website/full_javadoc/constant-values.html

   1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
   2 <!--NewPage-->\r
   3 <HTML>\r
   4 <HEAD>\r
   5 <!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:30:42 GMT 2011 -->\r
   6 <TITLE>\r
   7 Constant Field Values\r
   8 </TITLE>\r
   9 \r
  10 <META NAME="date" CONTENT="2011-12-07">\r
  11 \r
  12 <LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">\r
  13 \r
  14 <SCRIPT type="text/javascript">\r
  15 function windowTitle()\r
  16 {\r
  17     if (location.href.indexOf('is-external=true') == -1) {\r
  18         parent.document.title="Constant Field Values";\r
  19     }\r
  20 }\r
  21 </SCRIPT>\r
  22 <NOSCRIPT>\r
  23 </NOSCRIPT>\r
  24 \r
  25 </HEAD>\r
  26 \r
  27 <BODY BGCOLOR="white" onload="windowTitle();">\r
  28 <HR>\r
  29 \r
  30 \r
  31 <!-- ========= START OF TOP NAVBAR ======= -->\r
  32 <A NAME="navbar_top"><!-- --></A>\r
  33 <A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
  34 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
  35 <TR>\r
  36 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
  37 <A NAME="navbar_top_firstrow"><!-- --></A>\r
  38 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
  39   <TR ALIGN="center" VALIGN="top">\r
  40   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
  41   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
  42   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
  43   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
  44   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
  45   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
  46   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
  47   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
  48   </TR>\r
  49 </TABLE>\r
  50 </TD>\r
  51 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
  52 </EM>\r
  53 </TD>\r
  54 </TR>\r
  55 \r
  56 <TR>\r
  57 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
  58 &nbsp;PREV&nbsp;\r
  59 &nbsp;NEXT</FONT></TD>\r
  60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
  61   <A HREF="index.html?constant-values.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
  62 &nbsp;<A HREF="constant-values.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
  63 &nbsp;<SCRIPT type="text/javascript">\r
  64   <!--\r
  65   if(window==top) {\r
  66     document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');\r
  67   }\r
  68   //-->\r
  69 </SCRIPT>\r
  70 <NOSCRIPT>\r
  71   <A HREF="allclasses-noframe.html"><B>All Classes</B></A>\r
  72 </NOSCRIPT>\r
  73 \r
  74 \r
  75 </FONT></TD>\r
  76 </TR>\r
  77 </TABLE>\r
  78 <A NAME="skip-navbar_top"></A>\r
  79 <!-- ========= END OF TOP NAVBAR ========= -->\r
  80 \r
  81 <HR>\r
  82 <CENTER>\r
  83 <H1>\r
  84 Constant Field Values</H1>\r
  85 </CENTER>\r
  86 <HR SIZE="4" NOSHADE>\r
  87 <B>Contents</B><UL>\r
  88 <LI><A HREF="#compbio.data">compbio.data.*</A>\r
  89 <LI><A HREF="#compbio.engine">compbio.engine.*</A>\r
  90 <LI><A HREF="#compbio.metadata">compbio.metadata.*</A>\r
  91 <LI><A HREF="#compbio.runner">compbio.runner.*</A>\r
  92 <LI><A HREF="#compbio.ws">compbio.ws.*</A>\r
  93 </UL>\r
  94 \r
  95 <A NAME="compbio.data"><!-- --></A>\r
  96 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
  97 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
  98 <TH ALIGN="left"><FONT SIZE="+2">\r
  99 compbio.data.*</FONT></TH>\r
 100 </TR>\r
 101 </TABLE>\r
 102 \r
 103 <P>\r
 104 \r
 105 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 106 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 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>\r
 108 </TR>\r
 109 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 110 <A NAME="compbio.data.msa.Category.CATEGORY_ALIGNMENT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 111 <CODE>public&nbsp;static&nbsp;final&nbsp;<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
 112 <TD ALIGN="left"><CODE><A HREF="compbio/data/msa/Category.html#CATEGORY_ALIGNMENT">CATEGORY_ALIGNMENT</A></CODE></TD>\r
 113 <TD ALIGN="right"><CODE>"Alignment"</CODE></TD>\r
 114 </TR>\r
 115 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 116 <A NAME="compbio.data.msa.Category.CATEGORY_CONSERVATION"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 117 <CODE>public&nbsp;static&nbsp;final&nbsp;<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
