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  75 <h2 class="title">P</h2>
  76 <dl>
  77 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.Parameter.html#Parameter--">Parameter()</a></span> - Constructor for class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.Parameter.html" title="class in compbio.engine.client">CommandBuilder.Parameter</a></dt>
  78 <dd>&nbsp;</dd>
  79 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.Parameter.html#Parameter-java.lang.String-">Parameter(String)</a></span> - Constructor for class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.Parameter.html" title="class in compbio.engine.client">CommandBuilder.Parameter</a></dt>
  80 <dd>&nbsp;</dd>
  81 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.Parameter.html#Parameter-java.lang.String-java.lang.String-">Parameter(String, String)</a></span> - Constructor for class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.Parameter.html" title="class in compbio.engine.client">CommandBuilder.Parameter</a></dt>
  82 <dd>&nbsp;</dd>
  83 <dt><a href="../compbio/metadata/Parameter.html" title="class in compbio.metadata"><span class="typeNameLink">Parameter</span></a>&lt;<a href="../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</a>&gt; - Class in <a href="../compbio/metadata/package-summary.html">compbio.metadata</a></dt>
  84 <dd>
  85 <div class="block">A single value containing an option supported by the web service e.g.</div>
  86 </dd>
  87 <dt><span class="memberNameLink"><a href="../compbio/metadata/Parameter.html#Parameter--">Parameter()</a></span> - Constructor for class compbio.metadata.<a href="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</a></dt>
  88 <dd>&nbsp;</dd>
  89 <dt><span class="memberNameLink"><a href="../compbio/metadata/Parameter.html#Parameter-java.lang.String-java.lang.String-">Parameter(String, String)</a></span> - Constructor for class compbio.metadata.<a href="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</a></dt>
  90 <dd>&nbsp;</dd>
  91 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Constraints.html#parameterkey">parameterkey</a></span> - Static variable in class compbio.ws.client.<a href="../compbio/ws/client/Constraints.html" title="class in compbio.ws.client">Constraints</a></dt>
  92 <dd>&nbsp;</dd>
  93 <dt><span class="memberNameLink"><a href="../compbio/engine/client/RunConfiguration.html#parameters">parameters</a></span> - Variable in class compbio.engine.client.<a href="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</a></dt>
  94 <dd>
  95 <div class="block">Parameters</div>
  96 </dd>
  97 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#parameters">parameters</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
  98 <dd>&nbsp;</dd>
  99 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#parametersToCommandString-java.util.List-java.util.Map-">parametersToCommandString(List&lt;Parameter&lt;?&gt;&gt;, Map&lt;Parameter&lt;?&gt;, String&gt;)</a></span> - Method in class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
 100 <dd>&nbsp;</dd>
 101 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#parameterToString-java.util.List-">parameterToString(List&lt;CommandBuilder.Parameter&gt;)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
 102 <dd>&nbsp;</dd>
 103 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Constraints.html#paramFile">paramFile</a></span> - Static variable in class compbio.ws.client.<a href="../compbio/ws/client/Constraints.html" title="class in compbio.ws.client">Constraints</a></dt>
 104 <dd>&nbsp;</dd>
 105 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#paramList">paramList</a></span> - Variable in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
 106 <dd>&nbsp;</dd>
 107 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Constraints.html#paramList">paramList</a></span> - Static variable in class compbio.ws.client.<a href="../compbio/ws/client/Constraints.html" title="class in compbio.ws.client">Constraints</a></dt>
 108 <dd>&nbsp;</dd>
 109 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#paramValueUpdater--">paramValueUpdater()</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 110 <dd>
 111 <div class="block">This is a generic method of changing values of the parameters with
 112  properties
 113
 114  This method iterates via commands for an executable finding matches from
 115  the Executable.properties file and replacing values in CommandBuilder
 116  with a combination of value from CommandBuilder to merge path from
 117  properties</div>
 118 </dd>
 119 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#parseIUPredDomains-java.util.Scanner-">parseIUPredDomains(Scanner)</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>
 120 <dd>
 121 <div class="block"># P53_HUMA
 122
