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75 <h2 class="title">O</h2>
77 <dt><span class="memberNameLink"><a href="../compbio/ws/client/WSTester.html#OK">OK</a></span> - Static variable in class compbio.ws.client.<a href="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</a></dt>
79 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/ClustalAlignmentUtil.html#oneLineAlignmentLength">oneLineAlignmentLength</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</a></dt>
81 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#open">open</a></span> - Static variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</a></dt>
83 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#openInputStream-java.lang.String-">openInputStream(String)</a></span> - Static method in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
85 <div class="block">Reads and parses Fasta or Clustal formatted file into a list of
86 FastaSequence objects</div>
88 <dt><span class="memberNameLink"><a href="../compbio/ws/server/RegistryWS.html#operating">operating</a></span> - Static variable in class compbio.ws.server.<a href="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</a></dt>
90 <div class="block">Stores tested and passed (the test) services and their testing time</div>
92 <dt><a href="../compbio/metadata/Option.html" title="class in compbio.metadata"><span class="typeNameLink">Option</span></a><<a href="../compbio/metadata/Option.html" title="type parameter in Option">T</a>> - Class in <a href="../compbio/metadata/package-summary.html">compbio.metadata</a></dt>
94 <div class="block">Command line option/flag or multiple exclusive options with no value.</div>
96 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#Option--">Option()</a></span> - Constructor for class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
98 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#Option-java.lang.String-java.lang.String-">Option(String, String)</a></span> - Constructor for class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
100 <dt><span class="memberNameLink"><a href="../compbio/metadata/Preset.html#option">option</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a></dt>
102 <dt><a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner"><span class="typeNameLink">OptionCombinator</span></a> - Class in <a href="../compbio/runner/package-summary.html">compbio.runner</a></dt>
104 <div class="block">This class solve the following problems.</div>
106 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#OptionCombinator-compbio.metadata.RunnerConfig-">OptionCombinator(RunnerConfig<? extends Executable<?>>)</a></span> - Constructor for class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
108 <dt><span class="memberNameLink"><a href="../compbio/metadata/Option.html#optionNames">optionNames</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a></dt>
110 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAlign.html#options">options</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</a></dt>
112 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomAnalize.html#options">options</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</a></dt>
114 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CustomFold.html#options">options</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CustomFold.html" title="class in compbio.data.msa.jaxws">CustomFold</a></dt>
116 <dt><span class="memberNameLink"><a href="../compbio/metadata/RunnerConfig.html#options">options</a></span> - Variable in class compbio.metadata.<a href="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a></dt>
118 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#optionsToCommandString-java.util.List-">optionsToCommandString(List<Option<?>>)</a></span> - Method in class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
120 <dt><span class="memberNameLink"><a href="../compbio/runner/OptionCombinator.html#optionToCommandString-compbio.metadata.Option-">optionToCommandString(Option<?>)</a></span> - Static method in class compbio.runner.<a href="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</a></dt>
122 <dt><span class="memberNameLink"><a href="../compbio/engine/local/StreamGobbler.html#os">os</a></span> - Variable in class compbio.engine.local.<a href="../compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local">StreamGobbler</a></dt>
124 <dt><span class="memberNameLink"><a href="../compbio/engine/client/RunConfiguration.html#output">output</a></span> - Variable in class compbio.engine.client.<a href="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</a></dt>
126 <div class="block">Output</div>
128 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#OUTPUT">OUTPUT</a></span> - Static variable in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
130 <dt><span class="memberNameLink"><a href="../compbio/engine/client/SkeletalExecutable.html#outputFile">outputFile</a></span> - Variable in class compbio.engine.client.<a href="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></dt>
132 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Constraints.html#outputkey">outputkey</a></span> - Static variable in class compbio.ws.client.<a href="../compbio/ws/client/Constraints.html" title="class in compbio.ws.client">Constraints</a></dt>
134 <dt><span class="memberNameLink"><a href="../compbio/engine/local/StreamGobbler.OutputType.html#OutputType--">OutputType()</a></span> - Constructor for enum compbio.engine.local.<a href="../compbio/engine/local/StreamGobbler.OutputType.html" title="enum in compbio.engine.local">StreamGobbler.OutputType</a></dt>
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