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7 Uses of Interface compbio.engine.client.ConfiguredExecutable
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84 <B>Uses of Interface<br>compbio.engine.client.ConfiguredExecutable</B></H2>
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87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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90 Packages that use <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>
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92 <TR BGCOLOR="white" CLASS="TableRowColor">
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93 <TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>
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94 <TD> </TD>
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96 <TR BGCOLOR="white" CLASS="TableRowColor">
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97 <TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>
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98 <TD> </TD>
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100 <TR BGCOLOR="white" CLASS="TableRowColor">
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101 <TD><A HREF="#compbio.engine.cluster.drmaa"><B>compbio.engine.cluster.drmaa</B></A></TD>
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102 <TD> </TD>
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104 <TR BGCOLOR="white" CLASS="TableRowColor">
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105 <TD><A HREF="#compbio.engine.local"><B>compbio.engine.local</B></A></TD>
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106 <TD> </TD>
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108 <TR BGCOLOR="white" CLASS="TableRowColor">
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109 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>
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110 <TD>Utilities commonly used by all runners. </TD>
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112 <TR BGCOLOR="white" CLASS="TableRowColor">
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113 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>
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114 <TD> </TD>
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119 <A NAME="compbio.engine"><!-- --></A>
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120 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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121 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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122 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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123 Uses of <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A> in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>
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129 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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130 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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131 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> that return <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>
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133 <TR BGCOLOR="white" CLASS="TableRowColor">
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134 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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136 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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137 <TR ALIGN="right" VALIGN="">
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138 <TD NOWRAP><FONT SIZE="-1">
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139 <CODE><T> <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><T></CODE></FONT></TD>
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142 </CODE></FONT></TD>
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143 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T> executable)</CODE>
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146 </TD>
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148 <TR BGCOLOR="white" CLASS="TableRowColor">
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149 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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151 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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152 <TR ALIGN="right" VALIGN="">
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153 <TD NOWRAP><FONT SIZE="-1">
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154 <CODE><T> <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><T></CODE></FONT></TD>
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157 </CODE></FONT></TD>
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158 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, compbio.engine.client.Executable.ExecProvider)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T> executable,
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159 <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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162 </TD>
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164 <TR BGCOLOR="white" CLASS="TableRowColor">
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165 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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167 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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168 <TR ALIGN="right" VALIGN="">
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169 <TD NOWRAP><FONT SIZE="-1">
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170 <CODE><T> <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><T></CODE></FONT></TD>
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173 </CODE></FONT></TD>
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174 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, java.util.List)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T> executable,
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175 <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><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> dataSet)</CODE>
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178 </TD>
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180 <TR BGCOLOR="white" CLASS="TableRowColor">
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181 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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182 <CODE> <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
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183 <TD><CODE><B>Job.</B><B><A HREF="../../../../compbio/engine/Job.html#getConfExecutable()">getConfExecutable</A></B>()</CODE>
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186 </TD>
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188 <TR BGCOLOR="white" CLASS="TableRowColor">
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189 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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190 <CODE> <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
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191 <TD><CODE><B>AsyncExecutor.</B><B><A HREF="../../../../compbio/engine/AsyncExecutor.html#getResults(java.lang.String)">getResults</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> jobId)</CODE>
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194 Retrieve the results of the job.</TD>
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196 <TR BGCOLOR="white" CLASS="TableRowColor">
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197 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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198 <CODE> <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
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199 <TD><CODE><B>SyncExecutor.</B><B><A HREF="../../../../compbio/engine/SyncExecutor.html#waitForResult()">waitForResult</A></B>()</CODE>
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202 Call to this method block for as long as it is required for an executable to finish its job.</TD>
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208 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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209 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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210 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> that return types with arguments of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>
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212 <TR BGCOLOR="white" CLASS="TableRowColor">
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213 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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214 <CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/concurrent/Future.html?is-external=true" title="class or interface in java.util.concurrent">Future</A><<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?>></CODE></FONT></TD>
