website/full_javadoc/compbio/data/sequence/package-use.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 14:32:36 BST 2011 -->\r
   6 <TITLE>\r
   7 Uses of Package compbio.data.sequence\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="Uses of Package compbio.data.sequence";\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="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
  43   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&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&nbsp;\r
  59 &nbsp;NEXT</FONT></TD>\r
  60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
  61   <A HREF="../../../index.html?compbio/data/sequence/package-use.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
  62 &nbsp;<A HREF="package-use.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 </TABLE>\r
  78 <A NAME="skip-navbar_top"></A>\r
  79 <!-- ========= END OF TOP NAVBAR ========= -->\r
  80 \r
  81 <HR>\r
  82 <CENTER>\r
  83 <H2>\r
  84 <B>Uses of Package<br>compbio.data.sequence</B></H2>\r
  85 </CENTER>\r
  86 \r
  87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
  88 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
  89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
  90 Packages that use <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
  91 </TR>\r
  92 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  93 <TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
  94 <TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services.&nbsp;</TD>\r
  95 </TR>\r
  96 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  97 <TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>\r
  98 <TD>&nbsp;&nbsp;</TD>\r
  99 </TR>\r
 100 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 101 <TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
 102 <TD>A data model for multiple sequence alignment web services and utility methods
 103  that work on the objects of this model.&nbsp;</TD>\r
 104 </TR>\r
 105 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 106 <TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
 107 <TD>&nbsp;&nbsp;</TD>\r
 108 </TR>\r
 109 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 110 <TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
 111 <TD>A meta-data model for multiple sequence alignment web services
 112  Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
 113 </TR>\r
 114 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 115 <TD><A HREF="#compbio.pipeline._jpred"><B>compbio.pipeline._jpred</B></A></TD>\r
 116 <TD>&nbsp;&nbsp;</TD>\r
 117 </TR>\r
 118 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 119 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
 120 <TD>Utilities commonly used by all runners.&nbsp;</TD>\r
 121 </TR>\r
 122 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 123 <TD><A HREF="#compbio.runner.conservation"><B>compbio.runner.conservation</B></A></TD>\r
 124 <TD>&nbsp;&nbsp;</TD>\r
 125 </TR>\r
 126 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 127 <TD><A HREF="#compbio.runner.disorder"><B>compbio.runner.disorder</B></A></TD>\r
 128 <TD>&nbsp;&nbsp;</TD>\r
 129 </TR>\r
 130 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 131 <TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
 132 <TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
 133 </TR>\r
 134 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 135 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
 136 <TD>&nbsp;&nbsp;</TD>\r
 137 </TR>\r
 138 </TABLE>\r
 139 &nbsp;\r
 140 <P>\r
 141 <A NAME="compbio.data.msa"><!-- --></A>\r
 142 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 143 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 144 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 145 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
 146 </TR>\r
 147 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 148 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.msa"><B>Alignment</B></A></B>\r
 149 \r
 150 <BR>\r
 151 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
 152 </TR>\r
 153 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 154 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.msa"><B>FastaSequence</B></A></B>\r
 155 \r
 156 <BR>\r
 157 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
 158 </TR>\r
 159 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 160 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.data.msa"><B>ScoreManager</B></A></B>\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;\r
 167 <P>\r
 168 <A NAME="compbio.data.msa.jaxws"><!-- --></A>\r
 169 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 170 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 171 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 172 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>\r
 173 </TR>\r
 174 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 175 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.msa.jaxws"><B>Alignment</B></A></B>\r
 176 \r
 177 <BR>\r
 178 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
 179 </TR>\r
 180 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 181 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.msa.jaxws"><B>FastaSequence</B></A></B>\r
 182 \r
 183 <BR>\r
 184 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
 185 </TR>\r
 186 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 187 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.data.msa.jaxws"><B>ScoreManager</B></A></B>\r
 188 \r
 189 <BR>\r
 190 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 191 </TR>\r
 192 </TABLE>\r
 193 &nbsp;\r
 194 <P>\r
 195 <A NAME="compbio.data.sequence"><!-- --></A>\r
 196 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 197 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 198 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 199 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
 200 </TR>\r
