website/full_javadoc/compbio/runner/disorder/Disembl.html

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   7 Disembl\r
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  10 <META NAME="date" CONTENT="2011-08-12">\r
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  79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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  91 compbio.runner.disorder</FONT>\r
  92 <BR>\r
  93 Class Disembl</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 "><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">compbio.engine.client.SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;\r
  97       <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.disorder.Disembl</B>\r
  98 </PRE>\r
  99 <DL>\r
 100 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;, <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;</DD>\r
 101 </DL>\r
 102 <HR>\r
 103 <DL>\r
 104 <DT><PRE>public class <B>Disembl</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;<DT>implements <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;</DL>\r
 105 </PRE>\r
 106 \r
 107 <P>\r
 108 DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops
 109  fold_rem465 sequence_file print
 110
 111  'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out'
 112
 113  This version of DisEMBL is 1.4 (latest available for download in Feb 2011)
 114  capable of outputting raw values
 115
 116  The values of the parameters are hard coded in DisEMBL.py script.
 117  smooth_frame=8 peak_frame=8 join_frame=4 fold_coils=1.2 fold_hotloops=1.4
 118  fold_rem465=1.2
 119
 120  Changing these values are not recommended by developers, apart from smoothing
 121  window. However, 5 orders of magnitude changes in this parameter does not
 122  change the output so allowing this change also seems pointless. Finally, the
 123  binary, DisEMBL depends on - Tisean is not happy with arbitruary changes to
 124  these values, so changing them can lead to problems.
 125
 126
 127  This is not a standard DisEMBL! The script has been modified!\r
 128 <P>\r
 129 \r
 130 <P>\r
 131 <HR>\r
 132 \r
 133 <P>\r
 134 <!-- ======== NESTED CLASS SUMMARY ======== -->\r
 135 \r
 136 <A NAME="nested_class_summary"><!-- --></A>\r
 137 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 138 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 139 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 140 <B>Nested Class Summary</B></FONT></TH>\r
 141 </TR>\r
 142 </TABLE>\r
 143 &nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
 144 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 145 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 146 <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>\r
 147 </TR>\r
 148 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 149 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
 150 </TR>\r
 151 </TABLE>\r
 152 &nbsp;\r
 153 <!-- =========== FIELD SUMMARY =========== -->\r
 154 \r
 155 <A NAME="field_summary"><!-- --></A>\r
 156 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 157 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 158 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 159 <B>Field Summary</B></FONT></TH>\r
 160 </TR>\r
 161 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 162 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 163 <CODE>&nbsp;double</CODE></FONT></TD>\r
 164 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/Disembl.html#COILS_EXPECTATION_THRESHOLD">COILS_EXPECTATION_THRESHOLD</A></B></CODE>\r
 165 \r
 166 <BR>\r
 167 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;For the region to be considered disordered the values must exceed these</TD>\r
 168 </TR>\r
 169 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 170 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 171 <CODE>static&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
 172 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/Disembl.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></B></CODE>\r
 173 \r
 174 <BR>\r
 175 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 176 </TR>\r
 177 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 178 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 179 <CODE>&nbsp;double</CODE></FONT></TD>\r
 180 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/Disembl.html#LOOPS_EXPECTATION_THRESHOLD">LOOPS_EXPECTATION_THRESHOLD</A></B></CODE>\r
 181 \r
 182 <BR>\r
 183 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 184 </TR>\r
 185 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 186 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 187 <CODE>&nbsp;double</CODE></FONT></TD>\r
 188 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/Disembl.html#REM_EXPECTATION_THRESHOLD">REM_EXPECTATION_THRESHOLD</A></B></CODE>\r
 189 \r
 190 <BR>\r
 191 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 192 </TR>\r
 193 </TABLE>\r
 194 &nbsp;<A NAME="fields_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
 195 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 196 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 197 <TH ALIGN="left"><B>Fields inherited from class compbio.engine.client.<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A></B></TH>\r
 198 </TR>\r
 199 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 200 <TD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#ERROR">ERROR</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#INPUT">INPUT</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#OUTPUT">OUTPUT</A></CODE></TD>\r
 201 </TR>\r
 202 </TABLE>\r
 203 &nbsp;\r
