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  75 <h2 class="title">C</h2>
  76 <dl>
  77 <dt><span class="memberNameLink"><a href="../compbio/engine/PulledFileCache.html#CACHE">CACHE</a></span> - Static variable in class compbio.engine.<a href="../compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</a></dt>
  78 <dd>&nbsp;</dd>
  79 <dt><span class="memberNameLink"><a href="../compbio/engine/local/ExecutableWrapper.html#call--">call()</a></span> - Method in class compbio.engine.local.<a href="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</a></dt>
  80 <dd>
  81 <div class="block">It is vital that output and error streams are captured immediately for
  82  this call() to succeed.</div>
  83 </dd>
  84 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalExecutorService.html#canAcceptMoreWork--">canAcceptMoreWork()</a></span> - Method in class compbio.engine.local.<a href="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</a></dt>
  85 <dd>
  86 <div class="block">If the Executor queue is empty</div>
  87 </dd>
  88 <dt><a href="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">CancelJob</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
  89 <dd>&nbsp;</dd>
  90 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CancelJob.html#CancelJob--">CancelJob()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws">CancelJob</a></dt>
  91 <dd>&nbsp;</dd>
  92 <dt><span class="memberNameLink"><a href="../compbio/data/msa/JManagement.html#cancelJob-java.lang.String-">cancelJob(String)</a></span> - Method in interface compbio.data.msa.<a href="../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</a></dt>
  93 <dd>
  94 <div class="block">Stop running the job <code>jobId</code> but leave its output untouched</div>
  95 </dd>
  96 <dt><span class="memberNameLink"><a href="../compbio/engine/AsyncExecutor.html#cancelJob-java.lang.String-">cancelJob(String)</a></span> - Method in interface compbio.engine.<a href="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</a></dt>
  97 <dd>
  98 <div class="block">Stop running job.</div>
  99 </dd>
 100 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/AsyncClusterRunner.html#cancelJob-java.lang.String-">cancelJob(String)</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/AsyncClusterRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncClusterRunner</a></dt>
 101 <dd>&nbsp;</dd>
 102 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#cancelJob-java.lang.String-">cancelJob(String)</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</a></dt>
 103 <dd>&nbsp;</dd>
 104 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterEngineUtil.html#cancelJob-java.lang.String-compbio.engine.cluster.drmaa.ClusterSession-">cancelJob(String, ClusterSession)</a></span> - Static method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterEngineUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterEngineUtil</a></dt>
 105 <dd>&nbsp;</dd>
 106 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#cancelJob-java.lang.String-">cancelJob(String)</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterRunner.html" title="class in compbio.engine.cluster.drmaa">ClusterRunner</a></dt>
 107 <dd>&nbsp;</dd>
 108 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#cancelJob--">cancelJob()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterRunner.html" title="class in compbio.engine.cluster.drmaa">ClusterRunner</a></dt>
 109 <dd>&nbsp;</dd>
 110 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterUtil.html#cancelJob-java.lang.String-compbio.engine.cluster.drmaa.ClusterSession-">cancelJob(String, ClusterSession)</a></span> - 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></dt>
 111 <dd>&nbsp;</dd>
 112 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#cancelJob-java.lang.String-">cancelJob(String)</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</a></dt>
 113 <dd>&nbsp;</dd>
 114 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#cancelJob--">cancelJob()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</a></dt>
 115 <dd>&nbsp;</dd>
 116 <dt><span class="memberNameLink"><a href="../compbio/engine/local/AsyncLocalRunner.html#cancelJob-java.lang.String-">cancelJob(String)</a></span> - Method in class compbio.engine.local.<a href="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</a></dt>
 117 <dd>&nbsp;</dd>
 118 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalEngineUtil.html#cancelJob-java.util.concurrent.Future-java.lang.String-">cancelJob(Future&lt;ConfiguredExecutable&lt;?&gt;&gt;, String)</a></span> - Static method in class compbio.engine.local.<a href="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</a></dt>
 119 <dd>&nbsp;</dd>
 120 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalRunner.html#cancelJob--">cancelJob()</a></span> - Method in class compbio.engine.local.<a href="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</a></dt>
 121 <dd>&nbsp;</dd>
 122 <dt><span class="memberNameLink"><a href="../compbio/engine/SyncExecutor.html#cancelJob--">cancelJob()</a></span> - Method in interface compbio.engine.<a href="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</a></dt>
 123 <dd>
 124 <div class="block">Stops running job.</div>
 125 </dd>
 126 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalOWS.html#cancelJob-java.lang.String-">cancelJob(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</a></dt>
 127 <dd>&nbsp;</dd>
 128 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalWS.html#cancelJob-java.lang.String-">cancelJob(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</a></dt>
 129 <dd>&nbsp;</dd>
 130 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GenericMetadataService.html#cancelJob-java.lang.String-">cancelJob(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</a></dt>
 131 <dd>&nbsp;</dd>
 132 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GLprobsWS.html#cancelJob-java.lang.String-">cancelJob(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/GLprobsWS.html" title="class in compbio.ws.server">GLprobsWS</a></dt>
 133 <dd>&nbsp;</dd>
 134 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MafftWS.html#cancelJob-java.lang.String-">cancelJob(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</a></dt>
 135 <dd>&nbsp;</dd>
