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

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   7 Probcons\r
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   9 \r
  10 <META NAME="date" CONTENT="2010-02-17">\r
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  18         parent.document.title="Probcons";\r
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  58 &nbsp;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa"><B>PREV CLASS</B></A>&nbsp;\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
  82 </TR>\r
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  89 <H2>\r
  90 <FONT SIZE="-1">\r
  91 compbio.runner.msa</FONT>\r
  92 <BR>\r
  93 Class Probcons</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/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;\r
  97       <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.msa.Probcons</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/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;, <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</DD>\r
 101 </DL>\r
 102 <HR>\r
 103 <DL>\r
 104 <DT><PRE>public class <B>Probcons</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</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/Probcons.html" title="class in compbio.runner.msa">Probcons</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/Probcons.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/Probcons.html#Probcons()">Probcons</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/Probcons.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/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
 184 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Probcons.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/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
 192 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Probcons.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/Probcons.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>&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
 208 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Probcons.html#getType()">getType</A></B>()</CODE>\r
 209 \r
 210 <BR>\r
 211 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 212 </TR>\r
 213 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 214 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 215 <CODE>&nbsp;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></CODE></FONT></TD>\r
 216 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Probcons.html#setInput(java.lang.String)">setInput</A></B>(java.lang.String&nbsp;inFile)</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 </TABLE>\r
 222 &nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
 223 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 224 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 225 <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
 226 </TR>\r
 227 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 228 <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#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
 229 </TR>\r
 230 </TABLE>\r
 231 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 232 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 233 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 234 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
 235 </TR>\r
 236 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 237 <TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
 238 </TR>\r
 239 </TABLE>\r
 240 &nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></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 interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
 244 </TR>\r
 245 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 246 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/Executable.html#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
 247 </TR>\r
 248 </TABLE>\r
 249 &nbsp;\r
 250 <P>\r
 251 \r
 252 <!-- ============ FIELD DETAIL =========== -->\r
 253 \r
 254 <A NAME="field_detail"><!-- --></A>\r
 255 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 256 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 257 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 258 <B>Field Detail</B></FONT></TH>\r
 259 </TR>\r
 260 </TABLE>\r
 261 \r
 262 <A NAME="KEY_VALUE_SEPARATOR"><!-- --></A><H3>\r
 263 KEY_VALUE_SEPARATOR</H3>\r
 264 <PRE>\r
 265 public static final java.lang.String <B>KEY_VALUE_SEPARATOR</B></PRE>\r
 266 <DL>\r
 267 <DL>\r
 268 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.msa.Probcons.KEY_VALUE_SEPARATOR">Constant Field Values</A></DL>\r
 269 </DL>\r
 270 \r
 271 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 272 \r
 273 <A NAME="constructor_detail"><!-- --></A>\r
 274 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 275 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 276 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 277 <B>Constructor Detail</B></FONT></TH>\r
 278 </TR>\r
 279 </TABLE>\r
 280 \r
 281 <A NAME="Probcons()"><!-- --></A><H3>\r
 282 Probcons</H3>\r
 283 <PRE>\r
 284 public <B>Probcons</B>()</PRE>\r
 285 <DL>\r
 286 <DL>\r
 287 <DT><B>Parameters:</B><DD><CODE>workDirectory</CODE> - </DL>\r
 288 </DL>\r
 289 \r
 290 <!-- ============ METHOD DETAIL ========== -->\r
 291 \r
 292 <A NAME="method_detail"><!-- --></A>\r
 293 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 294 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 295 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 296 <B>Method Detail</B></FONT></TH>\r
