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

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   5 <!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:35 BST 2011 -->\r
   6 <TITLE>\r
   7 Muscle\r
   8 </TITLE>\r
   9 \r
  10 <META NAME="date" CONTENT="2011-08-12">\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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  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
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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 Muscle</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/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;<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/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;<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/Muscle.html#Muscle()">Muscle</A></B>()</CODE>\r
 167 \r
 168 <BR>\r
 169 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Default options are
 170
 171  -clwstrict - write output in clustal format</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="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<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>&gt;</CODE></FONT></TD>\r
 186 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
 187 \r
 188 <BR>\r
 189 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method cannot really tell whether the files has actually been
 190  created or not.</TD>\r
 191 </TR>\r
 192 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 193 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 194 <CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
 195 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.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
 196 \r
 197 <BR>\r
 198 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 199 </TR>\r
 200 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 201 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 202 <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
 203 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.html#getStatFile()">getStatFile</A></B>()</CODE>\r
 204 \r
 205 <BR>\r
 206 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 207 </TR>\r
 208 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 209 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 210 <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/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
 211 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.html#getType()">getType</A></B>()</CODE>\r
 212 \r
 213 <BR>\r
 214 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 215 </TR>\r
 216 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 217 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 218 <CODE>&nbsp;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></CODE></FONT></TD>\r
 219 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.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
 220 \r
 221 <BR>\r
 222 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 223 </TR>\r
 224 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 225 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 226 <CODE>&nbsp;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></CODE></FONT></TD>\r
 227 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.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
 228 \r
 229 <BR>\r
 230 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 231 </TR>\r
 232 </TABLE>\r
 233 &nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
 234 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 235 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 236 <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
 237 </TR>\r
 238 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 239 <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#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#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
 240 </TR>\r
 241 </TABLE>\r
 242 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 243 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 244 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 245 <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
 246 </TR>\r
 247 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 248 <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
 249 </TR>\r
 250 </TABLE>\r
 251 &nbsp;\r
 252 <P>\r
 253 \r
 254 <!-- ============ FIELD DETAIL =========== -->\r
 255 \r
 256 <A NAME="field_detail"><!-- --></A>\r
 257 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 258 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 259 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 260 <B>Field Detail</B></FONT></TH>\r
 261 </TR>\r
 262 </TABLE>\r
 263 \r
 264 <A NAME="KEY_VALUE_SEPARATOR"><!-- --></A><H3>\r
 265 KEY_VALUE_SEPARATOR</H3>\r
 266 <PRE>\r
 267 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
 268 <DL>\r
 269 <DL>\r
 270 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.msa.Muscle.KEY_VALUE_SEPARATOR">Constant Field Values</A></DL>\r
 271 </DL>\r
 272 \r
 273 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 274 \r
 275 <A NAME="constructor_detail"><!-- --></A>\r
 276 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 277 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 278 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 279 <B>Constructor Detail</B></FONT></TH>\r
 280 </TR>\r
 281 </TABLE>\r
 282 \r
 283 <A NAME="Muscle()"><!-- --></A><H3>\r
 284 Muscle</H3>\r
 285 <PRE>\r
 286 public <B>Muscle</B>()</PRE>\r
 287 <DL>\r
 288 <DD>Default options are
