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7 Constant Field Values
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18 parent.document.title="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.msa.<A HREF="compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A></TH>
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108 <TR BGCOLOR="white" CLASS="TableRowColor">
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109 <A NAME="compbio.data.msa.JABAService.SERVICE_NAMESPACE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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110 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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111 <TD ALIGN="left"><CODE><A HREF="compbio/data/msa/JABAService.html#SERVICE_NAMESPACE">SERVICE_NAMESPACE</A></CODE></TD>
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112 <TD ALIGN="right"><CODE>"http://msa.data.compbio/01/01/2010/"</CODE></TD>
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114 <TR BGCOLOR="white" CLASS="TableRowColor">
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115 <A NAME="compbio.data.msa.JABAService.V2_SERVICE_NAMESPACE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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116 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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117 <TD ALIGN="left"><CODE><A HREF="compbio/data/msa/JABAService.html#V2_SERVICE_NAMESPACE">V2_SERVICE_NAMESPACE</A></CODE></TD>
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118 <TD ALIGN="right"><CODE>"http://msa.data.compbio/01/12/2010/"</CODE></TD>
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128 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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129 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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130 <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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132 <TR BGCOLOR="white" CLASS="TableRowColor">
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133 <A NAME="compbio.data.sequence.ClustalAlignmentUtil.gapchar"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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134 <CODE>public static final char</CODE></FONT></TD>
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135 <TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/ClustalAlignmentUtil.html#gapchar">gapchar</A></CODE></TD>
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136 <TD ALIGN="right"><CODE>45</CODE></TD>
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146 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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147 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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148 <TH ALIGN="left" COLSPAN="3">compbio.data.sequence.<A HREF="compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></TH>
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150 <TR BGCOLOR="white" CLASS="TableRowColor">
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151 <A NAME="compbio.data.sequence.ScoreManager.SINGLE_ENTRY_KEY"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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152 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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153 <TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/ScoreManager.html#SINGLE_ENTRY_KEY">SINGLE_ENTRY_KEY</A></CODE></TD>
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154 <TD ALIGN="right"><CODE>"Alignment"</CODE></TD>
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164 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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165 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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166 <TH ALIGN="left" COLSPAN="3">compbio.data.sequence.<A HREF="compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A></TH>
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168 <TR BGCOLOR="white" CLASS="TableRowColor">
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169 <A NAME="compbio.data.sequence.SMERFSConstraints.DEFAULT_GAP_THRESHOLD"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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170 <CODE>public static final double</CODE></FONT></TD>
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171 <TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/SMERFSConstraints.html#DEFAULT_GAP_THRESHOLD">DEFAULT_GAP_THRESHOLD</A></CODE></TD>
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172 <TD ALIGN="right"><CODE>0.1</CODE></TD>
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174 <TR BGCOLOR="white" CLASS="TableRowColor">
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175 <A NAME="compbio.data.sequence.SMERFSConstraints.DEFAULT_WINDOW_SIZE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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176 <CODE>public static final int</CODE></FONT></TD>
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177 <TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/SMERFSConstraints.html#DEFAULT_WINDOW_SIZE">DEFAULT_WINDOW_SIZE</A></CODE></TD>
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178 <TD ALIGN="right"><CODE>7</CODE></TD>
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187 <A NAME="compbio.engine"><!-- --></A>
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188 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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189 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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190 <TH ALIGN="left"><FONT SIZE="+2">
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191 compbio.engine.*</FONT></TH>
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197 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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198 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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199 <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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201 <TR BGCOLOR="white" CLASS="TableRowColor">
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202 <A NAME="compbio.engine.client.ConfExecutable.CLUSTER_TASK_ID_PREFIX"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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203 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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204 <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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205 <TD ALIGN="right"><CODE>"@"</CODE></TD>
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215 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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216 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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217 <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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219 <TR BGCOLOR="white" CLASS="TableRowColor">
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220 <A NAME="compbio.engine.client.EnvVariableProcessor.PATH"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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221 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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222 <TD ALIGN="left"><CODE><A HREF="compbio/engine/client/EnvVariableProcessor.html#PATH">PATH</A></CODE></TD>
