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7 Uses of Interface compbio.engine.client.Executable
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42 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
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84 <B>Uses of Interface<br>compbio.engine.client.Executable</B></H2>
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87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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88 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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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/Executable.html" title="interface in compbio.engine.client">Executable</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>Classes and interfaces representing an input for engines. </TD>
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100 <TR BGCOLOR="white" CLASS="TableRowColor">
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101 <TD><A HREF="#compbio.engine.conf"><B>compbio.engine.conf</B></A></TD>
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102 <TD>Classes commonly used by both engines. </TD>
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104 <TR BGCOLOR="white" CLASS="TableRowColor">
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105 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>
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106 <TD>Utilities commonly used by all runners. </TD>
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108 <TR BGCOLOR="white" CLASS="TableRowColor">
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109 <TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>
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110 <TD> </TD>
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112 <TR BGCOLOR="white" CLASS="TableRowColor">
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113 <TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>
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114 <TD>Wrappers for native executables for multiple sequence alignment (msa) </TD>
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116 <TR BGCOLOR="white" CLASS="TableRowColor">
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117 <TD><A HREF="#compbio.runner.psiblast"><B>compbio.runner.psiblast</B></A></TD>
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118 <TD> </TD>
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123 <A NAME="compbio.engine"><!-- --></A>
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124 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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125 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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126 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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127 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>
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133 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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134 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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135 <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/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>
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137 <TR BGCOLOR="white" CLASS="TableRowColor">
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138 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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140 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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141 <TR ALIGN="right" VALIGN="">
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142 <TD NOWRAP><FONT SIZE="-1">
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143 <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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146 </CODE></FONT></TD>
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147 <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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150 </TD>
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152 <TR BGCOLOR="white" CLASS="TableRowColor">
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153 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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155 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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156 <TR ALIGN="right" VALIGN="">
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157 <TD NOWRAP><FONT SIZE="-1">
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158 <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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161 </CODE></FONT></TD>
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162 <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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163 <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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166 </TD>
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168 <TR BGCOLOR="white" CLASS="TableRowColor">
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169 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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171 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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172 <TR ALIGN="right" VALIGN="">
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173 <TD NOWRAP><FONT SIZE="-1">
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174 <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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177 </CODE></FONT></TD>
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178 <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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179 java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> dataSet)</CODE>
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182 </TD>
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184 <TR BGCOLOR="white" CLASS="TableRowColor">
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185 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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186 <CODE>static <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>
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187 <TD><CODE><B>LoadBalancer.</B><B><A HREF="../../../../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable)">getEngine</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?> executable)</CODE>
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190 </TD>
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192 <TR BGCOLOR="white" CLASS="TableRowColor">
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193 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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195 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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196 <TR ALIGN="right" VALIGN="">
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197 <TD NOWRAP><FONT SIZE="-1">
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198 <CODE><T,V> <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>
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201 </CODE></FONT></TD>
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202 <TD><CODE><B>LoadBalancer.</B><B><A HREF="../../../../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable, java.util.List)">getEngine</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><V> executable,
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203 java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> dataSet)</CODE>
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206 </TD>
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211 <A NAME="compbio.engine.client"><!-- --></A>
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212 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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213 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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214 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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215 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>
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221 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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222 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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223 <TH ALIGN="left" COLSPAN="2">Subinterfaces of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>
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225 <TR BGCOLOR="white" CLASS="TableRowColor">
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226 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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227 <CODE> interface</CODE></FONT></TD>
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228 <TD><CODE><B><A HREF="../../../../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client">ClusterNativeSpecExecutable<T></A></B></CODE>
