website/full_javadoc/compbio/data/sequence/class-use/FastaSequence.html

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   7 Uses of Class compbio.data.sequence.FastaSequence\r
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  83 <H2>\r
  84 <B>Uses of Class<br>compbio.data.sequence.FastaSequence</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/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</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.ws.server"><B>compbio.ws.server</B></A></TD>\r
 124 <TD>&nbsp;&nbsp;</TD>\r
 125 </TR>\r
 126 </TABLE>\r
 127 &nbsp;\r
 128 <P>\r
 129 <A NAME="compbio.data.msa"><!-- --></A>\r
 130 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 131 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 132 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 133 Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
 134 </TR>\r
 135 </TABLE>\r
 136 &nbsp;\r
 137 <P>\r
 138 \r
 139 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 140 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 141 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
 142 </TR>\r
 143 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 144 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 145 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 146 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 147 \r
 148 <BR>\r
 149 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with default settings.</TD>\r
 150 </TR>\r
 151 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 152 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 153 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 154 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 155             java.util.List&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&gt;&nbsp;options)</CODE>\r
 156 \r
 157 <BR>\r
 158 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with options.</TD>\r
 159 </TR>\r
 160 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 161 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 162 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 163 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 164             <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&nbsp;preset)</CODE>\r
 165 \r
 166 <BR>\r
 167 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with preset.</TD>\r
 168 </TR>\r
 169 </TABLE>\r
 170 &nbsp;\r
 171 <P>\r
 172 <A NAME="compbio.data.msa.jaxws"><!-- --></A>\r
 173 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 174 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 175 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 176 Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>\r
 177 </TR>\r
 178 </TABLE>\r
 179 &nbsp;\r
 180 <P>\r
 181 \r
 182 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 183 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 184 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> that return types with arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\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.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
 189 <TD><CODE><B>PresetAlign.</B><B><A HREF="../../../../compbio/data/msa/jaxws/PresetAlign.html#getFastaSequences()">getFastaSequences</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 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 195 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 196 <CODE>&nbsp;java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
 197 <TD><CODE><B>CustomAlign.</B><B><A HREF="../../../../compbio/data/msa/jaxws/CustomAlign.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>\r
 198 \r
 199 <BR>\r
 200 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 201 </TR>\r
 202 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 203 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 204 <CODE>&nbsp;java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
 205 <TD><CODE><B>Align.</B><B><A HREF="../../../../compbio/data/msa/jaxws/Align.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>\r
 206 \r
 207 <BR>\r
 208 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 209 </TR>\r
 210 </TABLE>\r
 211 &nbsp;\r
 212 <P>\r
 213 \r
 214 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 215 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 216 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
 217 </TR>\r
 218 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 219 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 220 <CODE>&nbsp;void</CODE></FONT></TD>\r
 221 <TD><CODE><B>PresetAlign.</B><B><A HREF="../../../../compbio/data/msa/jaxws/PresetAlign.html#setFastaSequences(java.util.List)">setFastaSequences</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;fastaSequences)</CODE>\r
 222 \r
 223 <BR>\r
 224 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 225 </TR>\r
 226 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 227 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 228 <CODE>&nbsp;void</CODE></FONT></TD>\r
 229 <TD><CODE><B>CustomAlign.</B><B><A HREF="../../../../compbio/data/msa/jaxws/CustomAlign.html#setFastaSequences(java.util.List)">setFastaSequences</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;fastaSequences)</CODE>\r
 230 \r
 231 <BR>\r
 232 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 233 </TR>\r
 234 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 235 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 236 <CODE>&nbsp;void</CODE></FONT></TD>\r
 237 <TD><CODE><B>Align.</B><B><A HREF="../../../../compbio/data/msa/jaxws/Align.html#setFastaSequences(java.util.List)">setFastaSequences</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;fastaSequences)</CODE>\r
 238 \r
 239 <BR>\r
 240 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 241 </TR>\r
 242 </TABLE>\r
 243 &nbsp;\r
 244 <P>\r
 245 <A NAME="compbio.data.sequence"><!-- --></A>\r
 246 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 247 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 248 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 249 Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
 250 </TR>\r
 251 </TABLE>\r
 252 &nbsp;\r
 253 <P>\r
 254 \r
 255 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 256 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 257 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return types with arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
 258 </TR>\r
 259 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 260 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 261 <CODE>&nbsp;java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
 262 <TD><CODE><B>Alignment.</B><B><A HREF="../../../../compbio/data/sequence/Alignment.html#getSequences()">getSequences</A></B>()</CODE>\r
 263 \r
 264 <BR>\r
 265 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 266 </TR>\r
