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  73 <!--   -->
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  75 <h2 class="title">M</h2>
  76 <dl>
  77 <dt><a href="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa"><span class="typeNameLink">Mafft</span></a> - Class in <a href="../compbio/runner/msa/package-summary.html">compbio.runner.msa</a></dt>
  78 <dd>&nbsp;</dd>
  79 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Mafft.html#Mafft--">Mafft()</a></span> - Constructor for class compbio.runner.msa.<a href="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a></dt>
  80 <dd>&nbsp;</dd>
  81 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EnvVariableProcessor.html#mafft_binaries">mafft_binaries</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>
  82 <dd>&nbsp;</dd>
  83 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#MAFFT_INFO">MAFFT_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>
  84 <dd>&nbsp;</dd>
  85 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MafftWS.html#mafftOptions">mafftOptions</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</a></dt>
  86 <dd>&nbsp;</dd>
  87 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MafftWS.html#mafftPresets">mafftPresets</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</a></dt>
  88 <dd>&nbsp;</dd>
  89 <dt><a href="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server"><span class="typeNameLink">MafftWS</span></a> - Class in <a href="../compbio/ws/server/package-summary.html">compbio.ws.server</a></dt>
  90 <dd>&nbsp;</dd>
  91 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MafftWS.html#MafftWS--">MafftWS()</a></span> - Constructor for class compbio.ws.server.<a href="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</a></dt>
  92 <dd>&nbsp;</dd>
  93 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#main-java.lang.String:A-">main(String[])</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructReader.html" title="class in compbio.data.sequence">RNAStructReader</a></dt>
  94 <dd>&nbsp;</dd>
  95 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/ExecutionStatCollector.html#main-java.lang.String:A-">main(String[])</a></span> - Static method in class compbio.stat.collector.<a href="../compbio/stat/collector/ExecutionStatCollector.html" title="class in compbio.stat.collector">ExecutionStatCollector</a></dt>
  96 <dd>
  97 <div class="block">Not in use</div>
  98 </dd>
  99 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/StatDB.html#main-java.lang.String:A-">main(String[])</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>
 100 <dd>&nbsp;</dd>
 101 <dt><span class="memberNameLink"><a href="../compbio/ws/client/AAConClient.html#main-java.lang.String:A-">main(String[])</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>
 102 <dd>
 103 <div class="block">Starts command line client, if no parameters are supplied prints help.</div>
 104 </dd>
 105 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Jws2Client.html#main-java.lang.String:A-">main(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>
 106 <dd>
 107 <div class="block">Starts command line client, if no parameter are supported print help.</div>
 108 </dd>
 109 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#main-java.lang.String:A-">main(String[])</a></span> - Static method in enum compbio.ws.client.<a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></dt>
 110 <dd>&nbsp;</dd>
 111 <dt><span class="memberNameLink"><a href="../compbio/ws/client/WSTester.html#main-java.lang.String:A-">main(String[])</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>
 112 <dd>
 113 <div class="block">Test JWS2 web services</div>
 114 </dd>
 115 <dt><span class="memberNameLink"><a href="../compbio/ws/server/SimpleWSPublisher.html#main-java.lang.String:A-">main(String[])</a></span> - Static method in class compbio.ws.server.<a href="../compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server">SimpleWSPublisher</a></dt>
 116 <dd>
 117 <div class="block"><span class="deprecatedLabel">Deprecated.</span></div>
 118 &nbsp;</dd>
 119 <dt><a href="../compbio/ws/server/MainManager.html" title="class in compbio.ws.server"><span class="typeNameLink">MainManager</span></a> - Class in <a href="../compbio/ws/server/package-summary.html">compbio.ws.server</a></dt>
 120 <dd>
 121 <div class="block">Two tasks:
 122  1.</div>
 123 </dd>
 124 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MainManager.html#MainManager--">MainManager()</a></span> - Constructor for class compbio.ws.server.<a href="../compbio/ws/server/MainManager.html" title="class in compbio.ws.server">MainManager</a></dt>
 125 <dd>&nbsp;</dd>
