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82 <A NAME="_A_"><!-- --></A><H2>
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85 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#AA"><B>AA</B></A> -
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86 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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87 <DD>Valid Amino acids
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88 <DT><A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation"><B>AACon</B></A> - Class in <A HREF="../compbio/runner/conservation/package-summary.html">compbio.runner.conservation</A><DD>Command line
90 java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out<DT><A HREF="../compbio/runner/conservation/AACon.html#AACon()"><B>AACon()</B></A> -
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91 Constructor for class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>
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93 <DT><A HREF="../compbio/ws/client/Services.html#AACON_INFO"><B>AACON_INFO</B></A> -
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94 Static variable in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>
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96 <DT><A HREF="../compbio/ws/client/AAConClient.html" title="class in compbio.ws.client"><B>AAConClient</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>A command line client for AACon web service<DT><A HREF="../compbio/ws/server/AAConWS.html" title="class in compbio.ws.server"><B>AAConWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD> <DT><A HREF="../compbio/ws/server/AAConWS.html#AAConWS()"><B>AAConWS()</B></A> -
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97 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/AAConWS.html" title="class in compbio.ws.server">AAConWS</A>
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99 <DT><A HREF="../compbio/metadata/RunnerConfig.html#addOption(compbio.metadata.Option)"><B>addOption(Option<T>)</B></A> -
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100 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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101 <DD>Adds Option to the internal list of options
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102 <DT><A HREF="../compbio/metadata/Option.html#addOptionNames(java.lang.String...)"><B>addOptionNames(String...)</B></A> -
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103 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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104 <DD>Adds an option to the optionName list
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105 <DT><A HREF="../compbio/metadata/Parameter.html#addOptionNames(java.lang.String...)"><B>addOptionNames(String...)</B></A> -
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106 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
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108 <DT><A HREF="../compbio/metadata/RunnerConfig.html#addParameter(compbio.metadata.Parameter)"><B>addParameter(Parameter<T>)</B></A> -
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109 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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110 <DD>Adds parameter to the internal parameter list
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111 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)"><B>addParameter(String)</B></A> -
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112 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>
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113 <DD><B>Deprecated.</B>
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114 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#addParameters(java.util.List)"><B>addParameters(List<String>)</B></A> -
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115 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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117 <DT><A HREF="../compbio/engine/client/Executable.html#addParameters(java.util.List)"><B>addParameters(List<String>)</B></A> -
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118 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>
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119 <DD>Adds parameter to the list of parameters for a native executable
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120 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)"><B>addParameters(List<String>)</B></A> -
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121 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>
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123 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#addParameters(java.util.List)"><B>addParameters(List<String>)</B></A> -
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124 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>
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126 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])"><B>addParameters(String[])</B></A> -
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127 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>
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128 <DD><B>Deprecated.</B>
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129 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)"><B>addParameters(List<String>)</B></A> -
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130 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>
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131 <DD><B>Deprecated.</B>
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132 <DT><A HREF="../compbio/runner/msa/Mafft.html#addParameters(java.util.List)"><B>addParameters(List<String>)</B></A> -
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133 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>
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134 <DD>Mafft input must always be the last parameter!
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135 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#addParams(java.util.List)"><B>addParams(List<String>)</B></A> -
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136 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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138 <DT><A HREF="../compbio/metadata/Parameter.html#addPossibleValues(java.lang.String...)"><B>addPossibleValues(String...)</B></A> -
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139 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
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141 <DT><A HREF="../compbio/engine/SubmissionManager.html#addTask(compbio.engine.client.ConfiguredExecutable, java.util.concurrent.Future)"><B>addTask(ConfiguredExecutable<?>, Future<ConfiguredExecutable<?>>)</B></A> -
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142 Static method in class compbio.engine.<A HREF="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</A>
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144 <DT><A HREF="../compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws"><B>Align</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/Align.html#Align()"><B>Align()</B></A> -
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145 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws">Align</A>
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147 <DT><A HREF="../compbio/data/msa/MsaWS.html#align(java.util.List)"><B>align(List<FastaSequence>)</B></A> -
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148 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>
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149 <DD>Align a list of sequences with default settings.