 267 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 268 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 269 <CODE>static&nbsp;java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
 270 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)">readFasta</A></B>(java.io.InputStream&nbsp;inStream)</CODE>\r
 271 \r
 272 <BR>\r
 273 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads fasta sequences from inStream into the list of FastaSequence
 274  objects</TD>\r
 275 </TR>\r
 276 </TABLE>\r
 277 &nbsp;\r
 278 <P>\r
 279 \r
 280 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 281 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 282 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
 283 </TR>\r
 284 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 285 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 286 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
 287 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence(compbio.data.sequence.FastaSequence)">isNucleotideSequence</A></B>(<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&nbsp;s)</CODE>\r
 288 \r
 289 <BR>\r
 290 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 291 </TR>\r
 292 </TABLE>\r
 293 &nbsp;\r
 294 <P>\r
 295 \r
 296 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 297 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 298 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
 299 </TR>\r
 300 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 301 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 302 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 303 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List)">writeFasta</A></B>(java.io.OutputStream&nbsp;os,\r
 304            java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 305 \r
 306 <BR>\r
 307 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Writes FastaSequence in the file, each sequence will take one line only</TD>\r
 308 </TR>\r
 309 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 310 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 311 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 312 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List, int)">writeFasta</A></B>(java.io.OutputStream&nbsp;outstream,\r
 313            java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 314            int&nbsp;width)</CODE>\r
 315 \r
 316 <BR>\r
 317 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Writes list of FastaSequeces into the outstream formatting the sequence
 318  so that it contains width chars on each line</TD>\r
 319 </TR>\r
 320 </TABLE>\r
 321 &nbsp;\r
 322 <P>\r
 323 \r
 324 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 325 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 326 <TH ALIGN="left" COLSPAN="2">Constructor parameters in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
 327 </TR>\r
 328 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 329 <TD><CODE><B><A HREF="../../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)">Alignment</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 330           <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>&nbsp;metadata)</CODE>\r
 331 \r
 332 <BR>\r
 333 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 334 </TR>\r
 335 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 336 <TD><CODE><B><A HREF="../../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)">Alignment</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 337           <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&nbsp;program,\r
 338           char&nbsp;gapchar)</CODE>\r
 339 \r
 340 <BR>\r
 341 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 342 </TR>\r
 343 </TABLE>\r
 344 &nbsp;\r
 345 <P>\r
 346 <A NAME="compbio.engine"><!-- --></A>\r
 347 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 348 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 349 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 350 Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
 351 </TR>\r
 352 </TABLE>\r
 353 &nbsp;\r
 354 <P>\r
 355 \r
 356 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 357 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 358 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
 359 </TR>\r
 360 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 361 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 362 <CODE>static\r
 363 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 364 <TR ALIGN="right" VALIGN="">\r
 365 <TD NOWRAP><FONT SIZE="-1">\r
 366 <CODE>&lt;T&gt; <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
 367 </TR>\r
 368 </TABLE>\r
 369 </CODE></FONT></TD>\r
 370 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, java.util.List)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable,\r
 371                     java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;dataSet)</CODE>\r
 372 \r
 373 <BR>\r
 374 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 375 </TR>\r
 376 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 377 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 378 <CODE>static\r
 379 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 380 <TR ALIGN="right" VALIGN="">\r
 381 <TD NOWRAP><FONT SIZE="-1">\r
 382 <CODE>&lt;T,V&gt; <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
 383 </TR>\r
 384 </TABLE>\r
 385 </CODE></FONT></TD>\r
 386 <TD><CODE><B>LoadBalancer.</B><B><A HREF="../../../../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable, java.util.List)">getEngine</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&nbsp;executable,\r
 387           java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;dataSet)</CODE>\r
 388 \r
 389 <BR>\r
 390 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 391 </TR>\r
 392 </TABLE>\r
 393 &nbsp;\r
 394 <P>\r
 395 <A NAME="compbio.metadata"><!-- --></A>\r
 396 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 397 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 398 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 399 Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
 400 </TR>\r
 401 </TABLE>\r
 402 &nbsp;\r
 403 <P>\r
 404 \r
 405 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 406 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 407 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/metadata/package-summary.html">compbio.metadata</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
 408 </TR>\r
 409 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 410 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 411 <CODE>static&nbsp;int</CODE></FONT></TD>\r
 412 <TD><CODE><B>Limit.</B><B><A HREF="../../../../compbio/metadata/Limit.html#getAvgSequenceLength(java.util.List)">getAvgSequenceLength</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;data)</CODE>\r
 413 \r
 414 <BR>\r
 415 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Calculates an average sequence length of the dataset</TD>\r