 136 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MSAprobsWS.html#cancelJob-java.lang.String-">cancelJob(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MSAprobsWS.html" title="class in compbio.ws.server">MSAprobsWS</a></dt>
 137 <dd>&nbsp;</dd>
 138 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MuscleWS.html#cancelJob-java.lang.String-">cancelJob(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</a></dt>
 139 <dd>&nbsp;</dd>
 140 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ProbconsWS.html#cancelJob-java.lang.String-">cancelJob(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</a></dt>
 141 <dd>&nbsp;</dd>
 142 <dt><span class="memberNameLink"><a href="../compbio/ws/server/TcoffeeWS.html#cancelJob-java.lang.String-">cancelJob(String)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</a></dt>
 143 <dd>&nbsp;</dd>
 144 <dt><span class="memberNameLink"><a href="../compbio/ws/server/WSUtil.html#cancelJob-java.lang.String-">cancelJob(String)</a></span> - Static method in class compbio.ws.server.<a href="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</a></dt>
 145 <dd>&nbsp;</dd>
 146 <dt><a href="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">CancelJobResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 147 <dd>&nbsp;</dd>
 148 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CancelJobResponse.html#CancelJobResponse--">CancelJobResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws">CancelJobResponse</a></dt>
 149 <dd>&nbsp;</dd>
 150 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/Totals.html#cancelled">cancelled</a></span> - Variable in class compbio.stat.servlet.util.<a href="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</a></dt>
 151 <dd>&nbsp;</dd>
 152 <dt><a href="../compbio/data/msa/Category.html" title="class in compbio.data.msa"><span class="typeNameLink">Category</span></a> - Class in <a href="../compbio/data/msa/package-summary.html">compbio.data.msa</a></dt>
 153 <dd>&nbsp;</dd>
 154 <dt><span class="memberNameLink"><a href="../compbio/data/msa/Category.html#Category-java.lang.String-java.util.Set-">Category(String, Set&lt;Services&gt;)</a></span> - Constructor for class compbio.data.msa.<a href="../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</a></dt>
 155 <dd>&nbsp;</dd>
 156 <dt><span class="memberNameLink"><a href="../compbio/data/msa/Category.html#Category--">Category()</a></span> - Constructor for class compbio.data.msa.<a href="../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</a></dt>
 157 <dd>&nbsp;</dd>
 158 <dt><span class="memberNameLink"><a href="../compbio/data/msa/Category.html#CATEGORY_ALIGNMENT">CATEGORY_ALIGNMENT</a></span> - Static variable in class compbio.data.msa.<a href="../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</a></dt>
 159 <dd>
 160 <div class="block">All of the Category names</div>
 161 </dd>
 162 <dt><span class="memberNameLink"><a href="../compbio/data/msa/Category.html#CATEGORY_CONSERVATION">CATEGORY_CONSERVATION</a></span> - Static variable in class compbio.data.msa.<a href="../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</a></dt>
 163 <dd>&nbsp;</dd>
 164 <dt><span class="memberNameLink"><a href="../compbio/data/msa/Category.html#CATEGORY_DISORDER">CATEGORY_DISORDER</a></span> - Static variable in class compbio.data.msa.<a href="../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</a></dt>
 165 <dd>&nbsp;</dd>
 166 <dt><span class="memberNameLink"><a href="../compbio/data/msa/Category.html#CATEGORY_PREDICTION">CATEGORY_PREDICTION</a></span> - Static variable in class compbio.data.msa.<a href="../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</a></dt>
 167 <dd>&nbsp;</dd>
 168 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#cbuilder">cbuilder</a></span> - Variable in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 169 <dd>
 170 <div class="block">This has to allow duplicate parameters as different options may have the
 171  same value e.g.</div>
 172 </dd>
 173 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#centStructP">centStructP</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructReader.html" title="class in compbio.data.sequence">RNAStructReader</a></dt>
 174 <dd>&nbsp;</dd>
 175 <dt><span class="memberNameLink"><a href="../compbio/engine/Job.html#cexecutable">cexecutable</a></span> - Variable in class compbio.engine.<a href="../compbio/engine/Job.html" title="class in compbio.engine">Job</a></dt>
 176 <dd>&nbsp;</dd>
 177 <dt><span class="memberNameLink"><a href="../compbio/ws/client/WSTester.html#checkService-compbio.data.msa.JABAService-compbio.ws.client.Services-">checkService(JABAService, Services)</a></span> - Method in class compbio.ws.client.<a href="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</a></dt>
 178 <dd>
 179 <div class="block">Call most of web services functions and check the output</div>
 180 </dd>
 181 <dt><span class="memberNameLink"><a href="../compbio/ws/client/WSTester.html#checkService-compbio.ws.client.Services-">checkService(Services)</a></span> - Method in class compbio.ws.client.<a href="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</a></dt>
 182 <dd>
 183 <div class="block">Test JABA web service</div>
 184 </dd>
 185 <dt><span class="memberNameLink"><a href="../compbio/metadata/ValueConstrain.html#checkValue-java.lang.String-">checkValue(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</a></dt>
 186 <dd>
 187 <div class="block">Validate that the value is within the constrain boundaries</div>
 188 </dd>
 189 <dt><span class="memberNameLink"><a href="../compbio/metadata/ChunkHolder.html#chunk">chunk</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</a></dt>
 190 <dd>&nbsp;</dd>
 191 <dt><a href="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><span class="typeNameLink">ChunkHolder</span></a> - Class in <a href="../compbio/metadata/package-summary.html">compbio.metadata</a></dt>
 192 <dd>
 193 <div class="block">Represents a chunk of a string data together with the position in a file for
 194  the next read operation.</div>
 195 </dd>
 196 <dt><span class="memberNameLink"><a href="../compbio/metadata/ChunkHolder.html#ChunkHolder--">ChunkHolder()</a></span> - Constructor for class compbio.metadata.<a href="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</a></dt>
 197 <dd>&nbsp;</dd>