 118 <TD ALIGN="left"><CODE><A HREF="compbio/data/msa/Category.html#CATEGORY_CONSERVATION">CATEGORY_CONSERVATION</A></CODE></TD>\r
 119 <TD ALIGN="right"><CODE>"Conservation"</CODE></TD>\r
 120 </TR>\r
 121 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 122 <A NAME="compbio.data.msa.Category.CATEGORY_DISORDER"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 123 <CODE>public&nbsp;static&nbsp;final&nbsp;<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
 124 <TD ALIGN="left"><CODE><A HREF="compbio/data/msa/Category.html#CATEGORY_DISORDER">CATEGORY_DISORDER</A></CODE></TD>\r
 125 <TD ALIGN="right"><CODE>"Protein Disorder"</CODE></TD>\r
 126 </TR>\r
 127 </FONT></TD>\r
 128 </TR>\r
 129 </TABLE>\r
 130 \r
 131 <P>\r
 132 \r
 133 <P>\r
 134 \r
 135 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 136 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 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>\r
 138 </TR>\r
 139 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 140 <A NAME="compbio.data.msa.JABAService.SERVICE_NAMESPACE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 141 <CODE>public&nbsp;static&nbsp;final&nbsp;<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
 142 <TD ALIGN="left"><CODE><A HREF="compbio/data/msa/JABAService.html#SERVICE_NAMESPACE">SERVICE_NAMESPACE</A></CODE></TD>\r
 143 <TD ALIGN="right"><CODE>"http://msa.data.compbio/01/01/2010/"</CODE></TD>\r
 144 </TR>\r
 145 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 146 <A NAME="compbio.data.msa.JABAService.V2_SERVICE_NAMESPACE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 147 <CODE>public&nbsp;static&nbsp;final&nbsp;<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
 148 <TD ALIGN="left"><CODE><A HREF="compbio/data/msa/JABAService.html#V2_SERVICE_NAMESPACE">V2_SERVICE_NAMESPACE</A></CODE></TD>\r
 149 <TD ALIGN="right"><CODE>"http://msa.data.compbio/01/12/2010/"</CODE></TD>\r
 150 </TR>\r
 151 </FONT></TD>\r
 152 </TR>\r
 153 </TABLE>\r
 154 \r
 155 <P>\r
 156 \r
 157 <P>\r
 158 \r
 159 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 160 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 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>\r
 162 </TR>\r
 163 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 164 <A NAME="compbio.data.sequence.ClustalAlignmentUtil.gapchar"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 165 <CODE>public&nbsp;static&nbsp;final&nbsp;char</CODE></FONT></TD>\r
 166 <TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/ClustalAlignmentUtil.html#gapchar">gapchar</A></CODE></TD>\r
 167 <TD ALIGN="right"><CODE>45</CODE></TD>\r
 168 </TR>\r
 169 </FONT></TD>\r
 170 </TR>\r
 171 </TABLE>\r
 172 \r
 173 <P>\r
 174 \r
 175 <P>\r
 176 \r
 177 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 178 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 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>\r
 180 </TR>\r
 181 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 182 <A NAME="compbio.data.sequence.ScoreManager.SINGLE_ENTRY_KEY"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 183 <CODE>public&nbsp;static&nbsp;final&nbsp;<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
 184 <TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/ScoreManager.html#SINGLE_ENTRY_KEY">SINGLE_ENTRY_KEY</A></CODE></TD>\r
 185 <TD ALIGN="right"><CODE>"Alignment"</CODE></TD>\r
 186 </TR>\r
 187 </FONT></TD>\r
 188 </TR>\r
 189 </TABLE>\r
 190 \r
 191 <P>\r
 192 \r
 193 <P>\r
 194 \r
 195 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 196 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 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>\r
 198 </TR>\r
 199 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 200 <A NAME="compbio.data.sequence.SMERFSConstraints.DEFAULT_GAP_THRESHOLD"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 201 <CODE>public&nbsp;static&nbsp;final&nbsp;double</CODE></FONT></TD>\r
 202 <TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/SMERFSConstraints.html#DEFAULT_GAP_THRESHOLD">DEFAULT_GAP_THRESHOLD</A></CODE></TD>\r
 203 <TD ALIGN="right"><CODE>0.1</CODE></TD>\r
 204 </TR>\r
 205 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 206 <A NAME="compbio.data.sequence.SMERFSConstraints.DEFAULT_WINDOW_SIZE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 207 <CODE>public&nbsp;static&nbsp;final&nbsp;int</CODE></FONT></TD>\r
