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  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/metadata/RunnerConfig.html#addOption(compbio.metadata.Option)"><B>addOption(Option&lt;T&gt;)</B></A> - \r
  89 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
  90 <DD>&nbsp;\r
  91 <DT><A HREF="../compbio/metadata/Option.html#addOptionNames(java.lang.String...)"><B>addOptionNames(String...)</B></A> - \r
  92 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
  93 <DD>Adds an option to the optionName list\r
  94 <DT><A HREF="../compbio/metadata/Parameter.html#addOptionNames(java.lang.String...)"><B>addOptionNames(String...)</B></A> - \r
  95 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
  96 <DD>&nbsp;\r
  97 <DT><A HREF="../compbio/metadata/RunnerConfig.html#addParameter(compbio.metadata.Parameter)"><B>addParameter(Parameter&lt;T&gt;)</B></A> - \r
  98 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
  99 <DD>&nbsp;\r
 100 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)"><B>addParameter(String)</B></A> - \r
 101 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 102 <DD>&nbsp;\r
 103 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#addParameters(java.util.List)"><B>addParameters(List&lt;String&gt;)</B></A> - \r
 104 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 105 <DD>&nbsp;\r
 106 <DT><A HREF="../compbio/engine/client/Executable.html#addParameters(java.util.List)"><B>addParameters(List&lt;String&gt;)</B></A> - \r
 107 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
 108 <DD>Adds parameter to the list of parameters for a native executable\r
 109 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)"><B>addParameters(List&lt;String&gt;)</B></A> - \r
 110 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 111 <DD>&nbsp;\r
 112 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#addParameters(java.util.List)"><B>addParameters(List&lt;String&gt;)</B></A> - \r
 113 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 114 <DD>&nbsp;\r
 115 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])"><B>addParameters(String[])</B></A> - \r
 116 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 117 <DD>&nbsp;\r
 118 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)"><B>addParameters(List&lt;String&gt;)</B></A> - \r
 119 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 120 <DD>&nbsp;\r
 121 <DT><A HREF="../compbio/runner/msa/Mafft.html#addParameters(java.util.List)"><B>addParameters(List&lt;String&gt;)</B></A> - \r
 122 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>\r
 123 <DD>Mafft input must always be the last parameter!\r
 124 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#addParams(java.util.List)"><B>addParams(List&lt;String&gt;)</B></A> - \r
 125 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 126 <DD>&nbsp;\r
 127 <DT><A HREF="../compbio/metadata/Parameter.html#addPossibleValues(java.lang.String...)"><B>addPossibleValues(String...)</B></A> - \r
 128 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
 129 <DD>&nbsp;\r
 130 <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
 131 Static method in class compbio.engine.<A HREF="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</A>\r
 132 <DD>&nbsp;\r
 133 <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
 134 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
 135 <DD>&nbsp;\r
 136 <DT><A HREF="../compbio/data/msa/MsaWS.html#align(java.util.List)"><B>align(List&lt;FastaSequence&gt;)</B></A> - \r
 137 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
 138 <DD>Align a list of sequences with default settings.\r
 139 <DT><A HREF="../compbio/ws/server/ClustalWS.html#align(java.util.List)"><B>align(List&lt;FastaSequence&gt;)</B></A> - \r
 140 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 141 <DD>&nbsp;\r
 142 <DT><A HREF="../compbio/ws/server/MafftWS.html#align(java.util.List)"><B>align(List&lt;FastaSequence&gt;)</B></A> - \r
 143 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
 144 <DD>&nbsp;\r
 145 <DT><A HREF="../compbio/ws/server/MuscleWS.html#align(java.util.List)"><B>align(List&lt;FastaSequence&gt;)</B></A> - \r
 146 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
 147 <DD>&nbsp;\r
 148 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#align(java.util.List)"><B>align(List&lt;FastaSequence&gt;)</B></A> - \r
 149 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
 150 <DD>&nbsp;\r
 151 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#align(java.util.List)"><B>align(List&lt;FastaSequence&gt;)</B></A> - \r
 152 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
 153 <DD>&nbsp;\r
 154 <DT><A HREF="../compbio/ws/server/WSUtil.html#align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String, compbio.metadata.Limit)"><B>align(List&lt;FastaSequence&gt;, ConfiguredExecutable&lt;T&gt;, Logger, WebServiceContext, String, Limit&lt;T&gt;)</B></A> - \r
 155 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
 156 <DD>&nbsp;\r
 157 <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
 158 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
 159 <DD>&nbsp;\r
 160 <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
 161 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
 162 <DD>&nbsp;\r
 163 <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
 164 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
 165 <DD>&nbsp;\r
 166 <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
 167 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
 168 <DD>&nbsp;\r
 169 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_AA"><B>AMBIGUOUS_AA</B></A> - \r
 170 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 171 <DD>Same as AA pattern but with two additional letters - XU\r
 172 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_NUCLEOTIDE"><B>AMBIGUOUS_NUCLEOTIDE</B></A> - \r
 173 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 174 <DD>Ambiguous nucleotide\r
 175 <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
 176  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
 177 Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
 178 <DD>&nbsp;\r
 179 <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
 180 Static method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
 181 <DD>&nbsp;\r
 182 <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,
 183  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
 184 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
 185 <DD>&nbsp;\r
 186 <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
 187 Constructor for class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
 188 <DD>&nbsp;\r
 189 <DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#awaitTermination(long, java.util.concurrent.TimeUnit)"><B>awaitTermination(long, TimeUnit)</B></A> - \r
 190 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
 191 <DD>&nbsp;\r
 192 </DL>\r
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