 204 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 205 \r
 206 <A NAME="constructor_summary"><!-- --></A>\r
 207 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 208 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 209 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 210 <B>Constructor Summary</B></FONT></TH>\r
 211 </TR>\r
 212 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 213 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/Disembl.html#Disembl()">Disembl</A></B>()</CODE>\r
 214 \r
 215 <BR>\r
 216 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 217 </TR>\r
 218 </TABLE>\r
 219 &nbsp;\r
 220 <!-- ========== METHOD SUMMARY =========== -->\r
 221 \r
 222 <A NAME="method_summary"><!-- --></A>\r
 223 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 224 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 225 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 226 <B>Method Summary</B></FONT></TH>\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;<A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>\r
 231 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/Disembl.html#getResults(java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory)</CODE>\r
 232 \r
 233 <BR>\r
 234 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 235 </TR>\r
 236 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 237 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 238 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;</CODE></FONT></TD>\r
 239 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/Disembl.html#getType()">getType</A></B>()</CODE>\r
 240 \r
 241 <BR>\r
 242 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 243 </TR>\r
 244 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 245 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 246 <CODE>&nbsp;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A></CODE></FONT></TD>\r
 247 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/Disembl.html#setInput(java.lang.String)">setInput</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;inFile)</CODE>\r
 248 \r
 249 <BR>\r
 250 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 251 </TR>\r
 252 </TABLE>\r
 253 &nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
 254 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 255 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 256 <TH ALIGN="left"><B>Methods inherited from class compbio.engine.client.<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A></B></TH>\r
 257 </TR>\r
 258 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 259 <TD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)">equals</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterCpuNum(java.lang.Class)">getClusterCpuNum</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterJobSettings()">getClusterJobSettings</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">getCreatedFiles</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#hashCode()">hashCode</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)">setError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)">setOutput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)">setParameter</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#toString()">toString</A></CODE></TD>\r
 260 </TR>\r
 261 </TABLE>\r
 262 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 263 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 264 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 265 <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
 266 </TR>\r
 267 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 268 <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
 269 </TR>\r
 270 </TABLE>\r
 271 &nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
 272 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 273 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 274 <TH ALIGN="left"><B>Methods inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
 275 </TR>\r
 276 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 277 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/engine/client/Executable.html#getClusterJobSettings()">getClusterJobSettings</A>, <A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A>, <A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></CODE></TD>\r
 278 </TR>\r
 279 </TABLE>\r
 280 &nbsp;\r
 281 <P>\r
 282 \r
 283 <!-- ============ FIELD DETAIL =========== -->\r
 284 \r
 285 <A NAME="field_detail"><!-- --></A>\r
 286 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 287 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 288 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 289 <B>Field Detail</B></FONT></TH>\r
 290 </TR>\r
 291 </TABLE>\r
 292 \r
 293 <A NAME="KEY_VALUE_SEPARATOR"><!-- --></A><H3>\r
 294 KEY_VALUE_SEPARATOR</H3>\r
 295 <PRE>\r
 296 public static final <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>KEY_VALUE_SEPARATOR</B></PRE>\r
 297 <DL>\r
 298 <DL>\r
 299 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.disorder.Disembl.KEY_VALUE_SEPARATOR">Constant Field Values</A></DL>\r
 300 </DL>\r
 301 <HR>\r
 302 \r
 303 <A NAME="COILS_EXPECTATION_THRESHOLD"><!-- --></A><H3>\r
 304 COILS_EXPECTATION_THRESHOLD</H3>\r
 305 <PRE>\r
 306 public final double <B>COILS_EXPECTATION_THRESHOLD</B></PRE>\r
 307 <DL>\r
 308 <DD>For the region to be considered disordered the values must exceed these\r
 309 <P>\r
 310 <DL>\r
 311 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.disorder.Disembl.COILS_EXPECTATION_THRESHOLD">Constant Field Values</A></DL>\r
 312 </DL>\r
 313 <HR>\r
 314 \r
 315 <A NAME="REM_EXPECTATION_THRESHOLD"><!-- --></A><H3>\r
