website/full_javadoc/index-files/index-3.html

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  82 <A NAME="_C_"><!-- --></A><H2>\r
  83 <B>C</B></H2>\r
  84 <DL>\r
  85 <DT><A HREF="../compbio/engine/local/ExecutableWrapper.html#call()"><B>call()</B></A> - \r
  86 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A>\r
  87 <DD>It is vital that output and error streams are captured immediately for
  88  this call() to succeed.\r
  89 <DT><A HREF="../compbio/engine/local/LocalExecutorService.html#canAcceptMoreWork()"><B>canAcceptMoreWork()</B></A> - \r
  90 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</A>\r
  91 <DD>If the Executor queue is empty\r
  92 <DT><A HREF="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws"><B>CancelJob</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/CancelJob.html#CancelJob()"><B>CancelJob()</B></A> - \r
  93 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws">CancelJob</A>\r
  94 <DD>&nbsp;\r
  95 <DT><A HREF="../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
  96 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
  97 <DD>Stop running job but leave its output untouched\r
  98 <DT><A HREF="../compbio/engine/AsyncExecutor.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
  99 Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
 100 <DD>Stop running job.\r
 101 <DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
 102 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
 103 <DD>&nbsp;\r
 104 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html#cancelJob(java.lang.String, compbio.engine.cluster.drmaa.ClusterSession)"><B>cancelJob(String, ClusterSession)</B></A> - \r
 105 Static method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterUtil</A>\r
 106 <DD>&nbsp;\r
 107 <DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#cancelJob()"><B>cancelJob()</B></A> - \r
 108 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
 109 <DD>&nbsp;\r
 110 <DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
 111 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
 112 <DD>&nbsp;\r
 113 <DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#cancelJob(java.util.concurrent.Future, java.lang.String)"><B>cancelJob(Future&lt;ConfiguredExecutable&lt;?&gt;&gt;, String)</B></A> - \r
 114 Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A>\r
 115 <DD>&nbsp;\r
 116 <DT><A HREF="../compbio/engine/local/LocalRunner.html#cancelJob()"><B>cancelJob()</B></A> - \r
 117 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
 118 <DD>&nbsp;\r
 119 <DT><A HREF="../compbio/engine/SyncExecutor.html#cancelJob()"><B>cancelJob()</B></A> - \r
 120 Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
 121 <DD>Stops running job.\r
 122 <DT><A HREF="../compbio/ws/server/ClustalWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
 123 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 124 <DD>&nbsp;\r
 125 <DT><A HREF="../compbio/ws/server/MafftWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
 126 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
 127 <DD>&nbsp;\r
 128 <DT><A HREF="../compbio/ws/server/MuscleWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
 129 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
 130 <DD>&nbsp;\r
 131 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
 132 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
 133 <DD>&nbsp;\r
 134 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
 135 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
 136 <DD>&nbsp;\r
 137 <DT><A HREF="../compbio/ws/server/WSUtil.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
 138 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
 139 <DD>&nbsp;\r
 140 <DT><A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws"><B>CancelJobResponse</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/CancelJobResponse.html#CancelJobResponse()"><B>CancelJobResponse()</B></A> - \r
 141 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws">CancelJobResponse</A>\r
 142 <DD>&nbsp;\r
 143 <DT><A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>ChunkHolder</B></A> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Represents a chunk of string data together with the position in a file from
 144  where corresponding to of the data.<DT><A HREF="../compbio/metadata/ChunkHolder.html#ChunkHolder(java.lang.String, long)"><B>ChunkHolder(String, long)</B></A> - \r
 145 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
 146 <DD>&nbsp;\r
 147 <DT><A HREF="../compbio/engine/Cleaner.html" title="class in compbio.engine"><B>Cleaner</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>&nbsp;<DT><A HREF="../compbio/engine/Cleaner.html#Cleaner()"><B>Cleaner()</B></A> - \r
 148 Constructor for class compbio.engine.<A HREF="../compbio/engine/Cleaner.html" title="class in compbio.engine">Cleaner</A>\r
 149 <DD>&nbsp;\r
 150 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#cleanSequence(java.lang.String)"><B>cleanSequence(String)</B></A> - \r
 151 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 152 <DD>Removes all whitespace chars in the sequence string\r
 153 <DT><A HREF="../compbio/engine/AsyncExecutor.html#cleanup(java.lang.String)"><B>cleanup(String)</B></A> - \r
 154 Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
 155 <DD>Remove all files and a job directory for a jobid.\r
 156 <DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#cleanup(java.lang.String)"><B>cleanup(String)</B></A> - \r
 157 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
