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

   1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
   2 <!--NewPage-->\r
   3 <HTML>\r
   4 <HEAD>\r
   5 <!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:35 BST 2011 -->\r
   6 <TITLE>\r
   7 IUPred\r
   8 </TITLE>\r
   9 \r
  10 <META NAME="date" CONTENT="2011-08-12">\r
  11 \r
  12 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
  13 \r
  14 <SCRIPT type="text/javascript">\r
  15 function windowTitle()\r
  16 {\r
  17     if (location.href.indexOf('is-external=true') == -1) {\r
  18         parent.document.title="IUPred";\r
  19     }\r
  20 }\r
  21 </SCRIPT>\r
  22 <NOSCRIPT>\r
  23 </NOSCRIPT>\r
  24 \r
  25 </HEAD>\r
  26 \r
  27 <BODY BGCOLOR="white" onload="windowTitle();">\r
  28 <HR>\r
  29 \r
  30 \r
  31 <!-- ========= START OF TOP NAVBAR ======= -->\r
  32 <A NAME="navbar_top"><!-- --></A>\r
  33 <A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
  34 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
  35 <TR>\r
  36 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
  37 <A NAME="navbar_top_firstrow"><!-- --></A>\r
  38 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
  39   <TR ALIGN="center" VALIGN="top">\r
  40   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
  41   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
  42   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
  43   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/IUPred.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
  44   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
  45   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
  46   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
  47   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
  48   </TR>\r
  49 </TABLE>\r
  50 </TD>\r
  51 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
  52 </EM>\r
  53 </TD>\r
  54 </TR>\r
  55 \r
  56 <TR>\r
  57 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
  58 &nbsp;<A HREF="../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder"><B>PREV CLASS</B></A>&nbsp;\r
  59 &nbsp;<A HREF="../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder"><B>NEXT CLASS</B></A></FONT></TD>\r
  60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
  61   <A HREF="../../../index.html?compbio/runner/disorder/IUPred.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
  62 &nbsp;<A HREF="IUPred.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
  63 &nbsp;<SCRIPT type="text/javascript">\r
  64   <!--\r
  65   if(window==top) {\r
  66     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
  67   }\r
  68   //-->\r
  69 </SCRIPT>\r
  70 <NOSCRIPT>\r
  71   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
  72 </NOSCRIPT>\r
  73 \r
  74 \r
  75 </FONT></TD>\r
  76 </TR>\r
  77 <TR>\r
  78 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
  79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#fields_inherited_from_class_compbio.engine.client.SkeletalExecutable">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
  80 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
  81 DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
  82 </TR>\r
  83 </TABLE>\r
  84 <A NAME="skip-navbar_top"></A>\r
  85 <!-- ========= END OF TOP NAVBAR ========= -->\r
  86 \r
  87 <HR>\r
  88 <!-- ======== START OF CLASS DATA ======== -->\r
  89 <H2>\r
  90 <FONT SIZE="-1">\r
  91 compbio.runner.disorder</FONT>\r
  92 <BR>\r
  93 Class IUPred</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/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>&gt;\r
  97       <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.disorder.IUPred</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/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>&gt;</DD>\r
 101 </DL>\r
 102 <HR>\r
 103 <DL>\r
 104 <DT><PRE>public class <B>IUPred</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>&gt;</DL>\r
 105 </PRE>\r
 106 \r
 107 <P>\r
 108 iupred sequenceFile <short long glob >
 109
 110  Maximum sequence length is 40000 chars. Single string length max is a 1000
 111  chars!\r
 112 <P>\r
 113 \r
 114 <P>\r
 115 <HR>\r
 116 \r
 117 <P>\r
 118 <!-- ======== NESTED CLASS SUMMARY ======== -->\r
 119 \r
 120 <A NAME="nested_class_summary"><!-- --></A>\r
 121 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 122 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 123 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 124 <B>Nested Class Summary</B></FONT></TH>\r
 125 </TR>\r
 126 </TABLE>\r
 127 &nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
 128 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 129 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 130 <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
 131 </TR>\r
 132 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 133 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
 134 </TR>\r
 135 </TABLE>\r
 136 &nbsp;\r
 137 <!-- =========== FIELD SUMMARY =========== -->\r
 138 \r
 139 <A NAME="field_summary"><!-- --></A>\r
 140 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 141 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 142 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 143 <B>Field Summary</B></FONT></TH>\r
 144 </TR>\r
 145 </TABLE>\r
 146 &nbsp;<A NAME="fields_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
 147 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 148 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 149 <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
 150 </TR>\r
 151 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 152 <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
 153 </TR>\r
 154 </TABLE>\r
 155 &nbsp;\r
 156 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 157 \r
 158 <A NAME="constructor_summary"><!-- --></A>\r
 159 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 160 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 161 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 162 <B>Constructor Summary</B></FONT></TH>\r
 163 </TR>\r
 164 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 165 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/IUPred.html#IUPred()">IUPred</A></B>()</CODE>\r
 166 \r
 167 <BR>\r
 168 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 169 </TR>\r
 170 </TABLE>\r
 171 &nbsp;\r
 172 <!-- ========== METHOD SUMMARY =========== -->\r
 173 \r
 174 <A NAME="method_summary"><!-- --></A>\r
 175 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 176 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 177 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 178 <B>Method Summary</B></FONT></TH>\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;<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
 183 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/IUPred.html#getOutput()">getOutput</A></B>()</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>&nbsp;<A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>\r
 191 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/IUPred.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
 192 \r
 193 <BR>\r
 194 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 195 </TR>\r
 196 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 197 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 198 <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/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>&gt;</CODE></FONT></TD>\r
 199 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/IUPred.html#getType()">getType</A></B>()</CODE>\r
 200 \r
 201 <BR>\r
