website/full_javadoc/compbio/engine/client/Executable.html

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   7 Executable\r
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   9 \r
  10 <META NAME="date" CONTENT="2010-02-17">\r
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  18         parent.document.title="Executable";\r
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  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/Executable.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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  58 &nbsp;<A HREF="../../../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
  59 &nbsp;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
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  79   SUMMARY:&nbsp;<A HREF="#nested_class_summary">NESTED</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&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;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.engine.client</FONT>\r
  92 <BR>\r
  93 Interface Executable&lt;T&gt;</H2>\r
  94 <DL>\r
  95 <DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - </DL>\r
  96 <DL>\r
  97 <DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client">ClusterNativeSpecExecutable</A>&lt;T&gt;, <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;, <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;T&gt;</DD>\r
  98 </DL>\r
  99 <DL>\r
 100 <DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>, <A HREF="../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>, <A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>, <A HREF="../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>, <A HREF="../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A>, <A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>, <A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>, <A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>, <A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>, <A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>, <A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>, <A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>, <A HREF="../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>, <A HREF="../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>, <A HREF="../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>, <A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></DD>\r
 101 </DL>\r
 102 <HR>\r
 103 <DL>\r
 104 <DT><PRE>public interface <B>Executable&lt;T&gt;</B></DL>\r
 105 </PRE>\r
 106 \r
 107 <P>\r
 108 Interface to a native executable.\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 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 128 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 129 <CODE>static&nbsp;class</CODE></FONT></TD>\r
 130 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></B></CODE>\r
 131 \r
 132 <BR>\r
 133 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 134 </TR>\r
 135 </TABLE>\r
 136 &nbsp;\r
 137 <!-- ========== METHOD SUMMARY =========== -->\r
 138 \r
 139 <A NAME="method_summary"><!-- --></A>\r
 140 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 141 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 142 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 143 <B>Method Summary</B></FONT></TH>\r
 144 </TR>\r
 145 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 146 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 147 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt;</CODE></FONT></TD>\r
 148 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</CODE>\r
 149 \r
 150 <BR>\r
 151 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds parameter to the list of parameters for a native executable</TD>\r
 152 </TR>\r
 153 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 154 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 155 <CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
 156 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
 157 \r
 158 <BR>\r
 159 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 160 </TR>\r
 161 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 162 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 163 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 164 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A></B>()</CODE>\r
 165 \r
 166 <BR>\r
 167 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\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;java.lang.String</CODE></FONT></TD>\r
 172 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</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="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt;</CODE></FONT></TD>\r
 180 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</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="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt;</CODE></FONT></TD>\r
 188 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</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>&nbsp;java.lang.String</CODE></FONT></TD>\r
 196 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</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>&nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt;</CODE></FONT></TD>\r
 204 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</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 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 210 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 211 <CODE>\r
 212 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 213 <TR ALIGN="right" VALIGN="">\r
 214 <TD NOWRAP><FONT SIZE="-1">\r
 215 <CODE>&lt;V&gt; V</CODE></FONT></TD>\r
 216 </TR>\r
 217 </TABLE>\r
 218 </CODE></FONT></TD>\r
 219 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;directory)</CODE>\r
 220 \r
 221 <BR>\r
 222 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 223 </TR>\r
 224 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 225 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 226 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
 227 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
 228 \r
 229 <BR>\r
 230 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 231 </TR>\r
 232 </TABLE>\r
 233 &nbsp;\r
 234 <P>\r
 235 \r
 236 <!-- ============ METHOD DETAIL ========== -->\r
 237 \r
 238 <A NAME="method_detail"><!-- --></A>\r
 239 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 240 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 241 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 242 <B>Method Detail</B></FONT></TH>\r
 243 </TR>\r
 244 </TABLE>\r
 245 \r
 246 <A NAME="addParameters(java.util.List)"><!-- --></A><H3>\r
 247 addParameters</H3>\r
 248 <PRE>\r
 249 <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt; <B>addParameters</B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</PRE>\r
 250 <DL>\r
 251 <DD>Adds parameter to the list of parameters for a native executable\r
 252 <P>\r
 253 <DD><DL>\r
 254 <DT><B>Parameters:</B><DD><CODE>parameters</CODE> - \r
 255 <DT><B>Returns:</B><DD>this Executable</DL>\r
 256 </DD>\r
 257 </DL>\r
 258 <HR>\r
 259 \r
 260 <A NAME="getCreatedFiles()"><!-- --></A><H3>\r
 261 getCreatedFiles</H3>\r
 262 <PRE>\r
 263 java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
 264 <DL>\r
 265 <DD><DL>\r
 266 </DL>\r
 267 </DD>\r
 268 </DL>\r
 269 <HR>\r
 270 \r
 271 <A NAME="getInput()"><!-- --></A><H3>\r
 272 getInput</H3>\r
 273 <PRE>\r
 274 java.lang.String <B>getInput</B>()</PRE>\r
 275 <DL>\r
 276 <DD><DL>\r
 277 </DL>\r
 278 </DD>\r
 279 </DL>\r
 280 <HR>\r
 281 \r
 282 <A NAME="getOutput()"><!-- --></A><H3>\r
 283 getOutput</H3>\r
 284 <PRE>\r
 285 java.lang.String <B>getOutput</B>()</PRE>\r
 286 <DL>\r
 287 <DD><DL>\r
 288 </DL>\r
 289 </DD>\r
 290 </DL>\r
 291 <HR>\r
 292 \r
 293 <A NAME="getError()"><!-- --></A><H3>\r
 294 getError</H3>\r
 295 <PRE>\r
 296 java.lang.String <B>getError</B>()</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="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
 305 getParameters</H3>\r
 306 <PRE>\r
 307 <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt; <B>getParameters</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</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="getResults(java.lang.String)"><!-- --></A><H3>\r
 316 getResults</H3>\r
 317 <PRE>\r
 318 &lt;V&gt; V <B>getResults</B>(java.lang.String&nbsp;directory)\r
 319              throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 320 <DL>\r
 321 <DD><DL>\r
 322 \r
 323 <DT><B>Throws:</B>\r
 324 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 325 </DD>\r
 326 </DL>\r
 327 <HR>\r
 328 \r
 329 <A NAME="loadRunConfiguration(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>\r
 330 loadRunConfiguration</H3>\r
 331 <PRE>\r
 332 <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt; <B>loadRunConfiguration</B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</PRE>\r
 333 <DL>\r
 334 <DD><DL>\r
 335 </DL>\r
 336 </DD>\r
 337 </DL>\r
 338 <HR>\r
 339 \r
 340 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
 341 getLimit</H3>\r
 342 <PRE>\r
 343 <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
 344 <DL>\r
 345 <DD><DL>\r
 346 </DL>\r
 347 </DD>\r
 348 </DL>\r
 349 <HR>\r
 350 \r
 351 <A NAME="getLimits()"><!-- --></A><H3>\r
 352 getLimits</H3>\r
 353 <PRE>\r
 354 <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt; <B>getLimits</B>()</PRE>\r
 355 <DL>\r
 356 <DD><DL>\r
 357 </DL>\r
 358 </DD>\r
 359 </DL>\r
 360 <!-- ========= END OF CLASS DATA ========= -->\r
 361 <HR>\r
 362 \r
 363 \r
 364 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 365 <A NAME="navbar_bottom"><!-- --></A>\r
 366 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 367 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 368 <TR>\r
 369 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 370 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 371 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 372   <TR ALIGN="center" VALIGN="top">\r
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