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215 <TD><CODE><B>SubmissionManager.</B><B><A HREF="../../../../compbio/engine/SubmissionManager.html#getTask(java.lang.String)">getTask</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> taskId)</CODE>
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218 </TD>
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224 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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225 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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226 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>
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228 <TR BGCOLOR="white" CLASS="TableRowColor">
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229 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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230 <CODE>static void</CODE></FONT></TD>
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231 <TD><CODE><B>SubmissionManager.</B><B><A HREF="../../../../compbio/engine/SubmissionManager.html#addTask(compbio.engine.client.ConfiguredExecutable, java.util.concurrent.Future)">addTask</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable,
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232 <A HREF="http://java.sun.com/javase/6/docs/api/java/util/concurrent/Future.html?is-external=true" title="class or interface in java.util.concurrent">Future</A><<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?>> future)</CODE>
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235 </TD>
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237 <TR BGCOLOR="white" CLASS="TableRowColor">
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238 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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239 <CODE>static boolean</CODE></FONT></TD>
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240 <TD><CODE><B>Cleaner.</B><B><A HREF="../../../../compbio/engine/Cleaner.html#deleteFiles(compbio.engine.client.ConfiguredExecutable)">deleteFiles</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> exec)</CODE>
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243 <B>Deprecated.</B> This method returns true if all files specified by List files were
244 successfully removed or there was no files to remove (files list was
247 <TR BGCOLOR="white" CLASS="TableRowColor">
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248 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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249 <CODE>static <A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></FONT></TD>
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250 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#getAsyncEngine(compbio.engine.client.ConfiguredExecutable)">getAsyncEngine</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable)</CODE>
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253 </TD>
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255 <TR BGCOLOR="white" CLASS="TableRowColor">
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256 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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257 <CODE>static <A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></FONT></TD>
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258 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#getAsyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)">getAsyncEngine</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable,
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259 <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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262 </TD>
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264 <TR BGCOLOR="white" CLASS="TableRowColor">
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265 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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266 <CODE>static <A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></FONT></TD>
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267 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable)">getSyncEngine</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable)</CODE>
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270 </TD>
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272 <TR BGCOLOR="white" CLASS="TableRowColor">
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273 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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274 <CODE>static <A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></FONT></TD>
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275 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)">getSyncEngine</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable,
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276 <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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279 </TD>
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281 <TR BGCOLOR="white" CLASS="TableRowColor">
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282 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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283 <CODE>static void</CODE></FONT></TD>
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284 <TD><CODE><B>SubmissionManager.</B><B><A HREF="../../../../compbio/engine/SubmissionManager.html#removeTask(compbio.engine.client.ConfiguredExecutable)">removeTask</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable)</CODE>
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287 </TD>
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289 <TR BGCOLOR="white" CLASS="TableRowColor">
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290 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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291 <CODE> <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>
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292 <TD><CODE><B>AsyncExecutor.</B><B><A HREF="../../../../compbio/engine/AsyncExecutor.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable)</CODE>
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295 Submits job for the execution
296 Immediate execution is not guaranteed, this method puts the job in the queue.</TD>
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302 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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303 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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304 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> with type arguments of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>
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306 <TR BGCOLOR="white" CLASS="TableRowColor">
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307 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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308 <CODE>static void</CODE></FONT></TD>
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309 <TD><CODE><B>SubmissionManager.</B><B><A HREF="../../../../compbio/engine/SubmissionManager.html#addTask(compbio.engine.client.ConfiguredExecutable, java.util.concurrent.Future)">addTask</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable,
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310 <A HREF="http://java.sun.com/javase/6/docs/api/java/util/concurrent/Future.html?is-external=true" title="class or interface in java.util.concurrent">Future</A><<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?>> future)</CODE>
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313 </TD>
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319 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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320 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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321 <TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>
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323 <TR BGCOLOR="white" CLASS="TableRowColor">
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324 <TD><CODE><B><A HREF="../../../../compbio/engine/Job.html#Job(java.lang.String, java.lang.String, compbio.engine.client.ConfiguredExecutable)">Job</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> taskId,
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325 <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> jobId,
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326 <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> cexecutable)</CODE>
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329 </TD>
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334 <A NAME="compbio.engine.client"><!-- --></A>
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335 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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336 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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337 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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338 Uses of <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>
