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  83 <B>N</B></H2>\r
  84 <DL>\r
  85 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl"><B>NetNglyc</B></A> - Class in <A HREF="../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A><DD>&nbsp;<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#NetNglyc()"><B>NetNglyc()</B></A> - \r
  86 Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
  87 <DD>&nbsp;\r
  88 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#newCommandBuilder(java.util.List, java.lang.String)"><B>newCommandBuilder(List&lt;? extends Option&lt;T&gt;&gt;, String)</B></A> - \r
  89 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
  90 <DD>This produces the same result as getCommands method.\r
  91 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#newConfExecutable(compbio.engine.client.RunConfiguration)"><B>newConfExecutable(RunConfiguration)</B></A> - \r
  92 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
  93 <DD>&nbsp;\r
  94 <DT><A HREF="../compbio/engine/FilePuller.html#newFilePuller(java.lang.String, int)"><B>newFilePuller(String, int)</B></A> - \r
  95 Static method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
  96 <DD>&nbsp;\r
  97 <DT><A HREF="../compbio/data/sequence/ScoreManager.html#newInstance(java.util.Map)"><B>newInstance(Map&lt;String, Set&lt;Score&gt;&gt;)</B></A> - \r
  98 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
  99 <DD>&nbsp;\r
 100 <DT><A HREF="../compbio/data/sequence/ScoreManager.html#newInstanceSingleScore(java.util.Map)"><B>newInstanceSingleScore(Map&lt;String, Score&gt;)</B></A> - \r
 101 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
 102 <DD>&nbsp;\r
 103 <DT><A HREF="../compbio/data/sequence/ScoreManager.html#newInstanceSingleSequence(java.util.Set)"><B>newInstanceSingleSequence(Set&lt;Score&gt;)</B></A> - \r
 104 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
 105 <DD>&nbsp;\r
 106 <DT><A HREF="../compbio/metadata/LimitExceededException.html#newLimitExceeded(compbio.metadata.Limit, java.util.List)"><B>newLimitExceeded(Limit&lt;?&gt;, List&lt;FastaSequence&gt;)</B></A> - \r
 107 Static method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
 108 <DD>&nbsp;\r
 109 <DT><A HREF="../compbio/engine/FilePuller.html#newProgressPuller(java.lang.String)"><B>newProgressPuller(String)</B></A> - \r
 110 Static method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
 111 <DD>Progress Puller is designed to read 3 characters from the beginning of
 112  the file, nothing more.\r
 113 <DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#newStatCollecton(java.util.Date, java.util.Date)"><B>newStatCollecton(Date, Date)</B></A> - \r
 114 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>\r
 115 <DD>&nbsp;\r
 116 <DT><A HREF="../compbio/data/sequence/FastaReader.html#next()"><B>next()</B></A> - \r
 117 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</A>\r
 118 <DD>Reads the next FastaSequence from the input\r
 119 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#NON_AA"><B>NON_AA</B></A> - \r
 120 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 121 <DD>inversion of AA pattern\r
 122 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#NON_NUCLEOTIDE"><B>NON_NUCLEOTIDE</B></A> - \r
 123 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 124 <DD>Non nucleotide\r
 125 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#NONWORD"><B>NONWORD</B></A> - \r
 126 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 127 <DD>Non word\r
 128 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#NUCLEOTIDE"><B>NUCLEOTIDE</B></A> - \r
 129 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 130 <DD>Nucleotides a, t, g, c, u\r
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