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

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   7 CommandBuilder\r
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  89 <H2>\r
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  91 compbio.engine.client</FONT>\r
  92 <BR>\r
  93 Class CommandBuilder&lt;T&gt;</H2>\r
  94 <PRE>\r
  95 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
  96   <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.client.CommandBuilder&lt;T&gt;</B>\r
  97 </PRE>\r
  98 <HR>\r
  99 <DL>\r
 100 <DT><PRE>public class <B>CommandBuilder&lt;T&gt;</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
 101 </PRE>\r
 102 \r
 103 <P>\r
 104 <HR>\r
 105 \r
 106 <P>\r
 107 \r
 108 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 109 \r
 110 <A NAME="constructor_summary"><!-- --></A>\r
 111 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 112 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 113 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 114 <B>Constructor Summary</B></FONT></TH>\r
 115 </TR>\r
 116 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 117 <TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#CommandBuilder(java.lang.String)">CommandBuilder</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;nameValueSeparator)</CODE>\r
 118 \r
 119 <BR>\r
 120 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 121 </TR>\r
 122 </TABLE>\r
 123 &nbsp;\r
 124 <!-- ========== METHOD SUMMARY =========== -->\r
 125 \r
 126 <A NAME="method_summary"><!-- --></A>\r
 127 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 128 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 129 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 130 <B>Method Summary</B></FONT></TH>\r
 131 </TR>\r
 132 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 133 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 134 <CODE>&nbsp;void</CODE></FONT></TD>\r
 135 <TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#addParams(java.util.List)">addParams</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>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt;&nbsp;params)</CODE>\r
 136 \r
 137 <BR>\r
 138 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 139 </TR>\r
 140 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 141 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 142 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 143 <TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A>&nbsp;obj)</CODE>\r
 144 \r
 145 <BR>\r
 146 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 147 </TR>\r
 148 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 149 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 150 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt;</CODE></FONT></TD>\r
 151 <TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#getCommands()">getCommands</A></B>()</CODE>\r
 152 \r
 153 <BR>\r
 154 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 155 </TR>\r
 156 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 157 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 158 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
 159 <TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#getCommandString()">getCommandString</A></B>()</CODE>\r
 160 \r
 161 <BR>\r
 162 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 163 </TR>\r
 164 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 165 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 166 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
 167 <TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#getParamValue(java.lang.String)">getParamValue</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;paramName)</CODE>\r
 168 \r
 169 <BR>\r
 170 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 171 </TR>\r
 172 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 173 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 174 <CODE>&nbsp;int</CODE></FONT></TD>\r
 175 <TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#hashCode()">hashCode</A></B>()</CODE>\r
 176 \r
 177 <BR>\r
 178 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 179 </TR>\r
 180 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 181 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 182 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 183 <TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#hasParam(java.lang.String)">hasParam</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;paramName)</CODE>\r
 184 \r
 185 <BR>\r
 186 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 187 </TR>\r
 188 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 189 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 190 <CODE>static\r
 191 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 192 <TR ALIGN="right" VALIGN="">\r
 193 <TD NOWRAP><FONT SIZE="-1">\r
 194 <CODE>&lt;T&gt; <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;T&gt;</CODE></FONT></TD>\r
 195 </TR>\r
 196 </TABLE>\r
 197 </CODE></FONT></TD>\r
 198 <TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#newCommandBuilder(java.util.List, java.lang.String)">newCommandBuilder</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>&lt;? extends <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;T&gt;&gt;&nbsp;arguments,\r
 199                   <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;nameValueSeparator)</CODE>\r
 200 \r
 201 <BR>\r
 202 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This produces the same result as getCommands method.</TD>\r
 203 </TR>\r
 204 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 205 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 206 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 207 <TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#removeParam(java.lang.String)">removeParam</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;paramName)</CODE>\r
