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7 Constant Field Values
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10 <META NAME="date" CONTENT="2011-12-07">
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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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92 <LI><A HREF="#compbio.ws">compbio.ws.*</A>
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95 <A NAME="compbio.data"><!-- --></A>
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96 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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97 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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98 <TH ALIGN="left"><FONT SIZE="+2">
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99 compbio.data.*</FONT></TH>
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105 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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106 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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107 <TH ALIGN="left" COLSPAN="3">compbio.data.msa.<A HREF="compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</A></TH>
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109 <TR BGCOLOR="white" CLASS="TableRowColor">
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110 <A NAME="compbio.data.msa.Category.CATEGORY_ALIGNMENT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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111 <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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112 <TD ALIGN="left"><CODE><A HREF="compbio/data/msa/Category.html#CATEGORY_ALIGNMENT">CATEGORY_ALIGNMENT</A></CODE></TD>
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113 <TD ALIGN="right"><CODE>"Alignment"</CODE></TD>
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115 <TR BGCOLOR="white" CLASS="TableRowColor">
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116 <A NAME="compbio.data.msa.Category.CATEGORY_CONSERVATION"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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117 <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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118 <TD ALIGN="left"><CODE><A HREF="compbio/data/msa/Category.html#CATEGORY_CONSERVATION">CATEGORY_CONSERVATION</A></CODE></TD>
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119 <TD ALIGN="right"><CODE>"Conservation"</CODE></TD>
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121 <TR BGCOLOR="white" CLASS="TableRowColor">
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122 <A NAME="compbio.data.msa.Category.CATEGORY_DISORDER"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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123 <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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124 <TD ALIGN="left"><CODE><A HREF="compbio/data/msa/Category.html#CATEGORY_DISORDER">CATEGORY_DISORDER</A></CODE></TD>
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125 <TD ALIGN="right"><CODE>"Protein Disorder"</CODE></TD>
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135 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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136 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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137 <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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139 <TR BGCOLOR="white" CLASS="TableRowColor">
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140 <A NAME="compbio.data.msa.JABAService.SERVICE_NAMESPACE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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141 <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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142 <TD ALIGN="left"><CODE><A HREF="compbio/data/msa/JABAService.html#SERVICE_NAMESPACE">SERVICE_NAMESPACE</A></CODE></TD>
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143 <TD ALIGN="right"><CODE>"http://msa.data.compbio/01/01/2010/"</CODE></TD>
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145 <TR BGCOLOR="white" CLASS="TableRowColor">
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146 <A NAME="compbio.data.msa.JABAService.V2_SERVICE_NAMESPACE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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147 <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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148 <TD ALIGN="left"><CODE><A HREF="compbio/data/msa/JABAService.html#V2_SERVICE_NAMESPACE">V2_SERVICE_NAMESPACE</A></CODE></TD>
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149 <TD ALIGN="right"><CODE>"http://msa.data.compbio/01/12/2010/"</CODE></TD>
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159 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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160 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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161 <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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163 <TR BGCOLOR="white" CLASS="TableRowColor">
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164 <A NAME="compbio.data.sequence.ClustalAlignmentUtil.gapchar"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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165 <CODE>public static final char</CODE></FONT></TD>
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166 <TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/ClustalAlignmentUtil.html#gapchar">gapchar</A></CODE></TD>
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167 <TD ALIGN="right"><CODE>45</CODE></TD>
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177 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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178 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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179 <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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181 <TR BGCOLOR="white" CLASS="TableRowColor">
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182 <A NAME="compbio.data.sequence.ScoreManager.SINGLE_ENTRY_KEY"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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183 <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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184 <TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/ScoreManager.html#SINGLE_ENTRY_KEY">SINGLE_ENTRY_KEY</A></CODE></TD>
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185 <TD ALIGN="right"><CODE>"Alignment"</CODE></TD>
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195 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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196 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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197 <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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199 <TR BGCOLOR="white" CLASS="TableRowColor">
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200 <A NAME="compbio.data.sequence.SMERFSConstraints.DEFAULT_GAP_THRESHOLD"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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201 <CODE>public static final double</CODE></FONT></TD>
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202 <TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/SMERFSConstraints.html#DEFAULT_GAP_THRESHOLD">DEFAULT_GAP_THRESHOLD</A></CODE></TD>
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203 <TD ALIGN="right"><CODE>0.1</CODE></TD>
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205 <TR BGCOLOR="white" CLASS="TableRowColor">
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206 <A NAME="compbio.data.sequence.SMERFSConstraints.DEFAULT_WINDOW_SIZE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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207 <CODE>public static final int</CODE></FONT></TD>
