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

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   5 <!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:34 BST 2011 -->\r
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   7 Mafft\r
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   9 \r
  10 <META NAME="date" CONTENT="2011-08-12">\r
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  16 {\r
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  18         parent.document.title="Mafft";\r
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  43   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Mafft.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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  58 &nbsp;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa"><B>PREV CLASS</B></A>&nbsp;\r
  59 &nbsp;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
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  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
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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 Mafft</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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;\r
  97       <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.msa.Mafft</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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;, <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</DD>\r
 101 </DL>\r
 102 <HR>\r
 103 <DL>\r
 104 <DT><PRE>public class <B>Mafft</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</DL>\r
 105 </PRE>\r
 106 \r
 107 <P>\r
 108 <DL>\r
 109 <DT><B>Author:</B></DT>\r
 110   <DD>pvtroshin</DD>\r
 111 </DL>\r
 112 <HR>\r
 113 \r
 114 <P>\r
 115 <!-- ======== NESTED CLASS SUMMARY ======== -->\r
 116 \r
 117 <A NAME="nested_class_summary"><!-- --></A>\r
 118 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 119 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 120 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 121 <B>Nested Class Summary</B></FONT></TH>\r
 122 </TR>\r
 123 </TABLE>\r
 124 &nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
 125 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 126 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 127 <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
 128 </TR>\r
 129 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 130 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
 131 </TR>\r
 132 </TABLE>\r
 133 &nbsp;\r
 134 <!-- =========== FIELD SUMMARY =========== -->\r
 135 \r
 136 <A NAME="field_summary"><!-- --></A>\r
 137 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 138 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 139 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 140 <B>Field Summary</B></FONT></TH>\r
 141 </TR>\r
 142 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 143 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 144 <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
 145 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Mafft.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></B></CODE>\r
 146 \r
 147 <BR>\r
 148 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 149 </TR>\r
 150 </TABLE>\r
 151 &nbsp;<A NAME="fields_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
 152 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 153 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 154 <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
 155 </TR>\r
 156 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 157 <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
 158 </TR>\r
 159 </TABLE>\r
 160 &nbsp;\r
 161 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 162 \r
 163 <A NAME="constructor_summary"><!-- --></A>\r
 164 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 165 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 166 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 167 <B>Constructor Summary</B></FONT></TH>\r
 168 </TR>\r
 169 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 170 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Mafft.html#Mafft()">Mafft</A></B>()</CODE>\r
 171 \r
 172 <BR>\r
 173 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 174 </TR>\r
 175 </TABLE>\r
 176 &nbsp;\r
 177 <!-- ========== METHOD SUMMARY =========== -->\r
 178 \r
 179 <A NAME="method_summary"><!-- --></A>\r
 180 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 181 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 182 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 183 <B>Method Summary</B></FONT></TH>\r
 184 </TR>\r
 185 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 186 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 187 <CODE>&nbsp;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></CODE></FONT></TD>\r
 188 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Mafft.html#addParameters(java.util.List)">addParameters</A></B>(<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;&nbsp;parameters)</CODE>\r
 189 \r
 190 <BR>\r
 191 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Mafft input must always be the last parameter!</TD>\r
 192 </TR>\r
 193 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 194 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 195 <CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
 196 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Mafft.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
 197 \r
 198 <BR>\r
 199 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 200 </TR>\r
 201 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 202 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 203 <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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></FONT></TD>\r
 204 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Mafft.html#getType()">getType</A></B>()</CODE>\r
 205 \r
 206 <BR>\r
 207 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 208 </TR>\r
 209 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 210 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 211 <CODE>&nbsp;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></CODE></FONT></TD>\r
 212 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Mafft.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
 213 \r
 214 <BR>\r
 215 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 216 </TR>\r
 217 </TABLE>\r
 218 &nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
 219 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 220 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 221 <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
 222 </TR>\r
 223 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 224 <TD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)">equals</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterCpuNum(java.lang.Class)">getClusterCpuNum</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterJobSettings()">getClusterJobSettings</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">getCreatedFiles</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#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#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
