website/full_javadoc/compbio/runner/msa/ClustalO.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 14:32:34 BST 2011 -->\r
   6 <TITLE>\r
   7 ClustalO\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="ClustalO";\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="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
  43   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ClustalO.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
  44   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-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 CLASS&nbsp;\r
  59 &nbsp;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
  60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
  61   <A HREF="../../../index.html?compbio/runner/msa/ClustalO.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
  62 &nbsp;<A HREF="ClustalO.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 <TR>\r
  78 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
  79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
  80 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
  81 DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
  82 </TR>\r
  83 </TABLE>\r
  84 <A NAME="skip-navbar_top"></A>\r
  85 <!-- ========= END OF TOP NAVBAR ========= -->\r
  86 \r
  87 <HR>\r
  88 <!-- ======== START OF CLASS DATA ======== -->\r
  89 <H2>\r
  90 <FONT SIZE="-1">\r
  91 compbio.runner.msa</FONT>\r
  92 <BR>\r
  93 Class ClustalO</H2>\r
  94 <PRE>\r
  95 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
  96   <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">compbio.engine.client.SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>&gt;\r
  97       <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.msa.ClustalO</B>\r
  98 </PRE>\r
  99 <DL>\r
 100 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>&gt;</DD>\r
 101 </DL>\r
 102 <HR>\r
 103 <DL>\r
 104 <DT><PRE>public class <B>ClustalO</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>&gt;</DL>\r
 105 </PRE>\r
 106 \r
 107 <P>\r
 108 <HR>\r
 109 \r
 110 <P>\r
 111 <!-- ======== NESTED CLASS SUMMARY ======== -->\r
 112 \r
 113 <A NAME="nested_class_summary"><!-- --></A>\r
 114 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 115 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 116 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 117 <B>Nested Class Summary</B></FONT></TH>\r
 118 </TR>\r
 119 </TABLE>\r
 120 &nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
 121 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 122 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 123 <TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
 124 </TR>\r
 125 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 126 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
 127 </TR>\r
 128 </TABLE>\r
 129 &nbsp;\r
 130 <!-- =========== FIELD SUMMARY =========== -->\r
 131 \r
 132 <A NAME="field_summary"><!-- --></A>\r
 133 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 134 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 135 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 136 <B>Field Summary</B></FONT></TH>\r
 137 </TR>\r
 138 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 139 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 140 <CODE>static&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
 141 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalO.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></B></CODE>\r
 142 \r
 143 <BR>\r
 144 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 145 </TR>\r
 146 </TABLE>\r
 147 &nbsp;<A NAME="fields_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
 148 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 149 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 150 <TH ALIGN="left"><B>Fields inherited from class compbio.engine.client.<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A></B></TH>\r
 151 </TR>\r
 152 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 153 <TD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#ERROR">ERROR</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#INPUT">INPUT</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#OUTPUT">OUTPUT</A></CODE></TD>\r
 154 </TR>\r
 155 </TABLE>\r
 156 &nbsp;\r
 157 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 158 \r
 159 <A NAME="constructor_summary"><!-- --></A>\r
 160 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 161 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 162 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 163 <B>Constructor Summary</B></FONT></TH>\r
 164 </TR>\r
 165 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 166 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalO.html#ClustalO()">ClustalO</A></B>()</CODE>\r
 167 \r
 168 <BR>\r
 169 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;--threads=<n> Number of processors to use
 170
 171  -l, --log=<file> Log all non-essential output to this file</TD>\r
 172 </TR>\r
 173 </TABLE>\r
 174 &nbsp;\r
 175 <!-- ========== METHOD SUMMARY =========== -->\r
 176 \r
 177 <A NAME="method_summary"><!-- --></A>\r
 178 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 179 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 180 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 181 <B>Method Summary</B></FONT></TH>\r
 182 </TR>\r
 183 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 184 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 185 <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
 186 <TD><CODE><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
 187 \r
 188 <BR>\r
