website/full_javadoc/compbio/runner/psiblast/PsiBlast.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_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
   6 <TITLE>\r
   7 PsiBlast\r
   8 </TITLE>\r
   9 \r
  10 <META NAME="date" CONTENT="2010-02-17">\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="PsiBlast";\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/PsiBlast.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;PREV CLASS&nbsp;\r
  59 &nbsp;NEXT CLASS</FONT></TD>\r
  60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
  61   <A HREF="../../../index.html?compbio/runner/psiblast/PsiBlast.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
  62 &nbsp;<A HREF="PsiBlast.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.runner.psiblast</FONT>\r
  92 <BR>\r
  93 Class PsiBlast</H2>\r
  94 <PRE>\r
  95 java.lang.Object\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/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>&gt;\r
  97       <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.psiblast.PsiBlast</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/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>&gt;</DD>\r
 101 </DL>\r
 102 <HR>\r
 103 <DL>\r
 104 <DT><PRE>public class <B>PsiBlast</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>&gt;</DL>\r
 105 </PRE>\r
 106 \r
 107 <P>\r
 108 <HR>\r
 109 \r
 110 <P>\r
 111 <!-- ======== NESTED CLASS SUMMARY ======== -->\r
 112 \r
 113 <A NAME="nested_class_summary"><!-- --></A>\r
 114 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 115 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 116 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 117 <B>Nested Class Summary</B></FONT></TH>\r
 118 </TR>\r
 119 </TABLE>\r
 120 &nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
 121 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 122 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 123 <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
 124 </TR>\r
 125 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 126 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
 127 </TR>\r
 128 </TABLE>\r
 129 &nbsp;\r
 130 \r
 131 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 132 \r
 133 <A NAME="constructor_summary"><!-- --></A>\r
 134 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 135 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 136 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 137 <B>Constructor Summary</B></FONT></TH>\r
 138 </TR>\r
 139 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 140 <TD><CODE><B><A HREF="../../../compbio/runner/psiblast/PsiBlast.html#PsiBlast()">PsiBlast</A></B>()</CODE>\r
 141 \r
 142 <BR>\r
 143 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 144 </TR>\r
 145 </TABLE>\r
 146 &nbsp;\r
 147 <!-- ========== METHOD SUMMARY =========== -->\r
 148 \r
 149 <A NAME="method_summary"><!-- --></A>\r
 150 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 151 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 152 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 153 <B>Method Summary</B></FONT></TH>\r
 154 </TR>\r
 155 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 156 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 157 <CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>&gt;</CODE></FONT></TD>\r
 158 <TD><CODE><B><A HREF="../../../compbio/runner/psiblast/PsiBlast.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
 159 \r
 160 <BR>\r
 161 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 162 </TR>\r
 163 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 164 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 165 <CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>&gt;</CODE></FONT></TD>\r
 166 <TD><CODE><B><A HREF="../../../compbio/runner/psiblast/PsiBlast.html#getLimits()">getLimits</A></B>()</CODE>\r
 167 \r
 168 <BR>\r
 169 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 170 </TR>\r
 171 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 172 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 173 <CODE>\r
 174 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 175 <TR ALIGN="right" VALIGN="">\r
 176 <TD NOWRAP><FONT SIZE="-1">\r
 177 <CODE>&lt;V&gt; V</CODE></FONT></TD>\r
 178 </TR>\r
 179 </TABLE>\r
 180 </CODE></FONT></TD>\r
 181 <TD><CODE><B><A HREF="../../../compbio/runner/psiblast/PsiBlast.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;directory)</CODE>\r
 182 \r
 183 <BR>\r
 184 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 185 </TR>\r
 186 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 187 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 188 <CODE>&nbsp;java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
 189 <TD><CODE><B><A HREF="../../../compbio/runner/psiblast/PsiBlast.html#getType()">getType</A></B>()</CODE>\r
 190 \r
 191 <BR>\r
 192 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 193 </TR>\r
 194 </TABLE>\r
 195 &nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
 196 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 197 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 198 <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
 199 </TR>\r
