website/full_javadoc/index-files/index-7.html

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  81 <A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
  82 <A NAME="_G_"><!-- --></A><H2>\r
  83 <B>G</B></H2>\r
  84 <DL>\r
  85 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#gapchar"><B>gapchar</B></A> - \r
  86 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
  87 <DD>Dash char to be used as gap char in the alignments\r
  88 <DT><A HREF="../compbio/ws/server/GAUtils.html" title="class in compbio.ws.server"><B>GAUtils</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/GAUtils.html#GAUtils()"><B>GAUtils()</B></A> - \r
  89 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/GAUtils.html" title="class in compbio.ws.server">GAUtils</A>\r
  90 <DD>&nbsp;\r
  91 <DT><A HREF="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server"><B>GenericMetadataService</B></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><DD>&nbsp;<DT><A HREF="../compbio/engine/PulledFileCache.html#get(java.lang.String)"><B>get(String)</B></A> - \r
  92 Static method in class compbio.engine.<A HREF="../compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</A>\r
  93 <DD>&nbsp;\r
  94 <DT><A HREF="../compbio/stat/servlet/util/Totals.html#getAbandoned()"><B>getAbandoned()</B></A> - \r
  95 Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>\r
  96 <DD>&nbsp;\r
  97 <DT><A HREF="../compbio/stat/collector/StatDB.html#getAbandonedCount(java.sql.Timestamp, java.sql.Timestamp)"><B>getAbandonedCount(Timestamp, Timestamp)</B></A> - \r
  98 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
  99 <DD>&nbsp;\r
 100 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#getAbandonedJobs()"><B>getAbandonedJobs()</B></A> - \r
 101 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
 102 <DD>Not collected.\r
 103 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getActualNumberofSequences()"><B>getActualNumberofSequences()</B></A> - \r
 104 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
 105 <DD>&nbsp;\r
 106 <DT><A HREF="../compbio/metadata/LimitExceededException.html#getActualNumberofSequences()"><B>getActualNumberofSequences()</B></A> - \r
 107 Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
 108 <DD>&nbsp;\r
 109 <DT><A HREF="../compbio/runner/OptionCombinator.html#getAllConstrainedParametersWithBorderValues(boolean)"><B>getAllConstrainedParametersWithBorderValues(boolean)</B></A> - \r
 110 Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
 111 <DD>&nbsp;\r
 112 <DT><A HREF="../compbio/runner/OptionCombinator.html#getAllConstrainedParametersWithRandomValues()"><B>getAllConstrainedParametersWithRandomValues()</B></A> - \r
 113 Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
 114 <DD>&nbsp;\r
 115 <DT><A HREF="../compbio/runner/OptionCombinator.html#getAllOptions()"><B>getAllOptions()</B></A> - \r
 116 Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
 117 <DD>&nbsp;\r
 118 <DT><A HREF="../compbio/runner/OptionCombinator.html#getAllParameters()"><B>getAllParameters()</B></A> - \r
 119 Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
 120 <DD>&nbsp;\r
 121 <DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#getAllStat()"><B>getAllStat()</B></A> - \r
 122 Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</A>\r
 123 <DD>&nbsp;\r
 124 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getAllStats()"><B>getAllStats()</B></A> - \r
 125 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 126 <DD>&nbsp;\r
 127 <DT><A HREF="../compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws"><B>GetAnnotation</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetAnnotation.html#GetAnnotation()"><B>GetAnnotation()</B></A> - \r
 128 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws">GetAnnotation</A>\r
 129 <DD>&nbsp;\r
 130 <DT><A HREF="../compbio/data/msa/SequenceAnnotation.html#getAnnotation(java.lang.String)"><B>getAnnotation(String)</B></A> - \r
 131 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>\r
 132 <DD>Return the result of the job.\r
 133 <DT><A HREF="../compbio/ws/server/SequenceAnnotationService.html#getAnnotation(java.lang.String)"><B>getAnnotation(String)</B></A> - \r
 134 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</A>\r
 135 <DD>&nbsp;\r
 136 <DT><A HREF="../compbio/ws/server/WSUtil.html#getAnnotation(java.lang.String, org.apache.log4j.Logger)"><B>getAnnotation(String, Logger)</B></A> - \r
 137 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
 138 <DD>&nbsp;\r
 139 <DT><A HREF="../compbio/data/sequence/ScoreManager.html#getAnnotationForSequence(java.lang.String)"><B>getAnnotationForSequence(String)</B></A> - \r
 140 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
 141 <DD>&nbsp;\r
 142 <DT><A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws"><B>GetAnnotationResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html#GetAnnotationResponse()"><B>GetAnnotationResponse()</B></A> - \r
 143 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws">GetAnnotationResponse</A>\r
 144 <DD>&nbsp;\r
 145 <DT><A HREF="../compbio/runner/_NativeSpecHelper.html#getApproprieteQueue()"><B>getApproprieteQueue()</B></A> - \r
 146 Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
 147 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 148 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTested.html#getArg0()"><B>getArg0()</B></A> - \r
 149 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws">GetLastTested</A>\r
 150 <DD>&nbsp;\r
 151 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html#getArg0()"><B>getArg0()</B></A> - \r
 152 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws">GetLastTestedOn</A>\r
 153 <DD>&nbsp;\r
 154 <DT><A HREF="../compbio/data/msa/jaxws/GetServiceDescription.html#getArg0()"><B>getArg0()</B></A> - \r
 155 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceDescription.html" title="class in compbio.data.msa.jaxws">GetServiceDescription</A>\r
 156 <DD>&nbsp;\r
 157 <DT><A HREF="../compbio/data/msa/jaxws/IsOperating.html#getArg0()"><B>getArg0()</B></A> - \r
 158 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperating.html" title="class in compbio.data.msa.jaxws">IsOperating</A>\r
 159 <DD>&nbsp;\r
 160 <DT><A HREF="../compbio/data/msa/jaxws/TestService.html#getArg0()"><B>getArg0()</B></A> - \r
 161 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestService.html" title="class in compbio.data.msa.jaxws">TestService</A>\r
 162 <DD>&nbsp;\r
 163 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)"><B>getArgument(String)</B></A> - \r
 164 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 165 <DD>Returns the argument by its name if found, NULL otherwise.\r
 166 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)"><B>getArgumentByOptionName(String)</B></A> - \r
 167 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 168 <DD>Returns the argument by option name, NULL if the argument is not found\r
 169 <DT><A HREF="../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)"><B>getArguments(RunnerConfig&lt;T&gt;)</B></A> - \r
 170 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
 171 <DD>Converts list of options as String to type Option\r
 172 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getArguments()"><B>getArguments()</B></A> - \r
 173 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 174 <DD>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
 175  runner\r
 176 <DT><A HREF="../compbio/engine/Configurator.html#getAsyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)"><B>getAsyncEngine(ConfiguredExecutable&lt;?&gt;, Executable.ExecProvider)</B></A> - \r
 177 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
 178 <DD>&nbsp;\r
 179 <DT><A HREF="../compbio/engine/Configurator.html#getAsyncEngine(compbio.engine.client.ConfiguredExecutable)"><B>getAsyncEngine(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
 180 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
 181 <DD>&nbsp;\r
 182 <DT><A HREF="../compbio/engine/Configurator.html#getAsyncEngine(java.lang.String)"><B>getAsyncEngine(String)</B></A> - \r
 183 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
 184 <DD>&nbsp;\r
 185 <DT><A HREF="../compbio/metadata/Limit.html#getAvgSeqLength()"><B>getAvgSeqLength()</B></A> - \r
 186 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
 187 <DD>&nbsp;\r
 188 <DT><A HREF="../compbio/metadata/Limit.html#getAvgSequenceLength(java.util.List)"><B>getAvgSequenceLength(List&lt;FastaSequence&gt;)</B></A> - \r
 189 Static method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
 190 <DD>Calculates an average sequence length of the dataset\r
 191 <DT><A HREF="../compbio/runner/_impl/Runners.html#getBlastAllRunnable(java.lang.String)"><B>getBlastAllRunnable(String)</B></A> - \r
 192 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
 193 <DD>&nbsp;\r
 194 <DT><A HREF="../compbio/runner/_impl/Environment.html#getBlastBinDir()"><B>getBlastBinDir()</B></A> - \r
 195 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl">Environment</A>\r
 196 <DD>&nbsp;\r
 197 <DT><A HREF="../compbio/runner/_impl/Environment.html#getBlastDatabasesDir()"><B>getBlastDatabasesDir()</B></A> - \r
 198 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl">Environment</A>\r
 199 <DD>&nbsp;\r
 200 <DT><A HREF="../compbio/engine/Job.html#getByJobId(java.lang.String, java.util.List)"><B>getByJobId(String, List&lt;Job&gt;)</B></A> - \r
 201 Static method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
 202 <DD>&nbsp;\r
 203 <DT><A HREF="../compbio/engine/Job.html#getByTaskId(java.lang.String, java.util.List)"><B>getByTaskId(String, List&lt;Job&gt;)</B></A> - \r
 204 Static method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
 205 <DD>&nbsp;\r
 206 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getCalculationTime()"><B>getCalculationTime()</B></A> - \r
 207 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 208 <DD>&nbsp;\r
 209 <DT><A HREF="../compbio/stat/servlet/util/Totals.html#getCancelled()"><B>getCancelled()</B></A> - \r
 210 Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>\r
 211 <DD>&nbsp;\r
 212 <DT><A HREF="../compbio/stat/collector/StatDB.html#getCancelledCount(java.sql.Timestamp, java.sql.Timestamp)"><B>getCancelledCount(Timestamp, Timestamp)</B></A> - \r
 213 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
 214 <DD>&nbsp;\r
 215 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#getCancelledJobs()"><B>getCancelledJobs()</B></A> - \r
 216 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
 217 <DD>&nbsp;\r
 218 <DT><A HREF="../compbio/data/msa/Category.html#getCategories()"><B>getCategories()</B></A> - \r
 219 Static method in class compbio.data.msa.<A HREF="../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</A>\r
 220 <DD>&nbsp;\r
 221 <DT><A HREF="../compbio/metadata/ChunkHolder.html#getChunk()"><B>getChunk()</B></A> - \r
 222 Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
 223 <DD>&nbsp;\r
 224 <DT><A HREF="../compbio/engine/conf/DirectoryManager.html#getClass(java.lang.String)"><B>getClass(String)</B></A> - \r
 225 Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</A>\r
 226 <DD>&nbsp;\r
 227 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getClusterCpuNum(java.lang.Class)"><B>getClusterCpuNum(Class&lt;? extends Executable&lt;?&gt;&gt;)</B></A> - \r
 228 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 229 <DD>&nbsp;\r
 230 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getClusterJobId(java.lang.String)"><B>getClusterJobId(String)</B></A> - \r
 231 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>\r
 232 <DD>&nbsp;\r
 233 <DT><A HREF="../compbio/stat/collector/JobStat.html#getClusterJobId()"><B>getClusterJobId()</B></A> - \r
 234 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
 235 <DD>&nbsp;\r
 236 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#getClusterJobs()"><B>getClusterJobs()</B></A> - \r
 237 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
 238 <DD>&nbsp;\r
 239 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getClusterJobSettings()"><B>getClusterJobSettings()</B></A> - \r
 240 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 241 <DD>&nbsp;\r
 242 <DT><A HREF="../compbio/engine/client/Executable.html#getClusterJobSettings()"><B>getClusterJobSettings()</B></A> - \r
 243 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
 244 <DD>&nbsp;\r
 245 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getClusterJobSettings()"><B>getClusterJobSettings()</B></A> - \r
 246 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 247 <DD>&nbsp;\r
 248 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getClusterJobSettings()"><B>getClusterJobSettings()</B></A> - \r
 249 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 250 <DD>&nbsp;\r
 251 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getClusterJobSettings()"><B>getClusterJobSettings()</B></A> - \r
 252 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 253 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 254 <DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#getClusterStat()"><B>getClusterStat()</B></A> - \r
 255 Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</A>\r
 256 <DD>&nbsp;\r