 416 </TR>\r
 417 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 418 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 419 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 420 <TD><CODE><B>Limit.</B><B><A HREF="../../../../compbio/metadata/Limit.html#isExceeded(java.util.List)">isExceeded</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;data)</CODE>\r
 421 \r
 422 <BR>\r
 423 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Checks if the number of sequences or their average length in the dataset
 424  exceeds limits the values defined by this Limit</TD>\r
 425 </TR>\r
 426 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 427 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 428 <CODE>static&nbsp;<A HREF="../../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE></FONT></TD>\r
 429 <TD><CODE><B>LimitExceededException.</B><B><A HREF="../../../../compbio/metadata/LimitExceededException.html#newLimitExceeded(compbio.metadata.Limit, java.util.List)">newLimitExceeded</A></B>(<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;?&gt;&nbsp;limit,\r
 430                  java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;seqs)</CODE>\r
 431 \r
 432 <BR>\r
 433 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 434 </TR>\r
 435 </TABLE>\r
 436 &nbsp;\r
 437 <P>\r
 438 <A NAME="compbio.pipeline._jpred"><!-- --></A>\r
 439 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 440 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 441 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 442 Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/pipeline/_jpred/package-summary.html">compbio.pipeline._jpred</A></FONT></TH>\r
 443 </TR>\r
 444 </TABLE>\r
 445 &nbsp;\r
 446 <P>\r
 447 \r
 448 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 449 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 450 <TH ALIGN="left" COLSPAN="2">Constructor parameters in <A HREF="../../../../compbio/pipeline/_jpred/package-summary.html">compbio.pipeline._jpred</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
 451 </TR>\r
 452 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 453 <TD><CODE><B><A HREF="../../../../compbio/pipeline/_jpred/Pairwise.html#Pairwise(java.util.List)">Pairwise</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 454 \r
 455 <BR>\r
 456 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 457 </TR>\r
 458 </TABLE>\r
 459 &nbsp;\r
 460 <P>\r
 461 <A NAME="compbio.runner"><!-- --></A>\r
 462 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 463 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 464 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 465 Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
 466 </TR>\r
 467 </TABLE>\r
 468 &nbsp;\r
 469 <P>\r
 470 \r
 471 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 472 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 473 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
 474 </TR>\r
 475 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 476 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 477 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 478 <TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)">writeInput</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 479            <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;exec)</CODE>\r
 480 \r
 481 <BR>\r
 482 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 483 </TR>\r
 484 </TABLE>\r
 485 &nbsp;\r
 486 <P>\r
 487 <A NAME="compbio.ws.server"><!-- --></A>\r
 488 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 489 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 490 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 491 Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
 492 </TR>\r
 493 </TABLE>\r
 494 &nbsp;\r
 495 <P>\r
 496 \r
 497 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 498 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 499 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
 500 </TR>\r
 501 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 502 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 503 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 504 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../../compbio/ws/server/TcoffeeWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 505 \r
 506 <BR>\r
 507 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 508 </TR>\r
 509 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 510 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 511 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 512 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 513 \r
 514 <BR>\r
 515 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 516 </TR>\r
 517 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 518 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 519 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 520 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 521 \r
 522 <BR>\r
 523 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 524 </TR>\r
 525 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 526 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 527 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 528 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../../compbio/ws/server/MafftWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 529 \r
 530 <BR>\r
 531 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 532 </TR>\r
 533 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 534 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 535 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 536 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 537 \r
 538 <BR>\r
 539 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 540 </TR>\r
 541 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 542 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 543 <CODE>static\r
 544 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 545 <TR ALIGN="right" VALIGN="">\r
 546 <TD NOWRAP><FONT SIZE="-1">\r
 547 <CODE>&lt;T&gt; java.lang.String</CODE></FONT></TD>\r
 548 </TR>\r
 549 </TABLE>\r
 550 </CODE></FONT></TD>\r
 551 <TD><CODE><B>WSUtil.</B><B><A HREF="../../../../compbio/ws/server/WSUtil.html#align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String, compbio.metadata.Limit)">align</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 552       <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;&nbsp;confExec,\r
 553       org.apache.log4j.Logger&nbsp;statLog,\r
 554       javax.xml.ws.WebServiceContext&nbsp;wsContext,\r
 555       java.lang.String&nbsp;callingMethod,\r
 556       <A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;T&gt;&nbsp;limit)</CODE>\r
 557 \r
 558 <BR>\r
 559 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 560 </TR>\r