 208 \r
 209 <BR>\r
 210 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 211 </TR>\r
 212 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 213 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 214 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 215 <TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#setFirst(java.lang.String)">setFirst</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;param)</CODE>\r
 216 \r
 217 <BR>\r
 218 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 219 </TR>\r
 220 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 221 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 222 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 223 <TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#setLast(java.lang.String)">setLast</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;paramName)</CODE>\r
 224 \r
 225 <BR>\r
 226 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 227 </TR>\r
 228 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 229 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 230 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 231 <TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#setLast(java.lang.String, java.lang.String)">setLast</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;paramName,\r
 232         <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;paramValue)</CODE>\r
 233 \r
 234 <BR>\r
 235 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 236 </TR>\r
 237 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 238 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 239 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 240 <TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#setParam(java.lang.String)">setParam</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;param)</CODE>\r
 241 \r
 242 <BR>\r
 243 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 244 </TR>\r
 245 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 246 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 247 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 248 <TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#setParam(java.lang.String, java.lang.String)">setParam</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;paramName,\r
 249          <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;paramValue)</CODE>\r
 250 \r
 251 <BR>\r
 252 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 253 </TR>\r
 254 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 255 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 256 <CODE>&nbsp;void</CODE></FONT></TD>\r
 257 <TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#setParams(java.util.List)">setParams</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>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt;&nbsp;params)</CODE>\r
 258 \r
 259 <BR>\r
 260 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 261 </TR>\r
 262 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 263 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 264 <CODE>&nbsp;int</CODE></FONT></TD>\r
 265 <TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#size()">size</A></B>()</CODE>\r
 266 \r
 267 <BR>\r
 268 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 269 </TR>\r
 270 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 271 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 272 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
 273 <TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#toString()">toString</A></B>()</CODE>\r
 274 \r
 275 <BR>\r
 276 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 277 </TR>\r
 278 </TABLE>\r
 279 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 280 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 281 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 282 <TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
 283 </TR>\r
 284 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 285 <TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
 286 </TR>\r
 287 </TABLE>\r
 288 &nbsp;\r
 289 <P>\r
 290 \r
 291 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 292 \r
 293 <A NAME="constructor_detail"><!-- --></A>\r
 294 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 295 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 296 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 297 <B>Constructor Detail</B></FONT></TH>\r
 298 </TR>\r
 299 </TABLE>\r
 300 \r
 301 <A NAME="CommandBuilder(java.lang.String)"><!-- --></A><H3>\r
 302 CommandBuilder</H3>\r
 303 <PRE>\r
 304 public <B>CommandBuilder</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;nameValueSeparator)</PRE>\r
 305 <DL>\r
 306 </DL>\r
 307 \r
 308 <!-- ============ METHOD DETAIL ========== -->\r
 309 \r
 310 <A NAME="method_detail"><!-- --></A>\r
 311 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 312 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 313 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 314 <B>Method Detail</B></FONT></TH>\r
 315 </TR>\r
 316 </TABLE>\r
 317 \r
 318 <A NAME="addParams(java.util.List)"><!-- --></A><H3>\r
 319 addParams</H3>\r
 320 <PRE>\r
 321 public void <B>addParams</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>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt;&nbsp;params)</PRE>\r
 322 <DL>\r
 323 <DD><DL>\r
 324 </DL>\r
 325 </DD>\r
 326 </DL>\r
 327 <HR>\r
 328 \r
 329 <A NAME="setParams(java.util.List)"><!-- --></A><H3>\r
 330 setParams</H3>\r
 331 <PRE>\r
 332 public void <B>setParams</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>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt;&nbsp;params)</PRE>\r
 333 <DL>\r
 334 <DD><DL>\r
 335 </DL>\r
 336 </DD>\r
 337 </DL>\r
 338 <HR>\r
 339 \r
 340 <A NAME="hasParam(java.lang.String)"><!-- --></A><H3>\r
 341 hasParam</H3>\r
