website/full_javadoc/compbio/runner/disorder/GlobPlot.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 GlobPlot\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="GlobPlot";\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/GlobPlot.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/Disembl.html" title="class in compbio.runner.disorder"><B>PREV CLASS</B></A>&nbsp;\r
  59 &nbsp;<A HREF="../../../compbio/runner/disorder/IUPred.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/GlobPlot.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
  62 &nbsp;<A HREF="GlobPlot.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="#field_summary">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;<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
  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 GlobPlot</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/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>&gt;\r
  97       <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.disorder.GlobPlot</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/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>&gt;, <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;<A HREF="../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>&gt;</DD>\r
 101 </DL>\r
 102 <HR>\r
 103 <DL>\r
 104 <DT><PRE>public class <B>GlobPlot</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</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/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>&gt;</DL>\r
 105 </PRE>\r
 106 \r
 107 <P>\r
 108 ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame
 109
 110  FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file'
 111  Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file'
 112
 113  Hard-coded values are 10 15 74 4 5.
 114
 115  Changing these values are not recommended by developers, apart from smoothing
 116  window. However, the binary, GlobPlot depends on - Tisean which is not happy
 117  with arbitrary changes to these values, so changing them can lead to
 118  problems. May be we can offer preset?
 119
 120  This is not a standard GlobPlot! The script has been modified!\r
 121 <P>\r
 122 \r
 123 <P>\r
 124 <HR>\r
 125 \r
 126 <P>\r
 127 <!-- ======== NESTED CLASS SUMMARY ======== -->\r
 128 \r
 129 <A NAME="nested_class_summary"><!-- --></A>\r
 130 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 131 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 132 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 133 <B>Nested Class Summary</B></FONT></TH>\r
 134 </TR>\r
 135 </TABLE>\r
 136 &nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
 137 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 138 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 139 <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
 140 </TR>\r
 141 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 142 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
 143 </TR>\r
 144 </TABLE>\r
 145 &nbsp;\r
 146 <!-- =========== FIELD SUMMARY =========== -->\r
 147 \r
 148 <A NAME="field_summary"><!-- --></A>\r
 149 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 150 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 151 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 152 <B>Field Summary</B></FONT></TH>\r
 153 </TR>\r
 154 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 155 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 156 <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
 157 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/GlobPlot.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></B></CODE>\r
 158 \r
 159 <BR>\r
 160 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 161 </TR>\r
 162 </TABLE>\r
 163 &nbsp;<A NAME="fields_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
 164 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 165 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 166 <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
 167 </TR>\r
 168 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 169 <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
 170 </TR>\r
 171 </TABLE>\r
 172 &nbsp;\r
 173 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 174 \r
 175 <A NAME="constructor_summary"><!-- --></A>\r
 176 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 177 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 178 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 179 <B>Constructor Summary</B></FONT></TH>\r
 180 </TR>\r
 181 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 182 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/GlobPlot.html#GlobPlot()">GlobPlot</A></B>()</CODE>\r
 183 \r
 184 <BR>\r
 185 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 186 </TR>\r
 187 </TABLE>\r
 188 &nbsp;\r
 189 <!-- ========== METHOD SUMMARY =========== -->\r
 190 \r
 191 <A NAME="method_summary"><!-- --></A>\r
 192 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 193 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 194 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 195 <B>Method Summary</B></FONT></TH>\r
 196 </TR>\r
 197 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 198 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 199 <CODE>&nbsp;<A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>\r
 200 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/GlobPlot.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
 201 \r
 202 <BR>\r
 203 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 204 </TR>\r
 205 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 206 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 207 <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/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>&gt;</CODE></FONT></TD>\r
 208 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/GlobPlot.html#getType()">getType</A></B>()</CODE>\r
 209 \r
 210 <BR>\r
 211 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 212 </TR>\r
 213 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 214 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 215 <CODE>&nbsp;<A HREF="../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A></CODE></FONT></TD>\r
 216 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/GlobPlot.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
 217 \r
 218 <BR>\r
 219 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 220 </TR>\r
 221 </TABLE>\r
 222 &nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
 223 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 224 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 225 <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
