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  83 <B>R</B></H2>\r
  84 <DL>\r
  85 <DT><A HREF="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence"><B>Range</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>&nbsp;<DT><A HREF="../compbio/data/sequence/Range.html#Range(int, int)"><B>Range(int, int)</B></A> - \r
  86 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>\r
  87 <DD>&nbsp;\r
  88 <DT><A HREF="../compbio/data/sequence/Range.html#Range(java.lang.String[])"><B>Range(String[])</B></A> - \r
  89 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>\r
  90 <DD>&nbsp;\r
  91 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readAAConResults(java.io.InputStream)"><B>readAAConResults(InputStream)</B></A> - \r
  92 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
  93 <DD>Read AACon result with no alignment files.\r
  94 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)"><B>readClustalFile(InputStream)</B></A> - \r
  95 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
  96 <DD>Read Clustal formatted alignment.\r
  97 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)"><B>readClustalFile(File)</B></A> - \r
  98 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
  99 <DD>&nbsp;\r
 100 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readDisembl(java.io.InputStream)"><B>readDisembl(InputStream)</B></A> - \r
 101 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 102 <DD>> Foobar_dundeefriends
 103
 104  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
 105
 106  # REM465 355-368
 107
 108  # HOTLOOPS 190-204
 109
 110  # RESIDUE COILS REM465 HOTLOOPS
 111
 112  M 0.86010 0.88512 0.37094
 113
 114  T 0.79983 0.85864 0.44331
 115
 116  >Next Sequence name\r
 117 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)"><B>readFasta(InputStream)</B></A> - \r
 118 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 119 <DD>Reads fasta sequences from inStream into the list of FastaSequence
 120  objects\r
 121 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readGlobPlot(java.io.InputStream)"><B>readGlobPlot(InputStream)</B></A> - \r
 122 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 123 <DD>> Foobar_dundeefriends
 124
 125  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
 126
 127  # REM465 355-368
 128
 129  # HOTLOOPS 190-204
 130
 131  # RESIDUE COILS REM465 HOTLOOPS
 132
 133  M 0.86010 0.88512 0.37094
 134
 135  T 0.79983 0.85864 0.44331
 136
 137  >Next Sequence name\r
 138 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readIUPred(java.io.File)"><B>readIUPred(File)</B></A> - \r
 139 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 140 <DD>Read IUPred output\r
 141 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.File)"><B>readJRonn(File)</B></A> - \r
 142 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 143 <DD>&nbsp;\r
 144 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.InputStream)"><B>readJRonn(InputStream)</B></A> - \r
 145 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 146 <DD>Reader for JRonn horizontal file format\r
 147 <DT><A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa"><B>RegistryWS</B></A> - Interface in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD>JABAWS services registry<DT><A HREF="../compbio/data/sequence/FastaReader.html#remove()"><B>remove()</B></A> - \r
 148 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</A>\r
 149 <DD>Not implemented\r
 150 <DT><A HREF="../compbio/metadata/RunnerConfig.html#removeArgument(java.lang.String)"><B>removeArgument(String)</B></A> - \r
 151 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 152 <DD>Removes the argument <A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> if found.\r
 153 <DT><A HREF="../compbio/metadata/RunnerConfig.html#removeArgumentByOptionName(java.lang.String)"><B>removeArgumentByOptionName(String)</B></A> - \r
 154 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 155 <DD>Removes the argument which can be a Parameter or an Option instance by
 156  the value in <optionNames> element of the runner configuration
 157  descriptor.\r
 158 <DT><A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>ResultNotAvailableException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>ResultNotAvailableException is thrown wherever the results of the calculation
 159  cannot be obtained.<DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String)"><B>ResultNotAvailableException(String)</B></A> - \r
 160 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
 161 <DD>&nbsp;\r
 162 <DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.Throwable)"><B>ResultNotAvailableException(Throwable)</B></A> - \r
 163 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
 164 <DD>&nbsp;\r
 165 <DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String, java.lang.Throwable)"><B>ResultNotAvailableException(String, Throwable)</B></A> - \r
 166 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
 167 <DD>&nbsp;\r
 168 <DT><A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>ResultNotAvailableExceptionBean</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/ResultNotAvailableExceptionBean.html#ResultNotAvailableExceptionBean()"><B>ResultNotAvailableExceptionBean()</B></A> - \r
 169 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws">ResultNotAvailableExceptionBean</A>\r
 170 <DD>&nbsp;\r
 171 <DT><A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><B>RunnerConfig</B></A>&lt;<A HREF="../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt; - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>The list of <A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.<DT><A HREF="../compbio/metadata/RunnerConfig.html#RunnerConfig()"><B>RunnerConfig()</B></A> - \r
 172 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 173 <DD>&nbsp;\r
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