 342 <PRE>\r
 343 public boolean <B>hasParam</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;paramName)</PRE>\r
 344 <DL>\r
 345 <DD><DL>\r
 346 </DL>\r
 347 </DD>\r
 348 </DL>\r
 349 <HR>\r
 350 \r
 351 <A NAME="setFirst(java.lang.String)"><!-- --></A><H3>\r
 352 setFirst</H3>\r
 353 <PRE>\r
 354 public boolean <B>setFirst</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;param)</PRE>\r
 355 <DL>\r
 356 <DD><DL>\r
 357 </DL>\r
 358 </DD>\r
 359 </DL>\r
 360 <HR>\r
 361 \r
 362 <A NAME="setParam(java.lang.String)"><!-- --></A><H3>\r
 363 setParam</H3>\r
 364 <PRE>\r
 365 public boolean <B>setParam</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;param)</PRE>\r
 366 <DL>\r
 367 <DD><DL>\r
 368 </DL>\r
 369 </DD>\r
 370 </DL>\r
 371 <HR>\r
 372 \r
 373 <A NAME="setLast(java.lang.String)"><!-- --></A><H3>\r
 374 setLast</H3>\r
 375 <PRE>\r
 376 public boolean <B>setLast</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;paramName)</PRE>\r
 377 <DL>\r
 378 <DD><DL>\r
 379 </DL>\r
 380 </DD>\r
 381 </DL>\r
 382 <HR>\r
 383 \r
 384 <A NAME="setLast(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
 385 setLast</H3>\r
 386 <PRE>\r
 387 public boolean <B>setLast</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;paramName,\r
 388                        <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;paramValue)</PRE>\r
 389 <DL>\r
 390 <DD><DL>\r
 391 </DL>\r
 392 </DD>\r
 393 </DL>\r
 394 <HR>\r
 395 \r
 396 <A NAME="getParamValue(java.lang.String)"><!-- --></A><H3>\r
 397 getParamValue</H3>\r
 398 <PRE>\r
 399 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getParamValue</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;paramName)</PRE>\r
 400 <DL>\r
 401 <DD><DL>\r
 402 </DL>\r
 403 </DD>\r
 404 </DL>\r
 405 <HR>\r
 406 \r
 407 <A NAME="removeParam(java.lang.String)"><!-- --></A><H3>\r
 408 removeParam</H3>\r
 409 <PRE>\r
 410 public boolean <B>removeParam</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;paramName)</PRE>\r
 411 <DL>\r
 412 <DD><DL>\r
 413 </DL>\r
 414 </DD>\r
 415 </DL>\r
 416 <HR>\r
 417 \r
 418 <A NAME="setParam(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
 419 setParam</H3>\r
 420 <PRE>\r
 421 public boolean <B>setParam</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;paramName,\r
 422                         <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;paramValue)</PRE>\r
 423 <DL>\r
 424 <DD><DL>\r
 425 </DL>\r
 426 </DD>\r
 427 </DL>\r
 428 <HR>\r
 429 \r
 430 <A NAME="getCommands()"><!-- --></A><H3>\r
 431 getCommands</H3>\r
 432 <PRE>\r
 433 public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt; <B>getCommands</B>()</PRE>\r
 434 <DL>\r
 435 <DD><DL>\r
 436 </DL>\r
 437 </DD>\r
 438 </DL>\r
 439 <HR>\r
 440 \r
 441 <A NAME="getCommandString()"><!-- --></A><H3>\r
 442 getCommandString</H3>\r
 443 <PRE>\r
 444 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getCommandString</B>()</PRE>\r
 445 <DL>\r
 446 <DD><DL>\r
 447 </DL>\r
 448 </DD>\r
 449 </DL>\r
 450 <HR>\r
 451 \r
 452 <A NAME="newCommandBuilder(java.util.List, java.lang.String)"><!-- --></A><H3>\r
 453 newCommandBuilder</H3>\r
 454 <PRE>\r
 455 public static &lt;T&gt; <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;T&gt; <B>newCommandBuilder</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>&lt;? extends <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;T&gt;&gt;&nbsp;arguments,\r
 456                                                       <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;nameValueSeparator)</PRE>\r
 457 <DL>\r
 458 <DD>This produces the same result as getCommands method. The only difference
 459  is that it accepts a List of Options as an input\r
 460 <P>\r
 461 <DD><DL>\r
 462 <DT><B>Parameters:</B><DD><CODE>arguments</CODE> - \r
 463 <DT><B>Returns:</B><DD>the instance of the CommandBuilder</DL>\r
 464 </DD>\r
 465 </DL>\r
 466 <HR>\r
 467 \r
 468 <A NAME="size()"><!-- --></A><H3>\r
 469 size</H3>\r
 470 <PRE>\r
 471 public int <B>size</B>()</PRE>\r
 472 <DL>\r
 473 <DD><DL>\r
 474 </DL>\r
 475 </DD>\r
 476 </DL>\r
 477 <HR>\r
 478 \r
 479 <A NAME="hashCode()"><!-- --></A><H3>\r
 480 hashCode</H3>\r
 481 <PRE>\r
 482 public int <B>hashCode</B>()</PRE>\r
 483 <DL>\r
 484 <DD><DL>\r
 485 <DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
 486 </DD>\r
 487 <DD><DL>\r
 488 </DL>\r
 489 </DD>\r
 490 </DL>\r
 491 <HR>\r
 492 \r
 493 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
 494 equals</H3>\r
 495 <PRE>\r
 496 public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A>&nbsp;obj)</PRE>\r
 497 <DL>\r
 498 <DD><DL>\r
 499 <DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
 500 </DD>\r
 501 <DD><DL>\r
 502 </DL>\r
 503 </DD>\r
 504 </DL>\r
 505 <HR>\r
 506 \r
 507 <A NAME="toString()"><!-- --></A><H3>\r
 508 toString</H3>\r
 509 <PRE>\r
 510 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>\r
 511 <DL>\r
 512 <DD><DL>\r
 513 <DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
 514 </DD>\r
 515 <DD><DL>\r
 516 </DL>\r
 517 </DD>\r
 518 </DL>\r
 519 <!-- ========= END OF CLASS DATA ========= -->\r
 520 <HR>\r
 521 \r
 522 \r
 523 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 524 <A NAME="navbar_bottom"><!-- --></A>\r
 525 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 526 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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 529 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 530 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 531   <TR ALIGN="center" VALIGN="top">\r
 532   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 533   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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 557   if(window==top) {\r
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 559   }\r
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