 257 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
 258 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 259 <DD>&nbsp;\r
 260 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
 261 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
 262 <DD>&nbsp;\r
 263 <DT><A HREF="../compbio/engine/client/Util.html#getCommand(compbio.engine.client.Executable.ExecProvider, java.lang.Class)"><B>getCommand(Executable.ExecProvider, Class&lt;?&gt;)</B></A> - \r
 264 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 265 <DD>&nbsp;\r
 266 <DT><A HREF="../compbio/runner/_impl/BlastAll.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
 267 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>\r
 268 <DD>&nbsp;\r
 269 <DT><A HREF="../compbio/runner/_impl/Mcl.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
 270 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
 271 <DD>&nbsp;\r
 272 <DT><A HREF="../compbio/runner/_impl/PSIBlast.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
 273 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
 274 <DD>&nbsp;\r
 275 <DT><A HREF="../compbio/runner/_impl/Ronn.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
 276 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
 277 <DD>&nbsp;\r
 278 <DT><A HREF="../compbio/runner/_impl/RPSBlast.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
 279 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
 280 <DD>&nbsp;\r
 281 <DT><A HREF="../compbio/runner/_impl/BlastAll.html#getCommandName()"><B>getCommandName()</B></A> - \r
 282 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>\r
 283 <DD>&nbsp;\r
 284 <DT><A HREF="../compbio/runner/_impl/Mcl.html#getCommandName()"><B>getCommandName()</B></A> - \r
 285 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
 286 <DD>&nbsp;\r
 287 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getCommandName()"><B>getCommandName()</B></A> - \r
 288 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 289 <DD>&nbsp;\r
 290 <DT><A HREF="../compbio/runner/_impl/PSIBlast.html#getCommandName()"><B>getCommandName()</B></A> - \r
 291 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
 292 <DD>&nbsp;\r
 293 <DT><A HREF="../compbio/runner/_impl/Ronn.html#getCommandName()"><B>getCommandName()</B></A> - \r
 294 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
 295 <DD>&nbsp;\r
 296 <DT><A HREF="../compbio/runner/_impl/RPSBlast.html#getCommandName()"><B>getCommandName()</B></A> - \r
 297 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
 298 <DD>&nbsp;\r
 299 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#getCommands()"><B>getCommands()</B></A> - \r
 300 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 301 <DD>&nbsp;\r
 302 <DT><A HREF="../compbio/ws/server/WSUtil.html#getCommands(java.util.List, java.lang.String)"><B>getCommands(List&lt;Option&lt;T&gt;&gt;, String)</B></A> - \r
 303 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
 304 <DD>&nbsp;\r
 305 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#getCommandString()"><B>getCommandString()</B></A> - \r
 306 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 307 <DD>&nbsp;\r
 308 <DT><A HREF="../compbio/engine/Job.html#getConfExecutable()"><B>getConfExecutable()</B></A> - \r
 309 Method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
 310 <DD>&nbsp;\r
 311 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getCPUTimeStat()"><B>getCPUTimeStat()</B></A> - \r
 312 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 313 <DD>&nbsp;\r
 314 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getCPUUsageTime()"><B>getCPUUsageTime()</B></A> - \r
 315 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 316 <DD>&nbsp;\r
 317 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 318 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 319 <DD>&nbsp;\r
 320 <DT><A HREF="../compbio/engine/client/Executable.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 321 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
 322 <DD><B>Deprecated.</B>&nbsp;\r
 323 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 324 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 325 <DD>This method cannot really tell whether the files has actually been
 326  created or not.\r
 327 <DT><A HREF="../compbio/runner/_impl/BlastAll.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 328 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>\r
 329 <DD>&nbsp;\r
 330 <DT><A HREF="../compbio/runner/_impl/Mcl.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 331 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
 332 <DD>&nbsp;\r
 333 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 334 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 335 <DD>&nbsp;\r
 336 <DT><A HREF="../compbio/runner/_impl/OB.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 337 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
 338 <DD>&nbsp;\r
 339 <DT><A HREF="../compbio/runner/_impl/PSIBlast.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 340 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
 341 <DD>&nbsp;\r
 342 <DT><A HREF="../compbio/runner/_impl/Ronn.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 343 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
 344 <DD>&nbsp;\r
 345 <DT><A HREF="../compbio/runner/_impl/RPSBlast.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 346 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
 347 <DD>&nbsp;\r
 348 <DT><A HREF="../compbio/runner/conservation/AACon.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 349 Method in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
 350 <DD>&nbsp;\r
 351 <DT><A HREF="../compbio/runner/disorder/Jronn.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 352 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
 353 <DD>&nbsp;\r
 354 <DT><A HREF="../compbio/runner/msa/ClustalW.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 355 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
 356 <DD>&nbsp;\r
 357 <DT><A HREF="../compbio/runner/msa/Muscle.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 358 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
 359 <DD>&nbsp;\r
 360 <DT><A HREF="../compbio/runner/msa/Probcons.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 361 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>\r
 362 <DD>&nbsp;\r
 363 <DT><A HREF="../compbio/runner/msa/Tcoffee.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 364 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
 365 <DD>&nbsp;\r
 366 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getDataTransfered()"><B>getDataTransfered()</B></A> - \r
 367 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 368 <DD>&nbsp;\r
 369 <DT><A HREF="../compbio/metadata/LimitsManager.html#getDefaultLimit()"><B>getDefaultLimit()</B></A> - \r
 370 Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
 371 <DD>&nbsp;\r
 372 <DT><A HREF="../compbio/metadata/Argument.html#getDefaultValue()"><B>getDefaultValue()</B></A> - \r
 373 Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
 374 <DD>&nbsp;\r
 375 <DT><A HREF="../compbio/metadata/Option.html#getDefaultValue()"><B>getDefaultValue()</B></A> - \r
 376 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 377 <DD>A default value of the option.\r
 378 <DT><A HREF="../compbio/engine/FilePuller.html#getDelay(java.util.concurrent.TimeUnit)"><B>getDelay(TimeUnit)</B></A> - \r
 379 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
 380 <DD>&nbsp;\r
 381 <DT><A HREF="../compbio/metadata/Argument.html#getDescription()"><B>getDescription()</B></A> - \r
 382 Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
 383 <DD>&nbsp;\r
 384 <DT><A HREF="../compbio/metadata/Option.html#getDescription()"><B>getDescription()</B></A> - \r
 385 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 386 <DD>A long description of the Option\r
 387 <DT><A HREF="../compbio/metadata/Preset.html#getDescription()"><B>getDescription()</B></A> - \r
 388 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
 389 <DD>&nbsp;\r
 390 <DT><A HREF="../compbio/stat/servlet/ServiceTestResult.html#getDetails()"><B>getDetails()</B></A> - \r
 391 Method in class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</A>\r
 392 <DD>&nbsp;\r
 393 <DT><A HREF="../compbio/stat/collector/StatDB.html#getEarliestRecord()"><B>getEarliestRecord()</B></A> - \r
 394 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
 395 <DD>&nbsp;\r
 396 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getEmail()"><B>getEmail()</B></A> - \r
 397 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 398 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 399 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getEndTime()"><B>getEndTime()</B></A> - \r
 400 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 401 <DD>&nbsp;\r
 402 <DT><A HREF="../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable)"><B>getEngine(Executable&lt;?&gt;)</B></A> - \r
 403 Static method in class compbio.engine.<A HREF="../compbio/engine/LoadBalancer.html" title="class in compbio.engine">LoadBalancer</A>\r
 404 <DD>&nbsp;\r
 405 <DT><A HREF="../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable, java.util.List)"><B>getEngine(Executable&lt;V&gt;, List&lt;FastaSequence&gt;)</B></A> - \r
 406 Static method in class compbio.engine.<A HREF="../compbio/engine/LoadBalancer.html" title="class in compbio.engine">LoadBalancer</A>\r
 407 <DD>&nbsp;\r
 408 <DT><A HREF="../compbio/ws/server/WSUtil.html#getEngine(compbio.engine.client.ConfiguredExecutable)"><B>getEngine(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
 409 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
 410 <DD>&nbsp;\r
 411 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getEnvironment()"><B>getEnvironment()</B></A> - \r
 412 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 413 <DD>&nbsp;\r
 414 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getEnvironment()"><B>getEnvironment()</B></A> - \r
 415 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
 416 <DD>&nbsp;\r
 417 <DT><A HREF="../compbio/engine/client/EnvVariableProcessor.html#getEnvVariables(java.lang.String, java.lang.Class)"><B>getEnvVariables(String, Class&lt;?&gt;)</B></A> - \r
 418 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</A>\r
 419 <DD>&nbsp;\r
 420 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getError()"><B>getError()</B></A> - \r
 421 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 422 <DD>&nbsp;\r
 423 <DT><A HREF="../compbio/engine/client/Executable.html#getError()"><B>getError()</B></A> - \r
 424 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
 425 <DD>&nbsp;\r
 426 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#getError()"><B>getError()</B></A> - \r
 427 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 428 <DD>&nbsp;\r
 429 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getError()"><B>getError()</B></A> - \r
 430 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 431 <DD>&nbsp;\r
 432 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getError()"><B>getError()</B></A> - \r
 433 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 434 <DD>&nbsp;\r
 435 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getError()"><B>getError()</B></A> - \r
 436 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 437 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 438 <DT><A HREF="../compbio/stat/collector/JobStat.html#getEscJobname()"><B>getEscJobname()</B></A> - \r
 439 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
 440 <DD>&nbsp;\r
 441 <DT><A HREF="../compbio/engine/client/Util.html#getExecProperty(java.lang.String, compbio.engine.client.Executable)"><B>getExecProperty(String, Executable&lt;?&gt;)</B></A> - \r
 442 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 443 <DD>&nbsp;\r
 444 <DT><A HREF="../compbio/engine/client/Util.html#getExecProperty(java.lang.String, java.lang.Class)"><B>getExecProperty(String, Class&lt;?&gt;)</B></A> - \r
 445 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 446 <DD>&nbsp;\r
 447 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getExecProvider()"><B>getExecProvider()</B></A> - \r
 448 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 449 <DD>&nbsp;\r
 450 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getExecProvider()"><B>getExecProvider()</B></A> - \r
 451 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
 452 <DD>&nbsp;\r
 453 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getExecutable()"><B>getExecutable()</B></A> - \r
 454 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 455 <DD>&nbsp;\r
 456 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getExecutable()"><B>getExecutable()</B></A> - \r
 457 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
 458 <DD>&nbsp;\r
 459 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getExecutionStat()"><B>getExecutionStat()</B></A> - \r
 460 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 461 <DD>&nbsp;\r
 462 <DT><A HREF="../compbio/engine/local/LocalExecutorService.html#getExecutor()"><B>getExecutor()</B></A> - \r
 463 Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</A>\r
