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7 Constant Field Values
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84 Constant Field Values</H1>
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86 <HR SIZE="4" NOSHADE>
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88 <LI><A HREF="#compbio.data">compbio.data.*</A>
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89 <LI><A HREF="#compbio.engine">compbio.engine.*</A>
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90 <LI><A HREF="#compbio.metadata">compbio.metadata.*</A>
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91 <LI><A HREF="#compbio.runner">compbio.runner.*</A>
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94 <A NAME="compbio.data"><!-- --></A>
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95 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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96 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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97 <TH ALIGN="left"><FONT SIZE="+2">
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98 compbio.data.*</FONT></TH>
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104 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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105 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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106 <TH ALIGN="left" COLSPAN="3">compbio.data.sequence.<A HREF="compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A></TH>
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108 <TR BGCOLOR="white" CLASS="TableRowColor">
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109 <A NAME="compbio.data.sequence.ClustalAlignmentUtil.gapchar"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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110 <CODE>public static final char</CODE></FONT></TD>
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111 <TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/ClustalAlignmentUtil.html#gapchar">gapchar</A></CODE></TD>
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112 <TD ALIGN="right"><CODE>45</CODE></TD>
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121 <A NAME="compbio.engine"><!-- --></A>
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122 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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123 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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124 <TH ALIGN="left"><FONT SIZE="+2">
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125 compbio.engine.*</FONT></TH>
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131 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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132 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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133 <TH ALIGN="left" COLSPAN="3">compbio.engine.client.<A HREF="compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A><<A HREF="compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></TH>
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135 <TR BGCOLOR="white" CLASS="TableRowColor">
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136 <A NAME="compbio.engine.client.ConfExecutable.CLUSTER_TASK_ID_PREFIX"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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137 <CODE>public static final java.lang.String</CODE></FONT></TD>
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138 <TD ALIGN="left"><CODE><A HREF="compbio/engine/client/ConfExecutable.html#CLUSTER_TASK_ID_PREFIX">CLUSTER_TASK_ID_PREFIX</A></CODE></TD>
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139 <TD ALIGN="right"><CODE>"@"</CODE></TD>
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149 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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150 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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151 <TH ALIGN="left" COLSPAN="3">compbio.engine.client.<A HREF="compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</A></TH>
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153 <TR BGCOLOR="white" CLASS="TableRowColor">
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154 <A NAME="compbio.engine.client.EnvVariableProcessor.PATH"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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155 <CODE>public static final java.lang.String</CODE></FONT></TD>
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156 <TD ALIGN="left"><CODE><A HREF="compbio/engine/client/EnvVariableProcessor.html#PATH">PATH</A></CODE></TD>
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157 <TD ALIGN="right"><CODE>"PATH"</CODE></TD>
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167 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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168 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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169 <TH ALIGN="left" COLSPAN="3">compbio.engine.client.<A HREF="compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A></TH>
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171 <TR BGCOLOR="white" CLASS="TableRowColor">
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172 <A NAME="compbio.engine.client.RunConfiguration.rconfigFile"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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173 <CODE>public static final java.lang.String</CODE></FONT></TD>
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174 <TD ALIGN="left"><CODE><A HREF="compbio/engine/client/RunConfiguration.html#rconfigFile">rconfigFile</A></CODE></TD>
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175 <TD ALIGN="right"><CODE>"RunnerConfig.xml"</CODE></TD>
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185 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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186 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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187 <TH ALIGN="left" COLSPAN="3">compbio.engine.cluster.drmaa.<A HREF="compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A></TH>
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189 <TR BGCOLOR="white" CLASS="TableRowColor">
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190 <A NAME="compbio.engine.cluster.drmaa.ClusterSession.JOBID"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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191 <CODE>public static final java.lang.String</CODE></FONT></TD>
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192 <TD ALIGN="left"><CODE><A HREF="compbio/engine/cluster/drmaa/ClusterSession.html#JOBID">JOBID</A></CODE></TD>
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193 <TD ALIGN="right"><CODE>"JOBID"</CODE></TD>
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203 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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204 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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205 <TH ALIGN="left" COLSPAN="3">compbio.engine.cluster.dundee.<A HREF="compbio/engine/cluster/dundee/_QueueConstraints.html" title="class in compbio.engine.cluster.dundee">_QueueConstraints</A></TH>