 198 <dt><span class="memberNameLink"><a href="../compbio/metadata/ChunkHolder.html#ChunkHolder-java.lang.String-long-">ChunkHolder(String, long)</a></span> - Constructor for class compbio.metadata.<a href="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</a></dt>
 199 <dd>&nbsp;</dd>
 200 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#chunkSize">chunkSize</a></span> - Variable in class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
 201 <dd>&nbsp;</dd>
 202 <dt><a href="../compbio/engine/Cleaner.html" title="class in compbio.engine"><span class="typeNameLink">Cleaner</span></a> - Class in <a href="../compbio/engine/package-summary.html">compbio.engine</a></dt>
 203 <dd>&nbsp;</dd>
 204 <dt><span class="memberNameLink"><a href="../compbio/engine/Cleaner.html#Cleaner--">Cleaner()</a></span> - Constructor for class compbio.engine.<a href="../compbio/engine/Cleaner.html" title="class in compbio.engine">Cleaner</a></dt>
 205 <dd>&nbsp;</dd>
 206 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#cleanProteinSequence-java.lang.String-">cleanProteinSequence(String)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 207 <dd>
 208 <div class="block">Remove all non AA chars from the sequence</div>
 209 </dd>
 210 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#cleanSequence-java.lang.String-">cleanSequence(String)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 211 <dd>
 212 <div class="block">Removes all whitespace chars in the sequence string</div>
 213 </dd>
 214 <dt><span class="memberNameLink"><a href="../compbio/engine/AsyncExecutor.html#cleanup-java.lang.String-">cleanup(String)</a></span> - Method in interface compbio.engine.<a href="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</a></dt>
 215 <dd>
 216 <div class="block">Remove all files and a job directory for a jobid.</div>
 217 </dd>
 218 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/AsyncClusterRunner.html#cleanup-java.lang.String-">cleanup(String)</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/AsyncClusterRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncClusterRunner</a></dt>
 219 <dd>&nbsp;</dd>
 220 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#cleanup-java.lang.String-">cleanup(String)</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</a></dt>
 221 <dd>&nbsp;</dd>
 222 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#cleanup--">cleanup()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterRunner.html" title="class in compbio.engine.cluster.drmaa">ClusterRunner</a></dt>
 223 <dd>&nbsp;</dd>
 224 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#cleanup--">cleanup()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</a></dt>
 225 <dd>&nbsp;</dd>
 226 <dt><span class="memberNameLink"><a href="../compbio/engine/local/AsyncLocalRunner.html#cleanup-java.lang.String-">cleanup(String)</a></span> - Method in class compbio.engine.local.<a href="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</a></dt>
 227 <dd>&nbsp;</dd>
 228 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalEngineUtil.html#cleanup-compbio.engine.client.ConfiguredExecutable-">cleanup(ConfiguredExecutable&lt;?&gt;)</a></span> - Static method in class compbio.engine.local.<a href="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</a></dt>
 229 <dd>&nbsp;</dd>
 230 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalRunner.html#cleanup--">cleanup()</a></span> - Method in class compbio.engine.local.<a href="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</a></dt>
 231 <dd>&nbsp;</dd>
 232 <dt><span class="memberNameLink"><a href="../compbio/engine/SyncExecutor.html#cleanup--">cleanup()</a></span> - Method in interface compbio.engine.<a href="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</a></dt>
 233 <dd>
 234 <div class="block">Clean up after the job</div>
 235 </dd>
 236 <dt><span class="memberNameLink"><a href="../compbio/engine/PulledFileCache.html#clear--">clear()</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</a></dt>
 237 <dd>&nbsp;</dd>
 238 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatDB.html#clearStatTable--">clearStatTable()</a></span> - Static method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</a></dt>
 239 <dd>&nbsp;</dd>
 240 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/FastaReader.html#close--">close()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</a></dt>
 241 <dd>
 242 <div class="block">Call this method to close the connection to the input file if you want to
 243  free up the resources.</div>
 244 </dd>
 245 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#close--">close()</a></span> - Method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</a></dt>
 246 <dd>&nbsp;</dd>
 247 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#closeSilently-java.util.logging.Logger-java.io.Closeable-">closeSilently(Logger, Closeable)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 248 <dd>
 249 <div class="block">Closes the Closable and logs the exception if any</div>
 250 </dd>
 251 <dt><span class="memberNameLink"><a href="../compbio/engine/local/StreamGobbler.html#closeSilently-java.io.Closeable-">closeSilently(Closeable)</a></span> - Static method in class compbio.engine.local.<a href="../compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local">StreamGobbler</a></dt>
 252 <dd>&nbsp;</dd>
 253 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#CLUSTAL_INFO">CLUSTAL_INFO</a></span> - Static variable in enum compbio.ws.client.<a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></dt>
 254 <dd>&nbsp;</dd>
 255 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#CLUSTAL_OMEGA_INFO">CLUSTAL_OMEGA_INFO</a></span> - Static variable in enum compbio.ws.client.<a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></dt>
 256 <dd>&nbsp;</dd>
 257 <dt><a href="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><span class="typeNameLink">ClustalAlignmentUtil</span></a> - Class in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
 258 <dd>
 259 <div class="block">Tools to read and write clustal formated files</div>
 260 </dd>
 261 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ClustalAlignmentUtil.html#ClustalAlignmentUtil--">ClustalAlignmentUtil()</a></span> - Constructor for class compbio.data.sequence.<a href="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</a></dt>