 464 <DD>This method returns the single instance of CachedThreadPoolExecutor which
 465  it cashes internally\r
 466 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getExitStatus()"><B>getExitStatus()</B></A> - \r
 467 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 468 <DD>&nbsp;\r
 469 <DT><A HREF="../compbio/stat/servlet/util/Totals.html#getFailed()"><B>getFailed()</B></A> - \r
 470 Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>\r
 471 <DD>&nbsp;\r
 472 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#getFailedJobs()"><B>getFailedJobs()</B></A> - \r
 473 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
 474 <DD>Started & finished but did not produce result\r
 475 <DT><A HREF="../compbio/data/msa/jaxws/Align.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
 476 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws">Align</A>\r
 477 <DD>&nbsp;\r
 478 <DT><A HREF="../compbio/data/msa/jaxws/Analize.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
 479 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Analize.html" title="class in compbio.data.msa.jaxws">Analize</A>\r
 480 <DD>&nbsp;\r
 481 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
 482 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>\r
 483 <DD>&nbsp;\r
 484 <DT><A HREF="../compbio/data/msa/jaxws/CustomAnalize.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
 485 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</A>\r
 486 <DD>&nbsp;\r
 487 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
 488 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>\r
 489 <DD>&nbsp;\r
 490 <DT><A HREF="../compbio/data/msa/jaxws/PresetAnalize.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
 491 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</A>\r
 492 <DD>&nbsp;\r
 493 <DT><A HREF="../compbio/engine/FilePuller.html#getFile()"><B>getFile()</B></A> - \r
 494 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
 495 <DD>&nbsp;\r
 496 <DT><A HREF="../compbio/stat/collector/JobStat.html#getFinish()"><B>getFinish()</B></A> - \r
 497 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
 498 <DD>&nbsp;\r
 499 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getFormatedSequence(int)"><B>getFormatedSequence(int)</B></A> - \r
 500 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
 501 <DD>Format sequence per width letter in one string.\r
 502 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getFormattedFasta()"><B>getFormattedFasta()</B></A> - \r
 503 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
 504 <DD>&nbsp;\r
 505 <DT><A HREF="../compbio/engine/client/Util.html#getFullPath(java.lang.String, java.lang.String)"><B>getFullPath(String, String)</B></A> - \r
 506 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 507 <DD>&nbsp;\r
 508 <DT><A HREF="../compbio/metadata/Argument.html#getFurtherDetails()"><B>getFurtherDetails()</B></A> - \r
 509 Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
 510 <DD>&nbsp;\r
 511 <DT><A HREF="../compbio/metadata/Option.html#getFurtherDetails()"><B>getFurtherDetails()</B></A> - \r
 512 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 513 <DD>The URL where further details about the option can be found\r
 514 <DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#getGapchar()"><B>getGapchar()</B></A> - \r
 515 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
 516 <DD>&nbsp;\r
 517 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getId()"><B>getId()</B></A> - \r
 518 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
 519 <DD>Gets the value of id\r
 520 <DT><A HREF="../compbio/stat/servlet/util/Totals.html#getIncomplete()"><B>getIncomplete()</B></A> - \r
 521 Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>\r
 522 <DD>&nbsp;\r
 523 <DT><A HREF="../compbio/stat/collector/StatDB.html#getIncompleteCount(java.sql.Timestamp, java.sql.Timestamp)"><B>getIncompleteCount(Timestamp, Timestamp)</B></A> - \r
 524 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
 525 <DD>&nbsp;\r
 526 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#getIncompleteJobs()"><B>getIncompleteJobs()</B></A> - \r
 527 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
 528 <DD>&nbsp;\r
 529 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getInput()"><B>getInput()</B></A> - \r
 530 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 531 <DD>Not all input paths are relative! Input path could be absolute!\r
 532 <DT><A HREF="../compbio/engine/client/Executable.html#getInput()"><B>getInput()</B></A> - \r
 533 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
 534 <DD>&nbsp;\r
 535 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#getInput()"><B>getInput()</B></A> - \r
 536 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 537 <DD>&nbsp;\r
 538 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getInput()"><B>getInput()</B></A> - \r
 539 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 540 <DD>&nbsp;\r
 541 <DT><A HREF="../compbio/runner/_impl/BlastAll.html#getInput()"><B>getInput()</B></A> - \r
 542 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>\r
 543 <DD>&nbsp;\r
 544 <DT><A HREF="../compbio/runner/_impl/Mcl.html#getInput()"><B>getInput()</B></A> - \r
 545 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
 546 <DD>&nbsp;\r
 547 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getInput()"><B>getInput()</B></A> - \r
 548 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 549 <DD>&nbsp;\r
 550 <DT><A HREF="../compbio/runner/_impl/OB.html#getInput()"><B>getInput()</B></A> - \r
 551 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
 552 <DD>&nbsp;\r
 553 <DT><A HREF="../compbio/runner/_impl/PSIBlast.html#getInput()"><B>getInput()</B></A> - \r
 554 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
 555 <DD>&nbsp;\r
 556 <DT><A HREF="../compbio/runner/_impl/Ronn.html#getInput()"><B>getInput()</B></A> - \r
 557 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
 558 <DD>&nbsp;\r
 559 <DT><A HREF="../compbio/runner/_impl/RPSBlast.html#getInput()"><B>getInput()</B></A> - \r
 560 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
 561 <DD>&nbsp;\r
 562 <DT><A HREF="../compbio/stat/collector/JobStat.html#getInputSize()"><B>getInputSize()</B></A> - \r
 563 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
 564 <DD>&nbsp;\r
 565 <DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#getInstance(compbio.engine.client.ConfiguredExecutable)"><B>getInstance(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
 566 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>\r
 567 <DD>&nbsp;\r
 568 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getIOWait()"><B>getIOWait()</B></A> - \r
 569 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 570 <DD>&nbsp;\r
 571 <DT><A HREF="../compbio/stat/collector/JobStat.html#getIsCancelled()"><B>getIsCancelled()</B></A> - \r
 572 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
 573 <DD>&nbsp;\r
 574 <DT><A HREF="../compbio/stat/collector/JobStat.html#getIsCollected()"><B>getIsCollected()</B></A> - \r
 575 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
 576 <DD>&nbsp;\r
 577 <DT><A HREF="../compbio/stat/collector/JobStat.html#getIsFinished()"><B>getIsFinished()</B></A> - \r
 578 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
 579 <DD>&nbsp;\r
 580 <DT><A HREF="../compbio/engine/client/Util.html#getJava()"><B>getJava()</B></A> - \r
 581 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 582 <DD>Returns the absolute path to the Java executable from JAVA_HOME\r
 583 <DT><A HREF="../compbio/data/msa/jaxws/CancelJob.html#getJobId()"><B>getJobId()</B></A> - \r
 584 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws">CancelJob</A>\r
 585 <DD>&nbsp;\r
 586 <DT><A HREF="../compbio/data/msa/jaxws/GetAnnotation.html#getJobId()"><B>getJobId()</B></A> - \r
 587 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws">GetAnnotation</A>\r
 588 <DD>&nbsp;\r
 589 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html#getJobId()"><B>getJobId()</B></A> - \r
 590 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws">GetJobStatus</A>\r
 591 <DD>&nbsp;\r
 592 <DT><A HREF="../compbio/data/msa/jaxws/GetResult.html#getJobId()"><B>getJobId()</B></A> - \r
 593 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws">GetResult</A>\r
 594 <DD>&nbsp;\r
 595 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#getJobId()"><B>getJobId()</B></A> - \r
 596 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>\r
 597 <DD>&nbsp;\r
 598 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getJobId()"><B>getJobId()</B></A> - \r
 599 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 600 <DD>&nbsp;\r
 601 <DT><A HREF="../compbio/engine/ClusterJobId.html#getJobId()"><B>getJobId()</B></A> - \r
 602 Method in class compbio.engine.<A HREF="../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>\r
 603 <DD>&nbsp;\r
 604 <DT><A HREF="../compbio/engine/Job.html#getJobId()"><B>getJobId()</B></A> - \r
 605 Method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
 606 <DD>&nbsp;\r
 607 <DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#getJobInfo()"><B>getJobInfo()</B></A> - \r
 608 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
 609 <DD>This method will block before the calculation has completed and then
 610  return the object containing a job execution statistics\r
 611 <DT><A HREF="../compbio/stat/collector/JobStat.html#getJobname()"><B>getJobname()</B></A> - \r
 612 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
 613 <DD>&nbsp;\r
 614 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#getJobNumber()"><B>getJobNumber()</B></A> - \r
 615 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
 616 <DD>&nbsp;\r
 617 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getJobPriority()"><B>getJobPriority()</B></A> - \r
 618 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 619 <DD>&nbsp;\r
 620 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#getJobs()"><B>getJobs()</B></A> - \r
 621 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
 622 <DD>&nbsp;\r
 623 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws"><B>GetJobStatus</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html#GetJobStatus()"><B>GetJobStatus()</B></A> - \r
 624 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws">GetJobStatus</A>\r
 625 <DD>&nbsp;\r
 626 <DT><A HREF="../compbio/data/msa/JManagement.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 627 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>\r
 628 <DD>Return the status of the job.\r
 629 <DT><A HREF="../compbio/engine/AsyncExecutor.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 630 Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
 631 <DD>Query the status of the job\r
 632 <DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 633 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
 634 <DD>This will never return clust.engine.JobStatus.CANCELLED as for sun grid
 635  engine cancelled job is the same as failed.\r
 636 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getJobStatus(compbio.engine.ClusterJobId)"><B>getJobStatus(ClusterJobId)</B></A> - \r
 637 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
 638 <DD>Apparently completed jobs cannot be found! If this happened most likely
 639  that the job is not running any more and Most likely it has been
 640  cancelled, finished or failed.\r
 641 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getJobStatus(int)"><B>getJobStatus(int)</B></A> - \r
 642 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>\r
 643 <DD><B>Deprecated.</B>&nbsp;\r
 644 <DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#getJobStatus()"><B>getJobStatus()</B></A> - \r
 645 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
 646 <DD>&nbsp;\r
 647 <DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 648 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
 649 <DD>&nbsp;\r
 650 <DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#getJobStatus(java.util.concurrent.Future)"><B>getJobStatus(Future&lt;ConfiguredExecutable&lt;?&gt;&gt;)</B></A> - \r
 651 Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A>\r
 652 <DD>&nbsp;\r
 653 <DT><A HREF="../compbio/engine/local/LocalRunner.html#getJobStatus()"><B>getJobStatus()</B></A> - \r
 654 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
 655 <DD>&nbsp;\r
 656 <DT><A HREF="../compbio/engine/SyncExecutor.html#getJobStatus()"><B>getJobStatus()</B></A> - \r
 657 Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
 658 <DD>Query the status of the job by its id.\r
 659 <DT><A HREF="../compbio/ws/server/ClustalOWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 660 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
 661 <DD>&nbsp;\r
 662 <DT><A HREF="../compbio/ws/server/ClustalWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 663 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 664 <DD>&nbsp;\r
 665 <DT><A HREF="../compbio/ws/server/GenericMetadataService.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 666 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A>\r
 667 <DD>&nbsp;\r
