website/full_javadoc/compbio/runner/_impl/Runners.html

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   7 Runners\r
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  10 <META NAME="date" CONTENT="2011-08-12">\r
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  18         parent.document.title="Runners";\r
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  79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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  81 DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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  89 <H2>\r
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  91 compbio.runner._impl</FONT>\r
  92 <BR>\r
  93 Class Runners</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 "><B>compbio.runner._impl.Runners</B>\r
  97 </PRE>\r
  98 <HR>\r
  99 <DL>\r
 100 <DT><PRE>public final class <B>Runners</B><DT>extends <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></DL>\r
 101 </PRE>\r
 102 \r
 103 <P>\r
 104 <HR>\r
 105 \r
 106 <P>\r
 107 \r
 108 <!-- ========== METHOD SUMMARY =========== -->\r
 109 \r
 110 <A NAME="method_summary"><!-- --></A>\r
 111 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 112 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 113 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 114 <B>Method Summary</B></FONT></TH>\r
 115 </TR>\r
 116 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 117 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 118 <CODE>static&nbsp;<A HREF="../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A></CODE></FONT></TD>\r
 119 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getBlastAllRunnable(java.lang.String)">getBlastAllRunnable</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
 120 \r
 121 <BR>\r
 122 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 123 </TR>\r
 124 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 125 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 126 <CODE>static&nbsp;<A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A></CODE></FONT></TD>\r
 127 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getMclRunnable(java.lang.String)">getMclRunnable</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
 128 \r
 129 <BR>\r
 130 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 131 </TR>\r
 132 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 133 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 134 <CODE>static&nbsp;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A></CODE></FONT></TD>\r
 135 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getNetNglycRunnable(java.lang.String)">getNetNglycRunnable</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
 136 \r
 137 <BR>\r
 138 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 139 </TR>\r
 140 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 141 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 142 <CODE>static&nbsp;<A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A></CODE></FONT></TD>\r
 143 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getOBRunnable(java.lang.String)">getOBRunnable</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
 144 \r
 145 <BR>\r
 146 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 147 </TR>\r
 148 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 149 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 150 <CODE>static&nbsp;<A HREF="../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A></CODE></FONT></TD>\r
 151 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getPSIBlastRunnable(java.lang.String)">getPSIBlastRunnable</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
 152 \r
 153 <BR>\r
 154 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 155 </TR>\r
 156 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 157 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 158 <CODE>static&nbsp;<A HREF="../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A></CODE></FONT></TD>\r
 159 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getRonnRunnable(java.lang.String)">getRonnRunnable</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
 160 \r
 161 <BR>\r
 162 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 163 </TR>\r
 164 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 165 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 166 <CODE>static&nbsp;<A HREF="../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A></CODE></FONT></TD>\r
 167 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getRPSBlastRunnable(java.lang.String)">getRPSBlastRunnable</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
 168 \r
 169 <BR>\r
 170 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\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>static&nbsp;compbio.runner._impl.Tmhmm2</CODE></FONT></TD>\r
 175 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getTmhmm2Runnable(java.lang.String)">getTmhmm2Runnable</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
 176 \r
 177 <BR>\r