 262 <dd>&nbsp;</dd>
 263 <dt><a href="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa"><span class="typeNameLink">ClustalO</span></a> - Class in <a href="../compbio/runner/msa/package-summary.html">compbio.runner.msa</a></dt>
 264 <dd>&nbsp;</dd>
 265 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/ClustalO.html#ClustalO--">ClustalO()</a></span> - Constructor for class compbio.runner.msa.<a href="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a></dt>
 266 <dd>
 267 <div class="block">--threads=<n> Number of processors to use
 268
 269  -l, --log=<file> Log all non-essential output to this file</div>
 270 </dd>
 271 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalOWS.html#clustalOptions">clustalOptions</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</a></dt>
 272 <dd>&nbsp;</dd>
 273 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalWS.html#clustalOptions">clustalOptions</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</a></dt>
 274 <dd>&nbsp;</dd>
 275 <dt><a href="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server"><span class="typeNameLink">ClustalOWS</span></a> - Class in <a href="../compbio/ws/server/package-summary.html">compbio.ws.server</a></dt>
 276 <dd>&nbsp;</dd>
 277 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalOWS.html#ClustalOWS--">ClustalOWS()</a></span> - Constructor for class compbio.ws.server.<a href="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</a></dt>
 278 <dd>&nbsp;</dd>
 279 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalOWS.html#clustalPresets">clustalPresets</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</a></dt>
 280 <dd>&nbsp;</dd>
 281 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalWS.html#clustalPresets">clustalPresets</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</a></dt>
 282 <dd>&nbsp;</dd>
 283 <dt><span class="memberNameLink"><a href="../compbio/ws/client/WSTester.html#clustalRNAAlignment">clustalRNAAlignment</a></span> - Static variable in class compbio.ws.client.<a href="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</a></dt>
 284 <dd>&nbsp;</dd>
 285 <dt><a href="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa"><span class="typeNameLink">ClustalW</span></a> - Class in <a href="../compbio/runner/msa/package-summary.html">compbio.runner.msa</a></dt>
 286 <dd>&nbsp;</dd>
 287 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/ClustalW.html#ClustalW--">ClustalW()</a></span> - Constructor for class compbio.runner.msa.<a href="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</a></dt>
 288 <dd>&nbsp;</dd>
 289 <dt><a href="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server"><span class="typeNameLink">ClustalWS</span></a> - Class in <a href="../compbio/ws/server/package-summary.html">compbio.ws.server</a></dt>
 290 <dd>&nbsp;</dd>
 291 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalWS.html#ClustalWS--">ClustalWS()</a></span> - Constructor for class compbio.ws.server.<a href="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</a></dt>
 292 <dd>&nbsp;</dd>
 293 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterEngineUtil.html#CLUSTER_STAT_IN_SEC">CLUSTER_STAT_IN_SEC</a></span> - Static variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterEngineUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterEngineUtil</a></dt>
 294 <dd>&nbsp;</dd>
 295 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterUtil.html#CLUSTER_STAT_IN_SEC">CLUSTER_STAT_IN_SEC</a></span> - Static variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterUtil</a></dt>
 296 <dd>&nbsp;</dd>
 297 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#CLUSTER_TASK_ID_PREFIX">CLUSTER_TASK_ID_PREFIX</a></span> - Static variable in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
 298 <dd>&nbsp;</dd>
 299 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#CLUSTER_WORK_DIRECTORY">CLUSTER_WORK_DIRECTORY</a></span> - Static variable in class compbio.engine.<a href="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></dt>
 300 <dd>&nbsp;</dd>
 301 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/StatisticCollector.html#clustercf">clustercf</a></span> - Variable in class compbio.stat.servlet.<a href="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</a></dt>
 302 <dd>&nbsp;</dd>
 303 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MainManager.html#clustercl">clustercl</a></span> - Variable in class compbio.ws.server.<a href="../compbio/ws/server/MainManager.html" title="class in compbio.ws.server">MainManager</a></dt>
 304 <dd>&nbsp;</dd>
 305 <dt><a href="../compbio/engine/cluster/drmaa/ClusterEngineUtil.html" title="class in compbio.engine.cluster.drmaa"><span class="typeNameLink">ClusterEngineUtil</span></a> - Class in <a href="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</a></dt>
 306 <dd>&nbsp;</dd>
 307 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterEngineUtil.html#ClusterEngineUtil--">ClusterEngineUtil()</a></span> - Constructor for class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterEngineUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterEngineUtil</a></dt>
 308 <dd>&nbsp;</dd>
 309 <dt><a href="../compbio/engine/ClusterJobId.html" title="class in compbio.engine"><span class="typeNameLink">ClusterJobId</span></a> - Class in <a href="../compbio/engine/package-summary.html">compbio.engine</a></dt>
 310 <dd>&nbsp;</dd>
 311 <dt><span class="memberNameLink"><a href="../compbio/engine/ClusterJobId.html#ClusterJobId-java.lang.String-">ClusterJobId(String)</a></span> - Constructor for class compbio.engine.<a href="../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</a></dt>
 312 <dd>&nbsp;</dd>
 313 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#clusterJobId">clusterJobId</a></span> - Variable in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 314 <dd>&nbsp;</dd>
 315 <dt><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html" title="class in compbio.engine.cluster.drmaa"><span class="typeNameLink">ClusterRunner</span></a> - Class in <a href="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</a></dt>
 316 <dd>
 317 <div class="block">Single cluster job runner class</div>
 318 </dd>