 668 <DT><A HREF="../compbio/ws/server/MafftWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 669 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
 670 <DD>&nbsp;\r
 671 <DT><A HREF="../compbio/ws/server/MuscleWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 672 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
 673 <DD>&nbsp;\r
 674 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 675 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
 676 <DD>&nbsp;\r
 677 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 678 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
 679 <DD>&nbsp;\r
 680 <DT><A HREF="../compbio/ws/server/WSUtil.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 681 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
 682 <DD>&nbsp;\r
 683 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws"><B>GetJobStatusResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html#GetJobStatusResponse()"><B>GetJobStatusResponse()</B></A> - \r
 684 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws">GetJobStatusResponse</A>\r
 685 <DD>&nbsp;\r
 686 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws"><B>GetLastTested</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLastTested.html#GetLastTested()"><B>GetLastTested()</B></A> - \r
 687 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws">GetLastTested</A>\r
 688 <DD>&nbsp;\r
 689 <DT><A HREF="../compbio/data/msa/RegistryWS.html#getLastTested(compbio.ws.client.Services)"><B>getLastTested(Services)</B></A> - \r
 690 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>\r
 691 <DD>Number of seconds since the last test.\r
 692 <DT><A HREF="../compbio/ws/server/RegistryWS.html#getLastTested(compbio.ws.client.Services)"><B>getLastTested(Services)</B></A> - \r
 693 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>\r
 694 <DD>&nbsp;\r
 695 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws"><B>GetLastTestedOn</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html#GetLastTestedOn()"><B>GetLastTestedOn()</B></A> - \r
 696 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws">GetLastTestedOn</A>\r
 697 <DD>&nbsp;\r
 698 <DT><A HREF="../compbio/data/msa/RegistryWS.html#getLastTestedOn(compbio.ws.client.Services)"><B>getLastTestedOn(Services)</B></A> - \r
 699 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>\r
 700 <DD>The date and time the service has been verified to work last time\r
 701 <DT><A HREF="../compbio/ws/server/RegistryWS.html#getLastTestedOn(compbio.ws.client.Services)"><B>getLastTestedOn(Services)</B></A> - \r
 702 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>\r
 703 <DD>Can potentially return null if the service has not been tested yet.\r
 704 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLastTestedOnResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html#GetLastTestedOnResponse()"><B>GetLastTestedOnResponse()</B></A> - \r
 705 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedOnResponse</A>\r
 706 <DD>&nbsp;\r
 707 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLastTestedResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html#GetLastTestedResponse()"><B>GetLastTestedResponse()</B></A> - \r
 708 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedResponse</A>\r
 709 <DD>&nbsp;\r
 710 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getLength()"><B>getLength()</B></A> - \r
 711 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
 712 <DD>&nbsp;\r
 713 <DT><A HREF="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws"><B>GetLimit</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLimit.html#GetLimit()"><B>GetLimit()</B></A> - \r
 714 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</A>\r
 715 <DD>&nbsp;\r
 716 <DT><A HREF="../compbio/data/msa/Metadata.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 717 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>\r
 718 <DD>Get a Limit for a preset.\r
 719 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 720 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 721 <DD>&nbsp;\r
 722 <DT><A HREF="../compbio/engine/client/Executable.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 723 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
 724 <DD>&nbsp;\r
 725 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 726 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 727 <DD>&nbsp;\r
 728 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 729 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 730 <DD>&nbsp;\r
 731 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 732 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 733 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 734 <DT><A HREF="../compbio/ws/server/ClustalOWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 735 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
 736 <DD>&nbsp;\r
 737 <DT><A HREF="../compbio/ws/server/ClustalWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 738 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 739 <DD>&nbsp;\r
 740 <DT><A HREF="../compbio/ws/server/GenericMetadataService.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 741 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A>\r
 742 <DD>&nbsp;\r
 743 <DT><A HREF="../compbio/ws/server/MafftWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 744 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
 745 <DD>&nbsp;\r
 746 <DT><A HREF="../compbio/ws/server/MuscleWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 747 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
 748 <DD>&nbsp;\r
 749 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 750 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
 751 <DD>&nbsp;\r
 752 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 753 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
 754 <DD>&nbsp;\r
 755 <DT><A HREF="../compbio/metadata/LimitsManager.html#getLimitByName(java.lang.String)"><B>getLimitByName(String)</B></A> - \r
 756 Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
 757 <DD>&nbsp;\r
 758 <DT><A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLimitResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html#GetLimitResponse()"><B>GetLimitResponse()</B></A> - \r
 759 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws">GetLimitResponse</A>\r
 760 <DD>&nbsp;\r
 761 <DT><A HREF="../compbio/data/msa/jaxws/GetLimits.html" title="class in compbio.data.msa.jaxws"><B>GetLimits</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLimits.html#GetLimits()"><B>GetLimits()</B></A> - \r
 762 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimits.html" title="class in compbio.data.msa.jaxws">GetLimits</A>\r
 763 <DD>&nbsp;\r
 764 <DT><A HREF="../compbio/data/msa/Metadata.html#getLimits()"><B>getLimits()</B></A> - \r
 765 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>\r
 766 <DD>List Limits supported by a web service.\r
 767 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getLimits()"><B>getLimits()</B></A> - \r
 768 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 769 <DD>&nbsp;\r
 770 <DT><A HREF="../compbio/engine/client/Executable.html#getLimits()"><B>getLimits()</B></A> - \r
 771 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
 772 <DD>&nbsp;\r
 773 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getLimits()"><B>getLimits()</B></A> - \r
 774 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 775 <DD>&nbsp;\r
 776 <DT><A HREF="../compbio/engine/client/Util.html#getLimits(java.lang.Class)"><B>getLimits(Class&lt;T&gt;)</B></A> - \r
 777 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 778 <DD>For now just assume that all parameters which came in needs setting it
 779  will be a client responsibility to prepare RunnerConfig object then\r
 780 <DT><A HREF="../compbio/metadata/LimitsManager.html#getLimits()"><B>getLimits()</B></A> - \r
 781 Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
 782 <DD>&nbsp;\r
 783 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getLimits()"><B>getLimits()</B></A> - \r
 784 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 785 <DD>&nbsp;\r
 786 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getLimits()"><B>getLimits()</B></A> - \r
 787 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 788 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 789 <DT><A HREF="../compbio/ws/server/ClustalOWS.html#getLimits()"><B>getLimits()</B></A> - \r
 790 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
 791 <DD>&nbsp;\r
 792 <DT><A HREF="../compbio/ws/server/ClustalWS.html#getLimits()"><B>getLimits()</B></A> - \r
 793 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 794 <DD>&nbsp;\r
 795 <DT><A HREF="../compbio/ws/server/GenericMetadataService.html#getLimits()"><B>getLimits()</B></A> - \r
 796 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A>\r
 797 <DD>&nbsp;\r
 798 <DT><A HREF="../compbio/ws/server/MafftWS.html#getLimits()"><B>getLimits()</B></A> - \r
 799 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
 800 <DD>&nbsp;\r
 801 <DT><A HREF="../compbio/ws/server/MuscleWS.html#getLimits()"><B>getLimits()</B></A> - \r
 802 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
 803 <DD>&nbsp;\r
 804 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#getLimits()"><B>getLimits()</B></A> - \r
 805 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
 806 <DD>&nbsp;\r
 807 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getLimits()"><B>getLimits()</B></A> - \r
 808 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
 809 <DD>&nbsp;\r
 810 <DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLimitsResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html#GetLimitsResponse()"><B>GetLimitsResponse()</B></A> - \r
 811 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws">GetLimitsResponse</A>\r
 812 <DD>&nbsp;\r
 813 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#getLocalJobs()"><B>getLocalJobs()</B></A> - \r
 814 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
 815 <DD>&nbsp;\r
 816 <DT><A HREF="../compbio/engine/conf/PropertyHelperManager.html#getLocalPath()"><B>getLocalPath()</B></A> - \r
 817 Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</A>\r
 818 <DD>Method return the absolute path to the project root directory.\r
 819 <DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#getLocalStat()"><B>getLocalStat()</B></A> - \r
 820 Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</A>\r
 821 <DD>&nbsp;\r
 822 <DT><A HREF="../compbio/metadata/ValueConstrain.html#getMax()"><B>getMax()</B></A> - \r
 823 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
 824 <DD>&nbsp;\r
 825 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getMaxVMem()"><B>getMaxVMem()</B></A> - \r
 826 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 827 <DD>&nbsp;\r
 828 <DT><A HREF="../compbio/runner/_impl/Runners.html#getMclRunnable(java.lang.String)"><B>getMclRunnable(String)</B></A> - \r
 829 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
 830 <DD>&nbsp;\r
 831 <DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#getMemoryLimit()"><B>getMemoryLimit()</B></A> - \r
 832 Method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
 833 <DD><B>Deprecated.</B>&nbsp;return max memory limit in Mb\r
 834 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getMemoryStat()"><B>getMemoryStat()</B></A> - \r
 835 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 836 <DD>&nbsp;\r
 837 <DT><A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
 838 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobSubmissionExceptionBean</A>\r
 839 <DD>&nbsp;\r
 840 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
 841 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
 842 <DD>&nbsp;\r
 843 <DT><A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
 844 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws">ResultNotAvailableExceptionBean</A>\r
 845 <DD>&nbsp;\r
 846 <DT><A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
 847 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html" title="class in compbio.data.msa.jaxws">UnsupportedRuntimeExceptionBean</A>\r
 848 <DD>&nbsp;\r
 849 <DT><A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
 850 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws">WrongParameterExceptionBean</A>\r
 851 <DD>&nbsp;\r
 852 <DT><A HREF="../compbio/data/sequence/Alignment.html#getMetadata()"><B>getMetadata()</B></A> - \r
 853 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
 854 <DD>&nbsp;\r
 855 <DT><A HREF="../compbio/data/sequence/ConservationMethod.html#getMethod(java.lang.String)"><B>getMethod(String)</B></A> - \r
 856 Static method in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence">ConservationMethod</A>\r
 857 <DD>&nbsp;\r
 858 <DT><A HREF="../compbio/data/sequence/Score.html#getMethod()"><B>getMethod()</B></A> - \r
 859 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
 860 <DD>Returns the ConservationMethod\r
 861 <DT><A HREF="../compbio/metadata/ValueConstrain.html#getMin()"><B>getMin()</B></A> - \r
 862 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
 863 <DD>&nbsp;\r
 864 <DT><A HREF="../compbio/metadata/Argument.html#getName()"><B>getName()</B></A> - \r
 865 Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
