website/full_javadoc/compbio/runner/msa/Tcoffee.html

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   5 <!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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   7 Tcoffee\r
   8 </TITLE>\r
   9 \r
  10 <META NAME="date" CONTENT="2010-02-17">\r
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  16 {\r
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  18         parent.document.title="Tcoffee";\r
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  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
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  85 <!-- ========= END OF TOP NAVBAR ========= -->\r
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  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 Tcoffee</H2>\r
  94 <PRE>\r
  95 java.lang.Object\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/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;\r
  97       <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.msa.Tcoffee</B>\r
  98 </PRE>\r
  99 <DL>\r
 100 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client">ClusterNativeSpecExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;, <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;, <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</DD>\r
 101 </DL>\r
 102 <HR>\r
 103 <DL>\r
 104 <DT><PRE>public class <B>Tcoffee</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;<DT>implements <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;, <A HREF="../../../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client">ClusterNativeSpecExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</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;java.lang.String</CODE></FONT></TD>\r
 141 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.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;\r
 148 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 149 \r
 150 <A NAME="constructor_summary"><!-- --></A>\r
 151 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 152 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 153 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 154 <B>Constructor Summary</B></FONT></TH>\r
 155 </TR>\r
 156 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 157 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#Tcoffee()">Tcoffee</A></B>()</CODE>\r
 158 \r
 159 <BR>\r
 160 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 161 </TR>\r
 162 </TABLE>\r
 163 &nbsp;\r
 164 <!-- ========== METHOD SUMMARY =========== -->\r
 165 \r
 166 <A NAME="method_summary"><!-- --></A>\r
 167 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 168 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 169 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 170 <B>Method Summary</B></FONT></TH>\r
 171 </TR>\r
 172 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 173 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 174 <CODE>static&nbsp;int</CODE></FONT></TD>\r
 175 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#getClusterCpuNum()">getClusterCpuNum</A></B>()</CODE>\r
 176 \r
 177 <BR>\r
 178 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 179 </TR>\r
 180 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 181 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 182 <CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
 183 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
 184 \r
 185 <BR>\r
 186 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method cannot really tell whether the files has actually been
 187  created or not.</TD>\r
 188 </TR>\r
 189 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 190 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 191 <CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
 192 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
 193 \r
 194 <BR>\r
 195 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 196 </TR>\r
 197 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 198 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 199 <CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
 200 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#getLimits()">getLimits</A></B>()</CODE>\r
 201 \r
 202 <BR>\r
 203 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\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;java.lang.String</CODE></FONT></TD>\r
 208 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#getNativeSpecs()">getNativeSpecs</A></B>()</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 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 214 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 215 <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
 216 <TD><CODE><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
 217 \r
 218 <BR>\r
 219 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 220 </TR>\r
 221 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 222 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 223 <CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
 224 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
 225 \r
 226 <BR>\r
 227 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 228 </TR>\r
 229 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 230 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 231 <CODE>&nbsp;java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
 232 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#getType()">getType</A></B>()</CODE>\r
 233 \r
 234 <BR>\r
 235 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 236 </TR>\r
 237 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 238 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 239 <CODE>&nbsp;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></CODE></FONT></TD>\r
