website/full_javadoc/compbio/pipeline/_jpred/Jpred4.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 Jpred4\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="Jpred4";\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/Jpred4.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/pipeline/_jpred/JackHmmerHitParser.html" title="class in compbio.pipeline._jpred"><B>PREV CLASS</B></A>&nbsp;\r
  59 &nbsp;<A HREF="../../../compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred"><B>NEXT CLASS</B></A></FONT></TD>\r
  60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
  61   <A HREF="../../../index.html?compbio/pipeline/_jpred/Jpred4.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
  62 &nbsp;<A HREF="Jpred4.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;FIELD&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.pipeline._jpred</FONT>\r
  92 <BR>\r
  93 Class Jpred4</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.pipeline._jpred.Jpred4</B>\r
  97 </PRE>\r
  98 <HR>\r
  99 <DL>\r
 100 <DT><PRE>public class <B>Jpred4</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 jpred --sequence <fasta file> OR --alignment <clustalW alignment> [--db
 105  <database>] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help]
 106
 107  jpred4 --sequence <fasta file> The path to the sequence (in FASTA format) you
 108  want to predict OR
 109
 110  [--alignment <clustalW alignment>] The alignment which to use for prediction
 111
 112  [--profile=<path to HMM profile>]
 113
 114  [--db <database>] Database to use for PSI-BLAST querying. Default: uniref90 (
 115  /homes/www-jpred/databases/uniref90.filt) Please note that database must be
 116  psi-blast indexed
 117
 118  [--pred-nohits] Toggle allowing Jpred to make predictions even when there are
 119  no PSI-BLAST hits.
 120
 121  [--logLevel=(ERROR|INFO|DEBUG)] one of ERROR, INFO, DEBUG [--help]\r
 122 <P>\r
 123 \r
 124 <P>\r
 125 <DL>\r
 126 <DT><B>Author:</B></DT>\r
 127   <DD>pvtroshin</DD>\r
 128 </DL>\r
 129 <HR>\r
 130 \r
 131 <P>\r
 132 \r
 133 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 134 \r
 135 <A NAME="constructor_summary"><!-- --></A>\r
 136 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 137 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 138 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 139 <B>Constructor Summary</B></FONT></TH>\r
 140 </TR>\r
 141 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 142 <TD><CODE><B><A HREF="../../../compbio/pipeline/_jpred/Jpred4.html#Jpred4()">Jpred4</A></B>()</CODE>\r
 143 \r
 144 <BR>\r
 145 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 146 </TR>\r
 147 </TABLE>\r
 148 &nbsp;\r
 149 <!-- ========== METHOD SUMMARY =========== -->\r
 150 \r
 151 <A NAME="method_summary"><!-- --></A>\r
 152 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 153 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 154 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 155 <B>Method Summary</B></FONT></TH>\r
 156 </TR>\r
 157 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 158 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 159 <CODE>&nbsp;void</CODE></FONT></TD>\r
 160 <TD><CODE><B><A HREF="../../../compbio/pipeline/_jpred/Jpred4.html#runPsiBlast()">runPsiBlast</A></B>()</CODE>\r
 161 \r
 162 <BR>\r
 163 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 164 </TR>\r
 165 </TABLE>\r
 166 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 167 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 168 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 169 <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
 170 </TR>\r
 171 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 172 <TD><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>, <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#hashCode()" title="class or interface in java.lang">hashCode</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#toString()" title="class or interface in java.lang">toString</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
 173 </TR>\r
 174 </TABLE>\r
 175 &nbsp;\r
 176 <P>\r
 177 \r
 178 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 179 \r
 180 <A NAME="constructor_detail"><!-- --></A>\r
 181 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 182 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 183 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 184 <B>Constructor Detail</B></FONT></TH>\r
 185 </TR>\r
 186 </TABLE>\r
 187 \r
 188 <A NAME="Jpred4()"><!-- --></A><H3>\r
 189 Jpred4</H3>\r
 190 <PRE>\r
 191 public <B>Jpred4</B>()</PRE>\r
 192 <DL>\r
 193 </DL>\r
 194 \r
 195 <!-- ============ METHOD DETAIL ========== -->\r
 196 \r
 197 <A NAME="method_detail"><!-- --></A>\r
 198 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 199 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 200 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 201 <B>Method Detail</B></FONT></TH>\r
 202 </TR>\r
 203 </TABLE>\r
 204 \r
 205 <A NAME="runPsiBlast()"><!-- --></A><H3>\r
 206 runPsiBlast</H3>\r
 207 <PRE>\r
 208 public void <B>runPsiBlast</B>()</PRE>\r
 209 <DL>\r
 210 <DD><DL>\r
 211 </DL>\r
 212 </DD>\r
 213 </DL>\r
 214 <!-- ========= END OF CLASS DATA ========= -->\r
 215 <HR>\r
 216 \r
 217 \r
 218 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 219 <A NAME="navbar_bottom"><!-- --></A>\r
 220 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 221 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 222 <TR>\r
 223 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 224 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 225 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 226   <TR ALIGN="center" VALIGN="top">\r
 227   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 228   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 229   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 230   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Jpred4.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 231   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 232   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 233   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 234   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 235   </TR>\r
 236 </TABLE>\r
 237 </TD>\r
 238 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 239 </EM>\r
 240 </TD>\r
 241 </TR>\r
 242 \r
 243 <TR>\r
 244 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 245 &nbsp;<A HREF="../../../compbio/pipeline/_jpred/JackHmmerHitParser.html" title="class in compbio.pipeline._jpred"><B>PREV CLASS</B></A>&nbsp;\r
 246 &nbsp;<A HREF="../../../compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred"><B>NEXT CLASS</B></A></FONT></TD>\r
 247 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 248   <A HREF="../../../index.html?compbio/pipeline/_jpred/Jpred4.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 249 &nbsp;<A HREF="Jpred4.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 250 &nbsp;<SCRIPT type="text/javascript">\r
 251   <!--\r
 252   if(window==top) {\r
 253     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 254   }\r
 255   //-->\r
 256 </SCRIPT>\r
 257 <NOSCRIPT>\r
 258   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 259 </NOSCRIPT>\r
 260 \r
 261 \r
 262 </FONT></TD>\r
 263 </TR>\r
 264 <TR>\r
 265 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 266   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
 267 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 268 DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
 269 </TR>\r
 270 </TABLE>\r
 271 <A NAME="skip-navbar_bottom"></A>\r
 272 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 273 \r
 274 <HR>\r
 275 \r
 276 </BODY>\r
 277 </HTML>\r