website/full_javadoc/compbio/engine/client/class-use/CommandBuilder.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 Fri Aug 12 14:32:36 BST 2011 -->\r
   6 <TITLE>\r
   7 Uses of Class compbio.engine.client.CommandBuilder\r
   8 </TITLE>\r
   9 \r
  10 <META NAME="date" CONTENT="2011-08-12">\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.engine.client.CommandBuilder";\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/engine/client/CommandBuilder.html" title="class in compbio.engine.client"><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/engine/client/\class-useCommandBuilder.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
  62 &nbsp;<A HREF="CommandBuilder.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.engine.client.CommandBuilder</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/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>\r
  91 </TR>\r
  92 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  93 <TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
  94 <TD>&nbsp;&nbsp;</TD>\r
  95 </TR>\r
  96 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  97 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
  98 <TD>Utilities commonly used by all runners.&nbsp;</TD>\r
  99 </TR>\r
 100 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 101 <TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
 102 <TD>&nbsp;&nbsp;</TD>\r
 103 </TR>\r
 104 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 105 <TD><A HREF="#compbio.runner.conservation"><B>compbio.runner.conservation</B></A></TD>\r
 106 <TD>&nbsp;&nbsp;</TD>\r
 107 </TR>\r
 108 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 109 <TD><A HREF="#compbio.runner.disorder"><B>compbio.runner.disorder</B></A></TD>\r
 110 <TD>&nbsp;&nbsp;</TD>\r
 111 </TR>\r
 112 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 113 <TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
 114 <TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
 115 </TR>\r
 116 </TABLE>\r
 117 &nbsp;\r
 118 <P>\r
 119 <A NAME="compbio.engine.client"><!-- --></A>\r
 120 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 121 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 122 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 123 Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
 124 </TR>\r
 125 </TABLE>\r
 126 &nbsp;\r
 127 <P>\r
 128 \r
 129 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 130 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 131 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>\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/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;?&gt;</CODE></FONT></TD>\r
 136 <TD><CODE><B>RunConfiguration.</B><B><A HREF="../../../../compbio/engine/client/RunConfiguration.html#getParameters()">getParameters</A></B>()</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/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="type parameter in ConfiguredExecutable">T</A>&gt;</CODE></FONT></TD>\r
 144 <TD><CODE><B>ConfiguredExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html#getParameters()">getParameters</A></B>()</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/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
 152 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getParameters()">getParameters</A></B>()</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 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 158 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 159 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt;</CODE></FONT></TD>\r
 160 <TD><CODE><B>Executable.</B><B><A HREF="../../../../compbio/engine/client/Executable.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
 161 \r
 162 <BR>\r
 163 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\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/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
 168 <TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.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
 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/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
 176 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.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
 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>static\r
 184 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 185 <TR ALIGN="right" VALIGN="">\r
 186 <TD NOWRAP><FONT SIZE="-1">\r
 187 <CODE>&lt;T&gt; <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;T&gt;</CODE></FONT></TD>\r
 188 </TR>\r
 189 </TABLE>\r
 190 </CODE></FONT></TD>\r
 191 <TD><CODE><B>CommandBuilder.</B><B><A HREF="../../../../compbio/engine/client/CommandBuilder.html#newCommandBuilder(java.util.List, java.lang.String)">newCommandBuilder</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;? extends <A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;T&gt;&gt;&nbsp;arguments,\r
 192                   <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>&nbsp;nameValueSeparator)</CODE>\r
 193 \r
 194 <BR>\r
 195 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This produces the same result as getCommands method.</TD>\r
 196 </TR>\r
 197 </TABLE>\r
 198 &nbsp;\r
 199 <P>\r
 200 \r
 201 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 202 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 203 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with parameters of type <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>\r
 204 </TR>\r
 205 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 206 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 207 <CODE>&nbsp;void</CODE></FONT></TD>\r
 208 <TD><CODE><B>RunConfiguration.</B><B><A HREF="../../../../compbio/engine/client/RunConfiguration.html#setParameters(compbio.engine.client.CommandBuilder)">setParameters</A></B>(<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;?&gt;&nbsp;parameters)</CODE>\r
 209 \r
 210 <BR>\r
 211 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 212 </TR>\r
 213 </TABLE>\r
 214 &nbsp;\r
 215 <P>\r
 216 <A NAME="compbio.runner"><!-- --></A>\r
 217 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 218 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 219 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 220 Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A> in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
 221 </TR>\r
 222 </TABLE>\r
 223 &nbsp;\r
 224 <P>\r
 225 \r
 226 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 227 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 228 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> that return <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>\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;<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
 233 <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
 234 \r
 235 <BR>\r
 236 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&nbsp;&nbsp;</TD>\r
 237 </TR>\r
 238 </TABLE>\r