 123  Number of globular domains: 2
 124
 125  globular domain 1.</div>
 126 </dd>
 127 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#parseIUPredScores-java.util.Scanner-">parseIUPredScores(Scanner)</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>
 128 <dd>&nbsp;</dd>
 129 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#parseRanges-java.lang.Enum-java.lang.String-">parseRanges(Enum, 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>
 130 <dd>
 131 <div class="block">Parsing:
 132
 133  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343,
 134  350-391, 429-485, 497-506, 539-547
 135
 136  # REM465 355-368
 137
 138  # HOTLOOPS 190-204</div>
 139 </dd>
 140 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EnvVariableProcessor.html#PATH">PATH</a></span> - Static variable in class compbio.engine.client.<a href="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</a></dt>
 141 <dd>
 142 <div class="block">Special variable keys Absolute path(s) will be merged with the content of
 143  the system PATH variable</div>
 144 </dd>
 145 <dt><a href="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client"><span class="typeNameLink">PathValidator</span></a> - Class in <a href="../compbio/engine/client/package-summary.html">compbio.engine.client</a></dt>
 146 <dd>&nbsp;</dd>
 147 <dt><span class="memberNameLink"><a href="../compbio/engine/client/PathValidator.html#PathValidator--">PathValidator()</a></span> - Constructor for class compbio.engine.client.<a href="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</a></dt>
 148 <dd>&nbsp;</dd>
 149 <dt><span class="memberNameLink"><a href="../compbio/engine/local/ExecutableWrapper.html#pbuilder">pbuilder</a></span> - Variable in class compbio.engine.local.<a href="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</a></dt>
 150 <dd>&nbsp;</dd>
 151 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#ph">ph</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>
 152 <dd>&nbsp;</dd>
 153 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EngineUtil.html#ph">ph</a></span> - Static variable in class compbio.engine.client.<a href="../compbio/engine/client/EngineUtil.html" title="class in compbio.engine.client">EngineUtil</a></dt>
 154 <dd>&nbsp;</dd>
 155 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#ph">ph</a></span> - Static variable in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
 156 <dd>&nbsp;</dd>
 157 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Util.html#ph">ph</a></span> - Static variable in class compbio.engine.client.<a href="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</a></dt>
 158 <dd>&nbsp;</dd>
 159 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#ph">ph</a></span> - Static variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</a></dt>
 160 <dd>&nbsp;</dd>
 161 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/PropertyHelperManager.html#ph">ph</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>
 162 <dd>&nbsp;</dd>
 163 <dt><span class="memberNameLink"><a href="../compbio/engine/Configurator.html#ph">ph</a></span> - Static variable in class compbio.engine.<a href="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</a></dt>
 164 <dd>&nbsp;</dd>
 165 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Tcoffee.html#ph">ph</a></span> - Static variable in class compbio.runner.msa.<a href="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</a></dt>
 166 <dd>&nbsp;</dd>
 167 <dt><span class="memberNameLink"><a href="../compbio/runner/Util.html#ph">ph</a></span> - Static variable in class compbio.runner.<a href="../compbio/runner/Util.html" title="class in compbio.runner">Util</a></dt>
 168 <dd>&nbsp;</dd>
 169 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/StatisticCollector.html#ph">ph</a></span> - Static variable in class compbio.stat.servlet.<a href="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</a></dt>
 170 <dd>&nbsp;</dd>
 171 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MainManager.html#ph">ph</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/MainManager.html" title="class in compbio.ws.server">MainManager</a></dt>
 172 <dd>&nbsp;</dd>
 173 <dt><a href="../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client"><span class="typeNameLink">PipedExecutable</span></a>&lt;<a href="../compbio/engine/client/PipedExecutable.html" title="type parameter in PipedExecutable">T</a>&gt; - Interface in <a href="../compbio/engine/client/package-summary.html">compbio.engine.client</a></dt>
 174 <dd>
 175 <div class="block">This is a marker interface to indicate that the output of the process must be
 176  captured.</div>
 177 </dd>
 178 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PullExecStatistics.html#position">position</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</a></dt>