 866 <DD>&nbsp;\r
 867 <DT><A HREF="../compbio/metadata/Option.html#getName()"><B>getName()</B></A> - \r
 868 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 869 <DD>Human readable name of the option\r
 870 <DT><A HREF="../compbio/metadata/Preset.html#getName()"><B>getName()</B></A> - \r
 871 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
 872 <DD>&nbsp;\r
 873 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getName()"><B>getName()</B></A> - \r
 874 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 875 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 876 <DT><A HREF="../compbio/runner/_NativeSpecHelper.html#getNativeSpec()"><B>getNativeSpec()</B></A> - \r
 877 Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
 878 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 879 <DT><A HREF="../compbio/runner/_impl/Runners.html#getNetNglycRunnable(java.lang.String)"><B>getNetNglycRunnable(String)</B></A> - \r
 880 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
 881 <DD>&nbsp;\r
 882 <DT><A HREF="../compbio/metadata/ChunkHolder.html#getNextPosition()"><B>getNextPosition()</B></A> - \r
 883 Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
 884 <DD>&nbsp;\r
 885 <DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#getNumberOfScores()"><B>getNumberOfScores()</B></A> - \r
 886 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
 887 <DD>&nbsp;\r
 888 <DT><A HREF="../compbio/data/sequence/ScoreManager.html#getNumberOfSeq()"><B>getNumberOfSeq()</B></A> - \r
 889 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
 890 <DD>&nbsp;\r
 891 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getNumberOfSequencesAllowed()"><B>getNumberOfSequencesAllowed()</B></A> - \r
 892 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
 893 <DD>&nbsp;\r
 894 <DT><A HREF="../compbio/metadata/LimitExceededException.html#getNumberOfSequencesAllowed()"><B>getNumberOfSequencesAllowed()</B></A> - \r
 895 Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
 896 <DD>&nbsp;\r
 897 <DT><A HREF="../compbio/runner/_impl/Runners.html#getOBRunnable(java.lang.String)"><B>getOBRunnable(String)</B></A> - \r
 898 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
 899 <DD>&nbsp;\r
 900 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getOnelineFasta()"><B>getOnelineFasta()</B></A> - \r
 901 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
 902 <DD>&nbsp;\r
 903 <DT><A HREF="../compbio/metadata/Parameter.html#getOptionName()"><B>getOptionName()</B></A> - \r
 904 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
 905 <DD>&nbsp;\r
 906 <DT><A HREF="../compbio/metadata/Option.html#getOptionNames()"><B>getOptionNames()</B></A> - \r
 907 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 908 <DD>&nbsp;\r
 909 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#getOptions()"><B>getOptions()</B></A> - \r
 910 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>\r
 911 <DD>&nbsp;\r
 912 <DT><A HREF="../compbio/data/msa/jaxws/CustomAnalize.html#getOptions()"><B>getOptions()</B></A> - \r
 913 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</A>\r
 914 <DD>&nbsp;\r
 915 <DT><A HREF="../compbio/metadata/Preset.html#getOptions()"><B>getOptions()</B></A> - \r
 916 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
 917 <DD>&nbsp;\r
 918 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getOptions()"><B>getOptions()</B></A> - \r
 919 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 920 <DD>Returns the list of the Options supported by the executable of type T\r
 921 <DT><A HREF="../compbio/runner/OptionCombinator.html#getOptionsAtRandom()"><B>getOptionsAtRandom()</B></A> - \r
 922 Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
 923 <DD>&nbsp;\r
 924 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getOutput()"><B>getOutput()</B></A> - \r
 925 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 926 <DD>&nbsp;\r
 927 <DT><A HREF="../compbio/engine/client/Executable.html#getOutput()"><B>getOutput()</B></A> - \r
 928 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
 929 <DD>&nbsp;\r
 930 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#getOutput()"><B>getOutput()</B></A> - \r
 931 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 932 <DD>&nbsp;\r
 933 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getOutput()"><B>getOutput()</B></A> - \r
 934 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 935 <DD>&nbsp;\r
 936 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getOutput()"><B>getOutput()</B></A> - \r
 937 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 938 <DD>&nbsp;\r
 939 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getOutput()"><B>getOutput()</B></A> - \r
 940 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 941 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 942 <DT><A HREF="../compbio/runner/disorder/IUPred.html#getOutput()"><B>getOutput()</B></A> - \r
 943 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>\r
 944 <DD>&nbsp;\r
 945 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getParameters()"><B>getParameters()</B></A> - \r
 946 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 947 <DD>&nbsp;\r
 948 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
 949 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 950 <DD>&nbsp;\r
 951 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getParameters()"><B>getParameters()</B></A> - \r
 952 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
 953 <DD>&nbsp;\r
 954 <DT><A HREF="../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
 955 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
 956 <DD>&nbsp;\r
 957 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#getParameters()"><B>getParameters()</B></A> - \r
 958 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 959 <DD>&nbsp;\r
 960 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
 961 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 962 <DD>&nbsp;\r
 963 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getParameters()"><B>getParameters()</B></A> - \r
 964 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 965 <DD>Returns the list of parameters supported executable of type T.\r
 966 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
 967 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 968 <DD>&nbsp;\r
 969 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
 970 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 971 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 972 <DT><A HREF="../compbio/runner/conservation/AACon.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
 973 Method in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
 974 <DD>&nbsp;\r
 975 <DT><A HREF="../compbio/runner/disorder/Jronn.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
 976 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
 977 <DD>&nbsp;\r
 978 <DT><A HREF="../compbio/runner/msa/ClustalO.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
 979 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>\r
 980 <DD>&nbsp;\r
 981 <DT><A HREF="../compbio/runner/msa/Tcoffee.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
 982 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
 983 <DD>&nbsp;\r
 984 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#getParamValue(java.lang.String)"><B>getParamValue(String)</B></A> - \r
 985 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 986 <DD>&nbsp;\r
 987 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#getPosition()"><B>getPosition()</B></A> - \r
 988 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>\r
 989 <DD>&nbsp;\r
 990 <DT><A HREF="../compbio/metadata/Argument.html#getPossibleValues()"><B>getPossibleValues()</B></A> - \r
 991 Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
 992 <DD>&nbsp;\r
 993 <DT><A HREF="../compbio/metadata/Option.html#getPossibleValues()"><B>getPossibleValues()</B></A> - \r
 994 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 995 <DD>List of possible optionNames\r
 996 <DT><A HREF="../compbio/metadata/Parameter.html#getPossibleValues()"><B>getPossibleValues()</B></A> - \r
 997 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
 998 <DD>List is more convenient to work with\r
 999 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#getPreset()"><B>getPreset()</B></A> - \r
1000 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>\r
1001 <DD>&nbsp;\r
1002 <DT><A HREF="../compbio/data/msa/jaxws/PresetAnalize.html#getPreset()"><B>getPreset()</B></A> - \r
1003 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</A>\r
1004 <DD>&nbsp;\r
1005 <DT><A HREF="../compbio/metadata/Limit.html#getPreset()"><B>getPreset()</B></A> - \r
1006 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
1007 <DD>&nbsp;\r
1008 <DT><A HREF="../compbio/metadata/PresetManager.html#getPresetByName(java.lang.String)"><B>getPresetByName(String)</B></A> - \r
1009 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
1010 <DD>&nbsp;\r
1011 <DT><A HREF="../compbio/data/msa/jaxws/GetLimit.html#getPresetName()"><B>getPresetName()</B></A> - \r
1012 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</A>\r
1013 <DD>&nbsp;\r
1014 <DT><A HREF="../compbio/data/msa/jaxws/GetPresets.html" title="class in compbio.data.msa.jaxws"><B>GetPresets</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetPresets.html#GetPresets()"><B>GetPresets()</B></A> - \r
1015 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetPresets.html" title="class in compbio.data.msa.jaxws">GetPresets</A>\r
1016 <DD>&nbsp;\r
1017 <DT><A HREF="../compbio/data/msa/Metadata.html#getPresets()"><B>getPresets()</B></A> - \r
1018 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>\r
1019 <DD>Get presets supported by a web service\r
1020 <DT><A HREF="../compbio/metadata/PresetManager.html#getPresets()"><B>getPresets()</B></A> - \r
1021 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
1022 <DD>&nbsp;\r
1023 <DT><A HREF="../compbio/runner/Util.html#getPresets(java.lang.Class)"><B>getPresets(Class&lt;? extends Executable&lt;T&gt;&gt;)</B></A> - \r
1024 Static method in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
1025 <DD>&nbsp;\r
1026 <DT><A HREF="../compbio/ws/server/ClustalOWS.html#getPresets()"><B>getPresets()</B></A> - \r
1027 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
1028 <DD>&nbsp;\r
1029 <DT><A HREF="../compbio/ws/server/ClustalWS.html#getPresets()"><B>getPresets()</B></A> - \r
1030 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
1031 <DD>&nbsp;\r
1032 <DT><A HREF="../compbio/ws/server/GenericMetadataService.html#getPresets()"><B>getPresets()</B></A> - \r
1033 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A>\r
1034 <DD>&nbsp;\r
1035 <DT><A HREF="../compbio/ws/server/MafftWS.html#getPresets()"><B>getPresets()</B></A> - \r
1036 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
1037 <DD>&nbsp;\r
1038 <DT><A HREF="../compbio/ws/server/MuscleWS.html#getPresets()"><B>getPresets()</B></A> - \r
1039 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
1040 <DD>&nbsp;\r
1041 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#getPresets()"><B>getPresets()</B></A> - \r
1042 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
1043 <DD>&nbsp;\r
1044 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getPresets()"><B>getPresets()</B></A> - \r
1045 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
1046 <DD>&nbsp;\r
1047 <DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws"><B>GetPresetsResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html#GetPresetsResponse()"><B>GetPresetsResponse()</B></A> - \r
1048 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws">GetPresetsResponse</A>\r
1049 <DD>&nbsp;\r
1050 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getPrmSeparator()"><B>getPrmSeparator()</B></A> - \r
1051 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
1052 <DD>&nbsp;\r
1053 <DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#getProgram()"><B>getProgram()</B></A> - \r
1054 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
1055 <DD>&nbsp;\r
1056 <DT><A HREF="../compbio/engine/FilePuller.html#getProgress()"><B>getProgress()</B></A> - \r
1057 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
1058 <DD>&nbsp;\r
1059 <DT><A HREF="../compbio/engine/ProgressGetter.html#getProgress(java.lang.String)"><B>getProgress(String)</B></A> - \r
1060 Static method in class compbio.engine.<A HREF="../compbio/engine/ProgressGetter.html" title="class in compbio.engine">ProgressGetter</A>\r
1061 <DD>&nbsp;\r
1062 <DT><A HREF="../compbio/ws/server/WSUtil.html#getProgress(java.lang.String)"><B>getProgress(String)</B></A> - \r
1063 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
1064 <DD>&nbsp;\r
1065 <DT><A HREF="../compbio/engine/conf/PropertyHelperManager.html#getPropertyHelper()"><B>getPropertyHelper()</B></A> - \r
1066 Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</A>\r
1067 <DD>Ways to fix path problem: 1) find a path to WEB-INF directory based on
1068  the path to a known class.\r
1069 <DT><A HREF="../compbio/runner/_impl/Runners.html#getPSIBlastRunnable(java.lang.String)"><B>getPSIBlastRunnable(String)</B></A> - \r