 226 </TR>\r
 227 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 228 <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
 229 </TR>\r
 230 </TABLE>\r
 231 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 232 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 233 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 234 <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
 235 </TR>\r
 236 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 237 <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
 238 </TR>\r
 239 </TABLE>\r
 240 &nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
 241 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 242 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 243 <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
 244 </TR>\r
 245 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 246 <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
 247 </TR>\r
 248 </TABLE>\r
 249 &nbsp;\r
 250 <P>\r
 251 \r
 252 <!-- ============ FIELD DETAIL =========== -->\r
 253 \r
 254 <A NAME="field_detail"><!-- --></A>\r
 255 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 256 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 257 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 258 <B>Field Detail</B></FONT></TH>\r
 259 </TR>\r
 260 </TABLE>\r
 261 \r
 262 <A NAME="KEY_VALUE_SEPARATOR"><!-- --></A><H3>\r
 263 KEY_VALUE_SEPARATOR</H3>\r
 264 <PRE>\r
 265 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
 266 <DL>\r
 267 <DL>\r
 268 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.disorder.GlobPlot.KEY_VALUE_SEPARATOR">Constant Field Values</A></DL>\r
 269 </DL>\r
 270 \r
 271 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 272 \r
 273 <A NAME="constructor_detail"><!-- --></A>\r
 274 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 275 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 276 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 277 <B>Constructor Detail</B></FONT></TH>\r
 278 </TR>\r
 279 </TABLE>\r
 280 \r
 281 <A NAME="GlobPlot()"><!-- --></A><H3>\r
 282 GlobPlot</H3>\r
 283 <PRE>\r
 284 public <B>GlobPlot</B>()</PRE>\r
 285 <DL>\r
 286 </DL>\r
 287 \r
 288 <!-- ============ METHOD DETAIL ========== -->\r
 289 \r
 290 <A NAME="method_detail"><!-- --></A>\r
 291 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 292 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 293 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 294 <B>Method Detail</B></FONT></TH>\r
 295 </TR>\r
 296 </TABLE>\r
 297 \r
 298 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
 299 getResults</H3>\r
 300 <PRE>\r
 301 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
 302                         throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 303 <DL>\r
 304 <DD><DL>\r
 305 <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/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>&gt;</CODE></DL>\r
 306 </DD>\r
 307 <DD><DL>\r
 308 \r
 309 <DT><B>Throws:</B>\r
 310 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 311 </DD>\r
 312 </DL>\r
 313 <HR>\r
 314 \r
 315 <A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
 316 setInput</H3>\r
 317 <PRE>\r
 318 public <A HREF="../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</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
 319 <DL>\r
 320 <DD><DL>\r
 321 <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/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>&gt;</CODE></DL>\r
 322 </DD>\r
 323 <DD><DL>\r
 324 </DL>\r
 325 </DD>\r
 326 </DL>\r
 327 <HR>\r
 328 \r
 329 <A NAME="getType()"><!-- --></A><H3>\r
 330 getType</H3>\r
 331 <PRE>\r
 332 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/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>&gt; <B>getType</B>()</PRE>\r
 333 <DL>\r
 334 <DD><DL>\r
 335 <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/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>&gt;</CODE></DL>\r
 336 </DD>\r
 337 <DD><DL>\r
 338 \r
 339 <DT><B>Returns:</B><DD>subclasses must return their type</DL>\r
 340 </DD>\r
 341 </DL>\r
 342 <!-- ========= END OF CLASS DATA ========= -->\r
 343 <HR>\r
 344 \r
 345 \r
 346 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 347 <A NAME="navbar_bottom"><!-- --></A>\r
 348 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 349 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 350 <TR>\r
 351 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 352 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 353 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 354   <TR ALIGN="center" VALIGN="top">\r
 355   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 356   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 357   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 358   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/GlobPlot.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 359   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 360   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 361   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 362   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 363   </TR>\r
 364 </TABLE>\r
 365 </TD>\r
 366 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 367 </EM>\r
 368 </TD>\r
 369 </TR>\r
 370 \r
 371 <TR>\r
 372 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 373 &nbsp;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder"><B>PREV CLASS</B></A>&nbsp;\r
 374 &nbsp;<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder"><B>NEXT CLASS</B></A></FONT></TD>\r
 375 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 376   <A HREF="../../../index.html?compbio/runner/disorder/GlobPlot.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 377 &nbsp;<A HREF="GlobPlot.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 378 &nbsp;<SCRIPT type="text/javascript">\r
 379   <!--\r
 380   if(window==top) {\r
 381     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 382   }\r
 383   //-->\r
 384 </SCRIPT>\r
 385 <NOSCRIPT>\r
 386   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 387 </NOSCRIPT>\r
 388 \r
 389 \r
 390 </FONT></TD>\r
 391 </TR>\r
 392 <TR>\r
 393 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 394   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
 395 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 396 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
 397 </TR>\r
 398 </TABLE>\r
 399 <A NAME="skip-navbar_bottom"></A>\r
 400 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 401 \r
 402 <HR>\r
 403 \r
 404 </BODY>\r
 405 </HTML>\r