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/JManagement.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
  96 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>\r
  97 <DD>Stop running the job <code>jobId</code> 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/ClustalOWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
 123 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
 124 <DD>&nbsp;\r
 125 <DT><A HREF="../compbio/ws/server/ClustalWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
 126 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 127 <DD>&nbsp;\r
 128 <DT><A HREF="../compbio/ws/server/GenericMetadataService.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
 129 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A>\r
 130 <DD>&nbsp;\r
 131 <DT><A HREF="../compbio/ws/server/MafftWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
 132 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
 133 <DD>&nbsp;\r
 134 <DT><A HREF="../compbio/ws/server/MuscleWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
 135 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
 136 <DD>&nbsp;\r
 137 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
 138 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
 139 <DD>&nbsp;\r
 140 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
 141 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
 142 <DD>&nbsp;\r
 143 <DT><A HREF="../compbio/ws/server/WSUtil.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
 144 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
 145 <DD>&nbsp;\r
 146 <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
 147 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
 148 <DD>&nbsp;\r
 149 <DT><A HREF="../compbio/ws/client/WSTester.html#checkService(compbio.ws.client.Services)"><B>checkService(Services)</B></A> - \r
 150 Method in class compbio.ws.client.<A HREF="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A>\r
 151 <DD>Test JABA web service\r
 152 <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 a string data together with the position in a file for
 153  the next read operation.<DT><A HREF="../compbio/metadata/ChunkHolder.html#ChunkHolder(java.lang.String, long)"><B>ChunkHolder(String, long)</B></A> - \r
 154 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
 155 <DD>&nbsp;\r
 156 <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><B>Deprecated.</B>&nbsp;<DT><A HREF="../compbio/engine/Cleaner.html#Cleaner()"><B>Cleaner()</B></A> - \r
 157 Constructor for class compbio.engine.<A HREF="../compbio/engine/Cleaner.html" title="class in compbio.engine">Cleaner</A>\r
 158 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 159 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#cleanProteinSequence(java.lang.String)"><B>cleanProteinSequence(String)</B></A> - \r
 160 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 161 <DD>Remove all non AA chars from the sequence\r
 162 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#cleanSequence(java.lang.String)"><B>cleanSequence(String)</B></A> - \r
 163 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 164 <DD>Removes all whitespace chars in the sequence string\r
 165 <DT><A HREF="../compbio/engine/AsyncExecutor.html#cleanup(java.lang.String)"><B>cleanup(String)</B></A> - \r
 166 Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
 167 <DD>Remove all files and a job directory for a jobid.\r
 168 <DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#cleanup(java.lang.String)"><B>cleanup(String)</B></A> - \r
 169 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
 170 <DD>&nbsp;\r
 171 <DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#cleanup()"><B>cleanup()</B></A> - \r
 172 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
 173 <DD>&nbsp;\r
 174 <DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#cleanup(java.lang.String)"><B>cleanup(String)</B></A> - \r
 175 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
 176 <DD>&nbsp;\r
 177 <DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#cleanup(compbio.engine.client.ConfiguredExecutable)"><B>cleanup(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
 178 Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A>\r
 179 <DD>&nbsp;\r
 180 <DT><A HREF="../compbio/engine/local/LocalRunner.html#cleanup()"><B>cleanup()</B></A> - \r
 181 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
 182 <DD>&nbsp;\r
 183 <DT><A HREF="../compbio/engine/SyncExecutor.html#cleanup()"><B>cleanup()</B></A> - \r
 184 Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
 185 <DD>Clean up after the job\r
 186 <DT><A HREF="../compbio/data/sequence/FastaReader.html#close()"><B>close()</B></A> - \r