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223 <TD ALIGN="right"><CODE>"PATH"</CODE></TD>
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233 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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234 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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235 <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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237 <TR BGCOLOR="white" CLASS="TableRowColor">
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238 <A NAME="compbio.engine.client.RunConfiguration.rconfigFile"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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239 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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240 <TD ALIGN="left"><CODE><A HREF="compbio/engine/client/RunConfiguration.html#rconfigFile">rconfigFile</A></CODE></TD>
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241 <TD ALIGN="right"><CODE>"RunnerConfig.xml"</CODE></TD>
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251 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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252 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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253 <TH ALIGN="left" COLSPAN="3">compbio.engine.client.<A HREF="compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></TH>
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255 <TR BGCOLOR="white" CLASS="TableRowColor">
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256 <A NAME="compbio.engine.client.SkeletalExecutable.ERROR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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257 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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258 <TD ALIGN="left"><CODE><A HREF="compbio/engine/client/SkeletalExecutable.html#ERROR">ERROR</A></CODE></TD>
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259 <TD ALIGN="right"><CODE>"error.txt"</CODE></TD>
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261 <TR BGCOLOR="white" CLASS="TableRowColor">
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262 <A NAME="compbio.engine.client.SkeletalExecutable.INPUT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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263 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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264 <TD ALIGN="left"><CODE><A HREF="compbio/engine/client/SkeletalExecutable.html#INPUT">INPUT</A></CODE></TD>
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265 <TD ALIGN="right"><CODE>"input.txt"</CODE></TD>
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267 <TR BGCOLOR="white" CLASS="TableRowColor">
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268 <A NAME="compbio.engine.client.SkeletalExecutable.OUTPUT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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269 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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270 <TD ALIGN="left"><CODE><A HREF="compbio/engine/client/SkeletalExecutable.html#OUTPUT">OUTPUT</A></CODE></TD>
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271 <TD ALIGN="right"><CODE>"result.txt"</CODE></TD>
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281 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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282 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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283 <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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285 <TR BGCOLOR="white" CLASS="TableRowColor">
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286 <A NAME="compbio.engine.cluster.drmaa.ClusterSession.JOBID"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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287 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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288 <TD ALIGN="left"><CODE><A HREF="compbio/engine/cluster/drmaa/ClusterSession.html#JOBID">JOBID</A></CODE></TD>
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289 <TD ALIGN="right"><CODE>"JOBID"</CODE></TD>
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299 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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300 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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301 <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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303 <TR BGCOLOR="white" CLASS="TableRowColor">
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304 <A NAME="compbio.engine.conf._Key.DELIM"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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305 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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306 <TD ALIGN="left"><CODE><A HREF="compbio/engine/conf/_Key.html#DELIM">DELIM</A></CODE></TD>
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307 <TD ALIGN="right"><CODE>"#"</CODE></TD>
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317 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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318 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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319 <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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321 <TR BGCOLOR="white" CLASS="TableRowColor">
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322 <A NAME="compbio.engine.conf.DirectoryManager.DELIM"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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323 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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324 <TD ALIGN="left"><CODE><A HREF="compbio/engine/conf/DirectoryManager.html#DELIM">DELIM</A></CODE></TD>
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325 <TD ALIGN="right"><CODE>"#"</CODE></TD>
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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.engine.local.<A HREF="compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A></TH>
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339 <TR BGCOLOR="white" CLASS="TableRowColor">
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340 <A NAME="compbio.engine.local.ExecutableWrapper.PROC_ERR_FILE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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341 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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342 <TD ALIGN="left"><CODE><A HREF="compbio/engine/local/ExecutableWrapper.html#PROC_ERR_FILE">PROC_ERR_FILE</A></CODE></TD>
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343 <TD ALIGN="right"><CODE>"procError.txt"</CODE></TD>
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345 <TR BGCOLOR="white" CLASS="TableRowColor">
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346 <A NAME="compbio.engine.local.ExecutableWrapper.PROC_OUT_FILE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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347 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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348 <TD ALIGN="left"><CODE><A HREF="compbio/engine/local/ExecutableWrapper.html#PROC_OUT_FILE">PROC_OUT_FILE</A></CODE></TD>
