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

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   7 ClustalW\r
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   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="ClustalW";\r
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  40   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
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  43   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ClustalW.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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  58 &nbsp;PREV CLASS&nbsp;\r
  59 &nbsp;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
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  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
  86 \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 ClustalW</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/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;\r
  97       <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.msa.ClustalW</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/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</DD>\r
 101 </DL>\r
 102 <HR>\r
 103 <DL>\r
 104 <DT><PRE>public class <B>ClustalW</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</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/ClustalW.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/ClustalW.html#ClustalW()">ClustalW</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>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
 175 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
 176 \r
 177 <BR>\r
 178 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method cannot really tell whether the files has actually been
 179  created or not.</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/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
 184 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</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 <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/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
 192 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#getLimits()">getLimits</A></B>()</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/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
 200 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</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>static&nbsp;java.lang.String</CODE></FONT></TD>\r
 208 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#getStatFile()">getStatFile</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;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
 216 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#getType()">getType</A></B>()</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/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></CODE></FONT></TD>\r
 224 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#setInput(java.lang.String)">setInput</A></B>(java.lang.String&nbsp;inFile)</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;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></CODE></FONT></TD>\r
 232 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#setOutput(java.lang.String)">setOutput</A></B>(java.lang.String&nbsp;outFile)</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 </TABLE>\r
 238 &nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
 239 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 240 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 241 <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
 242 </TR>\r
 243 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 244 <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#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</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
 245 </TR>\r
 246 </TABLE>\r
 247 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 248 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 249 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 250 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
 251 </TR>\r
 252 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 253 <TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
 254 </TR>\r
 255 </TABLE>\r
 256 &nbsp;\r
 257 <P>\r
 258 \r
 259 <!-- ============ FIELD DETAIL =========== -->\r
 260 \r
 261 <A NAME="field_detail"><!-- --></A>\r
 262 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 263 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 264 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 265 <B>Field Detail</B></FONT></TH>\r
 266 </TR>\r
 267 </TABLE>\r
 268 \r
 269 <A NAME="KEY_VALUE_SEPARATOR"><!-- --></A><H3>\r
 270 KEY_VALUE_SEPARATOR</H3>\r
 271 <PRE>\r
 272 public static final java.lang.String <B>KEY_VALUE_SEPARATOR</B></PRE>\r
 273 <DL>\r
 274 <DL>\r
 275 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.msa.ClustalW.KEY_VALUE_SEPARATOR">Constant Field Values</A></DL>\r
 276 </DL>\r
 277 \r
 278 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 279 \r
 280 <A NAME="constructor_detail"><!-- --></A>\r
 281 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 282 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 283 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 284 <B>Constructor Detail</B></FONT></TH>\r
 285 </TR>\r
 286 </TABLE>\r
 287 \r
 288 <A NAME="ClustalW()"><!-- --></A><H3>\r
 289 ClustalW</H3>\r
 290 <PRE>\r
 291 public <B>ClustalW</B>()</PRE>\r
 292 <DL>\r
 293 </DL>\r
 294 \r
 295 <!-- ============ METHOD DETAIL ========== -->\r
 296 \r
 297 <A NAME="method_detail"><!-- --></A>\r
 298 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 299 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 300 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 301 <B>Method Detail</B></FONT></TH>\r
