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  82 <A NAME="_A_"><!-- --></A><H2>\r
  83 <B>A</B></H2>\r
  84 <DL>\r
  85 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#AA"><B>AA</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>Valid Amino acids\r
  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
  89
  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> - \r
  91 Constructor for class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
  92 <DD>&nbsp;\r
  93 <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>&nbsp;<DT><A HREF="../compbio/ws/server/AAConWS.html#AAConWS()"><B>AAConWS()</B></A> - \r
  94 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/AAConWS.html" title="class in compbio.ws.server">AAConWS</A>\r
  95 <DD>&nbsp;\r
  96 <DT><A HREF="../compbio/metadata/RunnerConfig.html#addOption(compbio.metadata.Option)"><B>addOption(Option&lt;T&gt;)</B></A> - \r
  97 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
  98 <DD>Adds Option to the internal list of options\r
  99 <DT><A HREF="../compbio/metadata/Option.html#addOptionNames(java.lang.String...)"><B>addOptionNames(String...)</B></A> - \r
 100 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 101 <DD>Adds an option to the optionName list\r
 102 <DT><A HREF="../compbio/metadata/Parameter.html#addOptionNames(java.lang.String...)"><B>addOptionNames(String...)</B></A> - \r
 103 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
 104 <DD>&nbsp;\r
 105 <DT><A HREF="../compbio/metadata/RunnerConfig.html#addParameter(compbio.metadata.Parameter)"><B>addParameter(Parameter&lt;T&gt;)</B></A> - \r
 106 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 107 <DD>Adds parameter to the internal parameter list\r
 108 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)"><B>addParameter(String)</B></A> - \r
 109 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 110 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 111 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#addParameters(java.util.List)"><B>addParameters(List&lt;String&gt;)</B></A> - \r
 112 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 113 <DD>&nbsp;\r
 114 <DT><A HREF="../compbio/engine/client/Executable.html#addParameters(java.util.List)"><B>addParameters(List&lt;String&gt;)</B></A> - \r
 115 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
 116 <DD>Adds parameter to the list of parameters for a native executable\r
 117 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)"><B>addParameters(List&lt;String&gt;)</B></A> - \r
 118 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 119 <DD>&nbsp;\r
 120 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#addParameters(java.util.List)"><B>addParameters(List&lt;String&gt;)</B></A> - \r
 121 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 122 <DD>&nbsp;\r
 123 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])"><B>addParameters(String[])</B></A> - \r
 124 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 125 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 126 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)"><B>addParameters(List&lt;String&gt;)</B></A> - \r
 127 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 128 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 129 <DT><A HREF="../compbio/runner/msa/Mafft.html#addParameters(java.util.List)"><B>addParameters(List&lt;String&gt;)</B></A> - \r
 130 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>\r
 131 <DD>Mafft input must always be the last parameter!\r
 132 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#addParams(java.util.List)"><B>addParams(List&lt;String&gt;)</B></A> - \r
 133 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 134 <DD>&nbsp;\r
 135 <DT><A HREF="../compbio/metadata/Parameter.html#addPossibleValues(java.lang.String...)"><B>addPossibleValues(String...)</B></A> - \r
 136 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
 137 <DD>&nbsp;\r
 138 <DT><A HREF="../compbio/engine/SubmissionManager.html#addTask(compbio.engine.client.ConfiguredExecutable, java.util.concurrent.Future)"><B>addTask(ConfiguredExecutable&lt;?&gt;, Future&lt;ConfiguredExecutable&lt;?&gt;&gt;)</B></A> - \r
 139 Static method in class compbio.engine.<A HREF="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</A>\r
 140 <DD>&nbsp;\r
 141 <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>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/Align.html#Align()"><B>Align()</B></A> - \r
 142 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws">Align</A>\r
 143 <DD>&nbsp;\r
 144 <DT><A HREF="../compbio/data/msa/MsaWS.html#align(java.util.List)"><B>align(List&lt;FastaSequence&gt;)</B></A> - \r
 145 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
 146 <DD>Align a list of sequences with default settings.\r
 147 <DT><A HREF="../compbio/ws/server/_MsaService.html#align(java.util.List)"><B>align(List&lt;FastaSequence&gt;)</B></A> - \r
 148 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/_MsaService.html" title="class in compbio.ws.server">_MsaService</A>\r
 149 <DD>&nbsp;\r
 150 <DT><A HREF="../compbio/ws/server/ClustalOWS.html#align(java.util.List)"><B>align(List&lt;FastaSequence&gt;)</B></A> - \r
 151 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
 152 <DD>&nbsp;\r
 153 <DT><A HREF="../compbio/ws/server/ClustalWS.html#align(java.util.List)"><B>align(List&lt;FastaSequence&gt;)</B></A> - \r
 154 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 155 <DD>&nbsp;\r
 156 <DT><A HREF="../compbio/ws/server/MafftWS.html#align(java.util.List)"><B>align(List&lt;FastaSequence&gt;)</B></A> - \r
 157 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
 158 <DD>&nbsp;\r