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231 </TD>
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233 <TR BGCOLOR="white" CLASS="TableRowColor">
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234 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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235 <CODE> interface</CODE></FONT></TD>
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236 <TD><CODE><B><A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable<T></A></B></CODE>
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239 </TD>
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241 <TR BGCOLOR="white" CLASS="TableRowColor">
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242 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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243 <CODE> interface</CODE></FONT></TD>
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244 <TD><CODE><B><A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable<T></A></B></CODE>
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247 This is a marker interface to indicate that the output of the process must be
254 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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255 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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256 <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/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>
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258 <TR BGCOLOR="white" CLASS="TableRowColor">
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259 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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260 <CODE> class</CODE></FONT></TD>
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261 <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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264 </TD>
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266 <TR BGCOLOR="white" CLASS="TableRowColor">
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267 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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268 <CODE> class</CODE></FONT></TD>
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269 <TD><CODE><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable<T></A></B></CODE>
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272 </TD>
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278 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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279 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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280 <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/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>
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282 <TR BGCOLOR="white" CLASS="TableRowColor">
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283 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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284 <CODE> <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>
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285 <TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List<java.lang.String> parameters)</CODE>
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288 </TD>
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290 <TR BGCOLOR="white" CLASS="TableRowColor">
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291 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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292 <CODE> <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>></CODE></FONT></TD>
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293 <TD><CODE><B>Executable.</B><B><A HREF="../../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List<java.lang.String> parameters)</CODE>
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296 Adds parameter to the list of parameters for a native executable</TD>
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298 <TR BGCOLOR="white" CLASS="TableRowColor">
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299 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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300 <CODE> <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></FONT></TD>
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301 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List<java.lang.String> parameters)</CODE>
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304 </TD>
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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> <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="type parameter in ConfiguredExecutable">T</A>></CODE></FONT></TD>
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309 <TD><CODE><B>ConfiguredExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html#getExecutable()">getExecutable</A></B>()</CODE>
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312 </TD>
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314 <TR BGCOLOR="white" CLASS="TableRowColor">
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315 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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316 <CODE> <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></FONT></TD>
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317 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getExecutable()">getExecutable</A></B>()</CODE>
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320 </TD>
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322 <TR BGCOLOR="white" CLASS="TableRowColor">
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323 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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324 <CODE> <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?></CODE></FONT></TD>
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325 <TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> rconfig)</CODE>
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328 </TD>
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330 <TR BGCOLOR="white" CLASS="TableRowColor">
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331 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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332 <CODE> <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?></CODE></FONT></TD>
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333 <TD><CODE><B>Executable.</B><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> rconfig)</CODE>
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336 </TD>
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338 <TR BGCOLOR="white" CLASS="TableRowColor">
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339 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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340 <CODE> <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>
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341 <TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)">setParameter</A></B>(java.lang.String parameter)</CODE>
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344 </TD>
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350 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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351 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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352 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return types with arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>
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354 <TR BGCOLOR="white" CLASS="TableRowColor">
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355 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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356 <CODE>abstract java.lang.Class<? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>></CODE></FONT></TD>
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357 <TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#getType()">getType</A></B>()</CODE>
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360 </TD>
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366 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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367 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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368 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with parameters of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>
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370 <TR BGCOLOR="white" CLASS="TableRowColor">
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371 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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372 <CODE>static java.lang.String</CODE></FONT></TD>
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373 <TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/engine/client/Util.html#getExecProperty(java.lang.String, compbio.engine.client.Executable)">getExecProperty</A></B>(java.lang.String propertySpec,
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374 <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?> exec)</CODE>
