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   7 Util\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
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  91 compbio.runner</FONT>\r
  92 <BR>\r
  93 Class Util</H2>\r
  94 <PRE>\r
  95 java.lang.Object\r
  96   <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.Util</B>\r
  97 </PRE>\r
  98 <HR>\r
  99 <DL>\r
 100 <DT><PRE>public final class <B>Util</B><DT>extends java.lang.Object</DL>\r
 101 </PRE>\r
 102 \r
 103 <P>\r
 104 <HR>\r
 105 \r
 106 <P>\r
 107 <!-- =========== FIELD SUMMARY =========== -->\r
 108 \r
 109 <A NAME="field_summary"><!-- --></A>\r
 110 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 111 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 112 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 113 <B>Field Summary</B></FONT></TH>\r
 114 </TR>\r
 115 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 116 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 117 <CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
 118 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#SPACE">SPACE</A></B></CODE>\r
 119 \r
 120 <BR>\r
 121 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 122 </TR>\r
 123 </TABLE>\r
 124 &nbsp;\r
 125 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 126 \r
 127 <A NAME="constructor_summary"><!-- --></A>\r
 128 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 129 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 130 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 131 <B>Constructor Summary</B></FONT></TH>\r
 132 </TR>\r
 133 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 134 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#Util()">Util</A></B>()</CODE>\r
 135 \r
 136 <BR>\r
 137 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 138 </TR>\r
 139 </TABLE>\r
 140 &nbsp;\r
 141 <!-- ========== METHOD SUMMARY =========== -->\r
 142 \r
 143 <A NAME="method_summary"><!-- --></A>\r
 144 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 145 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 146 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 147 <B>Method Summary</B></FONT></TH>\r
 148 </TR>\r
 149 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 150 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 151 <CODE>static\r
 152 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 153 <TR ALIGN="right" VALIGN="">\r
 154 <TD NOWRAP><FONT SIZE="-1">\r
 155 <CODE>&lt;T&gt; <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;T&gt;</CODE></FONT></TD>\r
 156 </TR>\r
 157 </TABLE>\r
 158 </CODE></FONT></TD>\r
 159 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#getLimits(java.lang.Class)">getLimits</A></B>(java.lang.Class&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
 160 \r
 161 <BR>\r
 162 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;For now just assume that all parameters which came in needs setting it
 163  will be a client responsibility to prepare RunnerConfig object then</TD>\r
 164 </TR>\r
 165 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 166 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 167 <CODE>static\r
 168 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 169 <TR ALIGN="right" VALIGN="">\r
 170 <TD NOWRAP><FONT SIZE="-1">\r
 171 <CODE>&lt;T&gt; <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;T&gt;</CODE></FONT></TD>\r
 172 </TR>\r
 173 </TABLE>\r
 174 </CODE></FONT></TD>\r
 175 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#getPresets(java.lang.Class)">getPresets</A></B>(java.lang.Class&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
 176 \r
 177 <BR>\r
 178 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 179 </TR>\r
 180 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 181 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 182 <CODE>static\r
 183 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 184 <TR ALIGN="right" VALIGN="">\r
 185 <TD NOWRAP><FONT SIZE="-1">\r
 186 <CODE>&lt;T&gt; <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;T&gt;</CODE></FONT></TD>\r
 187 </TR>\r
 188 </TABLE>\r
 189 </CODE></FONT></TD>\r
 190 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#getSupportedOptions(java.lang.Class)">getSupportedOptions</A></B>(java.lang.Class&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
 191 \r
 192 <BR>\r
 193 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 194 </TR>\r
 195 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 196 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 197 <CODE>static&nbsp;<A HREF="../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
 198 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#readClustalFile(java.lang.String, java.lang.String)">readClustalFile</A></B>(java.lang.String&nbsp;workDirectory,\r
 199                 java.lang.String&nbsp;clustFile)</CODE>\r
 200 \r
 201 <BR>\r
 202 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 203 </TR>\r
 204 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 205 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 206 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 207 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)">writeInput</A></B>(java.util.List&lt;<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 208            <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;exec)</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 </TABLE>\r
 214 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 215 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 216 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 217 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
 218 </TR>\r
 219 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 220 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
 221 </TR>\r
 222 </TABLE>\r
 223 &nbsp;\r
 224 <P>\r
 225 \r
 226 <!-- ============ FIELD DETAIL =========== -->\r
 227 \r
 228 <A NAME="field_detail"><!-- --></A>\r
 229 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 230 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 231 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 232 <B>Field Detail</B></FONT></TH>\r
