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

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   5 <!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
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   7 Runners\r
   8 </TITLE>\r
   9 \r
  10 <META NAME="date" CONTENT="2010-02-17">\r
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  16 {\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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  89 <H2>\r
  90 <FONT SIZE="-1">\r
  91 compbio.runner._impl</FONT>\r
  92 <BR>\r
  93 Class Runners</H2>\r
  94 <PRE>\r
  95 java.lang.Object\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 java.lang.Object</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>(java.lang.String&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/Disembl.html" title="class in compbio.runner._impl">Disembl</A></CODE></FONT></TD>\r
 127 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getDisemblRunnable(java.lang.String)">getDisemblRunnable</A></B>(java.lang.String&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/Mcl.html" title="class in compbio.runner._impl">Mcl</A></CODE></FONT></TD>\r
 135 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getMclRunnable(java.lang.String)">getMclRunnable</A></B>(java.lang.String&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/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A></CODE></FONT></TD>\r
 143 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getNetNglycRunnable(java.lang.String)">getNetNglycRunnable</A></B>(java.lang.String&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/OB.html" title="class in compbio.runner._impl">OB</A></CODE></FONT></TD>\r
 151 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getOBRunnable(java.lang.String)">getOBRunnable</A></B>(java.lang.String&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/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A></CODE></FONT></TD>\r
 159 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getPSIBlastRunnable(java.lang.String)">getPSIBlastRunnable</A></B>(java.lang.String&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/Ronn.html" title="class in compbio.runner._impl">Ronn</A></CODE></FONT></TD>\r
 167 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getRonnRunnable(java.lang.String)">getRonnRunnable</A></B>(java.lang.String&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;<A HREF="../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A></CODE></FONT></TD>\r
 175 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getRPSBlastRunnable(java.lang.String)">getRPSBlastRunnable</A></B>(java.lang.String&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 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 181 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 182 <CODE>static&nbsp;compbio.runner._impl.Tmhmm2</CODE></FONT></TD>\r
 183 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getTmhmm2Runnable(java.lang.String)">getTmhmm2Runnable</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
 184 \r
 185 <BR>\r
 186 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 187 </TR>\r
 188 </TABLE>\r
 189 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 190 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 191 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 192 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
 193 </TR>\r
 194 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 195 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
 196 </TR>\r
 197 </TABLE>\r
 198 &nbsp;\r
 199 <P>\r
 200 \r
 201 <!-- ============ METHOD DETAIL ========== -->\r
 202 \r
 203 <A NAME="method_detail"><!-- --></A>\r
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 205 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 206 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 207 <B>Method Detail</B></FONT></TH>\r
 208 </TR>\r
 209 </TABLE>\r
 210 \r
 211 <A NAME="getMclRunnable(java.lang.String)"><!-- --></A><H3>\r
 212 getMclRunnable</H3>\r
 213 <PRE>\r
 214 public static <A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A> <B>getMclRunnable</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
 215 <DL>\r
 216 <DD><DL>\r
 217 </DL>\r
 218 </DD>\r
 219 </DL>\r
 220 <HR>\r
 221 \r
 222 <A NAME="getOBRunnable(java.lang.String)"><!-- --></A><H3>\r
 223 getOBRunnable</H3>\r
 224 <PRE>\r
 225 public static <A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A> <B>getOBRunnable</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
 226 <DL>\r
 227 <DD><DL>\r
 228 </DL>\r
 229 </DD>\r
 230 </DL>\r
 231 <HR>\r
 232 \r
 233 <A NAME="getDisemblRunnable(java.lang.String)"><!-- --></A><H3>\r
 234 getDisemblRunnable</H3>\r
 235 <PRE>\r
 236 public static <A HREF="../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A> <B>getDisemblRunnable</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
 237 <DL>\r
 238 <DD><DL>\r
 239 </DL>\r
 240 </DD>\r
 241 </DL>\r
 242 <HR>\r
 243 \r
 244 <A NAME="getNetNglycRunnable(java.lang.String)"><!-- --></A><H3>\r
 245 getNetNglycRunnable</H3>\r
 246 <PRE>\r
 247 public static <A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A> <B>getNetNglycRunnable</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
 248 <DL>\r
 249 <DD><DL>\r
 250 </DL>\r
 251 </DD>\r
 252 </DL>\r
 253 <HR>\r
 254 \r
 255 <A NAME="getRonnRunnable(java.lang.String)"><!-- --></A><H3>\r
 256 getRonnRunnable</H3>\r
 257 <PRE>\r
 258 public static <A HREF="../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A> <B>getRonnRunnable</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
 259 <DL>\r
 260 <DD><DL>\r
 261 </DL>\r
 262 </DD>\r
 263 </DL>\r
 264 <HR>\r
 265 \r
 266 <A NAME="getTmhmm2Runnable(java.lang.String)"><!-- --></A><H3>\r
 267 getTmhmm2Runnable</H3>\r
 268 <PRE>\r
 269 public static compbio.runner._impl.Tmhmm2 <B>getTmhmm2Runnable</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
 270 <DL>\r
 271 <DD><DL>\r
 272 </DL>\r
 273 </DD>\r
 274 </DL>\r
 275 <HR>\r
 276 \r
 277 <A NAME="getRPSBlastRunnable(java.lang.String)"><!-- --></A><H3>\r
 278 getRPSBlastRunnable</H3>\r
 279 <PRE>\r
 280 public static <A HREF="../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A> <B>getRPSBlastRunnable</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
 281 <DL>\r
 282 <DD><DL>\r
 283 </DL>\r
 284 </DD>\r
 285 </DL>\r
 286 <HR>\r
 287 \r
 288 <A NAME="getBlastAllRunnable(java.lang.String)"><!-- --></A><H3>\r
 289 getBlastAllRunnable</H3>\r
 290 <PRE>\r
 291 public static <A HREF="../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A> <B>getBlastAllRunnable</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
 292 <DL>\r
 293 <DD><DL>\r
 294 </DL>\r
 295 </DD>\r
 296 </DL>\r
 297 <HR>\r
 298 \r
 299 <A NAME="getPSIBlastRunnable(java.lang.String)"><!-- --></A><H3>\r
 300 getPSIBlastRunnable</H3>\r
 301 <PRE>\r
 302 public static <A HREF="../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A> <B>getPSIBlastRunnable</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
 303 <DL>\r
 304 <DD><DL>\r
 305 </DL>\r
 306 </DD>\r
 307 </DL>\r
 308 <!-- ========= END OF CLASS DATA ========= -->\r
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 360   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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