 187 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</A>\r
 188 <DD>Call this method to close the connection to the input file if you want to
 189  free up the resources.\r
 190 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#close()"><B>close()</B></A> - \r
 191 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
 192 <DD>&nbsp;\r
 193 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#closeSilently(java.util.logging.Logger, java.io.Closeable)"><B>closeSilently(Logger, Closeable)</B></A> - \r
 194 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 195 <DD>Closes the Closable and logs the exception if any\r
 196 <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
 197 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
 198 <DD>&nbsp;\r
 199 <DT><A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa"><B>ClustalO</B></A> - Class in <A HREF="../compbio/runner/msa/package-summary.html">compbio.runner.msa</A><DD>&nbsp;<DT><A HREF="../compbio/runner/msa/ClustalO.html#ClustalO()"><B>ClustalO()</B></A> - \r
 200 Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>\r
 201 <DD>--threads=<n> Number of processors to use
 202
 203  -l, --log=<file> Log all non-essential output to this file\r
 204 <DT><A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server"><B>ClustalOWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/ClustalOWS.html#ClustalOWS()"><B>ClustalOWS()</B></A> - \r
 205 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
 206 <DD>&nbsp;\r
 207 <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
 208 Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
 209 <DD>&nbsp;\r
 210 <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
 211 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 212 <DD>&nbsp;\r
 213 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html#CLUSTER_STAT_IN_SEC"><B>CLUSTER_STAT_IN_SEC</B></A> - \r
 214 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
 215 <DD>&nbsp;\r
 216 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#CLUSTER_TASK_ID_PREFIX"><B>CLUSTER_TASK_ID_PREFIX</B></A> - \r
 217 Static variable in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 218 <DD>&nbsp;\r
 219 <DT><A HREF="../compbio/engine/Configurator.html#CLUSTER_WORK_DIRECTORY"><B>CLUSTER_WORK_DIRECTORY</B></A> - \r
 220 Static variable 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/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
 223 Constructor for class compbio.engine.<A HREF="../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>\r
 224 <DD>&nbsp;\r
 225 <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
 226 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
 227 <DD>&nbsp;\r
 228 <DT><A HREF="../compbio/runner/disorder/Disembl.html#COILS_EXPECTATION_THRESHOLD"><B>COILS_EXPECTATION_THRESHOLD</B></A> - \r
 229 Variable in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>\r
 230 <DD>For the region to be considered disordered the values must exceed these\r
 231 <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
 232 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 233 <DD>&nbsp;\r
 234 <DT><A HREF="../compbio/pipeline/_jpred/Hit.EvalueComporator.html#compare(compbio.pipeline._jpred.Hit, compbio.pipeline._jpred.Hit)"><B>compare(Hit, Hit)</B></A> - \r
 235 Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Hit.EvalueComporator.html" title="class in compbio.pipeline._jpred">Hit.EvalueComporator</A>\r
 236 <DD>&nbsp;\r
 237 <DT><A HREF="../compbio/pipeline/_jpred/Hit.NumberComporator.html#compare(compbio.pipeline._jpred.Hit, compbio.pipeline._jpred.Hit)"><B>compare(Hit, Hit)</B></A> - \r
 238 Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Hit.NumberComporator.html" title="class in compbio.pipeline._jpred">Hit.NumberComporator</A>\r
 239 <DD>&nbsp;\r
 240 <DT><A HREF="../compbio/data/sequence/Range.html#compareTo(compbio.data.sequence.Range)"><B>compareTo(Range)</B></A> - \r
 241 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>\r
 242 <DD>&nbsp;\r
 243 <DT><A HREF="../compbio/data/sequence/Score.html#compareTo(compbio.data.sequence.Score)"><B>compareTo(Score)</B></A> - \r
 244 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
 245 <DD>&nbsp;\r
 246 <DT><A HREF="../compbio/engine/FilePuller.html#compareTo(java.util.concurrent.Delayed)"><B>compareTo(Delayed)</B></A> - \r
 247 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
 248 <DD>&nbsp;\r
 249 <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>Web Service interfaces for JAva Bioinformatics Analysis Web Services.<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/engine/conf/PropertyHelperManager.html#confDir"><B>confDir</B></A> - \r