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377 </TD>
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383 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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384 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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385 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with type arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>
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387 <TR BGCOLOR="white" CLASS="TableRowColor">
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388 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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390 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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391 <TR ALIGN="right" VALIGN="">
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392 <TD NOWRAP><FONT SIZE="-1">
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393 <CODE><V> <A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><V></CODE></FONT></TD>
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396 </CODE></FONT></TD>
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397 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getRunnerLimits(java.lang.Class)">getRunnerLimits</A></B>(java.lang.Class<? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><V>> clazz)</CODE>
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400 This method should be executed once and result of its execution reused.</TD>
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402 <TR BGCOLOR="white" CLASS="TableRowColor">
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403 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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405 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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406 <TR ALIGN="right" VALIGN="">
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407 <TD NOWRAP><FONT SIZE="-1">
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408 <CODE><V> <A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><V></CODE></FONT></TD>
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411 </CODE></FONT></TD>
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412 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getRunnerOptions(java.lang.Class)">getRunnerOptions</A></B>(java.lang.Class<? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><V>> clazz)</CODE>
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415 </TD>
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417 <TR BGCOLOR="white" CLASS="TableRowColor">
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418 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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420 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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421 <TR ALIGN="right" VALIGN="">
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422 <TD NOWRAP><FONT SIZE="-1">
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423 <CODE><V> <A HREF="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><V></CODE></FONT></TD>
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426 </CODE></FONT></TD>
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427 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getRunnerPresets(java.lang.Class)">getRunnerPresets</A></B>(java.lang.Class<? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><V>> clazz)</CODE>
\r
430 </TD>
\r
436 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
437 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
438 <TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with parameters of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>
\r
440 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
441 <TD><CODE><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#ConfExecutable(compbio.engine.client.Executable, java.lang.String)">ConfExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>> executable,
\r
442 java.lang.String taskDirectory)</CODE>
\r
445 </TD>
\r
450 <A NAME="compbio.engine.conf"><!-- --></A>
\r
451 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
452 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
453 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
454 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/engine/conf/package-summary.html">compbio.engine.conf</A></FONT></TH>
\r
460 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
461 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
462 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/conf/package-summary.html">compbio.engine.conf</A> that return types with arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>
\r
464 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
465 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
466 <CODE>static java.lang.Class<<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>></CODE></FONT></TD>
\r
467 <TD><CODE><B>DirectoryManager.</B><B><A HREF="../../../../compbio/engine/conf/DirectoryManager.html#getClass(java.lang.String)">getClass</A></B>(java.lang.String taskId)</CODE>
\r
470 </TD>
\r
475 <A NAME="compbio.runner"><!-- --></A>
\r
476 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
477 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
478 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
479 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>
\r
485 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
486 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
487 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> that implement <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>
\r
489 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
490 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
491 <CODE> class</CODE></FONT></TD>
\r
492 <TD><CODE><B><A HREF="../../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></B></CODE>
\r
495 </TD>
\r
501 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
502 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
503 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> that return <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>
\r
505 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
506 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
507 <CODE> <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?></CODE></FONT></TD>
\r
508 <TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> rconfig)</CODE>
\r
511 </TD>
\r
517 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
518 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
519 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> with type arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>
\r
521 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
522 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
523 <CODE>static java.util.List<java.lang.String></CODE></FONT></TD>
\r
524 <TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List, compbio.metadata.RunnerConfig)">argumentsToCommandString</A></B>(java.util.List<? extends <A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> arguments,
\r
525 <A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>> rconfig)</CODE>
\r
528 </TD>
\r
530 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
531 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
533 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
\r
534 <TR ALIGN="right" VALIGN="">
\r
535 <TD NOWRAP><FONT SIZE="-1">
\r
536 <CODE><T> <A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><T></CODE></FONT></TD>
\r
539 </CODE></FONT></TD>
\r
540 <TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#getLimits(java.lang.Class)">getLimits</A></B>(java.lang.Class<? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>> clazz)</CODE>
\r
543 For now just assume that all parameters which came in needs setting it
544 will be a client responsibility to prepare RunnerConfig object then</TD>
\r
546 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
547 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
549 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
\r
550 <TR ALIGN="right" VALIGN="">
\r
551 <TD NOWRAP><FONT SIZE="-1">
\r
552 <CODE><T> <A HREF="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><T></CODE></FONT></TD>
\r
555 </CODE></FONT></TD>
\r
556 <TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#getPresets(java.lang.Class)">getPresets</A></B>(java.lang.Class<? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>> clazz)</CODE>
\r
559 </TD>
\r
561 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
562 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
564 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
\r
565 <TR ALIGN="right" VALIGN="">
\r
566 <TD NOWRAP><FONT SIZE="-1">
\r
567 <CODE><T> <A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><T></CODE></FONT></TD>
\r
570 </CODE></FONT></TD>
\r
571 <TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#getSupportedOptions(java.lang.Class)">getSupportedOptions</A></B>(java.lang.Class<? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>> clazz)</CODE>
\r
574 </TD>
\r
580 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
581 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