 189 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 190 </TR>\r
 191 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 192 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 193 <CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
 194 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalO.html#getResults(java.lang.String)">getResults</A></B>(<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;workDirectory)</CODE>\r
 195 \r
 196 <BR>\r
 197 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 198 </TR>\r
 199 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 200 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 201 <CODE>static&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
 202 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalO.html#getStatFile()">getStatFile</A></B>()</CODE>\r
 203 \r
 204 <BR>\r
 205 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 206 </TR>\r
 207 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 208 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 209 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>&gt;</CODE></FONT></TD>\r
 210 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalO.html#getType()">getType</A></B>()</CODE>\r
 211 \r
 212 <BR>\r
 213 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 214 </TR>\r
 215 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 216 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 217 <CODE>&nbsp;<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A></CODE></FONT></TD>\r
 218 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalO.html#setInput(java.lang.String)">setInput</A></B>(<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;inFile)</CODE>\r
 219 \r
 220 <BR>\r
 221 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 222 </TR>\r
 223 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 224 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 225 <CODE>&nbsp;void</CODE></FONT></TD>\r
 226 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalO.html#setNCore(int)">setNCore</A></B>(int&nbsp;ncoreNumber)</CODE>\r
 227 \r
 228 <BR>\r
 229 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 230 </TR>\r
 231 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 232 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 233 <CODE>&nbsp;<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A></CODE></FONT></TD>\r
 234 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalO.html#setOutput(java.lang.String)">setOutput</A></B>(<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;outFile)</CODE>\r
 235 \r
 236 <BR>\r
 237 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 238 </TR>\r
 239 </TABLE>\r
 240 &nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
 241 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 242 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 243 <TH ALIGN="left"><B>Methods inherited from class compbio.engine.client.<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A></B></TH>\r
 244 </TR>\r
 245 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 246 <TD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)">equals</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterCpuNum(java.lang.Class)">getClusterCpuNum</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterJobSettings()">getClusterJobSettings</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">getCreatedFiles</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#hashCode()">hashCode</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)">setError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)">setParameter</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#toString()">toString</A></CODE></TD>\r
 247 </TR>\r
 248 </TABLE>\r
 249 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 250 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 251 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 252 <TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
 253 </TR>\r
 254 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 255 <TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
 256 </TR>\r
 257 </TABLE>\r
 258 &nbsp;\r
 259 <P>\r
 260 \r
 261 <!-- ============ FIELD DETAIL =========== -->\r
 262 \r
 263 <A NAME="field_detail"><!-- --></A>\r
 264 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 265 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 266 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 267 <B>Field Detail</B></FONT></TH>\r
 268 </TR>\r
 269 </TABLE>\r
 270 \r
 271 <A NAME="KEY_VALUE_SEPARATOR"><!-- --></A><H3>\r
 272 KEY_VALUE_SEPARATOR</H3>\r
 273 <PRE>\r
 274 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> <B>KEY_VALUE_SEPARATOR</B></PRE>\r
 275 <DL>\r
 276 <DL>\r
 277 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.msa.ClustalO.KEY_VALUE_SEPARATOR">Constant Field Values</A></DL>\r
 278 </DL>\r
 279 \r
 280 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 281 \r
 282 <A NAME="constructor_detail"><!-- --></A>\r
 283 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 284 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 285 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 286 <B>Constructor Detail</B></FONT></TH>\r
 287 </TR>\r
 288 </TABLE>\r
 289 \r
 290 <A NAME="ClustalO()"><!-- --></A><H3>\r
 291 ClustalO</H3>\r
 292 <PRE>\r
 293 public <B>ClustalO</B>()</PRE>\r
 294 <DL>\r
 295 <DD>--threads=<n> Number of processors to use
 296
 297  -l, --log=<file> Log all non-essential output to this file\r
 298 <P>\r
 299 </DL>\r
 300 \r
 301 <!-- ============ METHOD DETAIL ========== -->\r
 302 \r
 303 <A NAME="method_detail"><!-- --></A>\r