 240 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#setInput(java.lang.String)">setInput</A></B>(java.lang.String&nbsp;inFile)</CODE>\r
 241 \r
 242 <BR>\r
 243 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 244 </TR>\r
 245 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 246 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 247 <CODE>&nbsp;void</CODE></FONT></TD>\r
 248 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#setNCore(int)">setNCore</A></B>(int&nbsp;ncoreNumber)</CODE>\r
 249 \r
 250 <BR>\r
 251 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 252 </TR>\r
 253 </TABLE>\r
 254 &nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
 255 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 256 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 257 <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
 258 </TR>\r
 259 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 260 <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#getClusterSettings()">getClusterSettings</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#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#setOutput(java.lang.String)">setOutput</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
 261 </TR>\r
 262 </TABLE>\r
 263 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 264 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 265 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 266 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
 267 </TR>\r
 268 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 269 <TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
 270 </TR>\r
 271 </TABLE>\r
 272 &nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
 273 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 274 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 275 <TH ALIGN="left"><B>Methods inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
 276 </TR>\r
 277 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 278 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></CODE></TD>\r
 279 </TR>\r
 280 </TABLE>\r
 281 &nbsp;\r
 282 <P>\r
 283 \r
 284 <!-- ============ FIELD DETAIL =========== -->\r
 285 \r
 286 <A NAME="field_detail"><!-- --></A>\r
 287 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 288 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 289 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 290 <B>Field Detail</B></FONT></TH>\r
 291 </TR>\r
 292 </TABLE>\r
 293 \r
 294 <A NAME="KEY_VALUE_SEPARATOR"><!-- --></A><H3>\r
 295 KEY_VALUE_SEPARATOR</H3>\r
 296 <PRE>\r
 297 public static final java.lang.String <B>KEY_VALUE_SEPARATOR</B></PRE>\r
 298 <DL>\r
 299 <DL>\r
 300 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.msa.Tcoffee.KEY_VALUE_SEPARATOR">Constant Field Values</A></DL>\r
 301 </DL>\r
 302 \r
 303 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 304 \r
 305 <A NAME="constructor_detail"><!-- --></A>\r
 306 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 307 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 308 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 309 <B>Constructor Detail</B></FONT></TH>\r
 310 </TR>\r
 311 </TABLE>\r
 312 \r
 313 <A NAME="Tcoffee()"><!-- --></A><H3>\r
 314 Tcoffee</H3>\r
 315 <PRE>\r
 316 public <B>Tcoffee</B>()</PRE>\r
 317 <DL>\r
 318 <DL>\r
 319 <DT><B>Parameters:</B><DD><CODE>workDirectory</CODE> - </DL>\r
 320 </DL>\r
 321 \r
 322 <!-- ============ METHOD DETAIL ========== -->\r
 323 \r
 324 <A NAME="method_detail"><!-- --></A>\r
 325 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 326 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 327 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 328 <B>Method Detail</B></FONT></TH>\r
 329 </TR>\r
 330 </TABLE>\r
 331 \r
 332 <A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
 333 setInput</H3>\r
 334 <PRE>\r
 335 public <A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A> <B>setInput</B>(java.lang.String&nbsp;inFile)</PRE>\r
 336 <DL>\r
 337 <DD><DL>\r
 338 <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/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
 339 </DD>\r
 340 <DD><DL>\r
 341 </DL>\r
 342 </DD>\r
 343 </DL>\r
 344 <HR>\r
 345 \r
 346 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
 347 getResults</H3>\r
 348 <PRE>\r
 349 public <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResults</B>(java.lang.String&nbsp;workDirectory)\r
 350                      throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 351 <DL>\r
 352 <DD><DL>\r
 353 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</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/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
 354 </DD>\r
 355 <DD><DL>\r
 356 \r
 357 <DT><B>Throws:</B>\r
 358 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 359 </DD>\r
 360 </DL>\r
 361 <HR>\r
 362 \r
 363 <A NAME="getCreatedFiles()"><!-- --></A><H3>\r
 364 getCreatedFiles</H3>\r
 365 <PRE>\r
 366 public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
 367 <DL>\r
 368 <DD><B>Description copied from class: <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">SkeletalExecutable</A></CODE></B></DD>\r
 369 <DD>This method cannot really tell whether the files has actually been
 370  created or not. It must be overridden as required.\r
 371 <P>\r
 372 <DD><DL>\r
 373 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</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/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">getCreatedFiles</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/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