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208 <TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/SMERFSConstraints.html#DEFAULT_WINDOW_SIZE">DEFAULT_WINDOW_SIZE</A></CODE></TD>
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209 <TD ALIGN="right"><CODE>7</CODE></TD>
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218 <A NAME="compbio.engine"><!-- --></A>
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219 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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220 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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221 <TH ALIGN="left"><FONT SIZE="+2">
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222 compbio.engine.*</FONT></TH>
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228 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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229 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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230 <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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232 <TR BGCOLOR="white" CLASS="TableRowColor">
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233 <A NAME="compbio.engine.client.ConfExecutable.CLUSTER_TASK_ID_PREFIX"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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234 <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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235 <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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236 <TD ALIGN="right"><CODE>"@"</CODE></TD>
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246 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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247 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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248 <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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250 <TR BGCOLOR="white" CLASS="TableRowColor">
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251 <A NAME="compbio.engine.client.EnvVariableProcessor.PATH"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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252 <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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253 <TD ALIGN="left"><CODE><A HREF="compbio/engine/client/EnvVariableProcessor.html#PATH">PATH</A></CODE></TD>
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254 <TD ALIGN="right"><CODE>"PATH"</CODE></TD>
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264 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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265 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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266 <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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268 <TR BGCOLOR="white" CLASS="TableRowColor">
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269 <A NAME="compbio.engine.client.RunConfiguration.rconfigFile"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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270 <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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271 <TD ALIGN="left"><CODE><A HREF="compbio/engine/client/RunConfiguration.html#rconfigFile">rconfigFile</A></CODE></TD>
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272 <TD ALIGN="right"><CODE>"RunnerConfig.xml"</CODE></TD>
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282 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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283 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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284 <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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286 <TR BGCOLOR="white" CLASS="TableRowColor">
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287 <A NAME="compbio.engine.client.SkeletalExecutable.ERROR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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288 <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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289 <TD ALIGN="left"><CODE><A HREF="compbio/engine/client/SkeletalExecutable.html#ERROR">ERROR</A></CODE></TD>
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290 <TD ALIGN="right"><CODE>"error.txt"</CODE></TD>
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292 <TR BGCOLOR="white" CLASS="TableRowColor">
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293 <A NAME="compbio.engine.client.SkeletalExecutable.INPUT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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294 <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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295 <TD ALIGN="left"><CODE><A HREF="compbio/engine/client/SkeletalExecutable.html#INPUT">INPUT</A></CODE></TD>
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296 <TD ALIGN="right"><CODE>"input.txt"</CODE></TD>
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298 <TR BGCOLOR="white" CLASS="TableRowColor">
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299 <A NAME="compbio.engine.client.SkeletalExecutable.OUTPUT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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300 <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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301 <TD ALIGN="left"><CODE><A HREF="compbio/engine/client/SkeletalExecutable.html#OUTPUT">OUTPUT</A></CODE></TD>
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302 <TD ALIGN="right"><CODE>"result.txt"</CODE></TD>
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312 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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313 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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314 <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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316 <TR BGCOLOR="white" CLASS="TableRowColor">
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317 <A NAME="compbio.engine.cluster.drmaa.ClusterSession.JOBID"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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318 <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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319 <TD ALIGN="left"><CODE><A HREF="compbio/engine/cluster/drmaa/ClusterSession.html#JOBID">JOBID</A></CODE></TD>
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320 <TD ALIGN="right"><CODE>"JOBID"</CODE></TD>
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330 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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331 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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332 <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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334 <TR BGCOLOR="white" CLASS="TableRowColor">
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335 <A NAME="compbio.engine.conf._Key.DELIM"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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336 <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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337 <TD ALIGN="left"><CODE><A HREF="compbio/engine/conf/_Key.html#DELIM">DELIM</A></CODE></TD>
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338 <TD ALIGN="right"><CODE>"#"</CODE></TD>
