website/full_javadoc/compbio/runner/msa/Muscle.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 Muscle\r
   8 </TITLE>\r
   9 \r
  10 <META NAME="date" CONTENT="2010-02-17">\r
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  15 function windowTitle()\r
  16 {\r
  17     if (location.href.indexOf('is-external=true') == -1) {\r
  18         parent.document.title="Muscle";\r
  19     }\r
  20 }\r
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  26 \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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  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/Muscle.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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  58 &nbsp;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa"><B>PREV CLASS</B></A>&nbsp;\r
  59 &nbsp;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa"><B>NEXT CLASS</B></A></FONT></TD>\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
  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 Muscle</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/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;\r
  97       <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.msa.Muscle</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/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</DD>\r
 101 </DL>\r
 102 <HR>\r
 103 <DL>\r
 104 <DT><PRE>public class <B>Muscle</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</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/Muscle.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/Muscle.html#Muscle()">Muscle</A></B>()</CODE>\r
 158 \r
 159 <BR>\r
 160 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Default options are
 161
 162  -clwstrict - write output in clustal format</TD>\r
 163 </TR>\r
 164 </TABLE>\r
 165 &nbsp;\r
 166 <!-- ========== METHOD SUMMARY =========== -->\r
 167 \r
 168 <A NAME="method_summary"><!-- --></A>\r
 169 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 170 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 171 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 172 <B>Method Summary</B></FONT></TH>\r
 173 </TR>\r
 174 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 175 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 176 <CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
 177 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
 178 \r
 179 <BR>\r
 180 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method cannot really tell whether the files has actually been
 181  created or not.</TD>\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/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
 186 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</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/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
 194 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.html#getLimits()">getLimits</A></B>()</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>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
 202 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</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>static&nbsp;java.lang.String</CODE></FONT></TD>\r
 210 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.html#getStatFile()">getStatFile</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;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
 218 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.html#getType()">getType</A></B>()</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;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></CODE></FONT></TD>\r
 226 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.html#setInput(java.lang.String)">setInput</A></B>(java.lang.String&nbsp;inFile)</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/Muscle.html" title="class in compbio.runner.msa">Muscle</A></CODE></FONT></TD>\r
 234 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.html#setOutput(java.lang.String)">setOutput</A></B>(java.lang.String&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#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
 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.Object</B></TH>\r
 253 </TR>\r
 254 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 255 <TD><CODE>getClass, notify, notifyAll, wait, wait, wait</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 java.lang.String <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.Muscle.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="Muscle()"><!-- --></A><H3>\r
 291 Muscle</H3>\r
 292 <PRE>\r
 293 public <B>Muscle</B>()</PRE>\r
 294 <DL>\r
 295 <DD>Default options are
 296
 297  -clwstrict - write output in clustal format\r
 298 <P>\r
 299 <DL>\r
 300 <DT><B>Parameters:</B><DD><CODE>workDirectory</CODE> - </DL>\r
 301 </DL>\r
 302 \r
 303 <!-- ============ METHOD DETAIL ========== -->\r
 304 \r
 305 <A NAME="method_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>Method Detail</B></FONT></TH>\r
 310 </TR>\r
 311 </TABLE>\r
 312 \r
 313 <A NAME="setOutput(java.lang.String)"><!-- --></A><H3>\r
 314 setOutput</H3>\r
 315 <PRE>\r
 316 public <A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A> <B>setOutput</B>(java.lang.String&nbsp;outFile)</PRE>\r
 317 <DL>\r
 318 <DD><DL>\r
 319 <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/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></DL>\r
