website/full_javadoc/compbio/runner/class-use/_SkeletalCommandBuilder.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_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
   6 <TITLE>\r
   7 Uses of Class compbio.runner._SkeletalCommandBuilder\r
   8 </TITLE>\r
   9 \r
  10 <META NAME="date" CONTENT="2010-02-17">\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="Uses of Class compbio.runner._SkeletalCommandBuilder";\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">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
  42   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
  43   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></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?compbio/runner/\class-use_SkeletalCommandBuilder.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
  62 &nbsp;<A HREF="_SkeletalCommandBuilder.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 <H2>\r
  84 <B>Uses of Class<br>compbio.runner._SkeletalCommandBuilder</B></H2>\r
  85 </CENTER>\r
  86 \r
  87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
  88 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
  89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
  90 Packages that use <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></FONT></TH>\r
  91 </TR>\r
  92 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  93 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
  94 <TD>Utilities commonly used by all runners.&nbsp;</TD>\r
  95 </TR>\r
  96 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  97 <TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
  98 <TD>&nbsp;&nbsp;</TD>\r
  99 </TR>\r
 100 </TABLE>\r
 101 &nbsp;\r
 102 <P>\r
 103 <A NAME="compbio.runner"><!-- --></A>\r
 104 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 105 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 106 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 107 Uses of <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
 108 </TR>\r
 109 </TABLE>\r
 110 &nbsp;\r
 111 <P>\r
 112 \r
 113 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 114 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 115 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> that return <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></FONT></TH>\r
 116 </TR>\r
 117 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 118 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 119 <CODE>&nbsp;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
 120 <TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)">addParameter</A></B>(java.lang.String&nbsp;parameter)</CODE>\r
 121 \r
 122 <BR>\r
 123 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 124 </TR>\r
 125 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 126 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 127 <CODE>&nbsp;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
 128 <TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</CODE>\r
 129 \r
 130 <BR>\r
 131 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 132 </TR>\r
 133 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 134 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 135 <CODE>&nbsp;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
 136 <TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])">addParameters</A></B>(java.lang.String[]&nbsp;parameters)</CODE>\r
 137 \r
 138 <BR>\r
 139 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 140 </TR>\r
 141 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 142 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 143 <CODE>&nbsp;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
 144 <TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)">setEmail</A></B>(java.lang.String&nbsp;email)</CODE>\r
 145 \r
 146 <BR>\r
 147 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 148 </TR>\r
 149 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 150 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 151 <CODE>&nbsp;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
 152 <TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)">setName</A></B>(java.lang.String&nbsp;name)</CODE>\r
 153 \r
 154 <BR>\r
 155 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 156 </TR>\r
 157 </TABLE>\r
 158 &nbsp;\r
 159 <P>\r
 160 \r
 161 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 162 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 163 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> that return types with arguments of type <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></FONT></TH>\r
 164 </TR>\r
 165 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 166 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 167 <CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></FONT></TD>\r
 168 <TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
 169 \r
 170 <BR>\r
 171 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 172 </TR>\r
 173 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 174 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 175 <CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></FONT></TD>\r
 176 <TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimits()">getLimits</A></B>()</CODE>\r
 177 \r
 178 <BR>\r
 179 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 180 </TR>\r
 181 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 182 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 183 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></FONT></TD>\r
 184 <TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
 185 \r
 186 <BR>\r
 187 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 188 </TR>\r
 189 </TABLE>\r
 190 &nbsp;\r
 191 <P>\r
 192 <A NAME="compbio.runner._impl"><!-- --></A>\r
 193 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 194 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 195 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 196 Uses of <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> in <A HREF="../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
 197 </TR>\r
 198 </TABLE>\r
 199 &nbsp;\r
 200 <P>\r
 201 \r
 202 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 203 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 204 <TH ALIGN="left" COLSPAN="2">Subclasses of <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> in <A HREF="../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
 205 </TR>\r
 206 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 207 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 208 <CODE>&nbsp;class</CODE></FONT></TD>\r
 209 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A></B></CODE>\r
 210 \r
 211 <BR>\r
 212 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 213 </TR>\r
 214 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 215 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 216 <CODE>&nbsp;class</CODE></FONT></TD>\r
 217 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A></B></CODE>\r
 218 \r
 219 <BR>\r
 220 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 221 </TR>\r
 222 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 223 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 224 <CODE>&nbsp;class</CODE></FONT></TD>\r
 225 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A></B></CODE>\r
 226 \r
 227 <BR>\r
 228 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 229 </TR>\r
 230 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 231 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 232 <CODE>&nbsp;class</CODE></FONT></TD>\r
 233 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A></B></CODE>\r
 234 \r
 235 <BR>\r
 236 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;TODO this needs fixing! Executable does not work</TD>\r
 237 </TR>\r
 238 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 239 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 240 <CODE>&nbsp;class</CODE></FONT></TD>\r
 241 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A></B></CODE>\r
 242 \r
 243 <BR>\r
 244 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 245 </TR>\r
 246 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 247 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 248 <CODE>&nbsp;class</CODE></FONT></TD>\r
 249 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A></B></CODE>\r
 250 \r
 251 <BR>\r
 252 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 253 </TR>\r
 254 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 255 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 256 <CODE>&nbsp;class</CODE></FONT></TD>\r
 257 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A></B></CODE>\r
 258 \r
 259 <BR>\r
 260 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 261 </TR>\r
 262 </TABLE>\r
 263 &nbsp;\r
 264 <P>\r
 265 <HR>\r
 266 \r
 267 \r
 268 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 269 <A NAME="navbar_bottom"><!-- --></A>\r
 270 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 271 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 272 <TR>\r
 273 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 274 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 275 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 276   <TR ALIGN="center" VALIGN="top">\r
 277   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 278   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 279   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
 280   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
 281   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 282   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 283   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 284   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 285   </TR>\r
 286 </TABLE>\r
 287 </TD>\r
 288 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 289 </EM>\r
 290 </TD>\r
 291 </TR>\r
 292 \r
 293 <TR>\r
 294 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 295 &nbsp;PREV&nbsp;\r
 296 &nbsp;NEXT</FONT></TD>\r
 297 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 298   <A HREF="../../../index.html?compbio/runner/\class-use_SkeletalCommandBuilder.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 299 &nbsp;<A HREF="_SkeletalCommandBuilder.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 300 &nbsp;<SCRIPT type="text/javascript">\r
 301   <!--\r
 302   if(window==top) {\r
 303     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 304   }\r
 305   //-->\r
 306 </SCRIPT>\r
 307 <NOSCRIPT>\r
 308   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 309 </NOSCRIPT>\r
 310 \r
 311 \r
 312 </FONT></TD>\r
 313 </TR>\r
 314 </TABLE>\r
 315 <A NAME="skip-navbar_bottom"></A>\r
 316 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 317 \r
 318 <HR>\r
 319 \r
 320 </BODY>\r
 321 </HTML>\r