 319 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#ClusterRunner-compbio.engine.client.ConfiguredExecutable-">ClusterRunner(ConfiguredExecutable&lt;?&gt;)</a></span> - Constructor for class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterRunner.html" title="class in compbio.engine.cluster.drmaa">ClusterRunner</a></dt>
 320 <dd>&nbsp;</dd>
 321 <dt><a href="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa"><span class="typeNameLink">ClusterSession</span></a> - Class in <a href="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</a></dt>
 322 <dd>&nbsp;</dd>
 323 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#ClusterSession--">ClusterSession()</a></span> - Constructor for class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</a></dt>
 324 <dd>&nbsp;</dd>
 325 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/StatCollection.html#clusterStat">clusterStat</a></span> - Variable in class compbio.stat.servlet.util.<a href="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</a></dt>
 326 <dd>&nbsp;</dd>
 327 <dt><a href="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa"><span class="typeNameLink">ClusterUtil</span></a> - Class in <a href="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</a></dt>
 328 <dd>&nbsp;</dd>
 329 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterUtil.html#ClusterUtil--">ClusterUtil()</a></span> - Constructor for class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterUtil</a></dt>
 330 <dd>&nbsp;</dd>
 331 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#clustSession">clustSession</a></span> - Static variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterRunner.html" title="class in compbio.engine.cluster.drmaa">ClusterRunner</a></dt>
 332 <dd>&nbsp;</dd>
 333 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#clustSession">clustSession</a></span> - Static variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</a></dt>
 334 <dd>&nbsp;</dd>
 335 <dt><a href="../compbio/ws/client/CmdHelper.html" title="class in compbio.ws.client"><span class="typeNameLink">CmdHelper</span></a> - Class in <a href="../compbio/ws/client/package-summary.html">compbio.ws.client</a></dt>
 336 <dd>&nbsp;</dd>
 337 <dt><span class="memberNameLink"><a href="../compbio/ws/client/CmdHelper.html#CmdHelper--">CmdHelper()</a></span> - Constructor for class compbio.ws.client.<a href="../compbio/ws/client/CmdHelper.html" title="class in compbio.ws.client">CmdHelper</a></dt>
 338 <dd>&nbsp;</dd>
 339 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Disembl.html#COILS_EXPECTATION_THRESHOLD">COILS_EXPECTATION_THRESHOLD</a></span> - Variable in class compbio.runner.disorder.<a href="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</a></dt>
 340 <dd>
 341 <div class="block">For the region to be considered disordered the values must exceed these</div>
 342 </dd>
 343 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/StatisticCollector.html#collectClusterStats--">collectClusterStats()</a></span> - Static method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</a></dt>
 344 <dd>&nbsp;</dd>
 345 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/StatisticCollector.html#collectLocalStats--">collectLocalStats()</a></span> - Static method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</a></dt>
 346 <dd>&nbsp;</dd>
 347 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/ExecutionStatCollector.html#collectStatistics--">collectStatistics()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/ExecutionStatCollector.html" title="class in compbio.stat.collector">ExecutionStatCollector</a></dt>
 348 <dd>&nbsp;</dd>
 349 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/IUPred.html#combineScores-java.util.Map-java.util.Map-">combineScores(Map&lt;String, Set&lt;Score&gt;&gt;, Map&lt;String, Score&gt;)</a></span> - Method in class compbio.runner.disorder.<a href="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</a></dt>
 350 <dd>&nbsp;</dd>
 351 <dt><a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client"><span class="typeNameLink">CommandBuilder</span></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></dt>
 352 <dd>&nbsp;</dd>
 353 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#CommandBuilder--">CommandBuilder()</a></span> - Constructor for class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
 354 <dd>&nbsp;</dd>
 355 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#CommandBuilder-java.lang.String-">CommandBuilder(String)</a></span> - Constructor for class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
 356 <dd>&nbsp;</dd>
 357 <dt><a href="../compbio/engine/client/CommandBuilder.Parameter.html" title="class in compbio.engine.client"><span class="typeNameLink">CommandBuilder.Parameter</span></a> - Class in <a href="../compbio/engine/client/package-summary.html">compbio.engine.client</a></dt>
 358 <dd>&nbsp;</dd>
 359 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/InputFilter.html#compareClustalLines-java.io.File-java.lang.String:A-">compareClustalLines(File, String[])</a></span> - Static method in class compbio.stat.collector.<a href="../compbio/stat/collector/InputFilter.html" title="class in compbio.stat.collector">InputFilter</a></dt>
 360 <dd>&nbsp;</dd>
 361 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/InputFilter.html#compareLines-java.io.File-java.lang.String:A-">compareLines(File, String[])</a></span> - Static method in class compbio.stat.collector.<a href="../compbio/stat/collector/InputFilter.html" title="class in compbio.stat.collector">InputFilter</a></dt>
 362 <dd>&nbsp;</dd>
 363 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Range.html#compareTo-compbio.data.sequence.Range-">compareTo(Range)</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a></dt>
 364 <dd>&nbsp;</dd>
 365 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Score.html#compareTo-compbio.data.sequence.Score-">compareTo(Score)</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a></dt>
 366 <dd>&nbsp;</dd>
 367 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#compareTo-java.util.concurrent.Delayed-">compareTo(Delayed)</a></span> - Method in class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
 368 <dd>&nbsp;</dd>
 369 <dt><a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a> - package compbio.data.msa.jaxws</dt>
 370 <dd>&nbsp;</dd>