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349 <TD ALIGN="right"><CODE>"procOutput.txt"</CODE></TD>
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358 <A NAME="compbio.metadata"><!-- --></A>
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359 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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360 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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361 <TH ALIGN="left"><FONT SIZE="+2">
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362 compbio.metadata.*</FONT></TH>
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368 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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369 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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370 <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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372 <TR BGCOLOR="white" CLASS="TableRowColor">
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373 <A NAME="compbio.metadata.PresetManager.LOCAL_ENGINE_LIMIT_PRESET"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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374 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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375 <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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376 <TD ALIGN="right"><CODE>"# LocalEngineExecutionLimit #"</CODE></TD>
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385 <A NAME="compbio.runner"><!-- --></A>
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386 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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387 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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388 <TH ALIGN="left"><FONT SIZE="+2">
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389 compbio.runner.*</FONT></TH>
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395 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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396 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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397 <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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399 <TR BGCOLOR="white" CLASS="TableRowColor">
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400 <A NAME="compbio.runner.Util.SPACE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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401 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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402 <TD ALIGN="left"><CODE><A HREF="compbio/runner/Util.html#SPACE">SPACE</A></CODE></TD>
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403 <TD ALIGN="right"><CODE>" "</CODE></TD>
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413 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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414 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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415 <TH ALIGN="left" COLSPAN="3">compbio.runner.conservation.<A HREF="compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A></TH>
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417 <TR BGCOLOR="white" CLASS="TableRowColor">
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418 <A NAME="compbio.runner.conservation.AACon.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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419 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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420 <TD ALIGN="left"><CODE><A HREF="compbio/runner/conservation/AACon.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
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421 <TD ALIGN="right"><CODE>"="</CODE></TD>
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423 <TR BGCOLOR="white" CLASS="TableRowColor">
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424 <A NAME="compbio.runner.conservation.AACon.STAT_FILE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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425 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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426 <TD ALIGN="left"><CODE><A HREF="compbio/runner/conservation/AACon.html#STAT_FILE">STAT_FILE</A></CODE></TD>
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427 <TD ALIGN="right"><CODE>"stat.txt"</CODE></TD>
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437 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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438 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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439 <TH ALIGN="left" COLSPAN="3">compbio.runner.disorder.<A HREF="compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A></TH>
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441 <TR BGCOLOR="white" CLASS="TableRowColor">
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442 <A NAME="compbio.runner.disorder.Disembl.COILS_EXPECTATION_THRESHOLD"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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443 <CODE>public final double</CODE></FONT></TD>
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444 <TD ALIGN="left"><CODE><A HREF="compbio/runner/disorder/Disembl.html#COILS_EXPECTATION_THRESHOLD">COILS_EXPECTATION_THRESHOLD</A></CODE></TD>
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445 <TD ALIGN="right"><CODE>0.43</CODE></TD>
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447 <TR BGCOLOR="white" CLASS="TableRowColor">
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448 <A NAME="compbio.runner.disorder.Disembl.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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449 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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450 <TD ALIGN="left"><CODE><A HREF="compbio/runner/disorder/Disembl.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
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451 <TD ALIGN="right"><CODE>" "</CODE></TD>
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453 <TR BGCOLOR="white" CLASS="TableRowColor">
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454 <A NAME="compbio.runner.disorder.Disembl.LOOPS_EXPECTATION_THRESHOLD"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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455 <CODE>public final double</CODE></FONT></TD>
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456 <TD ALIGN="left"><CODE><A HREF="compbio/runner/disorder/Disembl.html#LOOPS_EXPECTATION_THRESHOLD">LOOPS_EXPECTATION_THRESHOLD</A></CODE></TD>
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457 <TD ALIGN="right"><CODE>0.086</CODE></TD>
\r
459 <TR BGCOLOR="white" CLASS="TableRowColor">
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460 <A NAME="compbio.runner.disorder.Disembl.REM_EXPECTATION_THRESHOLD"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
461 <CODE>public final double</CODE></FONT></TD>
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462 <TD ALIGN="left"><CODE><A HREF="compbio/runner/disorder/Disembl.html#REM_EXPECTATION_THRESHOLD">REM_EXPECTATION_THRESHOLD</A></CODE></TD>