 208 <TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/SMERFSConstraints.html#DEFAULT_WINDOW_SIZE">DEFAULT_WINDOW_SIZE</A></CODE></TD>\r
 209 <TD ALIGN="right"><CODE>7</CODE></TD>\r
 210 </TR>\r
 211 </FONT></TD>\r
 212 </TR>\r
 213 </TABLE>\r
 214 \r
 215 <P>\r
 216 \r
 217 <P>\r
 218 <A NAME="compbio.engine"><!-- --></A>\r
 219 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 220 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 221 <TH ALIGN="left"><FONT SIZE="+2">\r
 222 compbio.engine.*</FONT></TH>\r
 223 </TR>\r
 224 </TABLE>\r
 225 \r
 226 <P>\r
 227 \r
 228 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 229 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 230 <TH ALIGN="left" COLSPAN="3">compbio.engine.client.<A HREF="compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>&lt;<A HREF="compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</TH>\r
 231 </TR>\r
 232 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 233 <A NAME="compbio.engine.client.ConfExecutable.CLUSTER_TASK_ID_PREFIX"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 234 <CODE>public&nbsp;static&nbsp;final&nbsp;<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
 235 <TD ALIGN="left"><CODE><A HREF="compbio/engine/client/ConfExecutable.html#CLUSTER_TASK_ID_PREFIX">CLUSTER_TASK_ID_PREFIX</A></CODE></TD>\r
 236 <TD ALIGN="right"><CODE>"@"</CODE></TD>\r
 237 </TR>\r
 238 </FONT></TD>\r
 239 </TR>\r
 240 </TABLE>\r
 241 \r
 242 <P>\r
 243 \r
 244 <P>\r
 245 \r
 246 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 247 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 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>\r
 249 </TR>\r
 250 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 251 <A NAME="compbio.engine.client.EnvVariableProcessor.PATH"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 252 <CODE>public&nbsp;static&nbsp;final&nbsp;<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
 253 <TD ALIGN="left"><CODE><A HREF="compbio/engine/client/EnvVariableProcessor.html#PATH">PATH</A></CODE></TD>\r
 254 <TD ALIGN="right"><CODE>"PATH"</CODE></TD>\r
 255 </TR>\r
 256 </FONT></TD>\r
 257 </TR>\r
 258 </TABLE>\r
 259 \r
 260 <P>\r
 261 \r
 262 <P>\r
 263 \r
 264 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 265 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 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>\r
 267 </TR>\r
 268 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 269 <A NAME="compbio.engine.client.RunConfiguration.rconfigFile"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 270 <CODE>public&nbsp;static&nbsp;final&nbsp;<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
 271 <TD ALIGN="left"><CODE><A HREF="compbio/engine/client/RunConfiguration.html#rconfigFile">rconfigFile</A></CODE></TD>\r
 272 <TD ALIGN="right"><CODE>"RunnerConfig.xml"</CODE></TD>\r
 273 </TR>\r
 274 </FONT></TD>\r
 275 </TR>\r
 276 </TABLE>\r
 277 \r
 278 <P>\r
 279 \r
 280 <P>\r
 281 \r
 282 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 283 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 284 <TH ALIGN="left" COLSPAN="3">compbio.engine.client.<A HREF="compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</TH>\r
 285 </TR>\r
 286 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 287 <A NAME="compbio.engine.client.SkeletalExecutable.ERROR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 288 <CODE>public&nbsp;static&nbsp;final&nbsp;<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
 289 <TD ALIGN="left"><CODE><A HREF="compbio/engine/client/SkeletalExecutable.html#ERROR">ERROR</A></CODE></TD>\r
 290 <TD ALIGN="right"><CODE>"error.txt"</CODE></TD>\r
 291 </TR>\r
 292 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 293 <A NAME="compbio.engine.client.SkeletalExecutable.INPUT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 294 <CODE>public&nbsp;static&nbsp;final&nbsp;<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
 295 <TD ALIGN="left"><CODE><A HREF="compbio/engine/client/SkeletalExecutable.html#INPUT">INPUT</A></CODE></TD>\r
 296 <TD ALIGN="right"><CODE>"input.txt"</CODE></TD>\r
 297 </TR>\r