 179 <dd>&nbsp;</dd>
 180 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.Parameter.html#position">position</a></span> - Variable in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.Parameter.html" title="class in compbio.engine.client">CommandBuilder.Parameter</a></dt>
 181 <dd>&nbsp;</dd>
 182 <dt><span class="memberNameLink"><a href="../compbio/metadata/ChunkHolder.html#position">position</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</a></dt>
 183 <dd>&nbsp;</dd>
 184 <dt><span class="memberNameLink"><a href="../compbio/metadata/Parameter.html#possibleValues">possibleValues</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</a></dt>
 185 <dd>&nbsp;</dd>
 186 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetAlign.html#preset">preset</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</a></dt>
 187 <dd>&nbsp;</dd>
 188 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetAnalize.html#preset">preset</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</a></dt>
 189 <dd>&nbsp;</dd>
 190 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetFold.html#preset">preset</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PresetFold.html" title="class in compbio.data.msa.jaxws">PresetFold</a></dt>
 191 <dd>&nbsp;</dd>
 192 <dt><span class="memberNameLink"><a href="../compbio/metadata/Limit.html#preset">preset</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a></dt>
 193 <dd>&nbsp;</dd>
 194 <dt><a href="../compbio/metadata/Preset.html" title="class in compbio.metadata"><span class="typeNameLink">Preset</span></a>&lt;<a href="../compbio/metadata/Preset.html" title="type parameter in Preset">T</a>&gt; - Class in <a href="../compbio/metadata/package-summary.html">compbio.metadata</a></dt>
 195 <dd>
 196 <div class="block">Collection of Options and Parameters with their values</div>
 197 </dd>
 198 <dt><span class="memberNameLink"><a href="../compbio/metadata/Preset.html#Preset--">Preset()</a></span> - Constructor for class compbio.metadata.<a href="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a></dt>
 199 <dd>&nbsp;</dd>
 200 <dt><span class="memberNameLink"><a href="../compbio/metadata/PresetManager.html#preset">preset</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a></dt>
 201 <dd>&nbsp;</dd>
 202 <dt><a href="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">PresetAlign</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 203 <dd>&nbsp;</dd>
 204 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetAlign.html#PresetAlign--">PresetAlign()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</a></dt>
 205 <dd>&nbsp;</dd>
 206 <dt><span class="memberNameLink"><a href="../compbio/data/msa/MsaWS.html#presetAlign-java.util.List-compbio.metadata.Preset-">presetAlign(List&lt;FastaSequence&gt;, Preset&lt;T&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>
 207 <dd>
 208 <div class="block">Align a list of sequences with preset.</div>
 209 </dd>
 210 <dt><span class="memberNameLink"><a href="../compbio/ws/client/WSTester.html#presetAlign-compbio.data.msa.MsaWS-java.util.List-">presetAlign(MsaWS&lt;T&gt;, List&lt;Preset&lt;T&gt;&gt;)</a></span> - Method in class compbio.ws.client.<a href="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</a></dt>
 211 <dd>
 212 <div class="block">Calls alignment with preset</div>
 213 </dd>
 214 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalOWS.html#presetAlign-java.util.List-compbio.metadata.Preset-">presetAlign(List&lt;FastaSequence&gt;, Preset&lt;ClustalO&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>
 215 <dd>&nbsp;</dd>
 216 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalWS.html#presetAlign-java.util.List-compbio.metadata.Preset-">presetAlign(List&lt;FastaSequence&gt;, Preset&lt;ClustalW&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>
 217 <dd>&nbsp;</dd>
 218 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GLprobsWS.html#presetAlign-java.util.List-compbio.metadata.Preset-">presetAlign(List&lt;FastaSequence&gt;, Preset&lt;GLprobs&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>
 219 <dd>&nbsp;</dd>
 220 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MafftWS.html#presetAlign-java.util.List-compbio.metadata.Preset-">presetAlign(List&lt;FastaSequence&gt;, Preset&lt;Mafft&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>
 221 <dd>&nbsp;</dd>
 222 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MSAprobsWS.html#presetAlign-java.util.List-compbio.metadata.Preset-">presetAlign(List&lt;FastaSequence&gt;, Preset&lt;MSAprobs&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>
 223 <dd>&nbsp;</dd>
 224 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MuscleWS.html#presetAlign-java.util.List-compbio.metadata.Preset-">presetAlign(List&lt;FastaSequence&gt;, Preset&lt;Muscle&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>