1070 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
1071 <DD>&nbsp;\r
1072 <DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#getQueue(int, int)"><B>getQueue(int, int)</B></A> - \r
1073 Static method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
1074 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
1075 <DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#getQueue(java.lang.String)"><B>getQueue(String)</B></A> - \r
1076 Method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
1077 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
1078 <DT><A HREF="../compbio/runner/_NativeSpecHelper.html#getQueue()"><B>getQueue()</B></A> - \r
1079 Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
1080 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
1081 <DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#getQueueByMemoryRequirements(int)"><B>getQueueByMemoryRequirements(int)</B></A> - \r
1082 Static method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
1083 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
1084 <DT><A HREF="../compbio/data/sequence/Score.html#getRanges()"><B>getRanges()</B></A> - \r
1085 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
1086 <DD>Return Ranges if any Collections.EMPTY_SET otherwise\r
1087 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getRawUsage()"><B>getRawUsage()</B></A> - \r
1088 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
1089 <DD>&nbsp;\r
1090 <DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#getRecordedJobStatus(java.lang.String)"><B>getRecordedJobStatus(String)</B></A> - \r
1091 Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A>\r
1092 <DD>&nbsp;\r
1093 <DT><A HREF="../compbio/ws/server/_WSLogger.html#getRemoteAddress()"><B>getRemoteAddress()</B></A> - \r
1094 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/_WSLogger.html" title="class in compbio.ws.server">_WSLogger</A>\r
1095 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
1096 <DT><A HREF="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws"><B>GetResult</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetResult.html#GetResult()"><B>GetResult()</B></A> - \r
1097 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws">GetResult</A>\r
1098 <DD>&nbsp;\r
1099 <DT><A HREF="../compbio/data/msa/MsaWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
1100 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
1101 <DD>Return the result of the job.\r
1102 <DT><A HREF="../compbio/ws/server/_MsaService.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
1103 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/_MsaService.html" title="class in compbio.ws.server">_MsaService</A>\r
1104 <DD>&nbsp;\r
1105 <DT><A HREF="../compbio/ws/server/ClustalOWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
1106 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
1107 <DD>&nbsp;\r
1108 <DT><A HREF="../compbio/ws/server/ClustalWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
1109 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
1110 <DD>&nbsp;\r
1111 <DT><A HREF="../compbio/ws/server/MafftWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
1112 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
1113 <DD>&nbsp;\r
1114 <DT><A HREF="../compbio/ws/server/MuscleWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
1115 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
1116 <DD>&nbsp;\r
1117 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
1118 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
1119 <DD>&nbsp;\r
1120 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
1121 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
1122 <DD>&nbsp;\r
1123 <DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws"><B>GetResultResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html#GetResultResponse()"><B>GetResultResponse()</B></A> - \r
1124 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws">GetResultResponse</A>\r
1125 <DD>&nbsp;\r
1126 <DT><A HREF="../compbio/engine/AsyncExecutor.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1127 Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
1128 <DD>Retrieve the results of the job.\r
1129 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getResults()"><B>getResults()</B></A> - \r
1130 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
1131 <DD>&nbsp;\r
1132 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1133 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
1134 <DD>&nbsp;\r
1135 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getResults()"><B>getResults()</B></A> - \r
1136 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
1137 <DD>&nbsp;\r
1138 <DT><A HREF="../compbio/engine/client/Executable.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1139 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
1140 <DD>&nbsp;\r
1141 <DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1142 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
1143 <DD>&nbsp;\r
1144 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1145 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
1146 <DD>&nbsp;\r
1147 <DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1148 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
1149 <DD>&nbsp;\r
1150 <DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#getResults(java.util.concurrent.Future, java.lang.String)"><B>getResults(Future&lt;ConfiguredExecutable&lt;?&gt;&gt;, String)</B></A> - \r
1151 Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A>\r
1152 <DD>&nbsp;\r
1153 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1154 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
1155 <DD>&nbsp;\r
1156 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1157 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
1158 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
1159 <DT><A HREF="../compbio/runner/conservation/AACon.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1160 Method in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
1161 <DD>&nbsp;\r
1162 <DT><A HREF="../compbio/runner/disorder/Disembl.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1163 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>\r
1164 <DD>&nbsp;\r
1165 <DT><A HREF="../compbio/runner/disorder/GlobPlot.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1166 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>\r
1167 <DD>&nbsp;\r
1168 <DT><A HREF="../compbio/runner/disorder/IUPred.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1169 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>\r
1170 <DD>&nbsp;\r
1171 <DT><A HREF="../compbio/runner/disorder/Jronn.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1172 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
1173 <DD>&nbsp;\r
1174 <DT><A HREF="../compbio/runner/msa/ClustalO.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1175 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>\r
1176 <DD>&nbsp;\r
1177 <DT><A HREF="../compbio/runner/msa/ClustalW.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1178 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
1179 <DD>&nbsp;\r
1180 <DT><A HREF="../compbio/runner/msa/Mafft.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1181 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>\r
1182 <DD>&nbsp;\r
1183 <DT><A HREF="../compbio/runner/msa/Muscle.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1184 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
1185 <DD>&nbsp;\r
1186 <DT><A HREF="../compbio/runner/msa/Probcons.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1187 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>\r
1188 <DD>&nbsp;\r
1189 <DT><A HREF="../compbio/runner/msa/Tcoffee.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1190 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
1191 <DD>&nbsp;\r
1192 <DT><A HREF="../compbio/stat/collector/JobStat.html#getResultSize()"><B>getResultSize()</B></A> - \r
1193 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
1194 <DD>&nbsp;\r
1195 <DT><A HREF="../compbio/data/msa/jaxws/AlignResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1196 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws">AlignResponse</A>\r
1197 <DD>&nbsp;\r
1198 <DT><A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1199 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html" title="class in compbio.data.msa.jaxws">AnalizeResponse</A>\r
1200 <DD>&nbsp;\r
1201 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1202 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws">CustomAlignResponse</A>\r
1203 <DD>&nbsp;\r
1204 <DT><A HREF="../compbio/data/msa/jaxws/CustomAnalizeResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1205 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalizeResponse.html" title="class in compbio.data.msa.jaxws">CustomAnalizeResponse</A>\r
1206 <DD>&nbsp;\r
1207 <DT><A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1208 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws">GetAnnotationResponse</A>\r
1209 <DD>&nbsp;\r
1210 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1211 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws">GetJobStatusResponse</A>\r
1212 <DD>&nbsp;\r
1213 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1214 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedOnResponse</A>\r
1215 <DD>&nbsp;\r
1216 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1217 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedResponse</A>\r
1218 <DD>&nbsp;\r
1219 <DT><A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1220 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws">GetLimitResponse</A>\r
1221 <DD>&nbsp;\r
1222 <DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1223 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws">GetLimitsResponse</A>\r
1224 <DD>&nbsp;\r
1225 <DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1226 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws">GetPresetsResponse</A>\r
1227 <DD>&nbsp;\r
1228 <DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1229 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws">GetResultResponse</A>\r
1230 <DD>&nbsp;\r
1231 <DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1232 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws">GetRunnerOptionsResponse</A>\r
1233 <DD>&nbsp;\r
1234 <DT><A HREF="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1235 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html" title="class in compbio.data.msa.jaxws">GetServiceCategoriesResponse</A>\r
1236 <DD>&nbsp;\r
1237 <DT><A HREF="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1238 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html" title="class in compbio.data.msa.jaxws">GetServiceDescriptionResponse</A>\r
1239 <DD>&nbsp;\r
1240 <DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1241 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws">GetSupportedServicesResponse</A>\r
1242 <DD>&nbsp;\r
1243 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1244 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws">PresetAlignResponse</A>\r
1245 <DD>&nbsp;\r
1246 <DT><A HREF="../compbio/data/msa/jaxws/PresetAnalizeResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1247 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalizeResponse.html" title="class in compbio.data.msa.jaxws">PresetAnalizeResponse</A>\r
1248 <DD>&nbsp;\r
1249 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1250 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws">PullExecStatisticsResponse</A>\r
1251 <DD>&nbsp;\r
1252 <DT><A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1253 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html" title="class in compbio.data.msa.jaxws">TestAllServicesResponse</A>\r
1254 <DD>&nbsp;\r
1255 <DT><A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1256 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html" title="class in compbio.data.msa.jaxws">TestServiceResponse</A>\r
1257 <DD>&nbsp;\r
1258 <DT><A HREF="../compbio/runner/_impl/Runners.html#getRonnRunnable(java.lang.String)"><B>getRonnRunnable(String)</B></A> - \r
1259 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
1260 <DD>&nbsp;\r
1261 <DT><A HREF="../compbio/runner/_impl/Environment.html#getRPSBlastDatabasesDir()"><B>getRPSBlastDatabasesDir()</B></A> - \r
1262 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl">Environment</A>\r
1263 <DD>&nbsp;\r
1264 <DT><A HREF="../compbio/runner/_impl/Runners.html#getRPSBlastRunnable(java.lang.String)"><B>getRPSBlastRunnable(String)</B></A> - \r
1265 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
1266 <DD>&nbsp;\r
1267 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getRunConfiguration()"><B>getRunConfiguration()</B></A> - \r
1268 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
1269 <DD>&nbsp;\r
1270 <DT><A HREF="../compbio/ws/client/ServicesUtil.html#getRunnerByJobDirectory(java.io.File)"><B>getRunnerByJobDirectory(File)</B></A> - \r
1271 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</A>\r
1272 <DD>&nbsp;\r
1273 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#getRunnerClassName()"><B>getRunnerClassName()</B></A> - \r