 298 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 299 <A NAME="compbio.engine.client.SkeletalExecutable.OUTPUT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 300 <CODE>public&nbsp;static&nbsp;final&nbsp;<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
 301 <TD ALIGN="left"><CODE><A HREF="compbio/engine/client/SkeletalExecutable.html#OUTPUT">OUTPUT</A></CODE></TD>\r
 302 <TD ALIGN="right"><CODE>"result.txt"</CODE></TD>\r
 303 </TR>\r
 304 </FONT></TD>\r
 305 </TR>\r
 306 </TABLE>\r
 307 \r
 308 <P>\r
 309 \r
 310 <P>\r
 311 \r
 312 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 313 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 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>\r
 315 </TR>\r
 316 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 317 <A NAME="compbio.engine.cluster.drmaa.ClusterSession.JOBID"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 318 <CODE>public&nbsp;static&nbsp;final&nbsp;<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
 319 <TD ALIGN="left"><CODE><A HREF="compbio/engine/cluster/drmaa/ClusterSession.html#JOBID">JOBID</A></CODE></TD>\r
 320 <TD ALIGN="right"><CODE>"JOBID"</CODE></TD>\r
 321 </TR>\r
 322 </FONT></TD>\r
 323 </TR>\r
 324 </TABLE>\r
 325 \r
 326 <P>\r
 327 \r
 328 <P>\r
 329 \r
 330 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 331 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 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>\r
 333 </TR>\r
 334 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 335 <A NAME="compbio.engine.conf._Key.DELIM"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 336 <CODE>public&nbsp;static&nbsp;final&nbsp;<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
 337 <TD ALIGN="left"><CODE><A HREF="compbio/engine/conf/_Key.html#DELIM">DELIM</A></CODE></TD>\r
 338 <TD ALIGN="right"><CODE>"#"</CODE></TD>\r
 339 </TR>\r
 340 </FONT></TD>\r
 341 </TR>\r
 342 </TABLE>\r
 343 \r
 344 <P>\r
 345 \r
 346 <P>\r
 347 \r
 348 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 349 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 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>\r
 351 </TR>\r
 352 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 353 <A NAME="compbio.engine.conf.DirectoryManager.DELIM"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 354 <CODE>public&nbsp;static&nbsp;final&nbsp;<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
 355 <TD ALIGN="left"><CODE><A HREF="compbio/engine/conf/DirectoryManager.html#DELIM">DELIM</A></CODE></TD>\r
 356 <TD ALIGN="right"><CODE>"#"</CODE></TD>\r
 357 </TR>\r
 358 </FONT></TD>\r
 359 </TR>\r
 360 </TABLE>\r
 361 \r
 362 <P>\r
 363 \r
 364 <P>\r
 365 \r
 366 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 367 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 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>\r
 369 </TR>\r
 370 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 371 <A NAME="compbio.engine.local.ExecutableWrapper.PROC_ERR_FILE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 372 <CODE>public&nbsp;static&nbsp;final&nbsp;<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
 373 <TD ALIGN="left"><CODE><A HREF="compbio/engine/local/ExecutableWrapper.html#PROC_ERR_FILE">PROC_ERR_FILE</A></CODE></TD>\r
 374 <TD ALIGN="right"><CODE>"procError.txt"</CODE></TD>\r
 375 </TR>\r
 376 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 377 <A NAME="compbio.engine.local.ExecutableWrapper.PROC_OUT_FILE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 378 <CODE>public&nbsp;static&nbsp;final&nbsp;<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
 379 <TD ALIGN="left"><CODE><A HREF="compbio/engine/local/ExecutableWrapper.html#PROC_OUT_FILE">PROC_OUT_FILE</A></CODE></TD>\r
 380 <TD ALIGN="right"><CODE>"procOutput.txt"</CODE></TD>\r
 381 </TR>\r
 382 </FONT></TD>\r
 383 </TR>\r
 384 </TABLE>\r
 385 \r
 386 <P>\r
 387 \r
 388 <P>\r
 389 <A NAME="compbio.metadata"><!-- --></A>\r
 390 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 391 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 392 <TH ALIGN="left"><FONT SIZE="+2">\r
 393 compbio.metadata.*</FONT></TH>\r
 394 </TR>\r
 395 </TABLE>\r
 396 \r
 397 <P>\r
 398 \r
 399 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 400 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 401 <TH ALIGN="left" COLSPAN="3">compbio.metadata.<A HREF="compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt;</TH>\r