 225 <dd>&nbsp;</dd>
 226 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ProbconsWS.html#presetAlign-java.util.List-compbio.metadata.Preset-">presetAlign(List&lt;FastaSequence&gt;, Preset&lt;Probcons&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>
 227 <dd>&nbsp;</dd>
 228 <dt><span class="memberNameLink"><a href="../compbio/ws/server/TcoffeeWS.html#presetAlign-java.util.List-compbio.metadata.Preset-">presetAlign(List&lt;FastaSequence&gt;, Preset&lt;Tcoffee&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>
 229 <dd>&nbsp;</dd>
 230 <dt><a href="../compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">PresetAlignResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 231 <dd>&nbsp;</dd>
 232 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetAlignResponse.html#PresetAlignResponse--">PresetAlignResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws">PresetAlignResponse</a></dt>
 233 <dd>&nbsp;</dd>
 234 <dt><a href="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">PresetAnalize</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 235 <dd>&nbsp;</dd>
 236 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetAnalize.html#PresetAnalize--">PresetAnalize()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</a></dt>
 237 <dd>&nbsp;</dd>
 238 <dt><span class="memberNameLink"><a href="../compbio/data/msa/SequenceAnnotation.html#presetAnalize-java.util.List-compbio.metadata.Preset-">presetAnalize(List&lt;FastaSequence&gt;, Preset&lt;T&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>
 239 <dd>
 240 <div class="block">Analyse the sequences according to the preset settings.</div>
 241 </dd>
 242 <dt><span class="memberNameLink"><a href="../compbio/ws/server/AAConWS.html#presetAnalize-java.util.List-compbio.metadata.Preset-">presetAnalize(List&lt;FastaSequence&gt;, Preset&lt;AACon&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>
 243 <dd>&nbsp;</dd>
 244 <dt><span class="memberNameLink"><a href="../compbio/ws/server/DisemblWS.html#presetAnalize-java.util.List-compbio.metadata.Preset-">presetAnalize(List&lt;FastaSequence&gt;, Preset&lt;Disembl&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>
 245 <dd>&nbsp;</dd>
 246 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GlobPlotWS.html#presetAnalize-java.util.List-compbio.metadata.Preset-">presetAnalize(List&lt;FastaSequence&gt;, Preset&lt;GlobPlot&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>
 247 <dd>&nbsp;</dd>
 248 <dt><span class="memberNameLink"><a href="../compbio/ws/server/IUPredWS.html#presetAnalize-java.util.List-compbio.metadata.Preset-">presetAnalize(List&lt;FastaSequence&gt;, Preset&lt;IUPred&gt;)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/IUPredWS.html" title="class in compbio.ws.server">IUPredWS</a></dt>
 249 <dd>&nbsp;</dd>
 250 <dt><span class="memberNameLink"><a href="../compbio/ws/server/RNAalifoldWS.html#presetAnalize-java.util.List-compbio.metadata.Preset-">presetAnalize(List&lt;FastaSequence&gt;, Preset&lt;RNAalifold&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>
 251 <dd>&nbsp;</dd>
 252 <dt><span class="memberNameLink"><a href="../compbio/ws/server/SequenceAnnotationService.html#presetAnalize-java.util.List-compbio.metadata.Preset-">presetAnalize(List&lt;FastaSequence&gt;, Preset&lt;T&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>
 253 <dd>&nbsp;</dd>
 254 <dt><a href="../compbio/data/msa/jaxws/PresetAnalizeResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">PresetAnalizeResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 255 <dd>&nbsp;</dd>
 256 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetAnalizeResponse.html#PresetAnalizeResponse--">PresetAnalizeResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PresetAnalizeResponse.html" title="class in compbio.data.msa.jaxws">PresetAnalizeResponse</a></dt>
 257 <dd>&nbsp;</dd>
 258 <dt><a href="../compbio/data/msa/jaxws/PresetFold.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">PresetFold</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 259 <dd>&nbsp;</dd>
 260 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetFold.html#PresetFold--">PresetFold()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PresetFold.html" title="class in compbio.data.msa.jaxws">PresetFold</a></dt>
 261 <dd>&nbsp;</dd>
 262 <dt><a href="../compbio/data/msa/jaxws/PresetFoldResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">PresetFoldResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 263 <dd>&nbsp;</dd>
 264 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PresetFoldResponse.html#PresetFoldResponse--">PresetFoldResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PresetFoldResponse.html" title="class in compbio.data.msa.jaxws">PresetFoldResponse</a></dt>
 265 <dd>&nbsp;</dd>