 126 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#makeLocalPath-java.lang.String-">makeLocalPath(String)</a></span> - Static 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>
 127 <dd>&nbsp;</dd>
 128 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#makeLocalPath-java.lang.String-">makeLocalPath(String)</a></span> - Static method in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</a></dt>
 129 <dd>&nbsp;</dd>
 130 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Mafft.html#MATRIX_PAR_NAME">MATRIX_PAR_NAME</a></span> - Variable in class compbio.runner.msa.<a href="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a></dt>
 131 <dd>&nbsp;</dd>
 132 <dt><span class="memberNameLink"><a href="../compbio/metadata/ValueConstrain.html#max">max</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</a></dt>
 133 <dd>&nbsp;</dd>
 134 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ClustalAlignmentUtil.html#maxNameLength">maxNameLength</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</a></dt>
 135 <dd>&nbsp;</dd>
 136 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#MAXVALUE">MAXVALUE</a></span> - Static variable in class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
 137 <dd>&nbsp;</dd>
 138 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#maxvmem">maxvmem</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>
 139 <dd>&nbsp;</dd>
 140 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#MEAStructP">MEAStructP</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>
 141 <dd>&nbsp;</dd>
 142 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EngineUtil.html#mergeEnvVariables-java.util.Map-java.util.Map-">mergeEnvVariables(Map&lt;String, String&gt;, Map&lt;String, String&gt;)</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>
 143 <dd>&nbsp;</dd>
 144 <dt><span class="memberNameLink"><a href="../compbio/engine/client/Util.html#mergeEnvVariables-java.util.Map-java.util.Map-">mergeEnvVariables(Map&lt;String, String&gt;, Map&lt;String, String&gt;)</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>
 145 <dd>&nbsp;</dd>
 146 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html#message">message</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobSubmissionExceptionBean</a></dt>
 147 <dd>&nbsp;</dd>
 148 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#message">message</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</a></dt>
 149 <dd>&nbsp;</dd>
 150 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html#message">message</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws">ResultNotAvailableExceptionBean</a></dt>
 151 <dd>&nbsp;</dd>
 152 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html#message">message</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html" title="class in compbio.data.msa.jaxws">UnsupportedRuntimeExceptionBean</a></dt>
 153 <dd>&nbsp;</dd>
 154 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html#message">message</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws">WrongParameterExceptionBean</a></dt>
 155 <dd>&nbsp;</dd>
 156 <dt><a href="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa"><span class="typeNameLink">Metadata</span></a>&lt;<a href="../compbio/data/msa/Metadata.html" title="type parameter in Metadata">T</a>&gt; - Interface in <a href="../compbio/data/msa/package-summary.html">compbio.data.msa</a></dt>
 157 <dd>&nbsp;</dd>
 158 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Alignment.html#metadata">metadata</a></span> - Variable in class compbio.data.sequence.<a href="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></dt>
 159 <dd>&nbsp;</dd>
 160 <dt><a href="../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client"><span class="typeNameLink">MetadataHelper</span></a> - Class in <a href="../compbio/ws/client/package-summary.html">compbio.ws.client</a></dt>
 161 <dd>&nbsp;</dd>
 162 <dt><span class="memberNameLink"><a href="../compbio/ws/client/MetadataHelper.html#MetadataHelper--">MetadataHelper()</a></span> - Constructor for class compbio.ws.client.<a href="../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client">MetadataHelper</a></dt>
 163 <dd>&nbsp;</dd>
 164 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Score.html#method">method</a></span> - Variable in class compbio.data.sequence.<a href="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a></dt>
 165 <dd>&nbsp;</dd>
 166 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#mfeStructP">mfeStructP</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>
 167 <dd>&nbsp;</dd>
 168 <dt><span class="memberNameLink"><a href="../compbio/metadata/ValueConstrain.html#min">min</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</a></dt>