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348 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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349 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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350 <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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352 <TR BGCOLOR="white" CLASS="TableRowColor">
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353 <A NAME="compbio.engine.conf.DirectoryManager.DELIM"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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354 <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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355 <TD ALIGN="left"><CODE><A HREF="compbio/engine/conf/DirectoryManager.html#DELIM">DELIM</A></CODE></TD>
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356 <TD ALIGN="right"><CODE>"#"</CODE></TD>
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366 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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367 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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368 <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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370 <TR BGCOLOR="white" CLASS="TableRowColor">
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371 <A NAME="compbio.engine.local.ExecutableWrapper.PROC_ERR_FILE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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372 <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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373 <TD ALIGN="left"><CODE><A HREF="compbio/engine/local/ExecutableWrapper.html#PROC_ERR_FILE">PROC_ERR_FILE</A></CODE></TD>
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374 <TD ALIGN="right"><CODE>"procError.txt"</CODE></TD>
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376 <TR BGCOLOR="white" CLASS="TableRowColor">
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377 <A NAME="compbio.engine.local.ExecutableWrapper.PROC_OUT_FILE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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378 <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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379 <TD ALIGN="left"><CODE><A HREF="compbio/engine/local/ExecutableWrapper.html#PROC_OUT_FILE">PROC_OUT_FILE</A></CODE></TD>
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380 <TD ALIGN="right"><CODE>"procOutput.txt"</CODE></TD>
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389 <A NAME="compbio.metadata"><!-- --></A>
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390 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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391 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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392 <TH ALIGN="left"><FONT SIZE="+2">
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393 compbio.metadata.*</FONT></TH>
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399 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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400 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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401 <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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403 <TR BGCOLOR="white" CLASS="TableRowColor">
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404 <A NAME="compbio.metadata.PresetManager.LOCAL_ENGINE_LIMIT_PRESET"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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405 <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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406 <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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407 <TD ALIGN="right"><CODE>"# LocalEngineExecutionLimit #"</CODE></TD>
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416 <A NAME="compbio.runner"><!-- --></A>
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417 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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418 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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419 <TH ALIGN="left"><FONT SIZE="+2">
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420 compbio.runner.*</FONT></TH>
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426 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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427 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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428 <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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430 <TR BGCOLOR="white" CLASS="TableRowColor">
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431 <A NAME="compbio.runner.Util.SPACE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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432 <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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433 <TD ALIGN="left"><CODE><A HREF="compbio/runner/Util.html#SPACE">SPACE</A></CODE></TD>
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434 <TD ALIGN="right"><CODE>" "</CODE></TD>
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444 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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445 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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446 <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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448 <TR BGCOLOR="white" CLASS="TableRowColor">
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449 <A NAME="compbio.runner.conservation.AACon.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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450 <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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451 <TD ALIGN="left"><CODE><A HREF="compbio/runner/conservation/AACon.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
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452 <TD ALIGN="right"><CODE>"="</CODE></TD>
\r
454 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
455 <A NAME="compbio.runner.conservation.AACon.STAT_FILE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
456 <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
457 <TD ALIGN="left"><CODE><A HREF="compbio/runner/conservation/AACon.html#STAT_FILE">STAT_FILE</A></CODE></TD>
\r
458 <TD ALIGN="right"><CODE>"stat.txt"</CODE></TD>
\r
468 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
469 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
470 <TH ALIGN="left" COLSPAN="3">compbio.runner.disorder.<A HREF="compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A></TH>
\r
472 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
473 <A NAME="compbio.runner.disorder.Disembl.COILS_EXPECTATION_THRESHOLD"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
474 <CODE>public final double</CODE></FONT></TD>
\r
475 <TD ALIGN="left"><CODE><A HREF="compbio/runner/disorder/Disembl.html#COILS_EXPECTATION_THRESHOLD">COILS_EXPECTATION_THRESHOLD</A></CODE></TD>
\r
476 <TD ALIGN="right"><CODE>0.43</CODE></TD>
\r
478 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
479 <A NAME="compbio.runner.disorder.Disembl.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
480 <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
481 <TD ALIGN="left"><CODE><A HREF="compbio/runner/disorder/Disembl.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
\r
482 <TD ALIGN="right"><CODE>" "</CODE></TD>
\r
484 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
485 <A NAME="compbio.runner.disorder.Disembl.LOOPS_EXPECTATION_THRESHOLD"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
486 <CODE>public final double</CODE></FONT></TD>
\r
487 <TD ALIGN="left"><CODE><A HREF="compbio/runner/disorder/Disembl.html#LOOPS_EXPECTATION_THRESHOLD">LOOPS_EXPECTATION_THRESHOLD</A></CODE></TD>
\r
488 <TD ALIGN="right"><CODE>0.086</CODE></TD>