 266 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Constraints.html#presetkey">presetkey</a></span> - Static variable in class compbio.ws.client.<a href="../compbio/ws/client/Constraints.html" title="class in compbio.ws.client">Constraints</a></dt>
 267 <dd>&nbsp;</dd>
 268 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Constraints.html#presetList">presetList</a></span> - Static variable in class compbio.ws.client.<a href="../compbio/ws/client/Constraints.html" title="class in compbio.ws.client">Constraints</a></dt>
 269 <dd>&nbsp;</dd>
 270 <dt><a href="../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><span class="typeNameLink">PresetManager</span></a>&lt;<a href="../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</a>&gt; - Class in <a href="../compbio/metadata/package-summary.html">compbio.metadata</a></dt>
 271 <dd>
 272 <div class="block">Collection of presets and methods to manipulate them @see <a href="../compbio/metadata/Preset.html" title="class in compbio.metadata"><code>Preset</code></a></div>
 273 </dd>
 274 <dt><span class="memberNameLink"><a href="../compbio/metadata/PresetManager.html#PresetManager--">PresetManager()</a></span> - Constructor for class compbio.metadata.<a href="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a></dt>
 275 <dd>&nbsp;</dd>
 276 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetLimit.html#presetName">presetName</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</a></dt>
 277 <dd>&nbsp;</dd>
 278 <dt><span class="memberNameLink"><a href="../compbio/engine/PulledFileCache.html#print--">print()</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</a></dt>
 279 <dd>&nbsp;</dd>
 280 <dt><span class="memberNameLink"><a href="../compbio/ws/client/AAConClient.html#printUsage-int-">printUsage(int)</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>
 281 <dd>
 282 <div class="block">Prints AAConClient usage information to standard out</div>
 283 </dd>
 284 <dt><span class="memberNameLink"><a href="../compbio/ws/client/WSTester.html#printUsage--">printUsage()</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</a></dt>
 285 <dd>
 286 <div class="block">Prints usage</div>
 287 </dd>
 288 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#priority">priority</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>
 289 <dd>&nbsp;</dd>
 290 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#prmSeparator">prmSeparator</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
 291 <dd>&nbsp;</dd>
 292 <dt><a href="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa"><span class="typeNameLink">Probcons</span></a> - Class in <a href="../compbio/runner/msa/package-summary.html">compbio.runner.msa</a></dt>
 293 <dd>&nbsp;</dd>
 294 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Probcons.html#Probcons--">Probcons()</a></span> - Constructor for class compbio.runner.msa.<a href="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</a></dt>
 295 <dd>&nbsp;</dd>
 296 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#PROBCONS_INFO">PROBCONS_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>
 297 <dd>&nbsp;</dd>
 298 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ProbconsWS.html#probconsOptions">probconsOptions</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</a></dt>
 299 <dd>&nbsp;</dd>
 300 <dt><a href="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server"><span class="typeNameLink">ProbconsWS</span></a> - Class in <a href="../compbio/ws/server/package-summary.html">compbio.ws.server</a></dt>
 301 <dd>&nbsp;</dd>
 302 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ProbconsWS.html#ProbconsWS--">ProbconsWS()</a></span> - Constructor for class compbio.ws.server.<a href="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</a></dt>
 303 <dd>&nbsp;</dd>
 304 <dt><span class="memberNameLink"><a href="../compbio/engine/local/ExecutableWrapper.html#PROC_ERR_FILE">PROC_ERR_FILE</a></span> - Static variable in class compbio.engine.local.<a href="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</a></dt>
 305 <dd>&nbsp;</dd>
 306 <dt><span class="memberNameLink"><a href="../compbio/engine/local/ExecutableWrapper.html#PROC_IN_FILE">PROC_IN_FILE</a></span> - Static variable in class compbio.engine.local.<a href="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</a></dt>
 307 <dd>&nbsp;</dd>
 308 <dt><span class="memberNameLink"><a href="../compbio/engine/local/ExecutableWrapper.html#PROC_OUT_FILE">PROC_OUT_FILE</a></span> - Static variable in class compbio.engine.local.<a href="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</a></dt>
 309 <dd>&nbsp;</dd>