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150 <DT><A HREF="../compbio/ws/server/_MsaService.html#align(java.util.List)"><B>align(List<FastaSequence>)</B></A> -
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151 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/_MsaService.html" title="class in compbio.ws.server">_MsaService</A>
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153 <DT><A HREF="../compbio/ws/server/ClustalOWS.html#align(java.util.List)"><B>align(List<FastaSequence>)</B></A> -
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154 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>
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156 <DT><A HREF="../compbio/ws/server/ClustalWS.html#align(java.util.List)"><B>align(List<FastaSequence>)</B></A> -
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157 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>
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159 <DT><A HREF="../compbio/ws/server/MafftWS.html#align(java.util.List)"><B>align(List<FastaSequence>)</B></A> -
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160 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>
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162 <DT><A HREF="../compbio/ws/server/MuscleWS.html#align(java.util.List)"><B>align(List<FastaSequence>)</B></A> -
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163 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>
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165 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#align(java.util.List)"><B>align(List<FastaSequence>)</B></A> -
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166 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>
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168 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#align(java.util.List)"><B>align(List<FastaSequence>)</B></A> -
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169 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>
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171 <DT><A HREF="../compbio/ws/server/WSUtil.html#align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, java.lang.String, compbio.metadata.Limit)"><B>align(List<FastaSequence>, ConfiguredExecutable<T>, Logger, String, Limit<T>)</B></A> -
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172 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>
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174 <DT><A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence"><B>Alignment</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Multiple sequence alignment.<DT><A HREF="../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)"><B>Alignment(List<FastaSequence>, Program, char)</B></A> -
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175 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>
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177 <DT><A HREF="../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)"><B>Alignment(List<FastaSequence>, AlignmentMetadata)</B></A> -
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178 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>
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180 <DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>AlignmentMetadata</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Alignment metadata e.g.<DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#AlignmentMetadata(compbio.data.sequence.Program, char)"><B>AlignmentMetadata(Program, char)</B></A> -
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181 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>
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183 <DT><A HREF="../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws"><B>AlignResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/AlignResponse.html#AlignResponse()"><B>AlignResponse()</B></A> -
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184 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws">AlignResponse</A>
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186 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_AA"><B>AMBIGUOUS_AA</B></A> -
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187 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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188 <DD>Same as AA pattern but with two additional letters - XU
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189 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_NUCLEOTIDE"><B>AMBIGUOUS_NUCLEOTIDE</B></A> -
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190 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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191 <DD>Ambiguous nucleotide
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192 <DT><A HREF="../compbio/data/msa/jaxws/Analize.html" title="class in compbio.data.msa.jaxws"><B>Analize</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/Analize.html#Analize()"><B>Analize()</B></A> -
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193 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Analize.html" title="class in compbio.data.msa.jaxws">Analize</A>
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195 <DT><A HREF="../compbio/data/msa/SequenceAnnotation.html#analize(java.util.List)"><B>analize(List<FastaSequence>)</B></A> -
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196 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>
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197 <DD>Analyse the sequences.
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198 <DT><A HREF="../compbio/ws/server/AAConWS.html#analize(java.util.List)"><B>analize(List<FastaSequence>)</B></A> -
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199 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/AAConWS.html" title="class in compbio.ws.server">AAConWS</A>
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201 <DT><A HREF="../compbio/ws/server/SequenceAnnotationService.html#analize(java.util.List)"><B>analize(List<FastaSequence>)</B></A> -
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202 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</A>
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204 <DT><A HREF="../compbio/ws/server/WSUtil.html#analize(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, java.lang.String, compbio.metadata.Limit)"><B>analize(List<FastaSequence>, ConfiguredExecutable<T>, Logger, String, Limit<T>)</B></A> -
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205 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>
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207 <DT><A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html" title="class in compbio.data.msa.jaxws"><B>AnalizeResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html#AnalizeResponse()"><B>AnalizeResponse()</B></A> -
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208 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html" title="class in compbio.data.msa.jaxws">AnalizeResponse</A>
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210 <DT><A HREF="../compbio/stat/servlet/AnnualStat.html" title="class in compbio.stat.servlet"><B>AnnualStat</B></A> - Class in <A HREF="../compbio/stat/servlet/package-summary.html">compbio.stat.servlet</A><DD> <DT><A HREF="../compbio/stat/servlet/AnnualStat.html#AnnualStat()"><B>AnnualStat()</B></A> -
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211 Constructor for class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/AnnualStat.html" title="class in compbio.stat.servlet">AnnualStat</A>
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213 <DT><A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><B>Argument</B></A><<A HREF="../compbio/metadata/Argument.html" title="type parameter in Argument">T</A>> - Interface in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>An unmodifiable view for the options and parameters, with one exception - it
214 allows to set a value<DT><A HREF="../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List)"><B>argumentsToCommandString(List<? extends Option<?>>)</B></A> -
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215 Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>
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217 <DT><A HREF="../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List, compbio.metadata.RunnerConfig)"><B>argumentsToCommandString(List<? extends Option<?>>, RunnerConfig<? extends Executable<?>>)</B></A> -
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218 Static method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>
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220 <DT><A HREF="../compbio/data/sequence/ScoreManager.html#asMap()"><B>asMap()</B></A> -
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221 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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223 <DT><A HREF="../compbio/data/sequence/ScoreManager.html#asSet()"><B>asSet()</B></A> -
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224 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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226 <DT><A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine"><B>AsyncExecutor</B></A> - Interface in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>An asynchronous executor engine, capable of running, cancelling,
227 obtaining results calculated by a native executable wrapper in Executable interface.<DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa"><B>AsyncJobRunner</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD>Single cluster job runner class<DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#AsyncJobRunner()"><B>AsyncJobRunner()</B></A> -
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228 Constructor for class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>
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230 <DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local"><B>AsyncLocalRunner</B></A> - Class in <A HREF="../compbio/engine/local/package-summary.html">compbio.engine.local</A><DD> <DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#AsyncLocalRunner()"><B>AsyncLocalRunner()</B></A> -
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231 Constructor for class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>
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237 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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238 <A NAME="navbar_bottom"><!-- --></A>
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247 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
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248 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
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