 402 </TR>\r
 403 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 404 <A NAME="compbio.metadata.PresetManager.LOCAL_ENGINE_LIMIT_PRESET"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 405 <CODE>public&nbsp;static&nbsp;final&nbsp;<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
 406 <TD ALIGN="left"><CODE><A HREF="compbio/metadata/PresetManager.html#LOCAL_ENGINE_LIMIT_PRESET">LOCAL_ENGINE_LIMIT_PRESET</A></CODE></TD>\r
 407 <TD ALIGN="right"><CODE>"# LocalEngineExecutionLimit #"</CODE></TD>\r
 408 </TR>\r
 409 </FONT></TD>\r
 410 </TR>\r
 411 </TABLE>\r
 412 \r
 413 <P>\r
 414 \r
 415 <P>\r
 416 <A NAME="compbio.runner"><!-- --></A>\r
 417 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 418 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 419 <TH ALIGN="left"><FONT SIZE="+2">\r
 420 compbio.runner.*</FONT></TH>\r
 421 </TR>\r
 422 </TABLE>\r
 423 \r
 424 <P>\r
 425 \r
 426 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 427 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 428 <TH ALIGN="left" COLSPAN="3">compbio.runner.<A HREF="compbio/runner/Util.html" title="class in compbio.runner">Util</A></TH>\r
 429 </TR>\r
 430 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 431 <A NAME="compbio.runner.Util.SPACE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 432 <CODE>public&nbsp;static&nbsp;final&nbsp;<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
 433 <TD ALIGN="left"><CODE><A HREF="compbio/runner/Util.html#SPACE">SPACE</A></CODE></TD>\r
 434 <TD ALIGN="right"><CODE>" "</CODE></TD>\r
 435 </TR>\r
 436 </FONT></TD>\r
 437 </TR>\r
 438 </TABLE>\r
 439 \r
 440 <P>\r
 441 \r
 442 <P>\r
 443 \r
 444 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 445 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 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>\r
 447 </TR>\r
 448 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 449 <A NAME="compbio.runner.conservation.AACon.KEY_VALUE_SEPARATOR"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 450 <CODE>public&nbsp;static&nbsp;final&nbsp;<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
 451 <TD ALIGN="left"><CODE><A HREF="compbio/runner/conservation/AACon.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></CODE></TD>\r
 452 <TD ALIGN="right"><CODE>"="</CODE></TD>\r
 453 </TR>\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&nbsp;static&nbsp;final&nbsp;<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
 459 </TR>\r
 460 </FONT></TD>\r
 461 </TR>\r
 462 </TABLE>\r
 463 \r
 464 <P>\r
 465 \r
 466 <P>\r
 467 \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
 471 </TR>\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&nbsp;final&nbsp;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
 477 </TR>\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&nbsp;static&nbsp;final&nbsp;<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
 483 </TR>\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&nbsp;final&nbsp;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
 489 </TR>\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&nbsp;final&nbsp;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
 495 </TR>\r
 496 </FONT></TD>\r
 497 </TR>\r
 498 </TABLE>\r
 499 \r
 500 <P>\r
 501 \r
 502 <P>\r
 503 \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
 507 </TR>\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&nbsp;static&nbsp;final&nbsp;<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
 513 </TR>\r
 514 </FONT></TD>\r
 515 </TR>\r
 516 </TABLE>\r
 517 \r
 518 <P>\r
 519 \r
 520 <P>\r
 521 \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
 525 </TR>\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&nbsp;static&nbsp;final&nbsp;<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
 531 </TR>\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&nbsp;static&nbsp;final&nbsp;<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
 537 </TR>\r
 538 </FONT></TD>\r
 539 </TR>\r
 540 </TABLE>\r
 541 \r
 542 <P>\r
 543 \r
 544 <P>\r
 545 \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
 549 </TR>\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&nbsp;static&nbsp;final&nbsp;<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
 555 </TR>\r
 556 </FONT></TD>\r
 557 </TR>\r
 558 </TABLE>\r
 559 \r
 560 <P>\r
 561 \r
 562 <P>\r