 316 REM_EXPECTATION_THRESHOLD</H3>\r
 317 <PRE>\r
 318 public final double <B>REM_EXPECTATION_THRESHOLD</B></PRE>\r
 319 <DL>\r
 320 <DL>\r
 321 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.disorder.Disembl.REM_EXPECTATION_THRESHOLD">Constant Field Values</A></DL>\r
 322 </DL>\r
 323 <HR>\r
 324 \r
 325 <A NAME="LOOPS_EXPECTATION_THRESHOLD"><!-- --></A><H3>\r
 326 LOOPS_EXPECTATION_THRESHOLD</H3>\r
 327 <PRE>\r
 328 public final double <B>LOOPS_EXPECTATION_THRESHOLD</B></PRE>\r
 329 <DL>\r
 330 <DL>\r
 331 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.disorder.Disembl.LOOPS_EXPECTATION_THRESHOLD">Constant Field Values</A></DL>\r
 332 </DL>\r
 333 \r
 334 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 335 \r
 336 <A NAME="constructor_detail"><!-- --></A>\r
 337 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 338 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 339 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 340 <B>Constructor Detail</B></FONT></TH>\r
 341 </TR>\r
 342 </TABLE>\r
 343 \r
 344 <A NAME="Disembl()"><!-- --></A><H3>\r
 345 Disembl</H3>\r
 346 <PRE>\r
 347 public <B>Disembl</B>()</PRE>\r
 348 <DL>\r
 349 </DL>\r
 350 \r
 351 <!-- ============ METHOD DETAIL ========== -->\r
 352 \r
 353 <A NAME="method_detail"><!-- --></A>\r
 354 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 355 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 356 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 357 <B>Method Detail</B></FONT></TH>\r
 358 </TR>\r
 359 </TABLE>\r
 360 \r
 361 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
 362 getResults</H3>\r
 363 <PRE>\r
 364 public <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A> <B>getResults</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;workDirectory)\r
 365                         throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 366 <DL>\r
 367 <DD><DL>\r
 368 <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>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;</CODE></DL>\r
 369 </DD>\r
 370 <DD><DL>\r
 371 \r
 372 <DT><B>Throws:</B>\r
 373 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 374 </DD>\r
 375 </DL>\r
 376 <HR>\r
 377 \r
 378 <A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
 379 setInput</H3>\r
 380 <PRE>\r
 381 public <A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A> <B>setInput</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;inFile)</PRE>\r
 382 <DL>\r
 383 <DD><DL>\r
 384 <DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)">setInput</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;</CODE></DL>\r
 385 </DD>\r
 386 <DD><DL>\r
 387 </DL>\r
 388 </DD>\r
 389 </DL>\r
 390 <HR>\r
 391 \r
 392 <A NAME="getType()"><!-- --></A><H3>\r
 393 getType</H3>\r
 394 <PRE>\r
 395 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt; <B>getType</B>()</PRE>\r
 396 <DL>\r
 397 <DD><DL>\r
 398 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getType()">getType</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;</CODE></DL>\r
 399 </DD>\r
 400 <DD><DL>\r
 401 \r
 402 <DT><B>Returns:</B><DD>subclasses must return their type</DL>\r
 403 </DD>\r
 404 </DL>\r
 405 <!-- ========= END OF CLASS DATA ========= -->\r
 406 <HR>\r
 407 \r
 408 \r
 409 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 410 <A NAME="navbar_bottom"><!-- --></A>\r
 411 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 412 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 413 <TR>\r
 414 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 415 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 416 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 417   <TR ALIGN="center" VALIGN="top">\r
 418   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 419   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 420   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 421   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Disembl.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 422   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 423   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 424   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 425   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 426   </TR>\r
 427 </TABLE>\r
 428 </TD>\r
 429 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 430 </EM>\r
 431 </TD>\r
 432 </TR>\r
 433 \r
 434 <TR>\r
 435 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 436 &nbsp;PREV CLASS&nbsp;\r
 437 &nbsp;<A HREF="../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder"><B>NEXT CLASS</B></A></FONT></TD>\r
 438 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 439   <A HREF="../../../index.html?compbio/runner/disorder/Disembl.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 440 &nbsp;<A HREF="Disembl.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 441 &nbsp;<SCRIPT type="text/javascript">\r
 442   <!--\r
 443   if(window==top) {\r
 444     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 445   }\r
 446   //-->\r
 447 </SCRIPT>\r
 448 <NOSCRIPT>\r
 449   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 450 </NOSCRIPT>\r
 451 \r
 452 \r
 453 </FONT></TD>\r
 454 </TR>\r
 455 <TR>\r
 456 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 457   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
 458 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 459 DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
 460 </TR>\r
 461 </TABLE>\r
 462 <A NAME="skip-navbar_bottom"></A>\r
 463 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
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