 289
 290  -clwstrict - write output in clustal format\r
 291 <P>\r
 292 </DL>\r
 293 \r
 294 <!-- ============ METHOD DETAIL ========== -->\r
 295 \r
 296 <A NAME="method_detail"><!-- --></A>\r
 297 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 298 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 299 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 300 <B>Method Detail</B></FONT></TH>\r
 301 </TR>\r
 302 </TABLE>\r
 303 \r
 304 <A NAME="setOutput(java.lang.String)"><!-- --></A><H3>\r
 305 setOutput</H3>\r
 306 <PRE>\r
 307 public <A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</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
 308 <DL>\r
 309 <DD><DL>\r
 310 <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
 311 </DD>\r
 312 <DD><DL>\r
 313 </DL>\r
 314 </DD>\r
 315 </DL>\r
 316 <HR>\r
 317 \r
 318 <A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
 319 setInput</H3>\r
 320 <PRE>\r
 321 public <A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</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
 322 <DL>\r
 323 <DD><DL>\r
 324 <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
 325 </DD>\r
 326 <DD><DL>\r
 327 </DL>\r
 328 </DD>\r
 329 </DL>\r
 330 <HR>\r
 331 \r
 332 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
 333 getResults</H3>\r
 334 <PRE>\r
 335 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
 336                      throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 337 <DL>\r
 338 <DD><DL>\r
 339 \r
 340 <DT><B>Throws:</B>\r
 341 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 342 </DD>\r
 343 </DL>\r
 344 <HR>\r
 345 \r
 346 <A NAME="getCreatedFiles()"><!-- --></A><H3>\r
 347 getCreatedFiles</H3>\r
 348 <PRE>\r
 349 public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<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>&gt; <B>getCreatedFiles</B>()</PRE>\r
 350 <DL>\r
 351 <DD><B>Description copied from class: <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">SkeletalExecutable</A></CODE></B></DD>\r
 352 <DD>This method cannot really tell whether the files has actually been
 353  created or not. It must be overridden as required.\r
 354 <P>\r
 355 <DD><DL>\r
 356 <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
 357 </DD>\r
 358 <DD><DL>\r
 359 <DT><B>See Also:</B><DD><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()"><CODE>Executable.getCreatedFiles()</CODE></A></DL>\r
 360 </DD>\r
 361 </DL>\r
 362 <HR>\r
 363 \r
 364 <A NAME="getStatFile()"><!-- --></A><H3>\r
 365 getStatFile</H3>\r
 366 <PRE>\r
 367 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
 368 <DL>\r
 369 <DD><DL>\r
 370 </DL>\r
 371 </DD>\r
 372 </DL>\r
 373 <HR>\r
 374 \r
 375 <A NAME="getType()"><!-- --></A><H3>\r
 376 getType</H3>\r
 377 <PRE>\r
 378 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/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt; <B>getType</B>()</PRE>\r
 379 <DL>\r
 380 <DD><DL>\r
 381 <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
 382 </DD>\r
 383 <DD><DL>\r
 384 \r
 385 <DT><B>Returns:</B><DD>subclasses must return their type</DL>\r
 386 </DD>\r
 387 </DL>\r
 388 <!-- ========= END OF CLASS DATA ========= -->\r
 389 <HR>\r
 390 \r
 391 \r
 392 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 393 <A NAME="navbar_bottom"><!-- --></A>\r
 394 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 395 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 396 <TR>\r
 397 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 398 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 399 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 400   <TR ALIGN="center" VALIGN="top">\r
 401   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 402   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 403   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 404   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Muscle.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 405   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 406   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 407   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 408   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 409   </TR>\r
 410 </TABLE>\r
 411 </TD>\r
 412 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 413 </EM>\r
 414 </TD>\r
 415 </TR>\r
 416 \r
 417 <TR>\r
 418 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 419 &nbsp;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa"><B>PREV CLASS</B></A>&nbsp;\r
 420 &nbsp;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
 421 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 422   <A HREF="../../../index.html?compbio/runner/msa/Muscle.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 423 &nbsp;<A HREF="Muscle.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 424 &nbsp;<SCRIPT type="text/javascript">\r
 425   <!--\r
 426   if(window==top) {\r
 427     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 428   }\r
 429   //-->\r
 430 </SCRIPT>\r
 431 <NOSCRIPT>\r
 432   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 433 </NOSCRIPT>\r
 434 \r
 435 \r
 436 </FONT></TD>\r
 437 </TR>\r
 438 <TR>\r
 439 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 440   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
 441 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 442 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
 443 </TR>\r
 444 </TABLE>\r
 445 <A NAME="skip-navbar_bottom"></A>\r
 446 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 447 \r
 448 <HR>\r
 449 \r
 450 </BODY>\r
 451 </HTML>\r