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

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   5 <!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:35 BST 2011 -->\r
   6 <TITLE>\r
   7 OB\r
   8 </TITLE>\r
   9 \r
  10 <META NAME="date" CONTENT="2011-08-12">\r
  11 \r
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  15 function windowTitle()\r
  16 {\r
  17     if (location.href.indexOf('is-external=true') == -1) {\r
  18         parent.document.title="OB";\r
  19     }\r
  20 }\r
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  40   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
  41   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
  42   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
  43   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/OB.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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  58 &nbsp;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
  59 &nbsp;<A HREF="../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
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  76 </TR>\r
  77 <TR>\r
  78 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
  79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&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;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">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 OB</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/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">compbio.runner._SkeletalCommandBuilder</A>\r
  97       <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._impl.OB</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/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</DD>\r
 101 </DL>\r
 102 <HR>\r
 103 <DL>\r
 104 <DT><PRE>public class <B>OB</B><DT>extends <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></DL>\r
 105 </PRE>\r
 106 \r
 107 <P>\r
 108 TODO this needs fixing! Executable does not work\r
 109 <P>\r
 110 \r
 111 <P>\r
 112 <DL>\r
 113 <DT><B>Author:</B></DT>\r
 114   <DD>pvtroshin</DD>\r
 115 </DL>\r
 116 <HR>\r
 117 \r
 118 <P>\r
 119 <!-- ======== NESTED CLASS SUMMARY ======== -->\r
 120 \r
 121 <A NAME="nested_class_summary"><!-- --></A>\r
 122 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 123 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 124 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 125 <B>Nested Class Summary</B></FONT></TH>\r
 126 </TR>\r
 127 </TABLE>\r
 128 &nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
 129 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 130 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 131 <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
 132 </TR>\r
 133 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 134 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
 135 </TR>\r
 136 </TABLE>\r
 137 &nbsp;\r
 138 \r
 139 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 140 \r
 141 <A NAME="constructor_summary"><!-- --></A>\r
 142 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 143 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 144 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 145 <B>Constructor Summary</B></FONT></TH>\r
 146 </TR>\r
 147 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 148 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/OB.html#OB()">OB</A></B>()</CODE>\r
 149 \r
 150 <BR>\r
 151 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 152 </TR>\r
 153 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 154 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/OB.html#OB(java.lang.String)">OB</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
 155 \r
 156 <BR>\r
 157 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 158 </TR>\r
 159 </TABLE>\r
 160 &nbsp;\r
 161 <!-- ========== METHOD SUMMARY =========== -->\r
 162 \r
 163 <A NAME="method_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>Method Summary</B></FONT></TH>\r
 168 </TR>\r
 169 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 170 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 171 <CODE>&nbsp;<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;</CODE></FONT></TD>\r
 172 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/OB.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
 173 \r
 174 <BR>\r
 175 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 176 </TR>\r
 177 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 178 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 179 <CODE>&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
 180 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/OB.html#getInput()">getInput</A></B>()</CODE>\r
 181 \r
 182 <BR>\r
 183 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\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="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;</CODE></FONT></TD>\r
 188 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/OB.html#getTestArgs()">getTestArgs</A></B>()</CODE>\r
 189 \r
 190 <BR>\r
 191 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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>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
 196 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/OB.html#getTestCommand()">getTestCommand</A></B>()</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>static&nbsp;void</CODE></FONT></TD>\r
 204 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/OB.html#main(java.lang.String[])">main</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;args)</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 </TABLE>\r
 210 &nbsp;<A NAME="methods_inherited_from_class_compbio.runner._SkeletalCommandBuilder"><!-- --></A>\r
 211 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 212 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 213 <TH ALIGN="left"><B>Methods inherited from class compbio.runner.<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></B></TH>\r
 214 </TR>\r
 215 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 216 <TD><CODE><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)">addParameter</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getClusterJobSettings()">getClusterJobSettings</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getEmail()">getEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getError()">getError</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getName()">getName</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getResults(java.lang.String)">getResults</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)">setEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)">setName</A></CODE></TD>\r
 217 </TR>\r
 218 </TABLE>\r
 219 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 220 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 221 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 222 <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
 223 </TR>\r
 224 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 225 <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
 226 </TR>\r
 227 </TABLE>\r
 228 &nbsp;\r
 229 <P>\r
 230 \r
 231 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 232 \r
 233 <A NAME="constructor_detail"><!-- --></A>\r
 234 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 235 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 236 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 237 <B>Constructor Detail</B></FONT></TH>\r
 238 </TR>\r
 239 </TABLE>\r
 240 \r
 241 <A NAME="OB()"><!-- --></A><H3>\r
 242 OB</H3>\r
 243 <PRE>\r
 244 public <B>OB</B>()</PRE>\r
 245 <DL>\r
 246 </DL>\r
 247 <HR>\r
 248 \r
 249 <A NAME="OB(java.lang.String)"><!-- --></A><H3>\r
 250 OB</H3>\r
 251 <PRE>\r
 252 public <B>OB</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
 253 <DL>\r
 254 </DL>\r
 255 \r
 256 <!-- ============ METHOD DETAIL ========== -->\r
 257 \r
 258 <A NAME="method_detail"><!-- --></A>\r
 259 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 260 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 261 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 262 <B>Method Detail</B></FONT></TH>\r
 263 </TR>\r
 264 </TABLE>\r
 265 \r
 266 <A NAME="getTestCommand()"><!-- --></A><H3>\r
 267 getTestCommand</H3>\r
 268 <PRE>\r
 269 public static <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>getTestCommand</B>()</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="getTestArgs()"><!-- --></A><H3>\r
 278 getTestArgs</H3>\r
 279 <PRE>\r
 280 public <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; <B>getTestArgs</B>()</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="main(java.lang.String[])"><!-- --></A><H3>\r
 289 main</H3>\r
 290 <PRE>\r
 291 public static void <B>main</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;args)</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="getCreatedFiles()"><!-- --></A><H3>\r
 300 getCreatedFiles</H3>\r
 301 <PRE>\r
 302 public <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; <B>getCreatedFiles</B>()</PRE>\r
 303 <DL>\r
 304 <DD><DL>\r
 305 </DL>\r
 306 </DD>\r
 307 </DL>\r
 308 <HR>\r
 309 \r
 310 <A NAME="getInput()"><!-- --></A><H3>\r
 311 getInput</H3>\r
 312 <PRE>\r
 313 public <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>getInput</B>()</PRE>\r
 314 <DL>\r
 315 <DD><DL>\r
 316 </DL>\r
 317 </DD>\r
 318 </DL>\r
 319 <!-- ========= END OF CLASS DATA ========= -->\r
 320 <HR>\r
 321 \r
 322 \r
 323 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 324 <A NAME="navbar_bottom"><!-- --></A>\r
 325 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 326 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 327 <TR>\r
 328 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 329 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 330 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 331   <TR ALIGN="center" VALIGN="top">\r
 332   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
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