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344 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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345 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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346 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that implement <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>
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348 <TR BGCOLOR="white" CLASS="TableRowColor">
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349 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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350 <CODE> class</CODE></FONT></TD>
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351 <TD><CODE><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable<T></A></B></CODE>
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354 </TD>
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360 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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361 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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362 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>
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364 <TR BGCOLOR="white" CLASS="TableRowColor">
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365 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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366 <CODE>static <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
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367 <TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/engine/client/Util.html#loadExecutable(java.lang.String)">loadExecutable</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> taskId)</CODE>
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370 </TD>
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372 <TR BGCOLOR="white" CLASS="TableRowColor">
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373 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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374 <CODE> <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
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375 <TD><CODE><B>ConfiguredExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html#loadRunConfiguration(java.io.InputStream)">loadRunConfiguration</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> input)</CODE>
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378 </TD>
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380 <TR BGCOLOR="white" CLASS="TableRowColor">
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381 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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382 <CODE> <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
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383 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#loadRunConfiguration(java.io.InputStream)">loadRunConfiguration</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> input)</CODE>
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386 </TD>
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388 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
389 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
390 <CODE> <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
\r
391 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> rconf)</CODE>
\r
394 </TD>
\r
396 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
397 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
398 <CODE>static <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
\r
399 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#newConfExecutable(compbio.engine.client.RunConfiguration)">newConfExecutable</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> rconf)</CODE>
\r
402 </TD>
\r
407 <A NAME="compbio.engine.cluster.drmaa"><!-- --></A>
\r
408 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
409 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
410 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
411 Uses of <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A> in <A HREF="../../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A></FONT></TH>
\r
417 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
418 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
419 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> that return <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>
\r
421 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
422 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
423 <CODE> <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
\r
424 <TD><CODE><B>ClusterSession.</B><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#getResults(java.lang.String)">getResults</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> taskId)</CODE>
\r
427 </TD>
\r
429 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
430 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
431 <CODE> <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
\r
432 <TD><CODE><B>AsyncJobRunner.</B><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getResults(java.lang.String)">getResults</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> jobId)</CODE>
\r
435 </TD>
\r
437 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
438 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
439 <CODE> <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
\r
440 <TD><CODE><B>JobRunner.</B><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#waitForResult()">waitForResult</A></B>()</CODE>
\r
443 </TD>
\r
449 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
450 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
451 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>
\r
453 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
454 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
455 <CODE>static <A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A></CODE></FONT></TD>
\r
456 <TD><CODE><B>JobRunner.</B><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#getInstance(compbio.engine.client.ConfiguredExecutable)">getInstance</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable)</CODE>
\r
459 </TD>
\r
461 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
462 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
463 <CODE> <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
464 <TD><CODE><B>AsyncJobRunner.</B><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable)</CODE>
\r
467 </TD>
\r
473 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
474 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
475 <TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>
\r
477 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
478 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#JobRunner(compbio.engine.client.ConfiguredExecutable)">JobRunner</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> confExec)</CODE>
\r
481 </TD>
\r
486 <A NAME="compbio.engine.local"><!-- --></A>
\r
487 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
488 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
489 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
490 Uses of <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A> in <A HREF="../../../../compbio/engine/local/package-summary.html">compbio.engine.local</A></FONT></TH>
\r
496 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
497 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
498 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> that return <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>
\r
500 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
501 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
502 <CODE> <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
\r
503 <TD><CODE><B>ExecutableWrapper.</B><B><A HREF="../../../../compbio/engine/local/ExecutableWrapper.html#call()">call</A></B>()</CODE>
\r
506 It is vital that output and error streams are captured immediately for
507 this call() to succeed.</TD>
\r
509 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
510 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
511 <CODE>static <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
\r
512 <TD><CODE><B>LocalEngineUtil.</B><B><A HREF="../../../../compbio/engine/local/LocalEngineUtil.html#getResults(java.util.concurrent.Future, java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/concurrent/Future.html?is-external=true" title="class or interface in java.util.concurrent">Future</A><<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?>> future,
\r
513 <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> taskId)</CODE>
\r
516 </TD>
\r
518 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
519 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
520 <CODE> <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
\r