 302 </TR>\r
 303 </TABLE>\r
 304 \r
 305 <A NAME="setOutput(java.lang.String)"><!-- --></A><H3>\r
 306 setOutput</H3>\r
 307 <PRE>\r
 308 public <A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A> <B>setOutput</B>(java.lang.String&nbsp;outFile)</PRE>\r
 309 <DL>\r
 310 <DD><DL>\r
 311 <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/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></DL>\r
 312 </DD>\r
 313 <DD><DL>\r
 314 </DL>\r
 315 </DD>\r
 316 </DL>\r
 317 <HR>\r
 318 \r
 319 <A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
 320 setInput</H3>\r
 321 <PRE>\r
 322 public <A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A> <B>setInput</B>(java.lang.String&nbsp;inFile)</PRE>\r
 323 <DL>\r
 324 <DD><DL>\r
 325 <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/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></DL>\r
 326 </DD>\r
 327 <DD><DL>\r
 328 </DL>\r
 329 </DD>\r
 330 </DL>\r
 331 <HR>\r
 332 \r
 333 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
 334 getResults</H3>\r
 335 <PRE>\r
 336 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
 337                      throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 338 <DL>\r
 339 <DD><DL>\r
 340 \r
 341 <DT><B>Throws:</B>\r
 342 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 343 </DD>\r
 344 </DL>\r
 345 <HR>\r
 346 \r
 347 <A NAME="getCreatedFiles()"><!-- --></A><H3>\r
 348 getCreatedFiles</H3>\r
 349 <PRE>\r
 350 public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
 351 <DL>\r
 352 <DD><B>Description copied from class: <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">SkeletalExecutable</A></CODE></B></DD>\r
 353 <DD>This method cannot really tell whether the files has actually been
 354  created or not. It must be overridden as required.\r
 355 <P>\r
 356 <DD><DL>\r
 357 <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/ClustalW.html" title="class in compbio.runner.msa">ClustalW</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/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></DL>\r
 358 </DD>\r
 359 <DD><DL>\r
 360 <DT><B>See Also:</B><DD><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()"><CODE>Executable.getCreatedFiles()</CODE></A></DL>\r
 361 </DD>\r
 362 </DL>\r
 363 <HR>\r
 364 \r
 365 <A NAME="getStatFile()"><!-- --></A><H3>\r
 366 getStatFile</H3>\r
 367 <PRE>\r
 368 public static java.lang.String <B>getStatFile</B>()</PRE>\r
 369 <DL>\r
 370 <DD><DL>\r
 371 </DL>\r
 372 </DD>\r
 373 </DL>\r
 374 <HR>\r
 375 \r
 376 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
 377 getLimit</H3>\r
 378 <PRE>\r
 379 public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
 380 <DL>\r
 381 <DD><DL>\r
 382 </DL>\r
 383 </DD>\r
 384 </DL>\r
 385 <HR>\r
 386 \r
 387 <A NAME="getLimits()"><!-- --></A><H3>\r
 388 getLimits</H3>\r
 389 <PRE>\r
 390 public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt; <B>getLimits</B>()</PRE>\r
 391 <DL>\r
 392 <DD><DL>\r
 393 </DL>\r
 394 </DD>\r
 395 </DL>\r
 396 <HR>\r
 397 \r
 398 <A NAME="getType()"><!-- --></A><H3>\r
 399 getType</H3>\r
 400 <PRE>\r
 401 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
 402 <DL>\r
 403 <DD><DL>\r
 404 <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/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></DL>\r
 405 </DD>\r
 406 <DD><DL>\r
 407 </DL>\r
 408 </DD>\r
 409 </DL>\r
 410 <!-- ========= END OF CLASS DATA ========= -->\r
 411 <HR>\r
 412 \r
 413 \r
 414 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 415 <A NAME="navbar_bottom"><!-- --></A>\r
 416 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 417 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 418 <TR>\r
 419 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 420 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 421 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 422   <TR ALIGN="center" VALIGN="top">\r
 423   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 424   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 425   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 426   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ClustalW.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 427   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 428   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 429   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 430   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 431   </TR>\r
 432 </TABLE>\r
 433 </TD>\r
 434 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 435 </EM>\r
 436 </TD>\r
 437 </TR>\r
 438 \r
 439 <TR>\r
 440 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 441 &nbsp;PREV CLASS&nbsp;\r
 442 &nbsp;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
 443 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 444   <A HREF="../../../index.html?compbio/runner/msa/ClustalW.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 445 &nbsp;<A HREF="ClustalW.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 446 &nbsp;<SCRIPT type="text/javascript">\r
 447   <!--\r
 448   if(window==top) {\r
 449     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 450   }\r
 451   //-->\r
 452 </SCRIPT>\r
 453 <NOSCRIPT>\r
 454   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 455 </NOSCRIPT>\r
 456 \r
 457 \r
 458 </FONT></TD>\r
 459 </TR>\r
 460 <TR>\r
 461 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 462   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
 463 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 464 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
 465 </TR>\r
 466 </TABLE>\r
 467 <A NAME="skip-navbar_bottom"></A>\r
 468 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 469 \r
 470 <HR>\r
 471 \r
 472 </BODY>\r
 473 </HTML>\r