 202 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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;<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A></CODE></FONT></TD>\r
 207 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/IUPred.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
 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;<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A></CODE></FONT></TD>\r
 215 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/IUPred.html#setOutput(java.lang.String)">setOutput</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;outFile)</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 </TABLE>\r
 221 &nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
 222 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 223 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 224 <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
 225 </TR>\r
 226 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 227 <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#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#setParameter(java.lang.String)">setParameter</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#toString()">toString</A></CODE></TD>\r
 228 </TR>\r
 229 </TABLE>\r
 230 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 231 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 232 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 233 <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
 234 </TR>\r
 235 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 236 <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
 237 </TR>\r
 238 </TABLE>\r
 239 &nbsp;\r
 240 <P>\r
 241 \r
 242 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 243 \r
 244 <A NAME="constructor_detail"><!-- --></A>\r
 245 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 246 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 247 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 248 <B>Constructor Detail</B></FONT></TH>\r
 249 </TR>\r
 250 </TABLE>\r
 251 \r
 252 <A NAME="IUPred()"><!-- --></A><H3>\r
 253 IUPred</H3>\r
 254 <PRE>\r
 255 public <B>IUPred</B>()</PRE>\r
 256 <DL>\r
 257 </DL>\r
 258 \r
 259 <!-- ============ METHOD DETAIL ========== -->\r
 260 \r
 261 <A NAME="method_detail"><!-- --></A>\r
 262 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 263 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 264 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 265 <B>Method Detail</B></FONT></TH>\r
 266 </TR>\r
 267 </TABLE>\r
 268 \r
 269 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
 270 getResults</H3>\r
 271 <PRE>\r
 272 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
 273                         throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 274 <DL>\r
 275 <DD><DL>\r
 276 \r
 277 <DT><B>Throws:</B>\r
 278 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 279 </DD>\r
 280 </DL>\r
 281 <HR>\r
 282 \r
 283 <A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
 284 setInput</H3>\r
 285 <PRE>\r
 286 public <A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</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
 287 <DL>\r
 288 <DD><DL>\r
 289 <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/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>&gt;</CODE></DL>\r
 290 </DD>\r
 291 <DD><DL>\r
 292 </DL>\r
 293 </DD>\r
 294 </DL>\r
 295 <HR>\r
 296 \r
 297 <A NAME="setOutput(java.lang.String)"><!-- --></A><H3>\r
 298 setOutput</H3>\r
 299 <PRE>\r
 300 public <A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A> <B>setOutput</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;outFile)</PRE>\r
 301 <DL>\r
 302 <DD><DL>\r
 303 <DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)">setOutput</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/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>&gt;</CODE></DL>\r
 304 </DD>\r
 305 <DD><DL>\r
 306 </DL>\r
 307 </DD>\r
 308 </DL>\r
 309 <HR>\r
 310 \r
 311 <A NAME="getOutput()"><!-- --></A><H3>\r
 312 getOutput</H3>\r
 313 <PRE>\r
 314 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>getOutput</B>()</PRE>\r
 315 <DL>\r
 316 <DD><DL>\r
 317 <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>&lt;<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>&gt;</CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getOutput()">getOutput</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/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>&gt;</CODE></DL>\r
 318 </DD>\r
 319 <DD><DL>\r
 320 </DL>\r
 321 </DD>\r
 322 </DL>\r
 323 <HR>\r
 324 \r
 325 <A NAME="getType()"><!-- --></A><H3>\r
 326 getType</H3>\r
 327 <PRE>\r
 328 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/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>&gt; <B>getType</B>()</PRE>\r
 329 <DL>\r
 330 <DD><DL>\r
 331 <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/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>&gt;</CODE></DL>\r
 332 </DD>\r
 333 <DD><DL>\r
 334 \r
 335 <DT><B>Returns:</B><DD>subclasses must return their type</DL>\r
 336 </DD>\r
 337 </DL>\r
 338 <!-- ========= END OF CLASS DATA ========= -->\r
 339 <HR>\r
 340 \r
 341 \r
 342 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 343 <A NAME="navbar_bottom"><!-- --></A>\r
 344 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 345 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 346 <TR>\r
 347 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 348 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 349 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 350   <TR ALIGN="center" VALIGN="top">\r
 351   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 352   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 353   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 354   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/IUPred.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 355   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 356   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 357   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 358   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 359   </TR>\r
 360 </TABLE>\r
 361 </TD>\r
 362 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 363 </EM>\r
 364 </TD>\r
 365 </TR>\r
 366 \r
 367 <TR>\r
 368 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 369 &nbsp;<A HREF="../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder"><B>PREV CLASS</B></A>&nbsp;\r
 370 &nbsp;<A HREF="../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder"><B>NEXT CLASS</B></A></FONT></TD>\r
 371 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 372   <A HREF="../../../index.html?compbio/runner/disorder/IUPred.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 373 &nbsp;<A HREF="IUPred.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 374 &nbsp;<SCRIPT type="text/javascript">\r
 375   <!--\r
 376   if(window==top) {\r
 377     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 378   }\r
 379   //-->\r
 380 </SCRIPT>\r
 381 <NOSCRIPT>\r
 382   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 383 </NOSCRIPT>\r
 384 \r
 385 \r
 386 </FONT></TD>\r
 387 </TR>\r
 388 <TR>\r
 389 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 390   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#fields_inherited_from_class_compbio.engine.client.SkeletalExecutable">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
 391 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 392 DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
 393 </TR>\r
 394 </TABLE>\r
 395 <A NAME="skip-navbar_bottom"></A>\r
 396 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 397 \r
 398 <HR>\r
 399 \r
 400 </BODY>\r
 401 </HTML>\r