 297 </TR>\r
 298 </TABLE>\r
 299 \r
 300 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
 301 getResults</H3>\r
 302 <PRE>\r
 303 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
 304                      throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 305 <DL>\r
 306 <DD><DL>\r
 307 <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/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
 308 </DD>\r
 309 <DD><DL>\r
 310 \r
 311 <DT><B>Throws:</B>\r
 312 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 313 </DD>\r
 314 </DL>\r
 315 <HR>\r
 316 \r
 317 <A NAME="getCreatedFiles()"><!-- --></A><H3>\r
 318 getCreatedFiles</H3>\r
 319 <PRE>\r
 320 public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
 321 <DL>\r
 322 <DD><B>Description copied from class: <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">SkeletalExecutable</A></CODE></B></DD>\r
 323 <DD>This method cannot really tell whether the files has actually been
 324  created or not. It must be overridden as required.\r
 325 <P>\r
 326 <DD><DL>\r
 327 <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/Probcons.html" title="class in compbio.runner.msa">Probcons</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/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
 328 </DD>\r
 329 <DD><DL>\r
 330 <DT><B>See Also:</B><DD><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()"><CODE>Executable.getCreatedFiles()</CODE></A></DL>\r
 331 </DD>\r
 332 </DL>\r
 333 <HR>\r
 334 \r
 335 <A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
 336 setInput</H3>\r
 337 <PRE>\r
 338 public <A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A> <B>setInput</B>(java.lang.String&nbsp;inFile)</PRE>\r
 339 <DL>\r
 340 <DD><DL>\r
 341 <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/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
 342 </DD>\r
 343 <DD><DL>\r
 344 </DL>\r
 345 </DD>\r
 346 </DL>\r
 347 <HR>\r
 348 \r
 349 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
 350 getLimit</H3>\r
 351 <PRE>\r
 352 public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
 353 <DL>\r
 354 <DD><DL>\r
 355 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
 356 </DD>\r
 357 <DD><DL>\r
 358 </DL>\r
 359 </DD>\r
 360 </DL>\r
 361 <HR>\r
 362 \r
 363 <A NAME="getLimits()"><!-- --></A><H3>\r
 364 getLimits</H3>\r
 365 <PRE>\r
 366 public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt; <B>getLimits</B>()</PRE>\r
 367 <DL>\r
 368 <DD><DL>\r
 369 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
 370 </DD>\r
 371 <DD><DL>\r
 372 </DL>\r
 373 </DD>\r
 374 </DL>\r
 375 <HR>\r
 376 \r
 377 <A NAME="getType()"><!-- --></A><H3>\r
 378 getType</H3>\r
 379 <PRE>\r
 380 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
 381 <DL>\r
 382 <DD><DL>\r
 383 <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/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
 384 </DD>\r
 385 <DD><DL>\r
 386 </DL>\r
 387 </DD>\r
 388 </DL>\r
 389 <!-- ========= END OF CLASS DATA ========= -->\r
 390 <HR>\r
 391 \r
 392 \r
 393 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 394 <A NAME="navbar_bottom"><!-- --></A>\r
 395 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 396 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 397 <TR>\r
 398 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 399 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 400 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 401   <TR ALIGN="center" VALIGN="top">\r
 402   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 403   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 404   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 405   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Probcons.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 406   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 407   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 408   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 409   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 410   </TR>\r
 411 </TABLE>\r
 412 </TD>\r
 413 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 414 </EM>\r
 415 </TD>\r
 416 </TR>\r
 417 \r
 418 <TR>\r
 419 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 420 &nbsp;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa"><B>PREV CLASS</B></A>&nbsp;\r
 421 &nbsp;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
 422 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 423   <A HREF="../../../index.html?compbio/runner/msa/Probcons.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 424 &nbsp;<A HREF="Probcons.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 425 &nbsp;<SCRIPT type="text/javascript">\r
 426   <!--\r
 427   if(window==top) {\r
 428     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 429   }\r
 430   //-->\r
 431 </SCRIPT>\r
 432 <NOSCRIPT>\r
 433   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 434 </NOSCRIPT>\r
 435 \r
 436 \r
 437 </FONT></TD>\r
 438 </TR>\r
 439 <TR>\r
 440 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 441   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
 442 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 443 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
 444 </TR>\r
 445 </TABLE>\r
 446 <A NAME="skip-navbar_bottom"></A>\r
 447 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 448 \r
 449 <HR>\r
 450 \r
 451 </BODY>\r
 452 </HTML>\r