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  84 <DL>\r
  85 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#WHITE_SPACE"><B>WHITE_SPACE</B></A> - \r
  86 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
  87 <DD>A whitespace character: [\t\n\x0B\f\r]\r
  88 <DT><A HREF="../compbio/data/sequence/Score.html#write(java.util.TreeSet, java.io.Writer)"><B>write(TreeSet&lt;Score&gt;, Writer)</B></A> - \r
  89 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
  90 <DD>Outputs the List of Score objects into the Output stream.\r
  91 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment(java.io.Writer, compbio.data.sequence.Alignment)"><B>writeClustalAlignment(Writer, Alignment)</B></A> - \r
  92 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
  93 <DD>Write Clustal formatted alignment Limitations: does not record the
  94  consensus.\r
  95 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List, int)"><B>writeFasta(OutputStream, List&lt;FastaSequence&gt;, int)</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>Writes list of FastaSequeces into the outstream formatting the sequence
  98  so that it contains width chars on each line\r
  99 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List)"><B>writeFasta(OutputStream, List&lt;FastaSequence&gt;)</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>Writes FastaSequence in the file, each sequence will take one line only\r
 102 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#writeFastaKeepTheStream(java.io.OutputStream, java.util.List, int)"><B>writeFastaKeepTheStream(OutputStream, List&lt;FastaSequence&gt;, int)</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/data/sequence/ScoreManager.ScoreHolder.html#writeOut(java.io.Writer)"><B>writeOut(Writer)</B></A> - \r
 106 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
 107 <DD>&nbsp;\r
 108 <DT><A HREF="../compbio/data/sequence/ScoreManager.html#writeOut(java.io.Writer)"><B>writeOut(Writer)</B></A> - \r
 109 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
 110 <DD>&nbsp;\r
 111 <DT><A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata"><B>WrongParameterException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>WrongParameterException is thrown wherever the <A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
 112  does not match the actual runnable or then attempting to set the value of
 113  <A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.<DT><A HREF="../compbio/metadata/WrongParameterException.html#WrongParameterException(compbio.metadata.Option)"><B>WrongParameterException(Option&lt;?&gt;)</B></A> - \r
 114 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
 115 <DD>&nbsp;\r
 116 <DT><A HREF="../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.String)"><B>WrongParameterException(String)</B></A> - \r
 117 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
 118 <DD>&nbsp;\r
 119 <DT><A HREF="../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.Throwable)"><B>WrongParameterException(Throwable)</B></A> - \r
 120 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
 121 <DD>&nbsp;\r
 122 <DT><A HREF="../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.String, java.lang.Throwable)"><B>WrongParameterException(String, Throwable)</B></A> - \r
 123 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
 124 <DD>&nbsp;\r
 125 <DT><A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>WrongParameterExceptionBean</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>This class was generated by the JAX-WS RI.<DT><A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html#WrongParameterExceptionBean()"><B>WrongParameterExceptionBean()</B></A> - \r
 126 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws">WrongParameterExceptionBean</A>\r
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 129 Constructor for class compbio.ws.client.<A HREF="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A>\r
 130 <DD>Construct an instance of JABAWS tester\r
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