 371 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/PropertyHelperManager.html#confDir">confDir</a></span> - Static variable in class compbio.engine.conf.<a href="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</a></dt>
 372 <dd>&nbsp;</dd>
 373 <dt><span class="memberNameLink"><a href="../compbio/engine/local/ExecutableWrapper.html#confExec">confExec</a></span> - Variable in class compbio.engine.local.<a href="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</a></dt>
 374 <dd>&nbsp;</dd>
 375 <dt><a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client"><span class="typeNameLink">ConfExecutable</span></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></dt>
 376 <dd>&nbsp;</dd>
 377 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#ConfExecutable-compbio.engine.client.Executable-java.lang.String-">ConfExecutable(Executable&lt;T&gt;, String)</a></span> - Constructor for class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
 378 <dd>&nbsp;</dd>
 379 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#ConfExecutable-compbio.engine.client.RunConfiguration-">ConfExecutable(RunConfiguration)</a></span> - Constructor for class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
 380 <dd>&nbsp;</dd>
 381 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#confExecutable">confExecutable</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterRunner.html" title="class in compbio.engine.cluster.drmaa">ClusterRunner</a></dt>
 382 <dd>&nbsp;</dd>
 383 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#confExecutable">confExecutable</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</a></dt>
 384 <dd>&nbsp;</dd>
 385 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GAUtils.html#config">config</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/GAUtils.html" title="class in compbio.ws.server">GAUtils</a></dt>
 386 <dd>&nbsp;</dd>
 387 <dt><a href="../compbio/engine/Configurator.html" title="class in compbio.engine"><span class="typeNameLink">Configurator</span></a> - Class in <a href="../compbio/engine/package-summary.html">compbio.engine</a></dt>
 388 <dd>&nbsp;</dd>
 389 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#Configurator--">Configurator()</a></span> - Constructor for class compbio.engine.<a href="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></dt>
 390 <dd>&nbsp;</dd>
 391 <dt><a href="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client"><span class="typeNameLink">ConfiguredExecutable</span></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></dt>
 392 <dd>&nbsp;</dd>
 393 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#configureExecutable-compbio.engine.client.Executable-">configureExecutable(Executable&lt;T&gt;)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></dt>
 394 <dd>&nbsp;</dd>
 395 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#configureExecutable-compbio.engine.client.Executable-java.util.List-">configureExecutable(Executable&lt;T&gt;, List&lt;FastaSequence&gt;)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></dt>
 396 <dd>&nbsp;</dd>
 397 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#configureExecutable-compbio.engine.client.Executable-compbio.engine.client.Executable.ExecProvider-">configureExecutable(Executable&lt;T&gt;, Executable.ExecProvider)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></dt>
 398 <dd>&nbsp;</dd>
 399 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatDB.html#conn">conn</a></span> - Static variable in class compbio.stat.collector.<a href="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</a></dt>
 400 <dd>&nbsp;</dd>
 401 <dt><span class="memberNameLink"><a href="../compbio/ws/client/AAConClient.html#connect--">connect()</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/AAConClient.html" title="class in compbio.ws.client">AAConClient</a></dt>
 402 <dd>
 403 <div class="block">Connects to a AACon web service by the host and the service name</div>
 404 </dd>
 405 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Jws2Client.html#connect-java.lang.String-compbio.ws.client.Services-">connect(String, Services)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</a></dt>
 406 <dd>
 407 <div class="block">Connects to a web service by the host and the service name web service type</div>
 408 </dd>
 409 <dt><span class="memberNameLink"><a href="../compbio/ws/client/WSTester.html#connect-java.lang.String-compbio.ws.client.Services-">connect(String, Services)</a></span> - Method in class compbio.ws.client.<a href="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</a></dt>
 410 <dd>
 411 <div class="block">Connects to a web service by the host and the service name web service type</div>
 412 </dd>
 413 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Jws2Client.html#connectToRegistry-java.lang.String-">connectToRegistry(String)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</a></dt>
 414 <dd>
 415 <div class="block">Get a connection of JABAWS registry</div>
 416 </dd>
 417 <dt><a href="../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence"><span class="typeNameLink">ConservationMethod</span></a> - Enum in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
 418 <dd>
 419 <div class="block">Enumeration listing of all the supported methods.</div>
 420 </dd>
 421 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ConservationMethod.html#ConservationMethod--">ConservationMethod()</a></span> - Constructor for enum compbio.data.sequence.<a href="../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence">ConservationMethod</a></dt>
 422 <dd>&nbsp;</dd>
 423 <dt><a href="../compbio/ws/client/Constraints.html" title="class in compbio.ws.client"><span class="typeNameLink">Constraints</span></a> - Class in <a href="../compbio/ws/client/package-summary.html">compbio.ws.client</a></dt>
 424 <dd>&nbsp;</dd>
 425 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Constraints.html#Constraints--">Constraints()</a></span> - Constructor for class compbio.ws.client.<a href="../compbio/ws/client/Constraints.html" title="class in compbio.ws.client">Constraints</a></dt>
 426 <dd>&nbsp;</dd>
 427 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EnvVariableProcessor.html#containsMultipleVariables-java.lang.String-">containsMultipleVariables(String)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</a></dt>
