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   7 Uses of Package compbio.data.sequence\r
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  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>&nbsp;&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
 103  Classes in this package have no dependencies to other sources in the project.&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.msa"><B>compbio.runner.msa</B></A></TD>\r
 124 <TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
 125 </TR>\r
 126 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 127 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
 128 <TD>&nbsp;&nbsp;</TD>\r
 129 </TR>\r
 130 </TABLE>\r
 131 &nbsp;\r
 132 <P>\r
 133 <A NAME="compbio.data.msa"><!-- --></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 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
 138 </TR>\r
 139 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 140 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.msa"><B>Alignment</B></A></B>\r
 141 \r
 142 <BR>\r
 143 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
 144 </TR>\r
 145 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 146 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.msa"><B>FastaSequence</B></A></B>\r
 147 \r
 148 <BR>\r
 149 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
 150 </TR>\r
 151 </TABLE>\r
 152 &nbsp;\r
 153 <P>\r
 154 <A NAME="compbio.data.msa.jaxws"><!-- --></A>\r
 155 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 156 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 157 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 158 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
 159 </TR>\r
 160 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 161 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.msa.jaxws"><B>Alignment</B></A></B>\r
 162 \r
 163 <BR>\r
 164 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
 165 </TR>\r
 166 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 167 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.msa.jaxws"><B>FastaSequence</B></A></B>\r
 168 \r
 169 <BR>\r
 170 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
 171 </TR>\r
 172 </TABLE>\r
 173 &nbsp;\r
 174 <P>\r
 175 <A NAME="compbio.data.sequence"><!-- --></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 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
 180 </TR>\r
 181 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 182 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.sequence"><B>Alignment</B></A></B>\r
 183 \r
 184 <BR>\r
 185 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
 186 </TR>\r
 187 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 188 <TD><B><A HREF="../../../compbio/data/sequence/class-use/AlignmentMetadata.html#compbio.data.sequence"><B>AlignmentMetadata</B></A></B>\r
 189 \r
 190 <BR>\r
 191 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Alignment metadata e.g.</TD>\r
 192 </TR>\r
 193 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 194 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.sequence"><B>FastaSequence</B></A></B>\r
 195 \r
 196 <BR>\r
 197 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
 198 </TR>\r
 199 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 200 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Program.html#compbio.data.sequence"><B>Program</B></A></B>\r
 201 \r
 202 <BR>\r
 203 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Programmes that can produce alignments</TD>\r
 204 </TR>\r
 205 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 206 <TD><B><A HREF="../../../compbio/data/sequence/class-use/UnknownFileFormatException.html#compbio.data.sequence"><B>UnknownFileFormatException</B></A></B>\r
 207 \r
 208 <BR>\r
 209 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 210 </TR>\r
 211 </TABLE>\r
 212 &nbsp;\r
 213 <P>\r
 214 <A NAME="compbio.engine"><!-- --></A>\r
 215 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 216 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 217 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 218 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
 219 </TR>\r
 220 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 221 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.engine"><B>FastaSequence</B></A></B>\r
 222 \r
 223 <BR>\r
 224 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
 225 </TR>\r
 226 </TABLE>\r
 227 &nbsp;\r
 228 <P>\r
 229 <A NAME="compbio.metadata"><!-- --></A>\r
 230 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 231 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 232 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 233 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
 234 </TR>\r
 235 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 236 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.metadata"><B>FastaSequence</B></A></B>\r
 237 \r
 238 <BR>\r
 239 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
 240 </TR>\r
 241 </TABLE>\r
 242 &nbsp;\r
 243 <P>\r
 244 <A NAME="compbio.pipeline._jpred"><!-- --></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="2"><FONT SIZE="+2">\r
 248 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
 249 </TR>\r
 250 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 251 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.pipeline._jpred"><B>FastaSequence</B></A></B>\r
 252 \r
 253 <BR>\r
 254 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
 255 </TR>\r
 256 </TABLE>\r
 257 &nbsp;\r
 258 <P>\r
 259 <A NAME="compbio.runner"><!-- --></A>\r
 260 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 261 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 262 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 263 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
 264 </TR>\r
 265 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 266 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.runner"><B>Alignment</B></A></B>\r
 267 \r
 268 <BR>\r
 269 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
 270 </TR>\r
 271 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 272 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.runner"><B>FastaSequence</B></A></B>\r
 273 \r
 274 <BR>\r
 275 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
 276 </TR>\r
 277 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 278 <TD><B><A HREF="../../../compbio/data/sequence/class-use/UnknownFileFormatException.html#compbio.runner"><B>UnknownFileFormatException</B></A></B>\r
 279 \r
 280 <BR>\r
 281 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 282 </TR>\r
 283 </TABLE>\r
 284 &nbsp;\r
 285 <P>\r
 286 <A NAME="compbio.runner.msa"><!-- --></A>\r
 287 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 288 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 289 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 290 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
 291 </TR>\r
 292 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 293 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.runner.msa"><B>Alignment</B></A></B>\r
 294 \r
 295 <BR>\r
 296 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
 297 </TR>\r
 298 </TABLE>\r
 299 &nbsp;\r
 300 <P>\r
 301 <A NAME="compbio.ws.server"><!-- --></A>\r
 302 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 303 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 304 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 305 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
 306 </TR>\r
 307 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 308 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.ws.server"><B>Alignment</B></A></B>\r
 309 \r
 310 <BR>\r
 311 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
 312 </TR>\r
 313 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 314 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.ws.server"><B>FastaSequence</B></A></B>\r
 315 \r
 316 <BR>\r
 317 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
 318 </TR>\r
 319 </TABLE>\r
 320 &nbsp;\r
 321 <P>\r
 322 <HR>\r
 323 \r
 324 \r
 325 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 326 <A NAME="navbar_bottom"><!-- --></A>\r
 327 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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 331 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 332 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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 334   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
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