582 <TH ALIGN="left" COLSPAN="2">Constructor parameters in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> with type arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>
\r
584 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
585 <TD><CODE><B><A HREF="../../../../compbio/runner/OptionCombinator.html#OptionCombinator(compbio.metadata.RunnerConfig)">OptionCombinator</A></B>(<A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>> rconfig)</CODE>
\r
588 </TD>
\r
593 <A NAME="compbio.runner._impl"><!-- --></A>
\r
594 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
595 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
596 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
597 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>
\r
603 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
604 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
605 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that implement <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>
\r
607 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
608 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
609 <CODE> class</CODE></FONT></TD>
\r
610 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A></B></CODE>
\r
613 </TD>
\r
615 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
616 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
617 <CODE> class</CODE></FONT></TD>
\r
618 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A></B></CODE>
\r
621 </TD>
\r
623 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
624 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
625 <CODE> class</CODE></FONT></TD>
\r
626 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A></B></CODE>
\r
629 </TD>
\r
631 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
632 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
633 <CODE> class</CODE></FONT></TD>
\r
634 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A></B></CODE>
\r
637 </TD>
\r
639 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
640 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
641 <CODE> class</CODE></FONT></TD>
\r
642 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A></B></CODE>
\r
645 TODO this needs fixing! Executable does not work</TD>
\r
647 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
648 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
649 <CODE> class</CODE></FONT></TD>
\r
650 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A></B></CODE>
\r
653 </TD>
\r
655 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
656 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
657 <CODE> class</CODE></FONT></TD>
\r
658 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A></B></CODE>
\r
661 </TD>
\r
663 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
664 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
665 <CODE> class</CODE></FONT></TD>
\r
666 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A></B></CODE>
\r
669 </TD>
\r
675 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
676 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
677 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that return <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>
\r
679 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
680 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
681 <CODE> <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?></CODE></FONT></TD>
\r
682 <TD><CODE><B>NetNglyc.</B><B><A HREF="../../../../compbio/runner/_impl/NetNglyc.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> rconfig)</CODE>
\r
685 </TD>
\r
690 <A NAME="compbio.runner.msa"><!-- --></A>
\r
691 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
692 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
693 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
694 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>
\r
700 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
701 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
702 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that implement <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>
\r
704 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
705 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
706 <CODE> class</CODE></FONT></TD>
\r
707 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></B></CODE>
\r
710 </TD>
\r
712 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
713 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
714 <CODE> class</CODE></FONT></TD>
\r
715 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></B></CODE>
\r
718 </TD>
\r
720 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
721 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
722 <CODE> class</CODE></FONT></TD>
\r
723 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></B></CODE>
\r
726 </TD>
\r
728 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
729 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
730 <CODE> class</CODE></FONT></TD>
\r
731 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></B></CODE>
\r
734 </TD>
\r
736 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
737 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
738 <CODE> class</CODE></FONT></TD>
\r
739 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></B></CODE>
\r
742 </TD>
\r
748 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
749 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
750 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return types with arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>
\r
752 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
753 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
754 <CODE> java.lang.Class<? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>></CODE></FONT></TD>
\r
755 <TD><CODE><B>Tcoffee.</B><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html#getType()">getType</A></B>()</CODE>
\r
758 </TD>
\r
760 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
761 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
762 <CODE> java.lang.Class<? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>></CODE></FONT></TD>
\r
763 <TD><CODE><B>ClustalW.</B><B><A HREF="../../../../compbio/runner/msa/ClustalW.html#getType()">getType</A></B>()</CODE>
\r
766 </TD>
\r
768 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
769 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
770 <CODE> java.lang.Class<? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>></CODE></FONT></TD>
\r
771 <TD><CODE><B>Probcons.</B><B><A HREF="../../../../compbio/runner/msa/Probcons.html#getType()">getType</A></B>()</CODE>
\r
774 </TD>
\r
776 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
777 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
778 <CODE> java.lang.Class<? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>></CODE></FONT></TD>
\r
779 <TD><CODE><B>Muscle.</B><B><A HREF="../../../../compbio/runner/msa/Muscle.html#getType()">getType</A></B>()</CODE>
\r
782 </TD>
\r
784 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
785 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
786 <CODE> java.lang.Class<? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>></CODE></FONT></TD>
\r
787 <TD><CODE><B>Mafft.</B><B><A HREF="../../../../compbio/runner/msa/Mafft.html#getType()">getType</A></B>()</CODE>
\r
790 </TD>
\r
795 <A NAME="compbio.runner.psiblast"><!-- --></A>
\r
796 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
797 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
798 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
799 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A></FONT></TH>
\r
805 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
806 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
807 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A> that implement <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>
\r
809 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
810 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
811 <CODE> class</CODE></FONT></TD>
\r
812 <TD><CODE><B><A HREF="../../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A></B></CODE>
\r
815 </TD>
\r
821 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
822 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
823 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A> that return types with arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>
\r
825 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
826 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
827 <CODE> java.lang.Class<? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>></CODE></FONT></TD>
\r
828 <TD><CODE><B>PsiBlast.</B><B><A HREF="../../../../compbio/runner/psiblast/PsiBlast.html#getType()">getType</A></B>()</CODE>
\r
831 </TD>
\r
839 <!-- ======= START OF BOTTOM NAVBAR ====== -->
\r
840 <A NAME="navbar_bottom"><!-- --></A>
\r
841 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
\r
842 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
\r
844 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
\r
845 <A NAME="navbar_bottom_firstrow"><!-- --></A>
\r
846 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
\r
847 <TR ALIGN="center" VALIGN="top">
\r
848 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
\r
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