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463 <TD ALIGN="right"><CODE>0.5</CODE></TD>
\r
473 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
474 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
475 <TH ALIGN="left" COLSPAN="3">compbio.runner.disorder.<A HREF="compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A></TH>
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477 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
478 <A NAME="compbio.runner.disorder.GlobPlot.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
479 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
\r
480 <TD ALIGN="left"><CODE><A HREF="compbio/runner/disorder/GlobPlot.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
\r
481 <TD ALIGN="right"><CODE>" "</CODE></TD>
\r
491 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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492 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
493 <TH ALIGN="left" COLSPAN="3">compbio.runner.disorder.<A HREF="compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A></TH>
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495 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
496 <A NAME="compbio.runner.disorder.Jronn.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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497 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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498 <TD ALIGN="left"><CODE><A HREF="compbio/runner/disorder/Jronn.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
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499 <TD ALIGN="right"><CODE>" "</CODE></TD>
\r
501 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
502 <A NAME="compbio.runner.disorder.Jronn.STAT_FILE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
503 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
\r
504 <TD ALIGN="left"><CODE><A HREF="compbio/runner/disorder/Jronn.html#STAT_FILE">STAT_FILE</A></CODE></TD>
\r
505 <TD ALIGN="right"><CODE>"stat.txt"</CODE></TD>
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515 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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516 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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517 <TH ALIGN="left" COLSPAN="3">compbio.runner.msa.<A HREF="compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A></TH>
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519 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
520 <A NAME="compbio.runner.msa.ClustalO.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
521 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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522 <TD ALIGN="left"><CODE><A HREF="compbio/runner/msa/ClustalO.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
\r
523 <TD ALIGN="right"><CODE>"="</CODE></TD>
\r
533 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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534 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
535 <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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537 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
538 <A NAME="compbio.runner.msa.ClustalW.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
539 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
\r
540 <TD ALIGN="left"><CODE><A HREF="compbio/runner/msa/ClustalW.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
\r
541 <TD ALIGN="right"><CODE>"="</CODE></TD>
\r
551 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
552 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
553 <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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555 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
556 <A NAME="compbio.runner.msa.Mafft.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
557 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
\r
558 <TD ALIGN="left"><CODE><A HREF="compbio/runner/msa/Mafft.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
\r
559 <TD ALIGN="right"><CODE>" "</CODE></TD>
\r
569 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
570 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
571 <TH ALIGN="left" COLSPAN="3">compbio.runner.msa.<A HREF="compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></TH>
\r
573 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
574 <A NAME="compbio.runner.msa.Muscle.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
575 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
\r
576 <TD ALIGN="left"><CODE><A HREF="compbio/runner/msa/Muscle.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
\r
577 <TD ALIGN="right"><CODE>" "</CODE></TD>
\r
587 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
588 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
589 <TH ALIGN="left" COLSPAN="3">compbio.runner.msa.<A HREF="compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></TH>
\r
591 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
592 <A NAME="compbio.runner.msa.Probcons.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
593 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
\r
594 <TD ALIGN="left"><CODE><A HREF="compbio/runner/msa/Probcons.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
\r
595 <TD ALIGN="right"><CODE>" "</CODE></TD>
\r
605 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
606 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
607 <TH ALIGN="left" COLSPAN="3">compbio.runner.msa.<A HREF="compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></TH>
\r
609 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
610 <A NAME="compbio.runner.msa.Tcoffee.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
611 <CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
\r
612 <TD ALIGN="left"><CODE><A HREF="compbio/runner/msa/Tcoffee.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
\r
613 <TD ALIGN="right"><CODE>"="</CODE></TD>
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625 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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626 <A NAME="navbar_bottom"><!-- --></A>
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627 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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628 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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630 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
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631 <A NAME="navbar_bottom_firstrow"><!-- --></A>
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632 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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633 <TR ALIGN="center" VALIGN="top">
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634 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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635 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
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636 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
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640 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
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660 document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');
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