 250 Static variable in class compbio.engine.conf.<A HREF="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</A>\r
 251 <DD>&nbsp;\r
 252 <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
 253 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 254 <DD>&nbsp;\r
 255 <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
 256 Constructor for class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
 257 <DD>&nbsp;\r
 258 <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
 259 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
 260 <DD>&nbsp;\r
 261 <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
 262 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
 263 <DD>&nbsp;\r
 264 <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
 265 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
 266 <DD>&nbsp;\r
 267 <DT><A HREF="../compbio/ws/client/AAConClient.html#connect()"><B>connect()</B></A> - \r
 268 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/AAConClient.html" title="class in compbio.ws.client">AAConClient</A>\r
 269 <DD>Connects to a AACon web service by the host and the service name\r
 270 <DT><A HREF="../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Services)"><B>connect(String, Services)</B></A> - \r
 271 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
 272 <DD>Connects to a web service by the host and the service name web service
 273  type\r
 274 <DT><A HREF="../compbio/ws/client/Jws2Client.html#connectToRegistry(java.lang.String)"><B>connectToRegistry(String)</B></A> - \r
 275 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
 276 <DD>Get a connection of JABAWS registry\r
 277 <DT><A HREF="../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence"><B>ConservationMethod</B></A> - Enum in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Enumeration listing of all the supported methods.<DT><A HREF="../compbio/stat/servlet/StatisticCollector.html#contextDestroyed(javax.servlet.ServletContextEvent)"><B>contextDestroyed(ServletContextEvent)</B></A> - \r
 278 Method in class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</A>\r
 279 <DD>&nbsp;\r
 280 <DT><A HREF="../compbio/ws/server/ShutdownEngines.html#contextDestroyed(javax.servlet.ServletContextEvent)"><B>contextDestroyed(ServletContextEvent)</B></A> - \r
 281 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ShutdownEngines.html" title="class in compbio.ws.server">ShutdownEngines</A>\r
 282 <DD>&nbsp;\r
 283 <DT><A HREF="../compbio/stat/servlet/StatisticCollector.html#contextInitialized(javax.servlet.ServletContextEvent)"><B>contextInitialized(ServletContextEvent)</B></A> - \r
 284 Method in class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</A>\r
 285 <DD>&nbsp;\r
 286 <DT><A HREF="../compbio/ws/server/ShutdownEngines.html#contextInitialized(javax.servlet.ServletContextEvent)"><B>contextInitialized(ServletContextEvent)</B></A> - \r
 287 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ShutdownEngines.html" title="class in compbio.ws.server">ShutdownEngines</A>\r
 288 <DD>&nbsp;\r
 289 <DT><A HREF="../compbio/engine/client/Util.html#convertToAbsolute(java.lang.String)"><B>convertToAbsolute(String)</B></A> - \r
 290 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 291 <DD>&nbsp;\r
 292 <DT><A HREF="../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)"><B>copyAndValidateRConfig(RunnerConfig&lt;?&gt;)</B></A> - \r
 293 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 294 <DD>&nbsp;\r
 295 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#countMatchesInSequence(java.lang.String, java.lang.String)"><B>countMatchesInSequence(String, String)</B></A> - \r
 296 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
 297 <DD>&nbsp;\r
 298 <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
 299 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
 300 <DD>&nbsp;\r
 301 <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
 302 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
 303 <DD>Align a list of sequences with options.\r
 304 <DT><A HREF="../compbio/ws/server/_MsaService.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;T&gt;&gt;)</B></A> - \r
 305 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/_MsaService.html" title="class in compbio.ws.server">_MsaService</A>\r
 306 <DD>&nbsp;\r
 307 <DT><A HREF="../compbio/ws/server/ClustalOWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;ClustalO&gt;&gt;)</B></A> - \r
 308 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
 309 <DD>&nbsp;\r
 310 <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
 311 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 312 <DD>&nbsp;\r
 313 <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
