website/dm_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 14:32:04 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.metadata"><B>compbio.metadata</B></A></TD>\r
 107 <TD>A meta-data model for multiple sequence alignment web services
 108  Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
 109 </TR>\r
 110 </TABLE>\r
 111 &nbsp;\r
 112 <P>\r
 113 <A NAME="compbio.data.msa"><!-- --></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 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
 118 </TR>\r
 119 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 120 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.msa"><B>Alignment</B></A></B>\r
 121 \r
 122 <BR>\r
 123 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
 124 </TR>\r
 125 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 126 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.msa"><B>FastaSequence</B></A></B>\r
 127 \r
 128 <BR>\r
 129 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
 130 </TR>\r
 131 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 132 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.data.msa"><B>ScoreManager</B></A></B>\r
 133 \r
 134 <BR>\r
 135 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 136 </TR>\r
 137 </TABLE>\r
 138 &nbsp;\r
 139 <P>\r
 140 <A NAME="compbio.data.msa.jaxws"><!-- --></A>\r
 141 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 142 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 143 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 144 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
 145 </TR>\r
 146 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 147 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.msa.jaxws"><B>Alignment</B></A></B>\r
 148 \r
 149 <BR>\r
 150 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
 151 </TR>\r
 152 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 153 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.msa.jaxws"><B>FastaSequence</B></A></B>\r
 154 \r
 155 <BR>\r
 156 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
 157 </TR>\r
 158 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 159 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.data.msa.jaxws"><B>ScoreManager</B></A></B>\r
 160 \r
 161 <BR>\r
 162 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 163 </TR>\r
 164 </TABLE>\r
 165 &nbsp;\r
 166 <P>\r
 167 <A NAME="compbio.data.sequence"><!-- --></A>\r
 168 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 169 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 170 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 171 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
 172 </TR>\r
 173 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 174 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.sequence"><B>Alignment</B></A></B>\r
 175 \r
 176 <BR>\r
 177 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
 178 </TR>\r
 179 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 180 <TD><B><A HREF="../../../compbio/data/sequence/class-use/AlignmentMetadata.html#compbio.data.sequence"><B>AlignmentMetadata</B></A></B>\r
 181 \r
 182 <BR>\r
 183 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Alignment metadata e.g.</TD>\r
 184 </TR>\r
 185 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 186 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ConservationMethod.html#compbio.data.sequence"><B>ConservationMethod</B></A></B>\r
 187 \r
 188 <BR>\r
 189 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Enumeration listing of all the supported methods.</TD>\r
 190 </TR>\r
 191 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 192 <TD><B><A HREF="../../../compbio/data/sequence/class-use/DisorderMethod.html#compbio.data.sequence"><B>DisorderMethod</B></A></B>\r
 193 \r
 194 <BR>\r
 195 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 196 </TR>\r
 197 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 198 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.sequence"><B>FastaSequence</B></A></B>\r
 199 \r
 200 <BR>\r
 201 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
 202 </TR>\r
 203 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 204 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Program.html#compbio.data.sequence"><B>Program</B></A></B>\r
 205 \r
 206 <BR>\r
 207 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The list of programmes that can produce alignments</TD>\r
 208 </TR>\r
 209 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 210 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Range.html#compbio.data.sequence"><B>Range</B></A></B>\r
 211 \r
 212 <BR>\r
 213 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 214 </TR>\r
 215 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 216 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Score.html#compbio.data.sequence"><B>Score</B></A></B>\r
 217 \r
 218 <BR>\r
 219 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A value class for AACon annotation results storage.</TD>\r
 220 </TR>\r
 221 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 222 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.data.sequence"><B>ScoreManager</B></A></B>\r
 223 \r
 224 <BR>\r
 225 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 226 </TR>\r
 227 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 228 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.ScoreHolder.html#compbio.data.sequence"><B>ScoreManager.ScoreHolder</B></A></B>\r
 229 \r
 230 <BR>\r
 231 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 232 </TR>\r
 233 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 234 <TD><B><A HREF="../../../compbio/data/sequence/class-use/SMERFSConstraints.html#compbio.data.sequence"><B>SMERFSConstraints</B></A></B>\r
 235 \r
 236 <BR>\r
 237 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Enumeration defining two constraints for SMERFS columns score calculation.</TD>\r
 238 </TR>\r
 239 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 240 <TD><B><A HREF="../../../compbio/data/sequence/class-use/UnknownFileFormatException.html#compbio.data.sequence"><B>UnknownFileFormatException</B></A></B>\r
 241 \r
 242 <BR>\r
 243 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 244 </TR>\r
 245 </TABLE>\r
 246 &nbsp;\r
 247 <P>\r
 248 <A NAME="compbio.metadata"><!-- --></A>\r
 249 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 250 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 251 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 252 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
 253 </TR>\r
 254 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 255 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.metadata"><B>FastaSequence</B></A></B>\r
 256 \r
 257 <BR>\r
 258 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
 259 </TR>\r
 260 </TABLE>\r
 261 &nbsp;\r
 262 <P>\r
 263 <HR>\r
 264 \r
 265 \r
 266 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 267 <A NAME="navbar_bottom"><!-- --></A>\r
 268 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 269 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 270 <TR>\r
 271 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 272 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 273 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 274   <TR ALIGN="center" VALIGN="top">\r
 275   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 276   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 277   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
 278   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
 279   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 280   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 281   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 282   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 283   </TR>\r
 284 </TABLE>\r
 285 </TD>\r
 286 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 287 </EM>\r
 288 </TD>\r
 289 </TR>\r
 290 \r
 291 <TR>\r
 292 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 293 &nbsp;PREV&nbsp;\r
 294 &nbsp;NEXT</FONT></TD>\r
 295 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 296   <A HREF="../../../index.html?compbio/data/sequence/package-use.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 297 &nbsp;<A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 298 &nbsp;<SCRIPT type="text/javascript">\r
 299   <!--\r
 300   if(window==top) {\r
 301     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 302   }\r
 303   //-->\r
 304 </SCRIPT>\r
 305 <NOSCRIPT>\r
 306   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 307 </NOSCRIPT>\r
 308 \r
 309 \r
 310 </FONT></TD>\r
 311 </TR>\r
 312 </TABLE>\r
 313 <A NAME="skip-navbar_bottom"></A>\r
 314 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 315 \r
 316 <HR>\r
 317 \r
 318 </BODY>\r
 319 </HTML>\r