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82 <A NAME="_R_"><!-- --></A><H2>
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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> <DT><A HREF="../compbio/data/sequence/Range.html#Range(int, int)"><B>Range(int, int)</B></A> -
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86 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>
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88 <DT><A HREF="../compbio/data/sequence/Range.html#Range(java.lang.String[])"><B>Range(String[])</B></A> -
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89 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>
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91 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readAAConResults(java.io.InputStream)"><B>readAAConResults(InputStream)</B></A> -
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92 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>
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93 <DD>Read AACon result with no alignment files.
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94 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)"><B>readClustalFile(InputStream)</B></A> -
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95 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>
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96 <DD>Read Clustal formatted alignment.
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97 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)"><B>readClustalFile(File)</B></A> -
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98 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>
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100 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readDisembl(java.io.InputStream)"><B>readDisembl(InputStream)</B></A> -
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101 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>
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102 <DD>> Foobar_dundeefriends
104 # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
110 # RESIDUE COILS REM465 HOTLOOPS
112 M 0.86010 0.88512 0.37094
114 T 0.79983 0.85864 0.44331
116 >Next Sequence name
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117 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)"><B>readFasta(InputStream)</B></A> -
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118 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>
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119 <DD>Reads fasta sequences from inStream into the list of FastaSequence
121 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readGlobPlot(java.io.InputStream)"><B>readGlobPlot(InputStream)</B></A> -
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122 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>
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123 <DD>> Foobar_dundeefriends
125 # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
131 # RESIDUE COILS REM465 HOTLOOPS
133 M 0.86010 0.88512 0.37094
135 T 0.79983 0.85864 0.44331
137 >Next Sequence name
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138 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readIUPred(java.io.File)"><B>readIUPred(File)</B></A> -
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139 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>
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140 <DD>Read IUPred output
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141 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.File)"><B>readJRonn(File)</B></A> -
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142 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>
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144 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.InputStream)"><B>readJRonn(InputStream)</B></A> -
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145 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>
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146 <DD>Reader for JRonn horizontal file format
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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> -
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148 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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149 <DD>Not implemented
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150 <DT><A HREF="../compbio/metadata/RunnerConfig.html#removeArgument(java.lang.String)"><B>removeArgument(String)</B></A> -
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151 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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152 <DD>Removes the argument <A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> if found.
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153 <DT><A HREF="../compbio/metadata/RunnerConfig.html#removeArgumentByOptionName(java.lang.String)"><B>removeArgumentByOptionName(String)</B></A> -
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154 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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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
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> -
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160 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>
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162 <DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.Throwable)"><B>ResultNotAvailableException(Throwable)</B></A> -
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163 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>
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165 <DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String, java.lang.Throwable)"><B>ResultNotAvailableException(String, Throwable)</B></A> -
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166 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>
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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> -
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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>
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171 <DT><A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><B>RunnerConfig</B></A><<A HREF="../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> - 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> -
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172 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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