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207 <TR BGCOLOR="white" CLASS="TableRowColor">
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208 <A NAME="compbio.engine.cluster.dundee._QueueConstraints.FIRST_MEMORY_LIMIT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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209 <CODE>public static final int</CODE></FONT></TD>
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210 <TD ALIGN="left"><CODE><A HREF="compbio/engine/cluster/dundee/_QueueConstraints.html#FIRST_MEMORY_LIMIT">FIRST_MEMORY_LIMIT</A></CODE></TD>
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211 <TD ALIGN="right"><CODE>14000</CODE></TD>
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213 <TR BGCOLOR="white" CLASS="TableRowColor">
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214 <A NAME="compbio.engine.cluster.dundee._QueueConstraints.LONG_TIME_LIMIT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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215 <CODE>public static final int</CODE></FONT></TD>
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216 <TD ALIGN="left"><CODE><A HREF="compbio/engine/cluster/dundee/_QueueConstraints.html#LONG_TIME_LIMIT">LONG_TIME_LIMIT</A></CODE></TD>
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217 <TD ALIGN="right"><CODE>24</CODE></TD>
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219 <TR BGCOLOR="white" CLASS="TableRowColor">
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220 <A NAME="compbio.engine.cluster.dundee._QueueConstraints.MAX_MEMORY_LIMIT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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221 <CODE>public static final int</CODE></FONT></TD>
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222 <TD ALIGN="left"><CODE><A HREF="compbio/engine/cluster/dundee/_QueueConstraints.html#MAX_MEMORY_LIMIT">MAX_MEMORY_LIMIT</A></CODE></TD>
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223 <TD ALIGN="right"><CODE>30000</CODE></TD>
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225 <TR BGCOLOR="white" CLASS="TableRowColor">
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226 <A NAME="compbio.engine.cluster.dundee._QueueConstraints.SHORT_TIME_LIMIT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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227 <CODE>public static final int</CODE></FONT></TD>
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228 <TD ALIGN="left"><CODE><A HREF="compbio/engine/cluster/dundee/_QueueConstraints.html#SHORT_TIME_LIMIT">SHORT_TIME_LIMIT</A></CODE></TD>
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229 <TD ALIGN="right"><CODE>8</CODE></TD>
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239 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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240 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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241 <TH ALIGN="left" COLSPAN="3">compbio.engine.conf.<A HREF="compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A></TH>
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243 <TR BGCOLOR="white" CLASS="TableRowColor">
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244 <A NAME="compbio.engine.conf._Key.DELIM"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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245 <CODE>public static final java.lang.String</CODE></FONT></TD>
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246 <TD ALIGN="left"><CODE><A HREF="compbio/engine/conf/_Key.html#DELIM">DELIM</A></CODE></TD>
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247 <TD ALIGN="right"><CODE>"#"</CODE></TD>
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257 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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258 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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259 <TH ALIGN="left" COLSPAN="3">compbio.engine.conf.<A HREF="compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</A></TH>
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261 <TR BGCOLOR="white" CLASS="TableRowColor">
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262 <A NAME="compbio.engine.conf.DirectoryManager.DELIM"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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263 <CODE>public static final java.lang.String</CODE></FONT></TD>
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264 <TD ALIGN="left"><CODE><A HREF="compbio/engine/conf/DirectoryManager.html#DELIM">DELIM</A></CODE></TD>
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265 <TD ALIGN="right"><CODE>"#"</CODE></TD>
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275 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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276 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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277 <TH ALIGN="left" COLSPAN="3">compbio.engine.local.<A HREF="compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A></TH>
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279 <TR BGCOLOR="white" CLASS="TableRowColor">
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280 <A NAME="compbio.engine.local.ExecutableWrapper.PROC_ERR_FILE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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281 <CODE>public static final java.lang.String</CODE></FONT></TD>
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282 <TD ALIGN="left"><CODE><A HREF="compbio/engine/local/ExecutableWrapper.html#PROC_ERR_FILE">PROC_ERR_FILE</A></CODE></TD>
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283 <TD ALIGN="right"><CODE>"procError.txt"</CODE></TD>
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285 <TR BGCOLOR="white" CLASS="TableRowColor">
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286 <A NAME="compbio.engine.local.ExecutableWrapper.PROC_OUT_FILE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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287 <CODE>public static final java.lang.String</CODE></FONT></TD>
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288 <TD ALIGN="left"><CODE><A HREF="compbio/engine/local/ExecutableWrapper.html#PROC_OUT_FILE">PROC_OUT_FILE</A></CODE></TD>
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289 <TD ALIGN="right"><CODE>"procOutput.txt"</CODE></TD>
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298 <A NAME="compbio.metadata"><!-- --></A>
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299 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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300 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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301 <TH ALIGN="left"><FONT SIZE="+2">
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302 compbio.metadata.*</FONT></TH>
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308 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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309 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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310 <TH ALIGN="left" COLSPAN="3">compbio.metadata.<A HREF="compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>></TH>