 563 \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
 567 </TR>\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&nbsp;static&nbsp;final&nbsp;<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
 573 </TR>\r
 574 </FONT></TD>\r
 575 </TR>\r
 576 </TABLE>\r
 577 \r
 578 <P>\r
 579 \r
 580 <P>\r
 581 \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
 585 </TR>\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&nbsp;static&nbsp;final&nbsp;<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
 591 </TR>\r
 592 </FONT></TD>\r
 593 </TR>\r
 594 </TABLE>\r
 595 \r
 596 <P>\r
 597 \r
 598 <P>\r
 599 \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
 603 </TR>\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&nbsp;static&nbsp;final&nbsp;<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
 609 </TR>\r
 610 </FONT></TD>\r
 611 </TR>\r
 612 </TABLE>\r
 613 \r
 614 <P>\r
 615 \r
 616 <P>\r
 617 \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
 621 </TR>\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&nbsp;static&nbsp;final&nbsp;<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
 627 </TR>\r
 628 </FONT></TD>\r
 629 </TR>\r
 630 </TABLE>\r
 631 \r
 632 <P>\r
 633 \r
 634 <P>\r
 635 \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
 639 </TR>\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&nbsp;static&nbsp;final&nbsp;<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
 645 </TR>\r
 646 </FONT></TD>\r
 647 </TR>\r
 648 </TABLE>\r
 649 \r
 650 <P>\r
 651 \r
 652 <P>\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
 658 </TR>\r
 659 </TABLE>\r
 660 \r
 661 <P>\r
 662 \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
 666 </TR>\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&nbsp;static&nbsp;final&nbsp;<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>"&gt;Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n&gt;Bar\nASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n"</CODE></TD>\r
 672 </TR>\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&nbsp;static&nbsp;final&nbsp;<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>"&gt;Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n&gt;Bar\nASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n"</CODE></TD>\r
 678 </TR>\r
 679 </FONT></TD>\r
 680 </TR>\r
 681 </TABLE>\r
 682 \r
 683 <P>\r
 684 \r
 685 <P>\r
 686 <HR>\r
 687 \r
 688 \r
 689 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 690 <A NAME="navbar_bottom"><!-- --></A>\r
 691 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 692 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 693 <TR>\r
 694 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 695 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 696 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 697   <TR ALIGN="center" VALIGN="top">\r
 698   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 699   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
 700   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
 701   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
 702   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 703   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 704   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 705   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 706   </TR>\r
 707 </TABLE>\r
 708 </TD>\r
 709 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 710 </EM>\r
 711 </TD>\r
 712 </TR>\r
 713 \r
 714 <TR>\r
 715 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 716 &nbsp;PREV&nbsp;\r
 717 &nbsp;NEXT</FONT></TD>\r
 718 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 719   <A HREF="index.html?constant-values.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 720 &nbsp;<A HREF="constant-values.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 721 &nbsp;<SCRIPT type="text/javascript">\r
 722   <!--\r
 723   if(window==top) {\r
 724     document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');\r
 725   }\r
 726   //-->\r
 727 </SCRIPT>\r
 728 <NOSCRIPT>\r
 729   <A HREF="allclasses-noframe.html"><B>All Classes</B></A>\r
 730 </NOSCRIPT>\r
 731 \r
 732 \r
 733 </FONT></TD>\r
 734 </TR>\r
 735 </TABLE>\r
 736 <A NAME="skip-navbar_bottom"></A>\r
 737 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 738 \r
 739 <HR>\r
 740 \r
 741 </BODY>\r
 742 </HTML>\r