 178 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 179 </TR>\r
 180 </TABLE>\r
 181 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 182 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 183 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 184 <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
 185 </TR>\r
 186 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 187 <TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <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#hashCode()" title="class or interface in java.lang">hashCode</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#toString()" title="class or interface in java.lang">toString</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
 188 </TR>\r
 189 </TABLE>\r
 190 &nbsp;\r
 191 <P>\r
 192 \r
 193 <!-- ============ METHOD DETAIL ========== -->\r
 194 \r
 195 <A NAME="method_detail"><!-- --></A>\r
 196 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 197 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 198 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 199 <B>Method Detail</B></FONT></TH>\r
 200 </TR>\r
 201 </TABLE>\r
 202 \r
 203 <A NAME="getMclRunnable(java.lang.String)"><!-- --></A><H3>\r
 204 getMclRunnable</H3>\r
 205 <PRE>\r
 206 public static <A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A> <B>getMclRunnable</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)</PRE>\r
 207 <DL>\r
 208 <DD><DL>\r
 209 </DL>\r
 210 </DD>\r
 211 </DL>\r
 212 <HR>\r
 213 \r
 214 <A NAME="getOBRunnable(java.lang.String)"><!-- --></A><H3>\r
 215 getOBRunnable</H3>\r
 216 <PRE>\r
 217 public static <A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A> <B>getOBRunnable</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)</PRE>\r
 218 <DL>\r
 219 <DD><DL>\r
 220 </DL>\r
 221 </DD>\r
 222 </DL>\r
 223 <HR>\r
 224 \r
 225 <A NAME="getNetNglycRunnable(java.lang.String)"><!-- --></A><H3>\r
 226 getNetNglycRunnable</H3>\r
 227 <PRE>\r
 228 public static <A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A> <B>getNetNglycRunnable</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)</PRE>\r
 229 <DL>\r
 230 <DD><DL>\r
 231 </DL>\r
 232 </DD>\r
 233 </DL>\r
 234 <HR>\r
 235 \r
 236 <A NAME="getRonnRunnable(java.lang.String)"><!-- --></A><H3>\r
 237 getRonnRunnable</H3>\r
 238 <PRE>\r
 239 public static <A HREF="../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A> <B>getRonnRunnable</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)</PRE>\r
 240 <DL>\r
 241 <DD><DL>\r
 242 </DL>\r
 243 </DD>\r
 244 </DL>\r
 245 <HR>\r
 246 \r
 247 <A NAME="getTmhmm2Runnable(java.lang.String)"><!-- --></A><H3>\r
 248 getTmhmm2Runnable</H3>\r
 249 <PRE>\r
 250 public static compbio.runner._impl.Tmhmm2 <B>getTmhmm2Runnable</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)</PRE>\r
 251 <DL>\r
 252 <DD><DL>\r
 253 </DL>\r
 254 </DD>\r
 255 </DL>\r
 256 <HR>\r
 257 \r
 258 <A NAME="getRPSBlastRunnable(java.lang.String)"><!-- --></A><H3>\r
 259 getRPSBlastRunnable</H3>\r
 260 <PRE>\r
 261 public static <A HREF="../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A> <B>getRPSBlastRunnable</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)</PRE>\r
 262 <DL>\r
 263 <DD><DL>\r
 264 </DL>\r
 265 </DD>\r
 266 </DL>\r
 267 <HR>\r
 268 \r
 269 <A NAME="getBlastAllRunnable(java.lang.String)"><!-- --></A><H3>\r
 270 getBlastAllRunnable</H3>\r
 271 <PRE>\r
 272 public static <A HREF="../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A> <B>getBlastAllRunnable</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)</PRE>\r
 273 <DL>\r
 274 <DD><DL>\r
 275 </DL>\r
 276 </DD>\r
 277 </DL>\r
 278 <HR>\r
 279 \r
 280 <A NAME="getPSIBlastRunnable(java.lang.String)"><!-- --></A><H3>\r
 281 getPSIBlastRunnable</H3>\r
 282 <PRE>\r
 283 public static <A HREF="../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A> <B>getPSIBlastRunnable</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)</PRE>\r
 284 <DL>\r
 285 <DD><DL>\r
 286 </DL>\r
 287 </DD>\r
 288 </DL>\r
 289 <!-- ========= END OF CLASS DATA ========= -->\r
 290 <HR>\r
 291 \r
 292 \r
 293 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 294 <A NAME="navbar_bottom"><!-- --></A>\r
 295 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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 297 <TR>\r
 298 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 299 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 300 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 301   <TR ALIGN="center" VALIGN="top">\r
 302   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 303   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 304   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 305   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Runners.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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 313 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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 316 </TR>\r
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