 201 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 202 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.sequence"><B>Alignment</B></A></B>\r
 203 \r
 204 <BR>\r
 205 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
 206 </TR>\r
 207 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 208 <TD><B><A HREF="../../../compbio/data/sequence/class-use/AlignmentMetadata.html#compbio.data.sequence"><B>AlignmentMetadata</B></A></B>\r
 209 \r
 210 <BR>\r
 211 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Alignment metadata e.g.</TD>\r
 212 </TR>\r
 213 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 214 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ConservationMethod.html#compbio.data.sequence"><B>ConservationMethod</B></A></B>\r
 215 \r
 216 <BR>\r
 217 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Enumeration listing of all the supported methods.</TD>\r
 218 </TR>\r
 219 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 220 <TD><B><A HREF="../../../compbio/data/sequence/class-use/DisorderMethod.html#compbio.data.sequence"><B>DisorderMethod</B></A></B>\r
 221 \r
 222 <BR>\r
 223 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 224 </TR>\r
 225 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 226 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.sequence"><B>FastaSequence</B></A></B>\r
 227 \r
 228 <BR>\r
 229 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
 230 </TR>\r
 231 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 232 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Program.html#compbio.data.sequence"><B>Program</B></A></B>\r
 233 \r
 234 <BR>\r
 235 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The list of programmes that can produce alignments</TD>\r
 236 </TR>\r
 237 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 238 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Range.html#compbio.data.sequence"><B>Range</B></A></B>\r
 239 \r
 240 <BR>\r
 241 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 242 </TR>\r
 243 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 244 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Score.html#compbio.data.sequence"><B>Score</B></A></B>\r
 245 \r
 246 <BR>\r
 247 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A value class for AACon annotation results storage.</TD>\r
 248 </TR>\r
 249 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 250 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.data.sequence"><B>ScoreManager</B></A></B>\r
 251 \r
 252 <BR>\r
 253 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 254 </TR>\r
 255 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 256 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.ScoreHolder.html#compbio.data.sequence"><B>ScoreManager.ScoreHolder</B></A></B>\r
 257 \r
 258 <BR>\r
 259 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 260 </TR>\r
 261 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 262 <TD><B><A HREF="../../../compbio/data/sequence/class-use/SMERFSConstraints.html#compbio.data.sequence"><B>SMERFSConstraints</B></A></B>\r
 263 \r
 264 <BR>\r
 265 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Enumeration defining two constraints for SMERFS columns score calculation.</TD>\r
 266 </TR>\r
 267 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 268 <TD><B><A HREF="../../../compbio/data/sequence/class-use/UnknownFileFormatException.html#compbio.data.sequence"><B>UnknownFileFormatException</B></A></B>\r
 269 \r
 270 <BR>\r
 271 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 272 </TR>\r
 273 </TABLE>\r
 274 &nbsp;\r
 275 <P>\r
 276 <A NAME="compbio.engine"><!-- --></A>\r
 277 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 278 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 279 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 280 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
 281 </TR>\r
 282 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 283 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.engine"><B>FastaSequence</B></A></B>\r
 284 \r
 285 <BR>\r
 286 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
 287 </TR>\r
 288 </TABLE>\r
 289 &nbsp;\r
 290 <P>\r
 291 <A NAME="compbio.metadata"><!-- --></A>\r
 292 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 293 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 294 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 295 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
 296 </TR>\r
 297 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 298 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.metadata"><B>FastaSequence</B></A></B>\r
 299 \r
 300 <BR>\r
 301 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
 302 </TR>\r
 303 </TABLE>\r
 304 &nbsp;\r
 305 <P>\r
 306 <A NAME="compbio.pipeline._jpred"><!-- --></A>\r
 307 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 308 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 309 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 310 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/pipeline/_jpred/package-summary.html">compbio.pipeline._jpred</A></FONT></TH>\r
 311 </TR>\r
 312 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 313 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.pipeline._jpred"><B>FastaSequence</B></A></B>\r
 314 \r
 315 <BR>\r
 316 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
 317 </TR>\r
 318 </TABLE>\r
 319 &nbsp;\r
 320 <P>\r
 321 <A NAME="compbio.runner"><!-- --></A>\r
 322 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 323 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 324 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 325 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
 326 </TR>\r
 327 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 328 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.runner"><B>Alignment</B></A></B>\r
 329 \r
 330 <BR>\r