 310 <dt><span class="memberNameLink"><a href="../compbio/ws/client/MetadataHelper.html#processParameters-java.util.List-compbio.metadata.RunnerConfig-">processParameters(List&lt;String&gt;, RunnerConfig&lt;T&gt;)</a></span> - Static method in class compbio.ws.client.<a href="../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client">MetadataHelper</a></dt>
 311 <dd>
 312 <div class="block">Converts options supplied via parameters file into <code>Option</code> objects</div>
 313 </dd>
 314 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/AlignmentMetadata.html#program">program</a></span> - Variable in class compbio.data.sequence.<a href="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</a></dt>
 315 <dd>&nbsp;</dd>
 316 <dt><a href="../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><span class="typeNameLink">Program</span></a> - Enum in <a href="../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></dt>
 317 <dd>
 318 <div class="block">The list of programmes that can produce alignments</div>
 319 </dd>
 320 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Program.html#Program--">Program()</a></span> - Constructor for enum compbio.data.sequence.<a href="../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</a></dt>
 321 <dd>&nbsp;</dd>
 322 <dt><a href="../compbio/engine/ProgressGetter.html" title="class in compbio.engine"><span class="typeNameLink">ProgressGetter</span></a> - Class in <a href="../compbio/engine/package-summary.html">compbio.engine</a></dt>
 323 <dd>&nbsp;</dd>
 324 <dt><span class="memberNameLink"><a href="../compbio/engine/ProgressGetter.html#ProgressGetter--">ProgressGetter()</a></span> - Constructor for class compbio.engine.<a href="../compbio/engine/ProgressGetter.html" title="class in compbio.engine">ProgressGetter</a></dt>
 325 <dd>&nbsp;</dd>
 326 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GAUtils.html#PROP_HELPER">PROP_HELPER</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>
 327 <dd>&nbsp;</dd>
 328 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EnvVariableProcessor.html#PROP_NAME_VALUE_SEPARATOR">PROP_NAME_VALUE_SEPARATOR</a></span> - Static variable in class compbio.engine.client.<a href="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</a></dt>
 329 <dd>&nbsp;</dd>
 330 <dt><a href="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf"><span class="typeNameLink">PropertyHelperManager</span></a> - Class in <a href="../compbio/engine/conf/package-summary.html">compbio.engine.conf</a></dt>
 331 <dd>&nbsp;</dd>
 332 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/PropertyHelperManager.html#PropertyHelperManager--">PropertyHelperManager()</a></span> - Constructor for class compbio.engine.conf.<a href="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</a></dt>
 333 <dd>&nbsp;</dd>
 334 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatDB.html#protocol">protocol</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>
 335 <dd>&nbsp;</dd>
 336 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#provider">provider</a></span> - Variable in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
 337 <dd>&nbsp;</dd>
 338 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#ps">ps</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>
 339 <dd>&nbsp;</dd>
 340 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Constraints.html#pseparator">pseparator</a></span> - Static variable in class compbio.ws.client.<a href="../compbio/ws/client/Constraints.html" title="class in compbio.ws.client">Constraints</a></dt>
 341 <dd>&nbsp;</dd>
 342 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#PStructP">PStructP</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>
 343 <dd>&nbsp;</dd>
 344 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#pull-long-">pull(long)</a></span> - Method in class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
 345 <dd>&nbsp;</dd>
 346 <dt><span class="memberNameLink"><a href="../compbio/engine/ProgressGetter.html#pull-java.lang.String-long-long-java.util.concurrent.TimeUnit-">pull(String, long, long, TimeUnit)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/ProgressGetter.html" title="class in compbio.engine">ProgressGetter</a></dt>
 347 <dd>&nbsp;</dd>
 348 <dt><span class="memberNameLink"><a href="../compbio/engine/ProgressGetter.html#pull-java.lang.String-long-">pull(String, long)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/ProgressGetter.html" title="class in compbio.engine">ProgressGetter</a></dt>
 349 <dd>&nbsp;</dd>
 350 <dt><a href="../compbio/engine/PulledFileCache.html" title="class in compbio.engine"><span class="typeNameLink">PulledFileCache</span></a> - Class in <a href="../compbio/engine/package-summary.html">compbio.engine</a></dt>
 351 <dd>&nbsp;</dd>
 352 <dt><span class="memberNameLink"><a href="../compbio/engine/PulledFileCache.html#PulledFileCache--">PulledFileCache()</a></span> - Constructor for class compbio.engine.<a href="../compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</a></dt>
