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  83 <B>I</B></H2>\r
  84 <DL>\r
  85 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isAmbiguosProtein(java.lang.String)"><B>isAmbiguosProtein(String)</B></A> - \r
  86 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
  87 <DD>Check whether the sequence confirms to amboguous protein sequence\r
  88 <DT><A HREF="../compbio/metadata/Limit.html#isDefault()"><B>isDefault()</B></A> - \r
  89 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
  90 <DD>&nbsp;\r
  91 <DT><A HREF="../compbio/metadata/Limit.html#isExceeded(java.util.List)"><B>isExceeded(List&lt;FastaSequence&gt;)</B></A> - \r
  92 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
  93 <DD>Checks if the number of sequences or their average length in the dataset
  94  exceeds this limit.\r
  95 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isNonAmbNucleotideSequence(java.lang.String)"><B>isNonAmbNucleotideSequence(String)</B></A> - \r
  96 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
  97 <DD>Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
  98  (!) - B char\r
  99 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence(compbio.data.sequence.FastaSequence)"><B>isNucleotideSequence(FastaSequence)</B></A> - \r
 100 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 101 <DD>&nbsp;\r
 102 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isProteinSequence(java.lang.String)"><B>isProteinSequence(String)</B></A> - \r
 103 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 104 <DD>&nbsp;\r
 105 <DT><A HREF="../compbio/metadata/Option.html#isRequired"><B>isRequired</B></A> - \r
 106 Variable in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 107 <DD>&nbsp;\r
 108 <DT><A HREF="../compbio/metadata/Option.html#isRequired()"><B>isRequired()</B></A> - \r
 109 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 110 <DD>Flag that indicated that this option must be specified in the command
 111  line for an executable to run\r
 112 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#isValidClustalFile(java.io.InputStream)"><B>isValidClustalFile(InputStream)</B></A> - \r
 113 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
 114 <DD>Please note this method closes the input stream provided as a parameter\r
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