1274 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
1275 <DD>&nbsp;\r
1276 <DT><A HREF="../compbio/metadata/PresetManager.html#getRunnerClassName()"><B>getRunnerClassName()</B></A> - \r
1277 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
1278 <DD>&nbsp;\r
1279 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getRunnerClassName()"><B>getRunnerClassName()</B></A> - \r
1280 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
1281 <DD>&nbsp;\r
1282 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getRunnerLimits(java.lang.Class)"><B>getRunnerLimits(Class&lt;V&gt;)</B></A> - \r
1283 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
1284 <DD>This method should be executed once and result of its execution reused.\r
1285 <DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptions.html" title="class in compbio.data.msa.jaxws"><B>GetRunnerOptions</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptions.html#GetRunnerOptions()"><B>GetRunnerOptions()</B></A> - \r
1286 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetRunnerOptions.html" title="class in compbio.data.msa.jaxws">GetRunnerOptions</A>\r
1287 <DD>&nbsp;\r
1288 <DT><A HREF="../compbio/data/msa/Metadata.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
1289 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>\r
1290 <DD>Get options supported by a web service\r
1291 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getRunnerOptions(java.lang.Class)"><B>getRunnerOptions(Class&lt;? extends Executable&lt;V&gt;&gt;)</B></A> - \r
1292 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
1293 <DD>&nbsp;\r
1294 <DT><A HREF="../compbio/ws/server/ClustalOWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
1295 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
1296 <DD>&nbsp;\r
1297 <DT><A HREF="../compbio/ws/server/ClustalWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
1298 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
1299 <DD>&nbsp;\r
1300 <DT><A HREF="../compbio/ws/server/GenericMetadataService.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
1301 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A>\r
1302 <DD>&nbsp;\r
1303 <DT><A HREF="../compbio/ws/server/MafftWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
1304 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
1305 <DD>&nbsp;\r
1306 <DT><A HREF="../compbio/ws/server/MuscleWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
1307 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
1308 <DD>&nbsp;\r
1309 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
1310 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
1311 <DD>&nbsp;\r
1312 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
1313 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
1314 <DD>&nbsp;\r
1315 <DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws"><B>GetRunnerOptionsResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#GetRunnerOptionsResponse()"><B>GetRunnerOptionsResponse()</B></A> - \r
1316 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws">GetRunnerOptionsResponse</A>\r
1317 <DD>&nbsp;\r
1318 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getRunnerPresets(java.lang.Class)"><B>getRunnerPresets(Class&lt;? extends Executable&lt;V&gt;&gt;)</B></A> - \r
1319 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
1320 <DD>&nbsp;\r
1321 <DT><A HREF="../compbio/stat/collector/JobStat.html#getRuntime()"><B>getRuntime()</B></A> - \r
1322 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
1323 <DD>&nbsp;\r
1324 <DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#getSchema(java.lang.String)"><B>getSchema(String)</B></A> - \r
1325 Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
1326 <DD>&nbsp;\r
1327 <DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#getScoreByMethod(java.lang.Enum)"><B>getScoreByMethod(Enum&lt;?&gt;)</B></A> - \r
1328 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
1329 <DD>&nbsp;\r
1330 <DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#getScoreByMethod(java.lang.String)"><B>getScoreByMethod(String)</B></A> - \r
1331 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
1332 <DD>&nbsp;\r
1333 <DT><A HREF="../compbio/data/sequence/Score.html#getScores()"><B>getScores()</B></A> - \r
1334 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
1335 <DD>The column scores for the alignment\r
1336 <DT><A HREF="../compbio/metadata/Limit.html#getSeqNumber()"><B>getSeqNumber()</B></A> - \r
1337 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
1338 <DD>&nbsp;\r
1339 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getSequence()"><B>getSequence()</B></A> - \r
1340 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
1341 <DD>Gets the value of sequence\r
1342 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getSequenceLenghtActual()"><B>getSequenceLenghtActual()</B></A> - \r
1343 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
1344 <DD>&nbsp;\r
1345 <DT><A HREF="../compbio/metadata/LimitExceededException.html#getSequenceLenghtActual()"><B>getSequenceLenghtActual()</B></A> - \r
1346 Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
1347 <DD>&nbsp;\r
1348 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getSequenceLenghtAllowed()"><B>getSequenceLenghtAllowed()</B></A> - \r
1349 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
1350 <DD>&nbsp;\r
1351 <DT><A HREF="../compbio/metadata/LimitExceededException.html#getSequenceLenghtAllowed()"><B>getSequenceLenghtAllowed()</B></A> - \r
1352 Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
1353 <DD>&nbsp;\r
1354 <DT><A HREF="../compbio/data/sequence/Alignment.html#getSequences()"><B>getSequences()</B></A> - \r
1355 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
1356 <DD>&nbsp;\r
1357 <DT><A HREF="../compbio/stat/servlet/ServiceTestResult.html#getService()"><B>getService()</B></A> - \r
1358 Method in class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</A>\r
1359 <DD>&nbsp;\r
1360 <DT><A HREF="../compbio/ws/client/Services.html#getService(java.lang.String)"><B>getService(String)</B></A> - \r
1361 Static method in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
1362 <DD>&nbsp;\r
1363 <DT><A HREF="../compbio/ws/client/ServicesUtil.html#getServiceByJobDirectory(java.io.File)"><B>getServiceByJobDirectory(File)</B></A> - \r
1364 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</A>\r
1365 <DD>&nbsp;\r
1366 <DT><A HREF="../compbio/ws/client/ServicesUtil.html#getServiceByRunner(java.lang.Class)"><B>getServiceByRunner(Class&lt;? extends Executable&gt;)</B></A> - \r
1367 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</A>\r
1368 <DD>&nbsp;\r
1369 <DT><A HREF="../compbio/data/msa/jaxws/GetServiceCategories.html" title="class in compbio.data.msa.jaxws"><B>GetServiceCategories</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetServiceCategories.html#GetServiceCategories()"><B>GetServiceCategories()</B></A> - \r
1370 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceCategories.html" title="class in compbio.data.msa.jaxws">GetServiceCategories</A>\r
1371 <DD>&nbsp;\r
1372 <DT><A HREF="../compbio/data/msa/RegistryWS.html#getServiceCategories()"><B>getServiceCategories()</B></A> - \r
1373 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>\r
1374 <DD>Gets the list of services per category.\r
1375 <DT><A HREF="../compbio/ws/server/RegistryWS.html#getServiceCategories()"><B>getServiceCategories()</B></A> - \r
1376 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>\r
1377 <DD>&nbsp;\r
1378 <DT><A HREF="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html" title="class in compbio.data.msa.jaxws"><B>GetServiceCategoriesResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html#GetServiceCategoriesResponse()"><B>GetServiceCategoriesResponse()</B></A> - \r
1379 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html" title="class in compbio.data.msa.jaxws">GetServiceCategoriesResponse</A>\r
1380 <DD>&nbsp;\r
1381 <DT><A HREF="../compbio/data/msa/jaxws/GetServiceDescription.html" title="class in compbio.data.msa.jaxws"><B>GetServiceDescription</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetServiceDescription.html#GetServiceDescription()"><B>GetServiceDescription()</B></A> - \r
1382 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceDescription.html" title="class in compbio.data.msa.jaxws">GetServiceDescription</A>\r
1383 <DD>&nbsp;\r
1384 <DT><A HREF="../compbio/data/msa/RegistryWS.html#getServiceDescription(compbio.ws.client.Services)"><B>getServiceDescription(Services)</B></A> - \r
1385 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>\r
1386 <DD>Gives the description of the service.\r
1387 <DT><A HREF="../compbio/ws/server/RegistryWS.html#getServiceDescription(compbio.ws.client.Services)"><B>getServiceDescription(Services)</B></A> - \r
1388 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>\r
1389 <DD>&nbsp;\r
1390 <DT><A HREF="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html" title="class in compbio.data.msa.jaxws"><B>GetServiceDescriptionResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html#GetServiceDescriptionResponse()"><B>GetServiceDescriptionResponse()</B></A> - \r
1391 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html" title="class in compbio.data.msa.jaxws">GetServiceDescriptionResponse</A>\r
1392 <DD>&nbsp;\r
1393 <DT><A HREF="../compbio/ws/client/ServicesUtil.html#getServiceImpl(compbio.ws.client.Services)"><B>getServiceImpl(Services)</B></A> - \r
1394 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</A>\r
1395 <DD>&nbsp;\r
1396 <DT><A HREF="../compbio/ws/client/Services.html#getServiceInfo()"><B>getServiceInfo()</B></A> - \r
1397 Method in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
1398 <DD>&nbsp;\r
1399 <DT><A HREF="../compbio/data/msa/Category.html#getServices()"><B>getServices()</B></A> - \r
1400 Method in class compbio.data.msa.<A HREF="../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</A>\r
1401 <DD>&nbsp;\r
1402 <DT><A HREF="../compbio/ws/client/Jws2Client.html#getServices(java.lang.String)"><B>getServices(String)</B></A> - \r
1403 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
1404 <DD>&nbsp;\r
1405 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getSession()"><B>getSession()</B></A> - \r
1406 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
1407 <DD>&nbsp;\r
1408 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#getSingleWSStat(compbio.ws.client.Services)"><B>getSingleWSStat(Services)</B></A> - \r
1409 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
1410 <DD>&nbsp;\r
1411 <DT><A HREF="../compbio/data/sequence/Alignment.html#getSize()"><B>getSize()</B></A> - \r
1412 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
1413 <DD>&nbsp;\r
1414 <DT><A HREF="../compbio/data/sequence/SMERFSConstraints.html#getSMERFSColumnScore(java.lang.String)"><B>getSMERFSColumnScore(String)</B></A> - \r
1415 Static method in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A>\r
1416 <DD>&nbsp;\r
1417 <DT><A HREF="../compbio/stat/collector/JobStat.html#getStart()"><B>getStart()</B></A> - \r
1418 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
1419 <DD>&nbsp;\r
1420 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getStartTime()"><B>getStartTime()</B></A> - \r
1421 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
1422 <DD>&nbsp;\r
1423 <DT><A HREF="../compbio/runner/conservation/AACon.html#getStatFile()"><B>getStatFile()</B></A> - \r
1424 Static method in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
1425 <DD>&nbsp;\r
1426 <DT><A HREF="../compbio/runner/disorder/Jronn.html#getStatFile()"><B>getStatFile()</B></A> - \r
1427 Static method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
1428 <DD>&nbsp;\r
1429 <DT><A HREF="../compbio/runner/msa/ClustalO.html#getStatFile()"><B>getStatFile()</B></A> - \r
1430 Static method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>\r
1431 <DD>&nbsp;\r
1432 <DT><A HREF="../compbio/runner/msa/ClustalW.html#getStatFile()"><B>getStatFile()</B></A> - \r
1433 Static method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
1434 <DD>&nbsp;\r
1435 <DT><A HREF="../compbio/runner/msa/Muscle.html#getStatFile()"><B>getStatFile()</B></A> - \r
1436 Static method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
1437 <DD>&nbsp;\r
1438 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getStatistics(org.ggf.drmaa.JobInfo)"><B>getStatistics(JobInfo)</B></A> - \r
1439 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>\r
1440 <DD>&nbsp;\r
1441 <DT><A HREF="../compbio/ws/server/_WSLogger.html#getStatLogger(compbio.ws.client.Services, javax.xml.ws.WebServiceContext)"><B>getStatLogger(Services, WebServiceContext)</B></A> - \r
1442 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/_WSLogger.html" title="class in compbio.ws.server">_WSLogger</A>\r
1443 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
1444 <DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#getStats(int)"><B>getStats(int)</B></A> - \r
1445 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>\r
1446 <DD>&nbsp;\r
1447 <DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#getStats(java.util.Date)"><B>getStats(Date)</B></A> - \r
1448 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>\r