\r
490 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
491 <A NAME="compbio.runner.disorder.Disembl.REM_EXPECTATION_THRESHOLD"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
492 <CODE>public final double</CODE></FONT></TD>
\r
493 <TD ALIGN="left"><CODE><A HREF="compbio/runner/disorder/Disembl.html#REM_EXPECTATION_THRESHOLD">REM_EXPECTATION_THRESHOLD</A></CODE></TD>
\r
494 <TD ALIGN="right"><CODE>0.5</CODE></TD>
\r
504 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
505 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
506 <TH ALIGN="left" COLSPAN="3">compbio.runner.disorder.<A HREF="compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A></TH>
\r
508 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
509 <A NAME="compbio.runner.disorder.GlobPlot.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
510 <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
511 <TD ALIGN="left"><CODE><A HREF="compbio/runner/disorder/GlobPlot.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
\r
512 <TD ALIGN="right"><CODE>" "</CODE></TD>
\r
522 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
523 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
524 <TH ALIGN="left" COLSPAN="3">compbio.runner.disorder.<A HREF="compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A></TH>
\r
526 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
527 <A NAME="compbio.runner.disorder.Jronn.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
528 <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
529 <TD ALIGN="left"><CODE><A HREF="compbio/runner/disorder/Jronn.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
\r
530 <TD ALIGN="right"><CODE>" "</CODE></TD>
\r
532 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
533 <A NAME="compbio.runner.disorder.Jronn.STAT_FILE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
534 <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
535 <TD ALIGN="left"><CODE><A HREF="compbio/runner/disorder/Jronn.html#STAT_FILE">STAT_FILE</A></CODE></TD>
\r
536 <TD ALIGN="right"><CODE>"stat.txt"</CODE></TD>
\r
546 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
547 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
548 <TH ALIGN="left" COLSPAN="3">compbio.runner.msa.<A HREF="compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A></TH>
\r
550 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
551 <A NAME="compbio.runner.msa.ClustalO.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
552 <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
553 <TD ALIGN="left"><CODE><A HREF="compbio/runner/msa/ClustalO.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
\r
554 <TD ALIGN="right"><CODE>"="</CODE></TD>
\r
564 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
565 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
566 <TH ALIGN="left" COLSPAN="3">compbio.runner.msa.<A HREF="compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></TH>
\r
568 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
569 <A NAME="compbio.runner.msa.ClustalW.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
570 <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
571 <TD ALIGN="left"><CODE><A HREF="compbio/runner/msa/ClustalW.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
\r
572 <TD ALIGN="right"><CODE>"="</CODE></TD>
\r
582 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
583 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
584 <TH ALIGN="left" COLSPAN="3">compbio.runner.msa.<A HREF="compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></TH>
\r
586 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
587 <A NAME="compbio.runner.msa.Mafft.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
588 <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
589 <TD ALIGN="left"><CODE><A HREF="compbio/runner/msa/Mafft.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
\r
590 <TD ALIGN="right"><CODE>" "</CODE></TD>
\r
600 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
601 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
602 <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
604 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
605 <A NAME="compbio.runner.msa.Muscle.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
606 <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
607 <TD ALIGN="left"><CODE><A HREF="compbio/runner/msa/Muscle.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
\r
608 <TD ALIGN="right"><CODE>" "</CODE></TD>
\r
618 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
619 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
620 <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
622 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
623 <A NAME="compbio.runner.msa.Probcons.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
624 <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
625 <TD ALIGN="left"><CODE><A HREF="compbio/runner/msa/Probcons.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
\r
626 <TD ALIGN="right"><CODE>" "</CODE></TD>
\r
636 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
637 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
638 <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
640 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
641 <A NAME="compbio.runner.msa.Tcoffee.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
642 <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
643 <TD ALIGN="left"><CODE><A HREF="compbio/runner/msa/Tcoffee.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>
\r
644 <TD ALIGN="right"><CODE>"="</CODE></TD>
\r
653 <A NAME="compbio.ws"><!-- --></A>
\r
654 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
655 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
656 <TH ALIGN="left"><FONT SIZE="+2">
\r
657 compbio.ws.*</FONT></TH>
\r
663 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
664 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
665 <TH ALIGN="left" COLSPAN="3">compbio.ws.client.<A HREF="compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A></TH>
\r
667 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
668 <A NAME="compbio.ws.client.WSTester.fastaAlignment"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
669 <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
670 <TD ALIGN="left"><CODE><A HREF="compbio/ws/client/WSTester.html#fastaAlignment">fastaAlignment</A></CODE></TD>
\r
671 <TD ALIGN="right"><CODE>">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n>Bar\nASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n"</CODE></TD>
\r
673 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
674 <A NAME="compbio.ws.client.WSTester.fastaInput"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
\r
675 <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
676 <TD ALIGN="left"><CODE><A HREF="compbio/ws/client/WSTester.html#fastaInput">fastaInput</A></CODE></TD>
\r
677 <TD ALIGN="right"><CODE>">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n>Bar\nASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n"</CODE></TD>
\r
689 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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690 <A NAME="navbar_bottom"><!-- --></A>
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691 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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692 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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694 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
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695 <A NAME="navbar_bottom_firstrow"><!-- --></A>
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698 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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699 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
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700 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
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709 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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