 239 &nbsp;\r
 240 <P>\r
 241 <A NAME="compbio.runner._impl"><!-- --></A>\r
 242 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 243 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 244 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 245 Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A> in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
 246 </TR>\r
 247 </TABLE>\r
 248 &nbsp;\r
 249 <P>\r
 250 \r
 251 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 252 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 253 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that return <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>\r
 254 </TR>\r
 255 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 256 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 257 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></FONT></TD>\r
 258 <TD><CODE><B>NetNglyc.</B><B><A HREF="../../../../compbio/runner/_impl/NetNglyc.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
 259 \r
 260 <BR>\r
 261 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 262 </TR>\r
 263 </TABLE>\r
 264 &nbsp;\r
 265 <P>\r
 266 <A NAME="compbio.runner.conservation"><!-- --></A>\r
 267 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 268 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 269 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 270 Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A> in <A HREF="../../../../compbio/runner/conservation/package-summary.html">compbio.runner.conservation</A></FONT></TH>\r
 271 </TR>\r
 272 </TABLE>\r
 273 &nbsp;\r
 274 <P>\r
 275 \r
 276 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 277 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 278 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/conservation/package-summary.html">compbio.runner.conservation</A> that return <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>\r
 279 </TR>\r
 280 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 281 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 282 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>&gt;</CODE></FONT></TD>\r
 283 <TD><CODE><B>AACon.</B><B><A HREF="../../../../compbio/runner/conservation/AACon.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
 284 \r
 285 <BR>\r
 286 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 287 </TR>\r
 288 </TABLE>\r
 289 &nbsp;\r
 290 <P>\r
 291 <A NAME="compbio.runner.disorder"><!-- --></A>\r
 292 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 293 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 294 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 295 Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A> in <A HREF="../../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A></FONT></TH>\r
 296 </TR>\r
 297 </TABLE>\r
 298 &nbsp;\r
 299 <P>\r
 300 \r
 301 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 302 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 303 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A> that return <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>\r
 304 </TR>\r
 305 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 306 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 307 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>&gt;</CODE></FONT></TD>\r
 308 <TD><CODE><B>Jronn.</B><B><A HREF="../../../../compbio/runner/disorder/Jronn.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
 309 \r
 310 <BR>\r
 311 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 312 </TR>\r
 313 </TABLE>\r
 314 &nbsp;\r
 315 <P>\r
 316 <A NAME="compbio.runner.msa"><!-- --></A>\r
 317 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 318 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 319 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 320 Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
 321 </TR>\r
 322 </TABLE>\r
 323 &nbsp;\r
 324 <P>\r
 325 \r
 326 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 327 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 328 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>\r
 329 </TR>\r
 330 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 331 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 332 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
 333 <TD><CODE><B>Tcoffee.</B><B><A HREF="../../../../compbio/runner/msa/Tcoffee.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
 334 \r
 335 <BR>\r
 336 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 337 </TR>\r
 338 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 339 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 340 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>&gt;</CODE></FONT></TD>\r
 341 <TD><CODE><B>ClustalO.</B><B><A HREF="../../../../compbio/runner/msa/ClustalO.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
 342 \r
 343 <BR>\r
 344 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 345 </TR>\r
 346 </TABLE>\r
 347 &nbsp;\r
 348 <P>\r
 349 <HR>\r
 350 \r
 351 \r
 352 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 353 <A NAME="navbar_bottom"><!-- --></A>\r
 354 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 355 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 356 <TR>\r
 357 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 358 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 359 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 360   <TR ALIGN="center" VALIGN="top">\r
 361   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 362   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 363   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
 364   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
 365   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 366   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 367   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 368   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 369   </TR>\r
 370 </TABLE>\r
 371 </TD>\r
 372 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 373 </EM>\r
 374 </TD>\r
 375 </TR>\r
 376 \r
 377 <TR>\r
 378 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 379 &nbsp;PREV&nbsp;\r
 380 &nbsp;NEXT</FONT></TD>\r
 381 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 382   <A HREF="../../../../index.html?compbio/engine/client/\class-useCommandBuilder.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 383 &nbsp;<A HREF="CommandBuilder.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 384 &nbsp;<SCRIPT type="text/javascript">\r
 385   <!--\r
 386   if(window==top) {\r
 387     document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 388   }\r
 389   //-->\r
 390 </SCRIPT>\r
 391 <NOSCRIPT>\r
 392   <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 393 </NOSCRIPT>\r
 394 \r
 395 \r
 396 </FONT></TD>\r
 397 </TR>\r
 398 </TABLE>\r
 399 <A NAME="skip-navbar_bottom"></A>\r
 400 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 401 \r
 402 <HR>\r
 403 \r
 404 </BODY>\r
 405 </HTML>\r