 331 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
 332 </TR>\r
 333 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 334 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.runner"><B>FastaSequence</B></A></B>\r
 335 \r
 336 <BR>\r
 337 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
 338 </TR>\r
 339 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 340 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Score.html#compbio.runner"><B>Score</B></A></B>\r
 341 \r
 342 <BR>\r
 343 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A value class for AACon annotation results storage.</TD>\r
 344 </TR>\r
 345 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 346 <TD><B><A HREF="../../../compbio/data/sequence/class-use/UnknownFileFormatException.html#compbio.runner"><B>UnknownFileFormatException</B></A></B>\r
 347 \r
 348 <BR>\r
 349 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 350 </TR>\r
 351 </TABLE>\r
 352 &nbsp;\r
 353 <P>\r
 354 <A NAME="compbio.runner.conservation"><!-- --></A>\r
 355 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 356 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 357 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 358 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/runner/conservation/package-summary.html">compbio.runner.conservation</A></FONT></TH>\r
 359 </TR>\r
 360 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 361 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.runner.conservation"><B>ScoreManager</B></A></B>\r
 362 \r
 363 <BR>\r
 364 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 365 </TR>\r
 366 </TABLE>\r
 367 &nbsp;\r
 368 <P>\r
 369 <A NAME="compbio.runner.disorder"><!-- --></A>\r
 370 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 371 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 372 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 373 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A></FONT></TH>\r
 374 </TR>\r
 375 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 376 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.runner.disorder"><B>ScoreManager</B></A></B>\r
 377 \r
 378 <BR>\r
 379 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 380 </TR>\r
 381 </TABLE>\r
 382 &nbsp;\r
 383 <P>\r
 384 <A NAME="compbio.runner.msa"><!-- --></A>\r
 385 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 386 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 387 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 388 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
 389 </TR>\r
 390 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 391 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.runner.msa"><B>Alignment</B></A></B>\r
 392 \r
 393 <BR>\r
 394 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
 395 </TR>\r
 396 </TABLE>\r
 397 &nbsp;\r
 398 <P>\r
 399 <A NAME="compbio.ws.server"><!-- --></A>\r
 400 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 401 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 402 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 403 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
 404 </TR>\r
 405 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 406 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.ws.server"><B>Alignment</B></A></B>\r
 407 \r
 408 <BR>\r
 409 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
 410 </TR>\r
 411 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 412 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.ws.server"><B>FastaSequence</B></A></B>\r
 413 \r
 414 <BR>\r
 415 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
 416 </TR>\r
 417 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 418 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.ws.server"><B>ScoreManager</B></A></B>\r
 419 \r
 420 <BR>\r
 421 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 422 </TR>\r
 423 </TABLE>\r
 424 &nbsp;\r
 425 <P>\r
 426 <HR>\r
 427 \r
 428 \r
 429 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 430 <A NAME="navbar_bottom"><!-- --></A>\r
 431 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 432 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 433 <TR>\r
 434 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 435 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 436 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 437   <TR ALIGN="center" VALIGN="top">\r
 438   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 439   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 440   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
 441   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
 442   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 443   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 444   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 445   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 446   </TR>\r
 447 </TABLE>\r
 448 </TD>\r
 449 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 450 </EM>\r
 451 </TD>\r
 452 </TR>\r
 453 \r
 454 <TR>\r
 455 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 456 &nbsp;PREV&nbsp;\r
 457 &nbsp;NEXT</FONT></TD>\r
 458 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 459   <A HREF="../../../index.html?compbio/data/sequence/package-use.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 460 &nbsp;<A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 461 &nbsp;<SCRIPT type="text/javascript">\r
 462   <!--\r
 463   if(window==top) {\r
 464     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 465   }\r
 466   //-->\r
 467 </SCRIPT>\r
 468 <NOSCRIPT>\r
 469   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 470 </NOSCRIPT>\r
 471 \r
 472 \r
 473 </FONT></TD>\r
 474 </TR>\r
 475 </TABLE>\r
 476 <A NAME="skip-navbar_bottom"></A>\r
 477 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 478 \r
 479 <HR>\r
 480 \r
 481 </BODY>\r
 482 </HTML>\r