 304 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 305 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 306 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 307 <B>Method Detail</B></FONT></TH>\r
 308 </TR>\r
 309 </TABLE>\r
 310 \r
 311 <A NAME="setOutput(java.lang.String)"><!-- --></A><H3>\r
 312 setOutput</H3>\r
 313 <PRE>\r
 314 public <A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A> <B>setOutput</B>(<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;outFile)</PRE>\r
 315 <DL>\r
 316 <DD><DL>\r
 317 <DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)">setOutput</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>&gt;</CODE></DL>\r
 318 </DD>\r
 319 <DD><DL>\r
 320 </DL>\r
 321 </DD>\r
 322 </DL>\r
 323 <HR>\r
 324 \r
 325 <A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
 326 setInput</H3>\r
 327 <PRE>\r
 328 public <A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A> <B>setInput</B>(<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;inFile)</PRE>\r
 329 <DL>\r
 330 <DD><DL>\r
 331 <DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)">setInput</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>&gt;</CODE></DL>\r
 332 </DD>\r
 333 <DD><DL>\r
 334 </DL>\r
 335 </DD>\r
 336 </DL>\r
 337 <HR>\r
 338 \r
 339 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
 340 getResults</H3>\r
 341 <PRE>\r
 342 public <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResults</B>(<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;workDirectory)\r
 343                      throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 344 <DL>\r
 345 <DD><DL>\r
 346 \r
 347 <DT><B>Throws:</B>\r
 348 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 349 </DD>\r
 350 </DL>\r
 351 <HR>\r
 352 \r
 353 <A NAME="getStatFile()"><!-- --></A><H3>\r
 354 getStatFile</H3>\r
 355 <PRE>\r
 356 public static <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> <B>getStatFile</B>()</PRE>\r
 357 <DL>\r
 358 <DD><DL>\r
 359 </DL>\r
 360 </DD>\r
 361 </DL>\r
 362 <HR>\r
 363 \r
 364 <A NAME="getType()"><!-- --></A><H3>\r
 365 getType</H3>\r
 366 <PRE>\r
 367 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>&gt; <B>getType</B>()</PRE>\r
 368 <DL>\r
 369 <DD><DL>\r
 370 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getType()">getType</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>&gt;</CODE></DL>\r
 371 </DD>\r
 372 <DD><DL>\r
 373 \r
 374 <DT><B>Returns:</B><DD>subclasses must return their type</DL>\r
 375 </DD>\r
 376 </DL>\r
 377 <HR>\r
 378 \r
 379 <A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
 380 getParameters</H3>\r
 381 <PRE>\r
 382 public <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; <B>getParameters</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
 383 <DL>\r
 384 <DD><DL>\r
 385 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>&gt;</CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>&gt;</CODE></DL>\r
 386 </DD>\r
 387 <DD><DL>\r
 388 </DL>\r
 389 </DD>\r
 390 </DL>\r
 391 <HR>\r
 392 \r
 393 <A NAME="setNCore(int)"><!-- --></A><H3>\r
 394 setNCore</H3>\r
 395 <PRE>\r
 396 public void <B>setNCore</B>(int&nbsp;ncoreNumber)</PRE>\r
 397 <DL>\r
 398 <DD><DL>\r
 399 </DL>\r
 400 </DD>\r
 401 </DL>\r
 402 <!-- ========= END OF CLASS DATA ========= -->\r
 403 <HR>\r
 404 \r
 405 \r
 406 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 407 <A NAME="navbar_bottom"><!-- --></A>\r
 408 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 409 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 410 <TR>\r
 411 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 412 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 413 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 414   <TR ALIGN="center" VALIGN="top">\r
 415   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 416   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 417   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 418   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ClustalO.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 419   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 420   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 421   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 422   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 423   </TR>\r
 424 </TABLE>\r
 425 </TD>\r
 426 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 427 </EM>\r
 428 </TD>\r
 429 </TR>\r
 430 \r
 431 <TR>\r
 432 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 433 &nbsp;PREV CLASS&nbsp;\r
 434 &nbsp;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
 435 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 436   <A HREF="../../../index.html?compbio/runner/msa/ClustalO.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 437 &nbsp;<A HREF="ClustalO.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 438 &nbsp;<SCRIPT type="text/javascript">\r
 439   <!--\r
 440   if(window==top) {\r
 441     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 442   }\r
 443   //-->\r
 444 </SCRIPT>\r
 445 <NOSCRIPT>\r
 446   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 447 </NOSCRIPT>\r
 448 \r
 449 \r
 450 </FONT></TD>\r
 451 </TR>\r
 452 <TR>\r
 453 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 454   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
 455 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 456 DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
 457 </TR>\r
 458 </TABLE>\r
 459 <A NAME="skip-navbar_bottom"></A>\r
 460 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 461 \r
 462 <HR>\r
 463 \r
 464 </BODY>\r
 465 </HTML>\r