 200 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 201 <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#getClusterSettings()">getClusterSettings</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#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#setInput(java.lang.String)">setInput</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
 202 </TR>\r
 203 </TABLE>\r
 204 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 205 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 206 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 207 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
 208 </TR>\r
 209 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 210 <TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
 211 </TR>\r
 212 </TABLE>\r
 213 &nbsp;\r
 214 <P>\r
 215 \r
 216 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 217 \r
 218 <A NAME="constructor_detail"><!-- --></A>\r
 219 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 220 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 221 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 222 <B>Constructor Detail</B></FONT></TH>\r
 223 </TR>\r
 224 </TABLE>\r
 225 \r
 226 <A NAME="PsiBlast()"><!-- --></A><H3>\r
 227 PsiBlast</H3>\r
 228 <PRE>\r
 229 public <B>PsiBlast</B>()</PRE>\r
 230 <DL>\r
 231 </DL>\r
 232 \r
 233 <!-- ============ METHOD DETAIL ========== -->\r
 234 \r
 235 <A NAME="method_detail"><!-- --></A>\r
 236 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 237 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 238 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 239 <B>Method Detail</B></FONT></TH>\r
 240 </TR>\r
 241 </TABLE>\r
 242 \r
 243 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
 244 getResults</H3>\r
 245 <PRE>\r
 246 public &lt;V&gt; V <B>getResults</B>(java.lang.String&nbsp;directory)\r
 247              throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 248 <DL>\r
 249 <DD><DL>\r
 250 \r
 251 <DT><B>Throws:</B>\r
 252 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 253 </DD>\r
 254 </DL>\r
 255 <HR>\r
 256 \r
 257 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
 258 getLimit</H3>\r
 259 <PRE>\r
 260 public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
 261 <DL>\r
 262 <DD><DL>\r
 263 </DL>\r
 264 </DD>\r
 265 </DL>\r
 266 <HR>\r
 267 \r
 268 <A NAME="getLimits()"><!-- --></A><H3>\r
 269 getLimits</H3>\r
 270 <PRE>\r
 271 public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>&gt; <B>getLimits</B>()</PRE>\r
 272 <DL>\r
 273 <DD><DL>\r
 274 </DL>\r
 275 </DD>\r
 276 </DL>\r
 277 <HR>\r
 278 \r
 279 <A NAME="getType()"><!-- --></A><H3>\r
 280 getType</H3>\r
 281 <PRE>\r
 282 public java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt; <B>getType</B>()</PRE>\r
 283 <DL>\r
 284 <DD><DL>\r
 285 <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/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>&gt;</CODE></DL>\r
 286 </DD>\r
 287 <DD><DL>\r
 288 </DL>\r
 289 </DD>\r
 290 </DL>\r
 291 <!-- ========= END OF CLASS DATA ========= -->\r
 292 <HR>\r
 293 \r
 294 \r
 295 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 296 <A NAME="navbar_bottom"><!-- --></A>\r
 297 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 298 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 299 <TR>\r
 300 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 301 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 302 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 303   <TR ALIGN="center" VALIGN="top">\r
 304   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 305   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 306   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 307   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PsiBlast.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 308   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 309   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 310   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 311   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 312   </TR>\r
 313 </TABLE>\r
 314 </TD>\r
 315 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 316 </EM>\r
 317 </TD>\r
 318 </TR>\r
 319 \r
 320 <TR>\r
 321 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 322 &nbsp;PREV CLASS&nbsp;\r
 323 &nbsp;NEXT CLASS</FONT></TD>\r
 324 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 325   <A HREF="../../../index.html?compbio/runner/psiblast/PsiBlast.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 326 &nbsp;<A HREF="PsiBlast.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 327 &nbsp;<SCRIPT type="text/javascript">\r
 328   <!--\r
 329   if(window==top) {\r
 330     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 331   }\r
 332   //-->\r
 333 </SCRIPT>\r
 334 <NOSCRIPT>\r
 335   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 336 </NOSCRIPT>\r
 337 \r
 338 \r
 339 </FONT></TD>\r
 340 </TR>\r
 341 <TR>\r
 342 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 343   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
 344 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 345 DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
 346 </TR>\r
 347 </TABLE>\r
 348 <A NAME="skip-navbar_bottom"></A>\r
 349 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 350 \r
 351 <HR>\r
 352 \r
 353 </BODY>\r
 354 </HTML>\r