 320 </DD>\r
 321 <DD><DL>\r
 322 </DL>\r
 323 </DD>\r
 324 </DL>\r
 325 <HR>\r
 326 \r
 327 <A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
 328 setInput</H3>\r
 329 <PRE>\r
 330 public <A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A> <B>setInput</B>(java.lang.String&nbsp;inFile)</PRE>\r
 331 <DL>\r
 332 <DD><DL>\r
 333 <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/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></DL>\r
 334 </DD>\r
 335 <DD><DL>\r
 336 </DL>\r
 337 </DD>\r
 338 </DL>\r
 339 <HR>\r
 340 \r
 341 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
 342 getResults</H3>\r
 343 <PRE>\r
 344 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
 345                      throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 346 <DL>\r
 347 <DD><DL>\r
 348 \r
 349 <DT><B>Throws:</B>\r
 350 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 351 </DD>\r
 352 </DL>\r
 353 <HR>\r
 354 \r
 355 <A NAME="getCreatedFiles()"><!-- --></A><H3>\r
 356 getCreatedFiles</H3>\r
 357 <PRE>\r
 358 public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
 359 <DL>\r
 360 <DD><B>Description copied from class: <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">SkeletalExecutable</A></CODE></B></DD>\r
 361 <DD>This method cannot really tell whether the files has actually been
 362  created or not. It must be overridden as required.\r
 363 <P>\r
 364 <DD><DL>\r
 365 <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/Muscle.html" title="class in compbio.runner.msa">Muscle</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/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></DL>\r
 366 </DD>\r
 367 <DD><DL>\r
 368 <DT><B>See Also:</B><DD><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()"><CODE>Executable.getCreatedFiles()</CODE></A></DL>\r
 369 </DD>\r
 370 </DL>\r
 371 <HR>\r
 372 \r
 373 <A NAME="getStatFile()"><!-- --></A><H3>\r
 374 getStatFile</H3>\r
 375 <PRE>\r
 376 public static java.lang.String <B>getStatFile</B>()</PRE>\r
 377 <DL>\r
 378 <DD><DL>\r
 379 </DL>\r
 380 </DD>\r
 381 </DL>\r
 382 <HR>\r
 383 \r
 384 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
 385 getLimit</H3>\r
 386 <PRE>\r
 387 public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
 388 <DL>\r
 389 <DD><DL>\r
 390 </DL>\r
 391 </DD>\r
 392 </DL>\r
 393 <HR>\r
 394 \r
 395 <A NAME="getLimits()"><!-- --></A><H3>\r
 396 getLimits</H3>\r
 397 <PRE>\r
 398 public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt; <B>getLimits</B>()</PRE>\r
 399 <DL>\r
 400 <DD><DL>\r
 401 </DL>\r
 402 </DD>\r
 403 </DL>\r
 404 <HR>\r
 405 \r
 406 <A NAME="getType()"><!-- --></A><H3>\r
 407 getType</H3>\r
 408 <PRE>\r
 409 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
 410 <DL>\r
 411 <DD><DL>\r
 412 <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/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></DL>\r
 413 </DD>\r
 414 <DD><DL>\r
 415 </DL>\r
 416 </DD>\r
 417 </DL>\r
 418 <!-- ========= END OF CLASS DATA ========= -->\r
 419 <HR>\r
 420 \r
 421 \r
 422 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 423 <A NAME="navbar_bottom"><!-- --></A>\r
 424 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 425 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 426 <TR>\r
 427 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 428 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 429 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 430   <TR ALIGN="center" VALIGN="top">\r
 431   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 432   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 433   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 434   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Muscle.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 435   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 436   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 437   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 438   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 439   </TR>\r
 440 </TABLE>\r
 441 </TD>\r
 442 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 443 </EM>\r
 444 </TD>\r
 445 </TR>\r
 446 \r
 447 <TR>\r
 448 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 449 &nbsp;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa"><B>PREV CLASS</B></A>&nbsp;\r
 450 &nbsp;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
 451 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 452   <A HREF="../../../index.html?compbio/runner/msa/Muscle.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 453 &nbsp;<A HREF="Muscle.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 454 &nbsp;<SCRIPT type="text/javascript">\r
 455   <!--\r
 456   if(window==top) {\r
 457     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 458   }\r
 459   //-->\r
 460 </SCRIPT>\r
 461 <NOSCRIPT>\r
 462   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 463 </NOSCRIPT>\r
 464 \r
 465 \r
 466 </FONT></TD>\r
 467 </TR>\r
 468 <TR>\r
 469 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 470   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
 471 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 472 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
 473 </TR>\r
 474 </TABLE>\r
 475 <A NAME="skip-navbar_bottom"></A>\r
 476 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 477 \r
 478 <HR>\r
 479 \r
 480 </BODY>\r
 481 </HTML>\r