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