 159 <DT><A HREF="../compbio/ws/server/MuscleWS.html#align(java.util.List)"><B>align(List&lt;FastaSequence&gt;)</B></A> - \r
 160 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
 161 <DD>&nbsp;\r
 162 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#align(java.util.List)"><B>align(List&lt;FastaSequence&gt;)</B></A> - \r
 163 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
 164 <DD>&nbsp;\r
 165 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#align(java.util.List)"><B>align(List&lt;FastaSequence&gt;)</B></A> - \r
 166 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
 167 <DD>&nbsp;\r
 168 <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&lt;FastaSequence&gt;, ConfiguredExecutable&lt;T&gt;, Logger, String, Limit&lt;T&gt;)</B></A> - \r
 169 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
 170 <DD>&nbsp;\r
 171 <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&lt;FastaSequence&gt;, Program, char)</B></A> - \r
 172 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
 173 <DD>&nbsp;\r
 174 <DT><A HREF="../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)"><B>Alignment(List&lt;FastaSequence&gt;, AlignmentMetadata)</B></A> - \r
 175 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
 176 <DD>&nbsp;\r
 177 <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> - \r
 178 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
 179 <DD>&nbsp;\r
 180 <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>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/AlignResponse.html#AlignResponse()"><B>AlignResponse()</B></A> - \r
 181 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws">AlignResponse</A>\r
 182 <DD>&nbsp;\r
 183 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_AA"><B>AMBIGUOUS_AA</B></A> - \r
 184 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 185 <DD>Same as AA pattern but with two additional letters - XU\r
 186 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_NUCLEOTIDE"><B>AMBIGUOUS_NUCLEOTIDE</B></A> - \r
 187 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 188 <DD>Ambiguous nucleotide\r
 189 <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>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/Analize.html#Analize()"><B>Analize()</B></A> - \r
 190 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Analize.html" title="class in compbio.data.msa.jaxws">Analize</A>\r
 191 <DD>&nbsp;\r
 192 <DT><A HREF="../compbio/data/msa/SequenceAnnotation.html#analize(java.util.List)"><B>analize(List&lt;FastaSequence&gt;)</B></A> - \r
 193 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>\r
 194 <DD>Analyse the sequences.\r
 195 <DT><A HREF="../compbio/ws/server/AAConWS.html#analize(java.util.List)"><B>analize(List&lt;FastaSequence&gt;)</B></A> - \r
 196 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/AAConWS.html" title="class in compbio.ws.server">AAConWS</A>\r
 197 <DD>&nbsp;\r
 198 <DT><A HREF="../compbio/ws/server/SequenceAnnotationService.html#analize(java.util.List)"><B>analize(List&lt;FastaSequence&gt;)</B></A> - \r
 199 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</A>\r
 200 <DD>&nbsp;\r
 201 <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&lt;FastaSequence&gt;, ConfiguredExecutable&lt;T&gt;, Logger, String, Limit&lt;T&gt;)</B></A> - \r
 202 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
 203 <DD>&nbsp;\r
 204 <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>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html#AnalizeResponse()"><B>AnalizeResponse()</B></A> - \r
 205 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html" title="class in compbio.data.msa.jaxws">AnalizeResponse</A>\r
 206 <DD>&nbsp;\r
 207 <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>&nbsp;<DT><A HREF="../compbio/stat/servlet/AnnualStat.html#AnnualStat()"><B>AnnualStat()</B></A> - \r
 208 Constructor for class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/AnnualStat.html" title="class in compbio.stat.servlet">AnnualStat</A>\r
 209 <DD>&nbsp;\r
 210 <DT><A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><B>Argument</B></A>&lt;<A HREF="../compbio/metadata/Argument.html" title="type parameter in Argument">T</A>&gt; - 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
 211  allows to set a value<DT><A HREF="../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List)"><B>argumentsToCommandString(List&lt;? extends Option&lt;?&gt;&gt;)</B></A> - \r
 212 Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
 213 <DD>&nbsp;\r
 214 <DT><A HREF="../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List, compbio.metadata.RunnerConfig)"><B>argumentsToCommandString(List&lt;? extends Option&lt;?&gt;&gt;, RunnerConfig&lt;? extends Executable&lt;?&gt;&gt;)</B></A> - \r
 215 Static method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
 216 <DD>&nbsp;\r
 217 <DT><A HREF="../compbio/data/sequence/ScoreManager.html#asMap()"><B>asMap()</B></A> - \r
 218 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
 219 <DD>&nbsp;\r
 220 <DT><A HREF="../compbio/data/sequence/ScoreManager.html#asSet()"><B>asSet()</B></A> - \r
 221 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
 222 <DD>&nbsp;\r
 223 <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,
 224  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> - \r
 225 Constructor for class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
 226 <DD>&nbsp;\r
 227 <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>&nbsp;<DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#AsyncLocalRunner()"><B>AsyncLocalRunner()</B></A> - \r
 228 Constructor for class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
 229 <DD>&nbsp;\r
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