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10 <META NAME="date" CONTENT="2010-02-17">
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17 if (location.href.indexOf('is-external=true') == -1) {
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18 parent.document.title="NetNglyc";
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40 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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42 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
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63 <SCRIPT type="text/javascript">
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66 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
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71 <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
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78 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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79 SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
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81 DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
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84 <A NAME="skip-navbar_top"></A>
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85 <!-- ========= END OF TOP NAVBAR ========= -->
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88 <!-- ======== START OF CLASS DATA ======== -->
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91 compbio.runner._impl</FONT>
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96 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._impl.NetNglyc</B>
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99 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>></DD>
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103 <DT><PRE>public class <B>NetNglyc</B><DT>extends java.lang.Object<DT>implements <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>></DL>
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110 <!-- ======== NESTED CLASS SUMMARY ======== -->
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113 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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115 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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116 <B>Nested Class Summary</B></FONT></TH>
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119 <A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>
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120 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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121 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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122 <TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>
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124 <TR BGCOLOR="white" CLASS="TableRowColor">
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125 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>
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130 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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132 <A NAME="constructor_summary"><!-- --></A>
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133 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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134 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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135 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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136 <B>Constructor Summary</B></FONT></TH>
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138 <TR BGCOLOR="white" CLASS="TableRowColor">
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139 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#NetNglyc()">NetNglyc</A></B>()</CODE>
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142 </TD>
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146 <!-- ========== METHOD SUMMARY =========== -->
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148 <A NAME="method_summary"><!-- --></A>
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149 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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150 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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151 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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152 <B>Method Summary</B></FONT></TH>
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154 <TR BGCOLOR="white" CLASS="TableRowColor">
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155 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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156 <CODE> <A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A></CODE></FONT></TD>
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157 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List<java.lang.String> parameters)</CODE>
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160 Adds parameter to the list of parameters for a native executable</TD>
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162 <TR BGCOLOR="white" CLASS="TableRowColor">
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163 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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164 <CODE> java.lang.String</CODE></FONT></TD>
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165 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getCommandName()">getCommandName</A></B>()</CODE>
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168 </TD>
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170 <TR BGCOLOR="white" CLASS="TableRowColor">
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171 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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172 <CODE> java.util.List<java.lang.String></CODE></FONT></TD>
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173 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>
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176 </TD>
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178 <TR BGCOLOR="white" CLASS="TableRowColor">
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179 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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180 <CODE> java.lang.String</CODE></FONT></TD>
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181 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getError()">getError</A></B>()</CODE>
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184 </TD>
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186 <TR BGCOLOR="white" CLASS="TableRowColor">
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187 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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188 <CODE> java.lang.String</CODE></FONT></TD>
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189 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getInput()">getInput</A></B>()</CODE>
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192 </TD>
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194 <TR BGCOLOR="white" CLASS="TableRowColor">
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195 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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196 <CODE> <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>></CODE></FONT></TD>
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197 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String presetName)</CODE>
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200 </TD>
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202 <TR BGCOLOR="white" CLASS="TableRowColor">
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203 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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204 <CODE> <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>></CODE></FONT></TD>
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205 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getLimits()">getLimits</A></B>()</CODE>
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208 </TD>
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210 <TR BGCOLOR="white" CLASS="TableRowColor">
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211 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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212 <CODE> java.lang.String</CODE></FONT></TD>
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213 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getOutput()">getOutput</A></B>()</CODE>
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216 </TD>
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218 <TR BGCOLOR="white" CLASS="TableRowColor">
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219 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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220 <CODE> <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>></CODE></FONT></TD>
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221 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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224 </TD>
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226 <TR BGCOLOR="white" CLASS="TableRowColor">
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227 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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229 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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230 <TR ALIGN="right" VALIGN="">
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231 <TD NOWRAP><FONT SIZE="-1">
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232 <CODE><V> V</CODE></FONT></TD>
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235 </CODE></FONT></TD>
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236 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String directory)</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>static java.util.List<java.lang.String></CODE></FONT></TD>
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244 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getTestArgs()">getTestArgs</A></B>()</CODE>
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247 </TD>