521 <TD><CODE><B>AsyncLocalRunner.</B><B><A HREF="../../../../compbio/engine/local/AsyncLocalRunner.html#getResults(java.lang.String)">getResults</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> taskId)</CODE>
\r
524 </TD>
\r
526 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
527 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
528 <CODE> <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
\r
529 <TD><CODE><B>LocalRunner.</B><B><A HREF="../../../../compbio/engine/local/LocalRunner.html#waitForResult()">waitForResult</A></B>()</CODE>
\r
532 </TD>
\r
538 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
539 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
540 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>
\r
542 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
543 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
544 <CODE>static boolean</CODE></FONT></TD>
\r
545 <TD><CODE><B>LocalEngineUtil.</B><B><A HREF="../../../../compbio/engine/local/LocalEngineUtil.html#cleanup(compbio.engine.client.ConfiguredExecutable)">cleanup</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> confExecutable)</CODE>
\r
548 </TD>
\r
550 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
551 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
552 <CODE> <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
553 <TD><CODE><B>AsyncLocalRunner.</B><B><A HREF="../../../../compbio/engine/local/AsyncLocalRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable)</CODE>
\r
556 </TD>
\r
562 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
563 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
564 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> with type arguments of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>
\r
566 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
567 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
568 <CODE>static boolean</CODE></FONT></TD>
\r
569 <TD><CODE><B>LocalEngineUtil.</B><B><A HREF="../../../../compbio/engine/local/LocalEngineUtil.html#cancelJob(java.util.concurrent.Future, java.lang.String)">cancelJob</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/concurrent/Future.html?is-external=true" title="class or interface in java.util.concurrent">Future</A><<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?>> future,
\r
570 <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> workDirectory)</CODE>
\r
573 </TD>
\r
575 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
576 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
577 <CODE>static <A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>
\r
578 <TD><CODE><B>LocalEngineUtil.</B><B><A HREF="../../../../compbio/engine/local/LocalEngineUtil.html#getJobStatus(java.util.concurrent.Future)">getJobStatus</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/concurrent/Future.html?is-external=true" title="class or interface in java.util.concurrent">Future</A><<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?>> future)</CODE>
\r
581 </TD>
\r
583 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
584 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
585 <CODE>static <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
\r
586 <TD><CODE><B>LocalEngineUtil.</B><B><A HREF="../../../../compbio/engine/local/LocalEngineUtil.html#getResults(java.util.concurrent.Future, java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/concurrent/Future.html?is-external=true" title="class or interface in java.util.concurrent">Future</A><<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?>> future,
\r
587 <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> taskId)</CODE>
\r
590 </TD>
\r
596 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
597 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
598 <TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>
\r
600 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
601 <TD><CODE><B><A HREF="../../../../compbio/engine/local/ExecutableWrapper.html#ExecutableWrapper(compbio.engine.client.ConfiguredExecutable, java.lang.String)">ExecutableWrapper</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable,
\r
602 <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> workDirectory)</CODE>
\r
605 </TD>
\r
607 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
608 <TD><CODE><B><A HREF="../../../../compbio/engine/local/LocalRunner.html#LocalRunner(compbio.engine.client.ConfiguredExecutable)">LocalRunner</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable)</CODE>
\r
611 </TD>
\r
616 <A NAME="compbio.runner"><!-- --></A>
\r
617 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
618 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
619 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
620 Uses of <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A> in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>
\r
626 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
627 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
628 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>
\r
630 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
631 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
632 <CODE>static void</CODE></FONT></TD>
\r
633 <TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)">writeInput</A></B>(<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><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
634 <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> exec)</CODE>
\r
637 </TD>
\r
642 <A NAME="compbio.ws.server"><!-- --></A>
\r
643 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
644 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
645 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
646 Uses of <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A> in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>
\r
652 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
653 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
654 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>
\r
656 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
657 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
659 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
\r
660 <TR ALIGN="right" VALIGN="">
\r
661 <TD NOWRAP><FONT SIZE="-1">
\r
662 <CODE><T> <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
665 </CODE></FONT></TD>
\r
666 <TD><CODE><B>WSUtil.</B><B><A HREF="../../../../compbio/ws/server/WSUtil.html#align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, java.lang.String, compbio.metadata.Limit)">align</A></B>(<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><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
667 <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><T> confExec,
\r
668 org.apache.log4j.Logger logger,
\r
669 <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> callingMethod,
\r
670 <A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><T> limit)</CODE>
\r
673 </TD>
\r
675 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
676 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
678 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
\r
679 <TR ALIGN="right" VALIGN="">
\r
680 <TD NOWRAP><FONT SIZE="-1">
\r
681 <CODE><T> <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
684 </CODE></FONT></TD>
\r
685 <TD><CODE><B>WSUtil.</B><B><A HREF="../../../../compbio/ws/server/WSUtil.html#analize(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, java.lang.String, compbio.metadata.Limit)">analize</A></B>(<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><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
686 <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><T> confExec,
\r
687 org.apache.log4j.Logger log,
\r
688 <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> method,
\r
689 <A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><T> limit)</CODE>
\r
692 </TD>
\r
694 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
695 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
696 <CODE>static <A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></FONT></TD>
\r
697 <TD><CODE><B>WSUtil.</B><B><A HREF="../../../../compbio/ws/server/WSUtil.html#getEngine(compbio.engine.client.ConfiguredExecutable)">getEngine</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> confClustal)</CODE>
\r
700 </TD>
\r
708 <!-- ======= START OF BOTTOM NAVBAR ====== -->
\r
709 <A NAME="navbar_bottom"><!-- --></A>
\r
710 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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711 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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713 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
\r
714 <A NAME="navbar_bottom_firstrow"><!-- --></A>
\r
715 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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716 <TR ALIGN="center" VALIGN="top">
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717 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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718 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
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719 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
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