 158 <DD>&nbsp;\r
 159 <DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#cleanup()"><B>cleanup()</B></A> - \r
 160 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
 161 <DD>&nbsp;\r
 162 <DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#cleanup(java.lang.String)"><B>cleanup(String)</B></A> - \r
 163 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
 164 <DD>&nbsp;\r
 165 <DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#cleanup(compbio.engine.client.ConfiguredExecutable)"><B>cleanup(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
 166 Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A>\r
 167 <DD>&nbsp;\r
 168 <DT><A HREF="../compbio/engine/local/LocalRunner.html#cleanup()"><B>cleanup()</B></A> - \r
 169 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
 170 <DD>&nbsp;\r
 171 <DT><A HREF="../compbio/engine/SyncExecutor.html#cleanup()"><B>cleanup()</B></A> - \r
 172 Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
 173 <DD>Clean up after the job\r
 174 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#close()"><B>close()</B></A> - \r
 175 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
 176 <DD>&nbsp;\r
 177 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>ClustalAlignmentUtil</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Tools to read and write clustal formated files<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#ClustalAlignmentUtil()"><B>ClustalAlignmentUtil()</B></A> - \r
 178 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
 179 <DD>&nbsp;\r
 180 <DT><A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa"><B>ClustalW</B></A> - Class in <A HREF="../compbio/runner/msa/package-summary.html">compbio.runner.msa</A><DD>&nbsp;<DT><A HREF="../compbio/runner/msa/ClustalW.html#ClustalW()"><B>ClustalW()</B></A> - \r
 181 Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
 182 <DD>&nbsp;\r
 183 <DT><A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server"><B>ClustalWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/ClustalWS.html#ClustalWS()"><B>ClustalWS()</B></A> - \r
 184 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 185 <DD>&nbsp;\r
 186 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html#CLUSTER_STAT_IN_SEC"><B>CLUSTER_STAT_IN_SEC</B></A> - \r
 187 Static variable in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterUtil</A>\r
 188 <DD>&nbsp;\r
 189 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#CLUSTER_TASK_ID_PREFIX"><B>CLUSTER_TASK_ID_PREFIX</B></A> - \r
 190 Static variable in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 191 <DD>&nbsp;\r
 192 <DT><A HREF="../compbio/engine/Configurator.html#CLUSTER_WORK_DIRECTORY"><B>CLUSTER_WORK_DIRECTORY</B></A> - \r
 193 Static variable in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
 194 <DD>&nbsp;\r
 195 <DT><A HREF="../compbio/engine/ClusterJobId.html" title="class in compbio.engine"><B>ClusterJobId</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>&nbsp;<DT><A HREF="../compbio/engine/ClusterJobId.html#ClusterJobId(java.lang.String)"><B>ClusterJobId(String)</B></A> - \r
 196 Constructor for class compbio.engine.<A HREF="../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>\r
 197 <DD>&nbsp;\r
 198 <DT><A HREF="../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client"><B>ClusterNativeSpecExecutable</B></A>&lt;<A HREF="../compbio/engine/client/ClusterNativeSpecExecutable.html" title="type parameter in ClusterNativeSpecExecutable">T</A>&gt; - Interface in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>&nbsp;<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa"><B>ClusterSession</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD>&nbsp;<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa"><B>ClusterUtil</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD>&nbsp;<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html#ClusterUtil()"><B>ClusterUtil()</B></A> - \r
 199 Constructor for class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterUtil</A>\r
 200 <DD>&nbsp;\r
 201 <DT><A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client"><B>CommandBuilder</B></A>&lt;<A HREF="../compbio/engine/client/CommandBuilder.html" title="type parameter in CommandBuilder">T</A>&gt; - Class in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>&nbsp;<DT><A HREF="../compbio/engine/client/CommandBuilder.html#CommandBuilder(java.lang.String)"><B>CommandBuilder(String)</B></A> - \r
 202 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 203 <DD>&nbsp;\r
 204 <DT><A HREF="../compbio/engine/FilePuller.html#compareTo(java.util.concurrent.Delayed)"><B>compareTo(Delayed)</B></A> - \r
 205 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
 206 <DD>&nbsp;\r
 207 <DT><A HREF="../compbio/data/_structure/package-summary.html"><B>compbio.data._structure</B></A> - package compbio.data._structure<DD>&nbsp;<DT><A HREF="../compbio/data/msa/package-summary.html"><B>compbio.data.msa</B></A> - package compbio.data.msa<DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/package-summary.html"><B>compbio.data.msa.jaxws</B></A> - package compbio.data.msa.jaxws<DD>&nbsp;<DT><A HREF="../compbio/pipeline/_jpred/package-summary.html"><B>compbio.pipeline._jpred</B></A> - package compbio.pipeline._jpred<DD>&nbsp;<DT><A HREF="../compbio/runner/_jpred/package-summary.html"><B>compbio.runner._jpred</B></A> - package compbio.runner._jpred<DD>&nbsp;<DT><A HREF="../compbio/runner/psiblast/package-summary.html"><B>compbio.runner.psiblast</B></A> - package compbio.runner.psiblast<DD>&nbsp;<DT><A HREF="../compbio/ws/client/package-summary.html"><B>compbio.ws.client</B></A> - package compbio.ws.client<DD>&nbsp;<DT><A HREF="../compbio/ws/server/package-summary.html"><B>compbio.ws.server</B></A> - package compbio.ws.server<DD>&nbsp;<DT><A HREF="../compbio/engine/conf/PropertyHelperManager.html#confDir"><B>confDir</B></A> - \r
