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  75 <h2 class="title">N</h2>
  76 <dl>
  77 <dt><span class="memberNameLink"><a href="../compbio/data/msa/Category.html#name">name</a></span> - Variable in class compbio.data.msa.<a href="../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</a></dt>
  78 <dd>&nbsp;</dd>
  79 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.Parameter.html#name">name</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>
  80 <dd>&nbsp;</dd>
  81 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#name">name</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
  82 <dd>&nbsp;</dd>
  83 <dt><span class="memberNameLink"><a href="../compbio/metadata/Preset.html#name">name</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a></dt>
  84 <dd>&nbsp;</dd>
  85 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#nameValueSeparator">nameValueSeparator</a></span> - Variable in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
  86 <dd>&nbsp;</dd>
  87 <dt><span class="memberNameLink"><a href="../compbio/runner/conservation/AACon.html#ncoreNumber">ncoreNumber</a></span> - Variable in class compbio.runner.conservation.<a href="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a></dt>
  88 <dd>
  89 <div class="block">Number of cores to use, defaults to 1 for local execution or the value of
  90  "jronn.cluster.cpunum" property for cluster execution</div>
  91 </dd>
  92 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Jronn.html#ncoreNumber">ncoreNumber</a></span> - Variable in class compbio.runner.disorder.<a href="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</a></dt>
  93 <dd>&nbsp;</dd>
  94 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/ClustalO.html#ncoreNumber">ncoreNumber</a></span> - Variable in class compbio.runner.msa.<a href="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a></dt>
  95 <dd>
  96 <div class="block">Number of cores to use, defaults to 1 for local execution or the value of
  97  "tcoffee.cluster.cpunum" property for cluster execution</div>
  98 </dd>
  99 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Tcoffee.html#ncoreNumber">ncoreNumber</a></span> - Variable in class compbio.runner.msa.<a href="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</a></dt>
 100 <dd>
 101 <div class="block">Number of cores to use, defaults to 1 for local execution or the value of
 102  "tcoffee.cluster.cpunum" property for cluster execution</div>
 103 </dd>
 104 <dt><span class="memberNameLink"><a href="../compbio/runner/conservation/AACon.html#ncorePrm">ncorePrm</a></span> - Variable in class compbio.runner.conservation.<a href="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a></dt>
 105 <dd>&nbsp;</dd>
 106 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Jronn.html#ncorePrm">ncorePrm</a></span> - Variable in class compbio.runner.disorder.<a href="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</a></dt>
 107 <dd>&nbsp;</dd>
 108 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/ClustalO.html#ncorePrm">ncorePrm</a></span> - Static variable in class compbio.runner.msa.<a href="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a></dt>
 109 <dd>
 110 <div class="block">Number of cores parameter name</div>
 111 </dd>
 112 <dt><span class="memberNameLink"><a href="../compbio/runner/msa/Tcoffee.html#ncorePrm">ncorePrm</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>
 113 <dd>&nbsp;</dd>
 114 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#newCommandBuilder-java.util.List-java.lang.String-">newCommandBuilder(List&lt;? extends Option&lt;T&gt;&gt;, String)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
 115 <dd>
 116 <div class="block">This produces the same result as getCommands method.</div>
 117 </dd>
 118 <dt><span class="memberNameLink"><a href="../compbio/engine/client/ConfExecutable.html#newConfExecutable-compbio.engine.client.RunConfiguration-">newConfExecutable(RunConfiguration)</a></span> - Static method in class compbio.engine.client.<a href="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a></dt>
 119 <dd>&nbsp;</dd>
 120 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#newEmptyScore-java.lang.Enum-">newEmptyScore(Enum&lt;?&gt;)</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>
 121 <dd>&nbsp;</dd>
 122 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#newFilePuller-java.lang.String-int-">newFilePuller(String, int)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
 123 <dd>&nbsp;</dd>
 124 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#newIncompleteStat-java.lang.String-">newIncompleteStat(String)</a></span> - Static method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 125 <dd>&nbsp;</dd>
 126 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructScoreManager.html#newInstance-java.util.List-java.util.List-">newInstance(List&lt;String&gt;, List&lt;TreeSet&lt;Score&gt;&gt;)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructScoreManager.html" title="class in compbio.data.sequence">RNAStructScoreManager</a></dt>
 127 <dd>&nbsp;</dd>
 128 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ScoreManager.html#newInstance-java.util.Map-">newInstance(Map&lt;String, Set&lt;Score&gt;&gt;)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></dt>
 129 <dd>&nbsp;</dd>
 130 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#newInstance-compbio.ws.client.Services-java.lang.String-java.lang.String-long-long-long-long-boolean-boolean-">newInstance(Services, String, String, long, long, long, long, boolean, boolean)</a></span> - Static method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 131 <dd>&nbsp;</dd>