 233 </TR>\r
 234 </TABLE>\r
 235 \r
 236 <A NAME="SPACE"><!-- --></A><H3>\r
 237 SPACE</H3>\r
 238 <PRE>\r
 239 public static final java.lang.String <B>SPACE</B></PRE>\r
 240 <DL>\r
 241 <DL>\r
 242 <DT><B>See Also:</B><DD><A HREF="../../constant-values.html#compbio.runner.Util.SPACE">Constant Field Values</A></DL>\r
 243 </DL>\r
 244 \r
 245 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 246 \r
 247 <A NAME="constructor_detail"><!-- --></A>\r
 248 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 249 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 250 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 251 <B>Constructor Detail</B></FONT></TH>\r
 252 </TR>\r
 253 </TABLE>\r
 254 \r
 255 <A NAME="Util()"><!-- --></A><H3>\r
 256 Util</H3>\r
 257 <PRE>\r
 258 public <B>Util</B>()</PRE>\r
 259 <DL>\r
 260 </DL>\r
 261 \r
 262 <!-- ============ METHOD DETAIL ========== -->\r
 263 \r
 264 <A NAME="method_detail"><!-- --></A>\r
 265 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 266 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 267 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 268 <B>Method Detail</B></FONT></TH>\r
 269 </TR>\r
 270 </TABLE>\r
 271 \r
 272 <A NAME="getLimits(java.lang.Class)"><!-- --></A><H3>\r
 273 getLimits</H3>\r
 274 <PRE>\r
 275 public static &lt;T&gt; <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;T&gt; <B>getLimits</B>(java.lang.Class&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</PRE>\r
 276 <DL>\r
 277 <DD>For now just assume that all parameters which came in needs setting it
 278  will be a client responsibility to prepare RunnerConfig object then\r
 279 <P>\r
 280 <DD><DL>\r
 281 <DT><B>Parameters:</B><DD><CODE>rconfig</CODE> - \r
 282 <DT><B>Returns:</B><DD>public static List<String> toOptionString(RunnerConfig<?>
 283          rconfig) { String option = ""; List<String> options = new
 284          ArrayList<String>(); for (Parameter<?> par :
 285          rconfig.getParameters()) { if (par.getPossibleValues().isEmpty())
 286          { option = par.getOptionName(); } else { option =
 287          par.getOptionName() + "=" + par.getPossibleValues().get(0); } //
 288          separate options options.add(option); } return options; }</DL>\r
 289 </DD>\r
 290 </DL>\r
 291 <HR>\r
 292 \r
 293 <A NAME="getSupportedOptions(java.lang.Class)"><!-- --></A><H3>\r
 294 getSupportedOptions</H3>\r
 295 <PRE>\r
 296 public static &lt;T&gt; <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;T&gt; <B>getSupportedOptions</B>(java.lang.Class&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</PRE>\r
 297 <DL>\r
 298 <DD><DL>\r
 299 </DL>\r
 300 </DD>\r
 301 </DL>\r
 302 <HR>\r
 303 \r
 304 <A NAME="getPresets(java.lang.Class)"><!-- --></A><H3>\r
 305 getPresets</H3>\r
 306 <PRE>\r
 307 public static &lt;T&gt; <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;T&gt; <B>getPresets</B>(java.lang.Class&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</PRE>\r
 308 <DL>\r
 309 <DD><DL>\r
 310 </DL>\r
 311 </DD>\r
 312 </DL>\r
 313 <HR>\r
 314 \r
 315 <A NAME="readClustalFile(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
 316 readClustalFile</H3>\r
 317 <PRE>\r
 318 public static final <A HREF="../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>readClustalFile</B>(java.lang.String&nbsp;workDirectory,\r
 319                                               java.lang.String&nbsp;clustFile)\r
 320                                        throws <A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>,\r
 321                                               java.io.IOException,\r
 322                                               java.io.FileNotFoundException,\r
 323                                               java.lang.NullPointerException</PRE>\r
 324 <DL>\r
 325 <DD><DL>\r
 326 \r
 327 <DT><B>Throws:</B>\r
 328 <DD><CODE><A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE>\r
 329 <DD><CODE>java.io.IOException</CODE>\r
 330 <DD><CODE>java.io.FileNotFoundException</CODE>\r
 331 <DD><CODE>java.lang.NullPointerException</CODE></DL>\r
 332 </DD>\r
 333 </DL>\r
 334 <HR>\r
 335 \r
 336 <A NAME="writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
 337 writeInput</H3>\r
 338 <PRE>\r
 339 public static void <B>writeInput</B>(java.util.List&lt;<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 340                               <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;exec)</PRE>\r
 341 <DL>\r
 342 <DD><DL>\r
 343 </DL>\r
 344 </DD>\r
 345 </DL>\r
 346 <!-- ========= END OF CLASS DATA ========= -->\r
 347 <HR>\r
 348 \r
 349 \r
 350 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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 352 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 353 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 354 <TR>\r
 355 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 356 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 357 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 358   <TR ALIGN="center" VALIGN="top">\r
 359   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 360   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 361   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 362   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Util.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 363   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 364   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 365   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 366   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 367   </TR>\r
 368 </TABLE>\r
 369 </TD>\r
 370 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 371 </EM>\r
 372 </TD>\r
 373 </TR>\r
 374 \r
 375 <TR>\r
 376 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 377 &nbsp;<A HREF="../../compbio/runner/OptionCombinator.html" title="class in compbio.runner"><B>PREV CLASS</B></A>&nbsp;\r
 378 &nbsp;NEXT CLASS</FONT></TD>\r
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