 208 Static variable in class compbio.engine.conf.<A HREF="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</A>\r
 209 <DD>&nbsp;\r
 210 <DT><A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client"><B>ConfExecutable</B></A>&lt;<A HREF="../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt; - Class in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>&nbsp;<DT><A HREF="../compbio/engine/client/ConfExecutable.html#ConfExecutable(compbio.engine.client.Executable, java.lang.String)"><B>ConfExecutable(Executable&lt;T&gt;, String)</B></A> - \r
 211 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 212 <DD>&nbsp;\r
 213 <DT><A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine"><B>Configurator</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>&nbsp;<DT><A HREF="../compbio/engine/Configurator.html#Configurator()"><B>Configurator()</B></A> - \r
 214 Constructor for class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
 215 <DD>&nbsp;\r
 216 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client"><B>ConfiguredExecutable</B></A>&lt;<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="type parameter in ConfiguredExecutable">T</A>&gt; - Interface in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>&nbsp;<DT><A HREF="../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable)"><B>configureExecutable(Executable&lt;T&gt;)</B></A> - \r
 217 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
 218 <DD>&nbsp;\r
 219 <DT><A HREF="../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, java.util.List)"><B>configureExecutable(Executable&lt;T&gt;, List&lt;FastaSequence&gt;)</B></A> - \r
 220 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
 221 <DD>&nbsp;\r
 222 <DT><A HREF="../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, compbio.engine.client.Executable.ExecProvider)"><B>configureExecutable(Executable&lt;T&gt;, Executable.ExecProvider)</B></A> - \r
 223 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
 224 <DD>&nbsp;\r
 225 <DT><A HREF="../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Jws2Client.Services)"><B>connect(String, Jws2Client.Services)</B></A> - \r
 226 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
 227 <DD>Connects to a web service by the host and the service name\r
 228 <DT><A HREF="../compbio/engine/client/Util.html#convertToAbsolute(java.lang.String)"><B>convertToAbsolute(String)</B></A> - \r
 229 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 230 <DD>&nbsp;\r
 231 <DT><A HREF="../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)"><B>copyAndValidateRConfig(RunnerConfig&lt;?&gt;)</B></A> - \r
 232 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 233 <DD>&nbsp;\r
 234 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#countMatchesInSequence(java.lang.String, java.lang.String)"><B>countMatchesInSequence(String, String)</B></A> - \r
 235 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
 236 <DD>&nbsp;\r
 237 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws"><B>CustomAlign</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/CustomAlign.html#CustomAlign()"><B>CustomAlign()</B></A> - \r
 238 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>\r
 239 <DD>&nbsp;\r
 240 <DT><A HREF="../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;T&gt;&gt;)</B></A> - \r
 241 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
 242 <DD>Align a list of sequences with options.\r
 243 <DT><A HREF="../compbio/ws/server/ClustalWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;ClustalW&gt;&gt;)</B></A> - \r
 244 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 245 <DD>&nbsp;\r
 246 <DT><A HREF="../compbio/ws/server/MafftWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;Mafft&gt;&gt;)</B></A> - \r
 247 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
 248 <DD>&nbsp;\r
 249 <DT><A HREF="../compbio/ws/server/MuscleWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;Muscle&gt;&gt;)</B></A> - \r
 250 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
 251 <DD>&nbsp;\r
 252 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;Probcons&gt;&gt;)</B></A> - \r
 253 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
 254 <DD>&nbsp;\r
 255 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;Tcoffee&gt;&gt;)</B></A> - \r
 256 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
 257 <DD>&nbsp;\r
 258 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws"><B>CustomAlignResponse</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/CustomAlignResponse.html#CustomAlignResponse()"><B>CustomAlignResponse()</B></A> - \r
 259 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws">CustomAlignResponse</A>\r
 260 <DD>&nbsp;\r
 261 </DL>\r
 262 <HR>\r
 263 \r
 264 \r
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 266 <A NAME="navbar_bottom"><!-- --></A>\r
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 285 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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 294 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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