 353 <dd>&nbsp;</dd>
 354 <dt><a href="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">PullExecStatistics</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 355 <dd>&nbsp;</dd>
 356 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PullExecStatistics.html#PullExecStatistics--">PullExecStatistics()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</a></dt>
 357 <dd>&nbsp;</dd>
 358 <dt><span class="memberNameLink"><a href="../compbio/data/msa/JManagement.html#pullExecStatistics-java.lang.String-long-">pullExecStatistics(String, long)</a></span> - Method in interface compbio.data.msa.<a href="../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</a></dt>
 359 <dd>
 360 <div class="block">Reads 1kb chunk from the statistics file which is specific to a given web
 361  service from the <code>position</code>.</div>
 362 </dd>
 363 <dt><span class="memberNameLink"><a href="../compbio/ws/server/AAConWS.html#pullExecStatistics-java.lang.String-long-">pullExecStatistics(String, long)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/AAConWS.html" title="class in compbio.ws.server">AAConWS</a></dt>
 364 <dd>&nbsp;</dd>
 365 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalOWS.html#pullExecStatistics-java.lang.String-long-">pullExecStatistics(String, long)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</a></dt>
 366 <dd>&nbsp;</dd>
 367 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ClustalWS.html#pullExecStatistics-java.lang.String-long-">pullExecStatistics(String, long)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</a></dt>
 368 <dd>&nbsp;</dd>
 369 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GenericMetadataService.html#pullExecStatistics-java.lang.String-long-">pullExecStatistics(String, long)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</a></dt>
 370 <dd>
 371 <div class="block">Assume statistics is not supported</div>
 372 </dd>
 373 <dt><span class="memberNameLink"><a href="../compbio/ws/server/GLprobsWS.html#pullExecStatistics-java.lang.String-long-">pullExecStatistics(String, long)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/GLprobsWS.html" title="class in compbio.ws.server">GLprobsWS</a></dt>
 374 <dd>&nbsp;</dd>
 375 <dt><span class="memberNameLink"><a href="../compbio/ws/server/JronnWS.html#pullExecStatistics-java.lang.String-long-">pullExecStatistics(String, long)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/JronnWS.html" title="class in compbio.ws.server">JronnWS</a></dt>
 376 <dd>&nbsp;</dd>
 377 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MafftWS.html#pullExecStatistics-java.lang.String-long-">pullExecStatistics(String, long)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</a></dt>
 378 <dd>&nbsp;</dd>
 379 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MSAprobsWS.html#pullExecStatistics-java.lang.String-long-">pullExecStatistics(String, long)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MSAprobsWS.html" title="class in compbio.ws.server">MSAprobsWS</a></dt>
 380 <dd>&nbsp;</dd>
 381 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MuscleWS.html#pullExecStatistics-java.lang.String-long-">pullExecStatistics(String, long)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</a></dt>
 382 <dd>&nbsp;</dd>
 383 <dt><span class="memberNameLink"><a href="../compbio/ws/server/ProbconsWS.html#pullExecStatistics-java.lang.String-long-">pullExecStatistics(String, long)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</a></dt>
 384 <dd>&nbsp;</dd>
 385 <dt><span class="memberNameLink"><a href="../compbio/ws/server/TcoffeeWS.html#pullExecStatistics-java.lang.String-long-">pullExecStatistics(String, long)</a></span> - Method in class compbio.ws.server.<a href="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</a></dt>
 386 <dd>&nbsp;</dd>
 387 <dt><a href="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">PullExecStatisticsResponse</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 388 <dd>&nbsp;</dd>
 389 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#PullExecStatisticsResponse--">PullExecStatisticsResponse()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws">PullExecStatisticsResponse</a></dt>
 390 <dd>&nbsp;</dd>
 391 <dt><span class="memberNameLink"><a href="../compbio/ws/server/WSUtil.html#pullFile-java.lang.String-long-">pullFile(String, long)</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>
 392 <dd>&nbsp;</dd>
 393 <dt><span class="memberNameLink"><a href="../compbio/engine/PulledFileCache.html#put-compbio.engine.FilePuller-">put(FilePuller)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</a></dt>
 394 <dd>
 395 <div class="block">This method allows duplicates to be added.</div>
 396 </dd>
 397 </dl>
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