 428 <dd>&nbsp;</dd>
 429 <dt><span class="memberNameLink"><a href="../compbio/metadata/PresetManager.html#containsValue-java.util.List-java.lang.String-">containsValue(List&lt;String&gt;, String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a></dt>
 430 <dd>&nbsp;</dd>
 431 <dt><span class="memberNameLink"><a href="../compbio/metadata/Preset.html#containValue-java.lang.String-">containValue(String)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a></dt>
 432 <dd>&nbsp;</dd>
 433 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/StatisticCollector.html#contextDestroyed-javax.servlet.ServletContextEvent-">contextDestroyed(ServletContextEvent)</a></span> - Method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</a></dt>
 434 <dd>&nbsp;</dd>
 435 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MainManager.html#contextDestroyed-javax.servlet.ServletContextEvent-">contextDestroyed(ServletContextEvent)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MainManager.html" title="class in compbio.ws.server">MainManager</a></dt>
 436 <dd>&nbsp;</dd>
 437 <dt><span class="memberNameLink"><a href="../compbio/ws/server/SetExecutableFlag.html#contextDestroyed-javax.servlet.ServletContextEvent-">contextDestroyed(ServletContextEvent)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/SetExecutableFlag.html" title="class in compbio.ws.server">SetExecutableFlag</a></dt>
 438 <dd>&nbsp;</dd>
 439 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/StatisticCollector.html#contextInitialized-javax.servlet.ServletContextEvent-">contextInitialized(ServletContextEvent)</a></span> - Method in class compbio.stat.servlet.<a href="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</a></dt>
 440 <dd>&nbsp;</dd>
 441 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MainManager.html#contextInitialized-javax.servlet.ServletContextEvent-">contextInitialized(ServletContextEvent)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MainManager.html" title="class in compbio.ws.server">MainManager</a></dt>
 442 <dd>&nbsp;</dd>
 443 <dt><span class="memberNameLink"><a href="../compbio/ws/server/SetExecutableFlag.html#contextInitialized-javax.servlet.ServletContextEvent-">contextInitialized(ServletContextEvent)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/SetExecutableFlag.html" title="class in compbio.ws.server">SetExecutableFlag</a></dt>
 444 <dd>
 445 <div class="block">This listener is designed to run only once when the web application is
 446  deployed to set executable flag for binaries.</div>
 447 </dd>
 448 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/ClustalW.html#convertInputNameToTreeName--">convertInputNameToTreeName()</a></span> - Method in class compbio.runner.msa.<a href="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</a></dt>
 449 <dd>
 450 <div class="block">Clustal output tree with same name as input file but .dnd extension e.g.</div>
 451 </dd>
 452 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EngineUtil.html#convertToAbsolute-java.lang.String-">convertToAbsolute(String)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/EngineUtil.html" title="class in compbio.engine.client">EngineUtil</a></dt>
 453 <dd>&nbsp;</dd>
 454 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Util.html#convertToAbsolute-java.lang.String-">convertToAbsolute(String)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</a></dt>
 455 <dd>&nbsp;</dd>
 456 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#convertToNumber-java.lang.String:A-">convertToNumber(String[])</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 457 <dd>&nbsp;</dd>
 458 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig-compbio.metadata.RunnerConfig-">copyAndValidateRConfig(RunnerConfig&lt;?&gt;)</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
 459 <dd>&nbsp;</dd>
 460 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/FastaSequence.html#countMatchesInSequence-java.lang.String-java.lang.String-">countMatchesInSequence(String, String)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></dt>
 461 <dd>&nbsp;</dd>
 462 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#cpu">cpu</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 463 <dd>&nbsp;</dd>
 464 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/RunnerConfigMarshaller.MySchemaOutputResolver.html#createOutput-java.lang.String-java.lang.String-">createOutput(String, String)</a></span> - Method in class compbio.engine.conf.<a href="../compbio/engine/conf/RunnerConfigMarshaller.MySchemaOutputResolver.html" title="class in compbio.engine.conf">RunnerConfigMarshaller.MySchemaOutputResolver</a></dt>
 465 <dd>&nbsp;</dd>
 466 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatDB.html#createStatTable--">createStatTable()</a></span> - Method in class compbio.stat.collector.<a href="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</a></dt>
 467 <dd>
 468 <div class="block">rs.getBoolean(i) will return true for any non-zero value and false for 0
 469  on SMALLINT data column.</div>
 470 </dd>
 471 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/RunnerConfigMarshaller.html#ctx">ctx</a></span> - Variable in class compbio.engine.conf.<a href="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</a></dt>
 472 <dd>&nbsp;</dd>
 473 <dt><a href="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">CustomAlign</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 474 <dd>&nbsp;</dd>
 475 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAlign.html#CustomAlign--">CustomAlign()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</a></dt>
 476 <dd>&nbsp;</dd>
 477 <dt><span class="memberNameLink"><a href="../compbio/data/msa/MsaWS.html#customAlign-java.util.List-java.util.List-">customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;T&gt;&gt;)</a></span> - Method in interface compbio.data.msa.<a href="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a></dt>
 478 <dd>
 479 <div class="block">Align a list of sequences with options.</div>
 480 </dd>
 481 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalOWS.html#customAlign-java.util.List-java.util.List-">customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;ClustalO&gt;&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</a></dt>
 482 <dd>&nbsp;</dd>