 132 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#newInstance-compbio.ws.client.Services-java.lang.String-java.lang.String-java.sql.Timestamp-java.sql.Timestamp-long-long-boolean-boolean-">newInstance(Services, String, String, Timestamp, Timestamp, long, long, boolean, boolean)</a></span> - Static method in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 133 <dd>&nbsp;</dd>
 134 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ScoreManager.html#newInstanceSingleScore-java.util.Map-">newInstanceSingleScore(Map&lt;String, Score&gt;)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></dt>
 135 <dd>&nbsp;</dd>
 136 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ScoreManager.html#newInstanceSingleSequence-java.util.Set-">newInstanceSingleSequence(Set&lt;Score&gt;)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></dt>
 137 <dd>&nbsp;</dd>
 138 <dt><span class="memberNameLink"><a href="../compbio/metadata/LimitExceededException.html#newLimitExceeded-compbio.metadata.Limit-java.util.List-">newLimitExceeded(Limit&lt;?&gt;, List&lt;FastaSequence&gt;)</a></span> - Static method in exception compbio.metadata.<a href="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></dt>
 139 <dd>&nbsp;</dd>
 140 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#newLine">newLine</a></span> - Static 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>
 141 <dd>&nbsp;</dd>
 142 <dt><span class="memberNameLink"><a href="../compbio/engine/client/CommandBuilder.html#newParameter-java.lang.String-">newParameter(String)</a></span> - Method in class compbio.engine.client.<a href="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a></dt>
 143 <dd>&nbsp;</dd>
 144 <dt><span class="memberNameLink"><a href="../compbio/engine/FilePuller.html#newProgressPuller-java.lang.String-">newProgressPuller(String)</a></span> - Static method in class compbio.engine.<a href="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</a></dt>
 145 <dd>
 146 <div class="block">Progress Puller is designed to read 3 characters from the beginning of
 147  the file, nothing more.</div>
 148 </dd>
 149 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#newSetScore-java.lang.Enum-java.util.List-">newSetScore(Enum&lt;?&gt;, List&lt;Float&gt;)</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>
 150 <dd>&nbsp;</dd>
 151 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/util/StatCollection.html#newStatCollecton-java.util.Date-java.util.Date-">newStatCollecton(Date, Date)</a></span> - Static method in class compbio.stat.servlet.util.<a href="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</a></dt>
 152 <dd>&nbsp;</dd>
 153 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/IUPred.html#newUnsupportedOutputException--">newUnsupportedOutputException()</a></span> - Method in class compbio.runner.disorder.<a href="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</a></dt>
 154 <dd>&nbsp;</dd>
 155 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/FastaReader.html#next--">next()</a></span> - Method in class compbio.data.sequence.<a href="../compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</a></dt>
 156 <dd>
 157 <div class="block">Reads the next FastaSequence from the input</div>
 158 </dd>
 159 <dt><span class="memberNameLink"><a href="../compbio/engine/client/EnvVariableProcessor.html#NEXT_ENV_PROPERTY_DELIMITER">NEXT_ENV_PROPERTY_DELIMITER</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>
 160 <dd>&nbsp;</dd>
 161 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#NON_AA">NON_AA</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 162 <dd>
 163 <div class="block">inversion of AA pattern</div>
 164 </dd>
 165 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#NON_NUCLEOTIDE">NON_NUCLEOTIDE</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 166 <dd>
 167 <div class="block">Non nucleotide</div>
 168 </dd>
 169 <dt><span class="memberNameLink"><a href="../compbio/ws/server/RegistryWS.html#nonoperating">nonoperating</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</a></dt>
 170 <dd>&nbsp;</dd>
 171 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#NONWORD">NONWORD</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 172 <dd>
 173 <div class="block">Non word</div>
 174 </dd>
 175 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#notData">notData</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>
 176 <dd>&nbsp;</dd>
 177 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#NUCLEOTIDE">NUCLEOTIDE</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 178 <dd>
 179 <div class="block">Nucleotides a, t, g, c, u</div>
 180 </dd>
 181 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/Score.html#NUMBER_FORMAT">NUMBER_FORMAT</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a></dt>
 182 <dd>&nbsp;</dd>
 183 <dt><span class="memberNameLink"><a href="../compbio/metadata/Limit.html#numberOfLetters--">numberOfLetters()</a></span> - Method in class compbio.metadata.<a href="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a></dt>
 184 <dd>&nbsp;</dd>
 185 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#numberOfSequencesAllowed">numberOfSequencesAllowed</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>
 186 <dd>&nbsp;</dd>
 187 <dt><span class="memberNameLink"><a href="../compbio/metadata/LimitExceededException.html#numberOfSequencesAllowed">numberOfSequencesAllowed</a></span> - Variable in exception compbio.metadata.<a href="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></dt>
 188 <dd>&nbsp;</dd>
 189 <dt><span class="memberNameLink"><a href="../compbio/engine/local/LocalExecutorService.html#numTasks">numTasks</a></span> - Variable in class compbio.engine.local.<a href="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</a></dt>
 190 <dd>&nbsp;</dd>
 191 </dl>
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 202 <li><a href="../overview-summary.html">Overview</a></li>
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