobPlotWS.html#GlobPlotWS--">GlobPlotWS()</a></span> - Constructor for class compbio.ws.server.<a href="../compbio/ws/server/GlobPlotWS.html" title="class in compbio.ws.server">GlobPlotWS</a></dt>
1484 <dd>&nbsp;</dd>
1485 <dt><a href="../compbio/data/sequence/GlobProtResult.html" title="enum in compbio.data.sequence"><span class="typeNameLink">GlobProtResult</span></a> - Enum in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
1486 <dd>&nbsp;</dd>
1487 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/GlobProtResult.html#GlobProtResult--">GlobProtResult()</a></span> - Constructor for enum compbio.data.sequence.<a href="../compbio/data/sequence/GlobProtResult.html" title="enum in compbio.data.sequence">GlobProtResult</a></dt>
1488 <dd>&nbsp;</dd>
1489 <dt><a href="../compbio/runner/msa/GLprobs.html" title="class in compbio.runner.msa"><span class="typeNameLink">GLprobs</span></a> - Class in <a href="../compbio/runner/msa/package-summary.html">compbio.runner.msa</a></dt>
1490 <dd>&nbsp;</dd>
1491 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/GLprobs.html#GLprobs--">GLprobs()</a></span> - Constructor for class compbio.runner.msa.<a href="../compbio/runner/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a></dt>
1492 <dd>&nbsp;</dd>
1493 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#GLPROBS_INFO">GLPROBS_INFO</a></span> - Static variable in enum compbio.ws.client.<a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></dt>
1494 <dd>&nbsp;</dd>
1495 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GLprobsWS.html#GLprobsOptions">GLprobsOptions</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>
1496 <dd>&nbsp;</dd>
1497 <dt><a href="../compbio/ws/server/GLprobsWS.html" title="class in compbio.ws.server"><span class="typeNameLink">GLprobsWS</span></a> - Class in <a href="../compbio/ws/server/package-summary.html">compbio.ws.server</a></dt>
1498 <dd>&nbsp;</dd>
1499 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GLprobsWS.html#GLprobsWS--">GLprobsWS()</a></span> - Constructor for class compbio.ws.server.<a href="../compbio/ws/server/GLprobsWS.html" title="class in compbio.ws.server">GLprobsWS</a></dt>
1500 <dd>&nbsp;</dd>
1501 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/ServiceTestResult.html#group">group</a></span> - Variable in class compbio.stat.servlet.<a href="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</a></dt>
1502 <dd>&nbsp;</dd>
1503 </dl>
1504 <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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