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312 <TR BGCOLOR="white" CLASS="TableRowColor">
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313 <A NAME="compbio.metadata.PresetManager.LOCAL_ENGINE_LIMIT_PRESET"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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314 <CODE>public static final java.lang.String</CODE></FONT></TD>
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315 <TD ALIGN="left"><CODE><A HREF="compbio/metadata/PresetManager.html#LOCAL_ENGINE_LIMIT_PRESET">LOCAL_ENGINE_LIMIT_PRESET</A></CODE></TD>
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316 <TD ALIGN="right"><CODE>"# LocalEngineExecutionLimit #"</CODE></TD>
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325 <A NAME="compbio.runner"><!-- --></A>
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326 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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327 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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328 <TH ALIGN="left"><FONT SIZE="+2">
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329 compbio.runner.*</FONT></TH>
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335 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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336 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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337 <TH ALIGN="left" COLSPAN="3">compbio.runner.<A HREF="compbio/runner/Util.html" title="class in compbio.runner">Util</A></TH>
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339 <TR BGCOLOR="white" CLASS="TableRowColor">
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340 <A NAME="compbio.runner.Util.SPACE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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341 <CODE>public static final java.lang.String</CODE></FONT></TD>
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342 <TD ALIGN="left"><CODE><A HREF="compbio/runner/Util.html#SPACE">SPACE</A></CODE></TD>
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343 <TD ALIGN="right"><CODE>" "</CODE></TD>
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353 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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354 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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355 <TH ALIGN="left" COLSPAN="3">compbio.runner.msa.<A HREF="compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></TH>
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357 <TR BGCOLOR="white" CLASS="TableRowColor">
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358 <A NAME="compbio.runner.msa.ClustalW.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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359 <CODE>public static final java.lang.String</CODE></FONT></TD>
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360 <TD ALIGN="left"><CODE><A HREF="compbio/runner/msa/ClustalW.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
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361 <TD ALIGN="right"><CODE>"="</CODE></TD>
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371 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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372 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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373 <TH ALIGN="left" COLSPAN="3">compbio.runner.msa.<A HREF="compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></TH>
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375 <TR BGCOLOR="white" CLASS="TableRowColor">
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376 <A NAME="compbio.runner.msa.Mafft.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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377 <CODE>public static final java.lang.String</CODE></FONT></TD>
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378 <TD ALIGN="left"><CODE><A HREF="compbio/runner/msa/Mafft.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
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379 <TD ALIGN="right"><CODE>" "</CODE></TD>
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389 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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390 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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391 <TH ALIGN="left" COLSPAN="3">compbio.runner.msa.<A HREF="compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></TH>
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393 <TR BGCOLOR="white" CLASS="TableRowColor">
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394 <A NAME="compbio.runner.msa.Muscle.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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395 <CODE>public static final java.lang.String</CODE></FONT></TD>
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396 <TD ALIGN="left"><CODE><A HREF="compbio/runner/msa/Muscle.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
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397 <TD ALIGN="right"><CODE>" "</CODE></TD>
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407 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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408 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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409 <TH ALIGN="left" COLSPAN="3">compbio.runner.msa.<A HREF="compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></TH>
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411 <TR BGCOLOR="white" CLASS="TableRowColor">
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412 <A NAME="compbio.runner.msa.Probcons.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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413 <CODE>public static final java.lang.String</CODE></FONT></TD>
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414 <TD ALIGN="left"><CODE><A HREF="compbio/runner/msa/Probcons.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
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415 <TD ALIGN="right"><CODE>" "</CODE></TD>
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425 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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426 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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427 <TH ALIGN="left" COLSPAN="3">compbio.runner.msa.<A HREF="compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></TH>
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429 <TR BGCOLOR="white" CLASS="TableRowColor">
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430 <A NAME="compbio.runner.msa.Tcoffee.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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431 <CODE>public static final java.lang.String</CODE></FONT></TD>
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432 <TD ALIGN="left"><CODE><A HREF="compbio/runner/msa/Tcoffee.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
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433 <TD ALIGN="right"><CODE>"="</CODE></TD>
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