1449 <DD>&nbsp;\r
1450 <DT><A HREF="../compbio/stat/servlet/ServiceTestResult.html#getStatus()"><B>getStatus()</B></A> - \r
1451 Method in class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</A>\r
1452 <DD>&nbsp;\r
1453 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getSubmissionTime()"><B>getSubmissionTime()</B></A> - \r
1454 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
1455 <DD>&nbsp;\r
1456 <DT><A HREF="../compbio/runner/Util.html#getSupportedOptions(java.lang.Class)"><B>getSupportedOptions(Class&lt;? extends Executable&lt;T&gt;&gt;)</B></A> - \r
1457 Static method in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
1458 <DD>&nbsp;\r
1459 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getSupportedRuntimes()"><B>getSupportedRuntimes()</B></A> - \r
1460 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
1461 <DD>&nbsp;\r
1462 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getSupportedRuntimes()"><B>getSupportedRuntimes()</B></A> - \r
1463 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
1464 <DD>&nbsp;\r
1465 <DT><A HREF="../compbio/engine/client/Util.html#getSupportedRuntimes(java.lang.Class)"><B>getSupportedRuntimes(Class&lt;?&gt;)</B></A> - \r
1466 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
1467 <DD>&nbsp;\r
1468 <DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServices.html" title="class in compbio.data.msa.jaxws"><B>GetSupportedServices</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServices.html#GetSupportedServices()"><B>GetSupportedServices()</B></A> - \r
1469 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetSupportedServices.html" title="class in compbio.data.msa.jaxws">GetSupportedServices</A>\r
1470 <DD>&nbsp;\r
1471 <DT><A HREF="../compbio/data/msa/RegistryWS.html#getSupportedServices()"><B>getSupportedServices()</B></A> - \r
1472 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>\r
1473 <DD>List of services that are functioning on the server.\r
1474 <DT><A HREF="../compbio/ws/server/RegistryWS.html#getSupportedServices()"><B>getSupportedServices()</B></A> - \r
1475 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>\r
1476 <DD>&nbsp;\r
1477 <DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws"><B>GetSupportedServicesResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html#GetSupportedServicesResponse()"><B>GetSupportedServicesResponse()</B></A> - \r
1478 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws">GetSupportedServicesResponse</A>\r
1479 <DD>&nbsp;\r
1480 <DT><A HREF="../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)"><B>getSyncEngine(ConfiguredExecutable&lt;?&gt;, Executable.ExecProvider)</B></A> - \r
1481 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
1482 <DD>&nbsp;\r
1483 <DT><A HREF="../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable)"><B>getSyncEngine(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
1484 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
1485 <DD>&nbsp;\r
1486 <DT><A HREF="../compbio/engine/SubmissionManager.html#getTask(java.lang.String)"><B>getTask(String)</B></A> - \r
1487 Static method in class compbio.engine.<A HREF="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</A>\r
1488 <DD>&nbsp;\r
1489 <DT><A HREF="../compbio/engine/conf/DirectoryManager.html#getTaskDirectory(java.lang.Class)"><B>getTaskDirectory(Class&lt;?&gt;)</B></A> - \r
1490 Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</A>\r
1491 <DD>&nbsp;\r
1492 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getTaskId()"><B>getTaskId()</B></A> - \r
1493 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
1494 <DD>&nbsp;\r
1495 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getTaskId()"><B>getTaskId()</B></A> - \r
1496 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
1497 <DD>&nbsp;\r
1498 <DT><A HREF="../compbio/engine/Job.html#getTaskId()"><B>getTaskId()</B></A> - \r
1499 Method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
1500 <DD>&nbsp;\r
1501 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getTestArgs()"><B>getTestArgs()</B></A> - \r
1502 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
1503 <DD>&nbsp;\r
1504 <DT><A HREF="../compbio/runner/_impl/OB.html#getTestArgs()"><B>getTestArgs()</B></A> - \r
1505 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
1506 <DD>&nbsp;\r
1507 <DT><A HREF="../compbio/runner/_impl/Mcl.html#getTestCommand()"><B>getTestCommand()</B></A> - \r
1508 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
1509 <DD>&nbsp;\r
1510 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getTestCommand()"><B>getTestCommand()</B></A> - \r
1511 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
1512 <DD>&nbsp;\r
1513 <DT><A HREF="../compbio/runner/_impl/OB.html#getTestCommand()"><B>getTestCommand()</B></A> - \r
1514 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
1515 <DD>&nbsp;\r
1516 <DT><A HREF="../compbio/runner/_impl/Ronn.html#getTestCommand()"><B>getTestCommand()</B></A> - \r
1517 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
1518 <DD>&nbsp;\r
1519 <DT><A HREF="../compbio/runner/_impl/RPSBlast.html#getTestCommand()"><B>getTestCommand()</B></A> - \r
1520 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
1521 <DD>&nbsp;\r
1522 <DT><A HREF="../compbio/runner/_impl/Mcl.html#getTestParams()"><B>getTestParams()</B></A> - \r
1523 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
1524 <DD>&nbsp;\r
1525 <DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#getTimeLimit()"><B>getTimeLimit()</B></A> - \r
1526 Method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
1527 <DD><B>Deprecated.</B>&nbsp;0 - unlimited\r
1528 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getTimeStat()"><B>getTimeStat()</B></A> - \r
1529 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
1530 <DD>&nbsp;\r
1531 <DT><A HREF="../compbio/runner/_impl/Runners.html#getTmhmm2Runnable(java.lang.String)"><B>getTmhmm2Runnable(String)</B></A> - \r
1532 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
1533 <DD>&nbsp;\r
1534 <DT><A HREF="../compbio/stat/servlet/util/Totals.html#getTotal()"><B>getTotal()</B></A> - \r
1535 Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>\r
1536 <DD>&nbsp;\r
1537 <DT><A HREF="../compbio/stat/collector/StatDB.html#getTotalJobsCount(java.sql.Timestamp, java.sql.Timestamp)"><B>getTotalJobsCount(Timestamp, Timestamp)</B></A> - \r
1538 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
1539 <DD>&nbsp;\r
1540 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#getTotalRuntime()"><B>getTotalRuntime()</B></A> - \r
1541 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
1542 <DD>&nbsp;\r
1543 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getType()"><B>getType()</B></A> - \r
1544 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
1545 <DD>&nbsp;\r
1546 <DT><A HREF="../compbio/metadata/ValueConstrain.html#getType()"><B>getType()</B></A> - \r
1547 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
1548 <DD>&nbsp;\r
1549 <DT><A HREF="../compbio/runner/conservation/AACon.html#getType()"><B>getType()</B></A> - \r
1550 Method in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
1551 <DD>&nbsp;\r
1552 <DT><A HREF="../compbio/runner/disorder/Disembl.html#getType()"><B>getType()</B></A> - \r
1553 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>\r
1554 <DD>&nbsp;\r
1555 <DT><A HREF="../compbio/runner/disorder/GlobPlot.html#getType()"><B>getType()</B></A> - \r
1556 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>\r
1557 <DD>&nbsp;\r
1558 <DT><A HREF="../compbio/runner/disorder/IUPred.html#getType()"><B>getType()</B></A> - \r
1559 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>\r
1560 <DD>&nbsp;\r
1561 <DT><A HREF="../compbio/runner/disorder/Jronn.html#getType()"><B>getType()</B></A> - \r
1562 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
1563 <DD>&nbsp;\r
1564 <DT><A HREF="../compbio/runner/msa/ClustalO.html#getType()"><B>getType()</B></A> - \r
1565 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>\r
1566 <DD>&nbsp;\r
1567 <DT><A HREF="../compbio/runner/msa/ClustalW.html#getType()"><B>getType()</B></A> - \r
1568 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
1569 <DD>&nbsp;\r
1570 <DT><A HREF="../compbio/runner/msa/Mafft.html#getType()"><B>getType()</B></A> - \r
1571 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>\r
1572 <DD>&nbsp;\r
1573 <DT><A HREF="../compbio/runner/msa/Muscle.html#getType()"><B>getType()</B></A> - \r
1574 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
1575 <DD>&nbsp;\r
1576 <DT><A HREF="../compbio/runner/msa/Probcons.html#getType()"><B>getType()</B></A> - \r
1577 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>\r
1578 <DD>&nbsp;\r
1579 <DT><A HREF="../compbio/runner/msa/Tcoffee.html#getType()"><B>getType()</B></A> - \r
1580 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
1581 <DD>&nbsp;\r
1582 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getUsedSysTime()"><B>getUsedSysTime()</B></A> - \r
1583 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
1584 <DD>&nbsp;\r
1585 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getUsedUserTime()"><B>getUsedUserTime()</B></A> - \r
1586 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
1587 <DD>&nbsp;\r
1588 <DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#getValidator(java.lang.String)"><B>getValidator(String)</B></A> - \r
1589 Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
1590 <DD>&nbsp;\r
1591 <DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#getValidator(javax.xml.validation.Schema)"><B>getValidator(Schema)</B></A> - \r
1592 Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
1593 <DD>&nbsp;\r
1594 <DT><A HREF="../compbio/metadata/Parameter.html#getValidValue()"><B>getValidValue()</B></A> - \r
1595 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
1596 <DD>&nbsp;\r
1597 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getVMem()"><B>getVMem()</B></A> - \r
1598 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
1599 <DD>&nbsp;\r
1600 <DT><A HREF="../compbio/stat/collector/JobStat.html#getWebService()"><B>getWebService()</B></A> - \r
1601 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
1602 <DD>&nbsp;\r
1603 <DT><A HREF="../compbio/engine/AsyncExecutor.html#getWorkDirectory(java.lang.String)"><B>getWorkDirectory(String)</B></A> - \r
1604 Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
1605 <DD>&nbsp;\r
1606 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getWorkDirectory()"><B>getWorkDirectory()</B></A> - \r
1607 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
1608 <DD>&nbsp;\r
1609 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getWorkDirectory()"><B>getWorkDirectory()</B></A> - \r
1610 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
1611 <DD>&nbsp;\r
1612 <DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getWorkDirectory(java.lang.String)"><B>getWorkDirectory(String)</B></A> - \r
1613 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
1614 <DD>&nbsp;\r
1615 <DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#getWorkDirectory()"><B>getWorkDirectory()</B></A> - \r
1616 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
1617 <DD>&nbsp;\r
1618 <DT><A HREF="../compbio/engine/Configurator.html#getWorkDirectory(java.lang.String)"><B>getWorkDirectory(String)</B></A> - \r
1619 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
1620 <DD>&nbsp;\r
1621 <DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#getWorkDirectory(java.lang.String)"><B>getWorkDirectory(String)</B></A> - \r
1622 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
1623 <DD>&nbsp;\r
1624 <DT><A HREF="../compbio/engine/local/LocalRunner.html#getWorkDirectory()"><B>getWorkDirectory()</B></A> - \r
1625 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
1626 <DD>&nbsp;\r
1627 <DT><A HREF="../compbio/engine/SyncExecutor.html#getWorkDirectory()"><B>getWorkDirectory()</B></A> - \r
1628 Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
1629 <DD>&nbsp;\r
1630 <DT><A HREF="../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder"><B>GlobPlot</B></A> - Class in <A HREF="../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A><DD>./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame
1631
1632  FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file'
1633  Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file'
1634
1635  Hard-coded values are 10 15 74 4 5.<DT><A HREF="../compbio/runner/disorder/GlobPlot.html#GlobPlot()"><B>GlobPlot()</B></A> - \r
1636 Constructor for class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>\r
1637 <DD>&nbsp;\r
1638 <DT><A HREF="../compbio/ws/client/Services.html#GLOBPLOT_INFO"><B>GLOBPLOT_INFO</B></A> - \r
1639 Static variable in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
1640 <DD>&nbsp;\r
1641 <DT><A HREF="../compbio/ws/server/GlobPlotWS.html" title="class in compbio.ws.server"><B>GlobPlotWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/GlobPlotWS.html#GlobPlotWS()"><B>GlobPlotWS()</B></A> - \r
1642 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/GlobPlotWS.html" title="class in compbio.ws.server">GlobPlotWS</A>\r
1643 <DD>&nbsp;\r
1644 </DL>\r
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