 374 </DD>\r
 375 <DD><DL>\r
 376 <DT><B>See Also:</B><DD><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()"><CODE>Executable.getCreatedFiles()</CODE></A></DL>\r
 377 </DD>\r
 378 </DL>\r
 379 <HR>\r
 380 \r
 381 <A NAME="setNCore(int)"><!-- --></A><H3>\r
 382 setNCore</H3>\r
 383 <PRE>\r
 384 public void <B>setNCore</B>(int&nbsp;ncoreNumber)</PRE>\r
 385 <DL>\r
 386 <DD><DL>\r
 387 </DL>\r
 388 </DD>\r
 389 <DD><DL>\r
 390 </DL>\r
 391 </DD>\r
 392 </DL>\r
 393 <HR>\r
 394 \r
 395 <A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
 396 getParameters</H3>\r
 397 <PRE>\r
 398 public <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; <B>getParameters</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
 399 <DL>\r
 400 <DD><DL>\r
 401 <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/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</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/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
 402 </DD>\r
 403 <DD><DL>\r
 404 </DL>\r
 405 </DD>\r
 406 </DL>\r
 407 <HR>\r
 408 \r
 409 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
 410 getLimit</H3>\r
 411 <PRE>\r
 412 public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
 413 <DL>\r
 414 <DD><DL>\r
 415 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</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/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
 416 </DD>\r
 417 <DD><DL>\r
 418 </DL>\r
 419 </DD>\r
 420 </DL>\r
 421 <HR>\r
 422 \r
 423 <A NAME="getLimits()"><!-- --></A><H3>\r
 424 getLimits</H3>\r
 425 <PRE>\r
 426 public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt; <B>getLimits</B>()</PRE>\r
 427 <DL>\r
 428 <DD><DL>\r
 429 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</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/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
 430 </DD>\r
 431 <DD><DL>\r
 432 </DL>\r
 433 </DD>\r
 434 </DL>\r
 435 <HR>\r
 436 \r
 437 <A NAME="getNativeSpecs()"><!-- --></A><H3>\r
 438 getNativeSpecs</H3>\r
 439 <PRE>\r
 440 public java.lang.String <B>getNativeSpecs</B>()</PRE>\r
 441 <DL>\r
 442 <DD><DL>\r
 443 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ClusterNativeSpecExecutable.html#getNativeSpecs()">getNativeSpecs</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client">ClusterNativeSpecExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
 444 </DD>\r
 445 <DD><DL>\r
 446 </DL>\r
 447 </DD>\r
 448 </DL>\r
 449 <HR>\r
 450 \r
 451 <A NAME="getClusterCpuNum()"><!-- --></A><H3>\r
 452 getClusterCpuNum</H3>\r
 453 <PRE>\r
 454 public static int <B>getClusterCpuNum</B>()</PRE>\r
 455 <DL>\r
 456 <DD><DL>\r
 457 </DL>\r
 458 </DD>\r
 459 <DD><DL>\r
 460 \r
 461 <DT><B>Returns:</B><DD>number of cpus to use on the cluster or 0 if the value is
 462          undefined</DL>\r
 463 </DD>\r
 464 </DL>\r
 465 <HR>\r
 466 \r
 467 <A NAME="getType()"><!-- --></A><H3>\r
 468 getType</H3>\r
 469 <PRE>\r
 470 public java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt; <B>getType</B>()</PRE>\r
 471 <DL>\r
 472 <DD><DL>\r
 473 <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/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
 474 </DD>\r
 475 <DD><DL>\r
 476 </DL>\r
 477 </DD>\r
 478 </DL>\r
 479 <!-- ========= END OF CLASS DATA ========= -->\r
 480 <HR>\r
 481 \r
 482 \r
 483 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 484 <A NAME="navbar_bottom"><!-- --></A>\r
 485 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 486 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 487 <TR>\r
 488 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 489 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 490 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 491   <TR ALIGN="center" VALIGN="top">\r
 492   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 493   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 494   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 495   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Tcoffee.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 496   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 497   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 498   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 499   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 500   </TR>\r
 501 </TABLE>\r
 502 </TD>\r
 503 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 504 </EM>\r
 505 </TD>\r
 506 </TR>\r
 507 \r
 508 <TR>\r
 509 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 510 &nbsp;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa"><B>PREV CLASS</B></A>&nbsp;\r
 511 &nbsp;NEXT CLASS</FONT></TD>\r
 512 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 513   <A HREF="../../../index.html?compbio/runner/msa/Tcoffee.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 514 &nbsp;<A HREF="Tcoffee.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 515 &nbsp;<SCRIPT type="text/javascript">\r
 516   <!--\r
 517   if(window==top) {\r
 518     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 519   }\r
 520   //-->\r
 521 </SCRIPT>\r
 522 <NOSCRIPT>\r
 523   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 524 </NOSCRIPT>\r
 525 \r
 526 \r
 527 </FONT></TD>\r
 528 </TR>\r
 529 <TR>\r
 530 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 531   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
 532 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 533 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
 534 </TR>\r
 535 </TABLE>\r
 536 <A NAME="skip-navbar_bottom"></A>\r
 537 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 538 \r
 539 <HR>\r
 540 \r
 541 </BODY>\r
 542 </HTML>\r