 483 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalWS.html#customAlign-java.util.List-java.util.List-">customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;ClustalW&gt;&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</a></dt>
 484 <dd>&nbsp;</dd>
 485 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GLprobsWS.html#customAlign-java.util.List-java.util.List-">customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;GLprobs&gt;&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/GLprobsWS.html" title="class in compbio.ws.server">GLprobsWS</a></dt>
 486 <dd>&nbsp;</dd>
 487 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MafftWS.html#customAlign-java.util.List-java.util.List-">customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;Mafft&gt;&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</a></dt>
 488 <dd>&nbsp;</dd>
 489 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MSAprobsWS.html#customAlign-java.util.List-java.util.List-">customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;MSAprobs&gt;&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MSAprobsWS.html" title="class in compbio.ws.server">MSAprobsWS</a></dt>
 490 <dd>&nbsp;</dd>
 491 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MuscleWS.html#customAlign-java.util.List-java.util.List-">customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;Muscle&gt;&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</a></dt>
 492 <dd>&nbsp;</dd>
 493 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ProbconsWS.html#customAlign-java.util.List-java.util.List-">customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;Probcons&gt;&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</a></dt>
 494 <dd>&nbsp;</dd>
 495 <dt><span class="memberNameLink"><a href="../compbio/ws/server/TcoffeeWS.html#customAlign-java.util.List-java.util.List-">customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;Tcoffee&gt;&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</a></dt>
 496 <dd>&nbsp;</dd>
 497 <dt><a href="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">CustomAlignResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 498 <dd>&nbsp;</dd>
 499 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAlignResponse.html#CustomAlignResponse--">CustomAlignResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws">CustomAlignResponse</a></dt>
 500 <dd>&nbsp;</dd>
 501 <dt><a href="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">CustomAnalize</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 502 <dd>&nbsp;</dd>
 503 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAnalize.html#CustomAnalize--">CustomAnalize()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</a></dt>
 504 <dd>&nbsp;</dd>
 505 <dt><span class="memberNameLink"><a href="../compbio/data/msa/SequenceAnnotation.html#customAnalize-java.util.List-java.util.List-">customAnalize(List&lt;FastaSequence&gt;, List&lt;Option&lt;T&gt;&gt;)</a></span> - Method in interface compbio.data.msa.<a href="../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</a></dt>
 506 <dd>
 507 <div class="block">Analyse the sequences according to custom settings defined in options
 508  list.</div>
 509 </dd>
 510 <dt><span class="memberNameLink"><a href="../compbio/ws/server/AAConWS.html#customAnalize-java.util.List-java.util.List-">customAnalize(List&lt;FastaSequence&gt;, List&lt;Option&lt;AACon&gt;&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/AAConWS.html" title="class in compbio.ws.server">AAConWS</a></dt>
 511 <dd>&nbsp;</dd>
 512 <dt><span class="memberNameLink"><a href="../compbio/ws/server/DisemblWS.html#customAnalize-java.util.List-java.util.List-">customAnalize(List&lt;FastaSequence&gt;, List&lt;Option&lt;Disembl&gt;&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/DisemblWS.html" title="class in compbio.ws.server">DisemblWS</a></dt>
 513 <dd>&nbsp;</dd>
 514 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GlobPlotWS.html#customAnalize-java.util.List-java.util.List-">customAnalize(List&lt;FastaSequence&gt;, List&lt;Option&lt;GlobPlot&gt;&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/GlobPlotWS.html" title="class in compbio.ws.server">GlobPlotWS</a></dt>
 515 <dd>&nbsp;</dd>
 516 <dt><span class="memberNameLink"><a href="../compbio/ws/server/RNAalifoldWS.html#customAnalize-java.util.List-java.util.List-">customAnalize(List&lt;FastaSequence&gt;, List&lt;Option&lt;RNAalifold&gt;&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/RNAalifoldWS.html" title="class in compbio.ws.server">RNAalifoldWS</a></dt>
 517 <dd>&nbsp;</dd>
 518 <dt><span class="memberNameLink"><a href="../compbio/ws/server/SequenceAnnotationService.html#customAnalize-java.util.List-java.util.List-">customAnalize(List&lt;FastaSequence&gt;, List&lt;Option&lt;T&gt;&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</a></dt>
 519 <dd>&nbsp;</dd>
 520 <dt><a href="../compbio/data/msa/jaxws/CustomAnalizeResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">CustomAnalizeResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 521 <dd>&nbsp;</dd>
 522 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAnalizeResponse.html#CustomAnalizeResponse--">CustomAnalizeResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomAnalizeResponse.html" title="class in compbio.data.msa.jaxws">CustomAnalizeResponse</a></dt>
 523 <dd>&nbsp;</dd>
 524 <dt><a href="../compbio/data/msa/jaxws/CustomFold.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">CustomFold</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 525 <dd>&nbsp;</dd>
 526 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomFold.html#CustomFold--">CustomFold()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomFold.html" title="class in compbio.data.msa.jaxws">CustomFold</a></dt>
 527 <dd>&nbsp;</dd>
 528 <dt><a href="../compbio/data/msa/jaxws/CustomFoldResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">CustomFoldResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 529 <dd>&nbsp;</dd>
 530 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomFoldResponse.html#CustomFoldResponse--">CustomFoldResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomFoldResponse.html" title="class in compbio.data.msa.jaxws">CustomFoldResponse</a></dt>
 531 <dd>&nbsp;</dd>
 532 </dl>
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