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  82 <A NAME="_T_"><!-- --></A><H2>\r
  83 <B>T</B></H2>\r
  84 <DL>\r
  85 <DT><A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa"><B>Tcoffee</B></A> - Class in <A HREF="../compbio/runner/msa/package-summary.html">compbio.runner.msa</A><DD>&nbsp;<DT><A HREF="../compbio/runner/msa/Tcoffee.html#Tcoffee()"><B>Tcoffee()</B></A> - \r
  86 Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
  87 <DD>&nbsp;\r
  88 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server"><B>TcoffeeWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#TcoffeeWS()"><B>TcoffeeWS()</B></A> - \r
  89 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
  90 <DD>&nbsp;\r
  91 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#termSignal()"><B>termSignal()</B></A> - \r
  92 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
  93 <DD>&nbsp;\r
  94 <DT><A HREF="../compbio/metadata/Option.html#toCommand(java.lang.String)"><B>toCommand(String)</B></A> - \r
  95 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
  96 <DD>Convert the option to the command string.\r
  97 <DT><A HREF="../compbio/metadata/Parameter.html#toCommand(java.lang.String)"><B>toCommand(String)</B></A> - \r
  98 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
  99 <DD>&nbsp;\r
 100 <DT><A HREF="../compbio/data/sequence/Alignment.html#toString()"><B>toString()</B></A> - \r
 101 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
 102 <DD>&nbsp;\r
 103 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#toString()"><B>toString()</B></A> - \r
 104 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
 105 <DD>Same as oneLineFasta\r
 106 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#toString()"><B>toString()</B></A> - \r
 107 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 108 <DD>&nbsp;\r
 109 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#toString()"><B>toString()</B></A> - \r
 110 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 111 <DD>&nbsp;\r
 112 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#toString()"><B>toString()</B></A> - \r
 113 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 114 <DD>&nbsp;\r
 115 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#toString()"><B>toString()</B></A> - \r
 116 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 117 <DD>&nbsp;\r
 118 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#toString()"><B>toString()</B></A> - \r
 119 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 120 <DD>&nbsp;\r
 121 <DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#toString()"><B>toString()</B></A> - \r
 122 Method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
 123 <DD>&nbsp;\r
 124 <DT><A HREF="../compbio/engine/conf/_Key.html#toString()"><B>toString()</B></A> - \r
 125 Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A>\r
 126 <DD>&nbsp;\r
 127 <DT><A HREF="../compbio/engine/FilePuller.html#toString()"><B>toString()</B></A> - \r
 128 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
 129 <DD>&nbsp;\r
 130 <DT><A HREF="../compbio/engine/Job.html#toString()"><B>toString()</B></A> - \r
 131 Method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
 132 <DD>&nbsp;\r
 133 <DT><A HREF="../compbio/metadata/ChunkHolder.html#toString()"><B>toString()</B></A> - \r
 134 Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
 135 <DD>&nbsp;\r
 136 <DT><A HREF="../compbio/metadata/Limit.html#toString()"><B>toString()</B></A> - \r
 137 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
 138 <DD>&nbsp;\r
 139 <DT><A HREF="../compbio/metadata/LimitsManager.html#toString()"><B>toString()</B></A> - \r
 140 Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
 141 <DD>&nbsp;\r
 142 <DT><A HREF="../compbio/metadata/Option.html#toString()"><B>toString()</B></A> - \r
 143 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 144 <DD>&nbsp;\r
 145 <DT><A HREF="../compbio/metadata/Parameter.html#toString()"><B>toString()</B></A> - \r
 146 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
 147 <DD>&nbsp;\r
 148 <DT><A HREF="../compbio/metadata/Preset.html#toString()"><B>toString()</B></A> - \r
 149 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
 150 <DD>&nbsp;\r
 151 <DT><A HREF="../compbio/metadata/PresetManager.html#toString()"><B>toString()</B></A> - \r
 152 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
 153 <DD>&nbsp;\r
 154 <DT><A HREF="../compbio/metadata/RunnerConfig.html#toString()"><B>toString()</B></A> - \r
 155 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 156 <DD>&nbsp;\r
 157 <DT><A HREF="../compbio/metadata/ValueConstrain.html#toString()"><B>toString()</B></A> - \r
 158 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
 159 <DD>&nbsp;\r
 160 <DT><A HREF="../compbio/pipeline/_jpred/PScore.html#toString()"><B>toString()</B></A> - \r
 161 Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred">PScore</A>\r
 162 <DD>&nbsp;\r
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