 314 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
 315 <DD>&nbsp;\r
 316 <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
 317 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
 318 <DD>&nbsp;\r
 319 <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
 320 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
 321 <DD>&nbsp;\r
 322 <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
 323 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
 324 <DD>&nbsp;\r
 325 <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
 326 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
 327 <DD>&nbsp;\r
 328 <DT><A HREF="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws"><B>CustomAnalize</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/CustomAnalize.html#CustomAnalize()"><B>CustomAnalize()</B></A> - \r
 329 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</A>\r
 330 <DD>&nbsp;\r
 331 <DT><A HREF="../compbio/data/msa/SequenceAnnotation.html#customAnalize(java.util.List, java.util.List)"><B>customAnalize(List&lt;FastaSequence&gt;, List&lt;Option&lt;T&gt;&gt;)</B></A> - \r
 332 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>\r
 333 <DD>Analyse the sequences according to custom settings defined in options
 334  list.\r
 335 <DT><A HREF="../compbio/ws/server/DisemblWS.html#customAnalize(java.util.List, java.util.List)"><B>customAnalize(List&lt;FastaSequence&gt;, List&lt;Option&lt;Disembl&gt;&gt;)</B></A> - \r
 336 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/DisemblWS.html" title="class in compbio.ws.server">DisemblWS</A>\r
 337 <DD>&nbsp;\r
 338 <DT><A HREF="../compbio/ws/server/GlobPlotWS.html#customAnalize(java.util.List, java.util.List)"><B>customAnalize(List&lt;FastaSequence&gt;, List&lt;Option&lt;GlobPlot&gt;&gt;)</B></A> - \r
 339 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/GlobPlotWS.html" title="class in compbio.ws.server">GlobPlotWS</A>\r
 340 <DD>&nbsp;\r
 341 <DT><A HREF="../compbio/ws/server/SequenceAnnotationService.html#customAnalize(java.util.List, java.util.List)"><B>customAnalize(List&lt;FastaSequence&gt;, List&lt;Option&lt;T&gt;&gt;)</B></A> - \r
 342 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</A>\r
 343 <DD>&nbsp;\r
 344 <DT><A HREF="../compbio/data/msa/jaxws/CustomAnalizeResponse.html" title="class in compbio.data.msa.jaxws"><B>CustomAnalizeResponse</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/CustomAnalizeResponse.html#CustomAnalizeResponse()"><B>CustomAnalizeResponse()</B></A> - \r
 345 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalizeResponse.html" title="class in compbio.data.msa.jaxws">CustomAnalizeResponse</A>\r
 346 <DD>&nbsp;\r
 347 </DL>\r
 348 <HR>\r
 349 \r
 350 \r
 351 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 352 <A NAME="navbar_bottom"><!-- --></A>\r
 353 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 354 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 355 <TR>\r
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 358 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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 360   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 361   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
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 363   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
 364   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 365   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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 367   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 368   </TR>\r
 369 </TABLE>\r
 370 </TD>\r
 371 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 372 </EM>\r
 373 </TD>\r
 374 </TR>\r
 375 \r
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 377 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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 380 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 381   <A HREF="../index.html?index-filesindex-3.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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 383 &nbsp;<SCRIPT type="text/javascript">\r
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 386     document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
 387   }\r
 388   //-->\r
 389 </SCRIPT>\r
 390 <NOSCRIPT>\r
 391   <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
 392 </NOSCRIPT>\r
 393 \r
 394 \r
 395 </FONT></TD>\r
 396 </TR>\r
 397 </TABLE>\r
 398 <A NAME="skip-navbar_bottom"></A>\r
 399 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 400 \r
 401 <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
 402 \r
 403 </BODY>\r
 404 </HTML>\r