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249 <TR BGCOLOR="white" CLASS="TableRowColor">
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250 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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251 <CODE>static java.lang.String</CODE></FONT></TD>
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252 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getTestCommand()">getTestCommand</A></B>()</CODE>
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255 </TD>
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257 <TR BGCOLOR="white" CLASS="TableRowColor">
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258 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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259 <CODE> <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?></CODE></FONT></TD>
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260 <TD><CODE><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>
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263 </TD>
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266 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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267 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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268 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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269 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>
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271 <TR BGCOLOR="white" CLASS="TableRowColor">
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272 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
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278 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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280 <A NAME="constructor_detail"><!-- --></A>
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281 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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282 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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283 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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284 <B>Constructor Detail</B></FONT></TH>
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288 <A NAME="NetNglyc()"><!-- --></A><H3>
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291 public <B>NetNglyc</B>()</PRE>
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295 <!-- ============ METHOD DETAIL ========== -->
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297 <A NAME="method_detail"><!-- --></A>
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298 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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299 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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300 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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301 <B>Method Detail</B></FONT></TH>
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305 <A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>
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308 public <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>> <B>getParameters</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</PRE>
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311 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>></CODE></DL>
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319 <A NAME="getTestArgs()"><!-- --></A><H3>
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322 public static java.util.List<java.lang.String> <B>getTestArgs</B>()</PRE>
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333 <A NAME="addParameters(java.util.List)"><!-- --></A><H3>
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336 public <A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A> <B>addParameters</B>(java.util.List<java.lang.String> parameters)</PRE>
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338 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">Executable</A></CODE></B></DD>
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339 <DD>Adds parameter to the list of parameters for a native executable
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342 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>></CODE></DL>
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346 <DT><B>Returns:</B><DD>this Executable</DL>
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351 <A NAME="getTestCommand()"><!-- --></A><H3>
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352 getTestCommand</H3>
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354 public static java.lang.String <B>getTestCommand</B>()</PRE>
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365 <A NAME="getCommandName()"><!-- --></A><H3>
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366 getCommandName</H3>
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368 public java.lang.String <B>getCommandName</B>()</PRE>
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379 <A NAME="getCreatedFiles()"><!-- --></A><H3>
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380 getCreatedFiles</H3>
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382 public java.util.List<java.lang.String> <B>getCreatedFiles</B>()</PRE>
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385 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>></CODE></DL>
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393 <A NAME="getInput()"><!-- --></A><H3>
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396 public java.lang.String <B>getInput</B>()</PRE>
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399 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>></CODE></DL>
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407 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>
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410 public <V> V <B>getResults</B>(java.lang.String directory)</PRE>
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413 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>></CODE></DL>
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421 <A NAME="loadRunConfiguration(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>
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422 loadRunConfiguration</H3>
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424 public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?> <B>loadRunConfiguration</B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> rconfig)</PRE>
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427 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>></CODE></DL>
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435 <A NAME="getOutput()"><!-- --></A><H3>
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438 public java.lang.String <B>getOutput</B>()</PRE>
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441 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>></CODE></DL>
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449 <A NAME="getError()"><!-- --></A><H3>
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452 public java.lang.String <B>getError</B>()</PRE>
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455 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>></CODE></DL>
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463 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>
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466 public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>> <B>getLimit</B>(java.lang.String presetName)</PRE>
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469 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>></CODE></DL>
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477 <A NAME="getLimits()"><!-- --></A><H3>
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480 public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>> <B>getLimits</B>()</PRE>
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483 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>></CODE></DL>
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489 <!-- ========= END OF CLASS DATA ========= -->
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493 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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494 <A NAME="navbar_bottom"><!-- --></A>
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495 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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496 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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498 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
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499 <A NAME="navbar_bottom_firstrow"><!-- --></A>
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500 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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501 <TR ALIGN="center" VALIGN="top">
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502 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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503 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
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504 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
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505 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/NetNglyc.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
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506 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
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507 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
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508 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
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509 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
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513 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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519 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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520 <A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>
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