 225 </TR>\r
 226 </TABLE>\r
 227 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 228 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 229 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 230 <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
 231 </TR>\r
 232 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 233 <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
 234 </TR>\r
 235 </TABLE>\r
 236 &nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
 237 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 238 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 239 <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
 240 </TR>\r
 241 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 242 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getClusterJobSettings()">getClusterJobSettings</A>, <A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</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#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></CODE></TD>\r
 243 </TR>\r
 244 </TABLE>\r
 245 &nbsp;\r
 246 <P>\r
 247 \r
 248 <!-- ============ FIELD DETAIL =========== -->\r
 249 \r
 250 <A NAME="field_detail"><!-- --></A>\r
 251 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 252 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 253 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 254 <B>Field Detail</B></FONT></TH>\r
 255 </TR>\r
 256 </TABLE>\r
 257 \r
 258 <A NAME="KEY_VALUE_SEPARATOR"><!-- --></A><H3>\r
 259 KEY_VALUE_SEPARATOR</H3>\r
 260 <PRE>\r
 261 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
 262 <DL>\r
 263 <DL>\r
 264 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.msa.Mafft.KEY_VALUE_SEPARATOR">Constant Field Values</A></DL>\r
 265 </DL>\r
 266 \r
 267 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 268 \r
 269 <A NAME="constructor_detail"><!-- --></A>\r
 270 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 271 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 272 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 273 <B>Constructor Detail</B></FONT></TH>\r
 274 </TR>\r
 275 </TABLE>\r
 276 \r
 277 <A NAME="Mafft()"><!-- --></A><H3>\r
 278 Mafft</H3>\r
 279 <PRE>\r
 280 public <B>Mafft</B>()</PRE>\r
 281 <DL>\r
 282 </DL>\r
 283 \r
 284 <!-- ============ METHOD DETAIL ========== -->\r
 285 \r
 286 <A NAME="method_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>Method Detail</B></FONT></TH>\r
 291 </TR>\r
 292 </TABLE>\r
 293 \r
 294 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
 295 getResults</H3>\r
 296 <PRE>\r
 297 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
 298                      throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 299 <DL>\r
 300 <DD><DL>\r
 301 <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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></DL>\r
 302 </DD>\r
 303 <DD><DL>\r
 304 \r
 305 <DT><B>Throws:</B>\r
 306 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 307 </DD>\r
 308 </DL>\r
 309 <HR>\r
 310 \r
 311 <A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
 312 setInput</H3>\r
 313 <PRE>\r
 314 public <A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</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
 315 <DL>\r
 316 <DD><DL>\r
 317 <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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></DL>\r
 318 </DD>\r
 319 <DD><DL>\r
 320 </DL>\r
 321 </DD>\r
 322 </DL>\r
 323 <HR>\r
 324 \r
 325 <A NAME="addParameters(java.util.List)"><!-- --></A><H3>\r
 326 addParameters</H3>\r
 327 <PRE>\r
 328 public <A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A> <B>addParameters</B>(<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;&nbsp;parameters)</PRE>\r
 329 <DL>\r
 330 <DD>Mafft input must always be the last parameter!\r
 331 <P>\r
 332 <DD><DL>\r
 333 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)">addParameters</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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></DL>\r
 334 </DD>\r
 335 <DD><DL>\r
 336 \r
 337 <DT><B>Returns:</B><DD>this Executable</DL>\r
 338 </DD>\r
 339 </DL>\r
 340 <HR>\r
 341 \r
 342 <A NAME="getType()"><!-- --></A><H3>\r
 343 getType</H3>\r
 344 <PRE>\r
 345 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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt; <B>getType</B>()</PRE>\r
 346 <DL>\r
 347 <DD><DL>\r
 348 <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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></DL>\r
 349 </DD>\r
 350 <DD><DL>\r
 351 \r
 352 <DT><B>Returns:</B><DD>subclasses must return their type</DL>\r
 353 </DD>\r
 354 </DL>\r
 355 <!-- ========= END OF CLASS DATA ========= -->\r
 356 <HR>\r
 357 \r
 358 \r
 359 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 360 <A NAME="navbar_bottom"><!-- --></A>\r
 361 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 362 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 363 <TR>\r
 364 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 365 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 366 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 367   <TR ALIGN="center" VALIGN="top">\r
 368   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 369   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 370   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 371   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Mafft.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 372   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 373   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 374   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 375   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 376   </TR>\r
 377 </TABLE>\r
 378 </TD>\r
 379 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 380 </EM>\r
 381 </TD>\r
 382 </TR>\r
 383 \r
 384 <TR>\r
 385 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 386 &nbsp;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa"><B>PREV CLASS</B></A>&nbsp;\r
 387 &nbsp;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
 388 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 389   <A HREF="../../../index.html?compbio/runner/msa/Mafft.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 390 &nbsp;<A HREF="Mafft.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 391 &nbsp;<SCRIPT type="text/javascript">\r
 392   <!--\r
 393   if(window==top) {\r
 394     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 395   }\r
 396   //-->\r
 397 </SCRIPT>\r
 398 <NOSCRIPT>\r
 399   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 400 </NOSCRIPT>\r
 401 \r
 402 \r
 403 </FONT></TD>\r
 404 </TR>\r
 405 <TR>\r
 406 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 407   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
 408 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 409 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
 410 </TR>\r
 411 </TABLE>\r
 412 <A NAME="skip-navbar_bottom"></A>\r
 413 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 414 \r
 415 <HR>\r
 416 \r
 417 </BODY>\r
 418 </HTML>\r