 561 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 562 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 563 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 564 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 565             java.util.List&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;&gt;&nbsp;options)</CODE>\r
 566 \r
 567 <BR>\r
 568 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 569 </TR>\r
 570 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 571 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 572 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 573 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../../compbio/ws/server/MafftWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 574             java.util.List&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;&gt;&nbsp;options)</CODE>\r
 575 \r
 576 <BR>\r
 577 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 578 </TR>\r
 579 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 580 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 581 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 582 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 583             java.util.List&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&gt;&nbsp;options)</CODE>\r
 584 \r
 585 <BR>\r
 586 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 587 </TR>\r
 588 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 589 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 590 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 591 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 592             java.util.List&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&gt;&nbsp;options)</CODE>\r
 593 \r
 594 <BR>\r
 595 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 596 </TR>\r
 597 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 598 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 599 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 600 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../../compbio/ws/server/TcoffeeWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 601             java.util.List&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;&gt;&nbsp;options)</CODE>\r
 602 \r
 603 <BR>\r
 604 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 605 </TR>\r
 606 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 607 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 608 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 609 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 610             <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;&nbsp;preset)</CODE>\r
 611 \r
 612 <BR>\r
 613 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 614 </TR>\r
 615 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 616 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 617 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 618 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../../compbio/ws/server/MafftWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 619             <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;&nbsp;preset)</CODE>\r
 620 \r
 621 <BR>\r
 622 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 623 </TR>\r
 624 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 625 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 626 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 627 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 628             <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&nbsp;preset)</CODE>\r
 629 \r
 630 <BR>\r
 631 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 632 </TR>\r
 633 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 634 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 635 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 636 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 637             <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&nbsp;preset)</CODE>\r
 638 \r
 639 <BR>\r
 640 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 641 </TR>\r
 642 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 643 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 644 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 645 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../../compbio/ws/server/TcoffeeWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 646             <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;&nbsp;preset)</CODE>\r
 647 \r
 648 <BR>\r
 649 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 650 </TR>\r
 651 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 652 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 653 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 654 <TD><CODE><B>WSUtil.</B><B><A HREF="../../../../compbio/ws/server/WSUtil.html#validateFastaInput(java.util.List)">validateFastaInput</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 655 \r
 656 <BR>\r
 657 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 658 </TR>\r
 659 </TABLE>\r
 660 &nbsp;\r
 661 <P>\r
 662 <HR>\r
 663 \r
 664 \r
 665 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 666 <A NAME="navbar_bottom"><!-- --></A>\r
 667 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 668 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 669 <TR>\r
 670 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 671 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 672 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 673   <TR ALIGN="center" VALIGN="top">\r
 674   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 675   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 676   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
 677   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
 678   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 679   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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 682   </TR>\r
 683 </TABLE>\r
 684 </TD>\r
 685 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 686 </EM>\r
 687 </TD>\r
 688 </TR>\r
 689 \r
 690 <TR>\r
 691 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 692 &nbsp;PREV&nbsp;\r
 693 &nbsp;NEXT</FONT></TD>\r
 694 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 695   <A HREF="../../../../index.html?compbio/data/sequence/\class-useFastaSequence.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 696 &nbsp;<A HREF="FastaSequence.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 697 &nbsp;<SCRIPT type="text/javascript">\r
 698   <!--\r
 699   if(window==top) {\r
 700     document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 701   }\r
 702   //-->\r
 703 </SCRIPT>\r
 704 <NOSCRIPT>\r
 705   <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 706 </NOSCRIPT>\r
 707 \r
 708 \r
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 710 </TR>\r
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 712 <A NAME="skip-navbar_bottom"></A>\r
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