 169 <dd>&nbsp;</dd>
 170 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ClustalAlignmentUtil.html#minNameHolderLength">minNameHolderLength</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</a></dt>
 171 <dd>&nbsp;</dd>
 172 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#MINVALUE">MINVALUE</a></span> - Static variable in class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
 173 <dd>&nbsp;</dd>
 174 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.ServiceInfo.html#moreinfo">moreinfo</a></span> - Variable in class compbio.ws.client.<a href="../compbio/ws/client/Services.ServiceInfo.html" title="class in compbio.ws.client">Services.ServiceInfo</a></dt>
 175 <dd>&nbsp;</dd>
 176 <dt><a href="../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa"><span class="typeNameLink">MSAprobs</span></a> - Class in <a href="../compbio/runner/msa/package-summary.html">compbio.runner.msa</a></dt>
 177 <dd>&nbsp;</dd>
 178 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/MSAprobs.html#MSAprobs--">MSAprobs()</a></span> - Constructor for class compbio.runner.msa.<a href="../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a></dt>
 179 <dd>&nbsp;</dd>
 180 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#MSAPROBS_INFO">MSAPROBS_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>
 181 <dd>&nbsp;</dd>
 182 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MSAprobsWS.html#MSAprobsOptions">MSAprobsOptions</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/MSAprobsWS.html" title="class in compbio.ws.server">MSAprobsWS</a></dt>
 183 <dd>&nbsp;</dd>
 184 <dt><a href="../compbio/ws/server/MSAprobsWS.html" title="class in compbio.ws.server"><span class="typeNameLink">MSAprobsWS</span></a> - Class in <a href="../compbio/ws/server/package-summary.html">compbio.ws.server</a></dt>
 185 <dd>&nbsp;</dd>
 186 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MSAprobsWS.html#MSAprobsWS--">MSAprobsWS()</a></span> - Constructor for class compbio.ws.server.<a href="../compbio/ws/server/MSAprobsWS.html" title="class in compbio.ws.server">MSAprobsWS</a></dt>
 187 <dd>&nbsp;</dd>
 188 <dt><a href="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><span class="typeNameLink">MsaWS</span></a>&lt;<a href="../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</a>&gt; - Interface in <a href="../compbio/data/msa/package-summary.html">compbio.data.msa</a></dt>
 189 <dd>
 190 <div class="block">Multiple Sequence Alignment (MSA) Web Services Interface</div>
 191 </dd>
 192 <dt><a href="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa"><span class="typeNameLink">Muscle</span></a> - Class in <a href="../compbio/runner/msa/package-summary.html">compbio.runner.msa</a></dt>
 193 <dd>&nbsp;</dd>
 194 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Muscle.html#Muscle--">Muscle()</a></span> - Constructor for class compbio.runner.msa.<a href="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</a></dt>
 195 <dd>
 196 <div class="block">Default options are
 197
 198  -clwstrict - write output in clustal format</div>
 199 </dd>
 200 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#MUSCLE_INFO">MUSCLE_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>
 201 <dd>&nbsp;</dd>
 202 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MuscleWS.html#muscleOptions">muscleOptions</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</a></dt>
 203 <dd>&nbsp;</dd>
 204 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MuscleWS.html#musclePresets">musclePresets</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</a></dt>
 205 <dd>&nbsp;</dd>
 206 <dt><a href="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server"><span class="typeNameLink">MuscleWS</span></a> - Class in <a href="../compbio/ws/server/package-summary.html">compbio.ws.server</a></dt>
 207 <dd>&nbsp;</dd>
 208 <dt><span class="memberNameLink"><a href="../compbio/ws/server/MuscleWS.html#MuscleWS--">MuscleWS()</a></span> - Constructor for class compbio.ws.server.<a href="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</a></dt>
 209 <dd>&nbsp;</dd>
 210 <dt><span class="memberNameLink"><a href="../compbio/engine/conf/RunnerConfigMarshaller.MySchemaOutputResolver.html#MySchemaOutputResolver-java.lang.String-java.lang.String-">MySchemaOutputResolver(String, String)</a></span> - Constructor for class compbio.engine.conf.<a href="../compbio/engine/conf/RunnerConfigMarshaller.MySchemaOutputResolver.html" title="class in compbio.engine.conf">RunnerConfigMarshaller.MySchemaOutputResolver</a></dt>
 211 <dd>&nbsp;</dd>
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