website/dm_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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  84 <B>Uses of Class<br>compbio.data.sequence.FastaSequence</B></H2>\r
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  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>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.sequence"><B>compbio.data.sequence</B></A></TD>\r
  98 <TD>A data model for multiple sequence alignment web services and utility methods
  99  that work on the objects of this model.&nbsp;</TD>\r
 100 </TR>\r
 101 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 102 <TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
 103 <TD>A meta-data model for multiple sequence alignment web services
 104  Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
 105 </TR>\r
 106 </TABLE>\r
 107 &nbsp;\r
 108 <P>\r
 109 <A NAME="compbio.data.msa"><!-- --></A>\r
 110 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 111 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 112 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 113 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
 114 </TR>\r
 115 </TABLE>\r
 116 &nbsp;\r
 117 <P>\r
 118 \r
 119 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 120 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 121 <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
 122 </TR>\r
 123 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 124 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 125 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
 126 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 127 \r
 128 <BR>\r
 129 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with default settings.</TD>\r
 130 </TR>\r
 131 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 132 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 133 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
 134 <TD><CODE><B>Annotation.</B><B><A HREF="../../../../compbio/data/msa/Annotation.html#analize(java.util.List)">analize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 135 \r
 136 <BR>\r
 137 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Analyse the sequences.</TD>\r
 138 </TR>\r
 139 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 140 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 141 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
 142 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 143             <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&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
 144 \r
 145 <BR>\r
 146 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with options.</TD>\r
 147 </TR>\r
 148 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 149 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 150 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
 151 <TD><CODE><B>Annotation.</B><B><A HREF="../../../../compbio/data/msa/Annotation.html#customAnalize(java.util.List, java.util.List)">customAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 152               <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../../compbio/data/msa/Annotation.html" title="type parameter in Annotation">T</A>&gt;&gt;&nbsp;options)</CODE>\r
 153 \r
 154 <BR>\r
 155 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Analyse the sequences according to custom settings defined in options
 156  list.</TD>\r
 157 </TR>\r
 158 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 159 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 160 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
 161 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 162             <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
 163 \r
 164 <BR>\r
 165 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with preset.</TD>\r
 166 </TR>\r
 167 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 168 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 169 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
 170 <TD><CODE><B>Annotation.</B><B><A HREF="../../../../compbio/data/msa/Annotation.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 171               <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../../compbio/data/msa/Annotation.html" title="type parameter in Annotation">T</A>&gt;&nbsp;preset)</CODE>\r
 172 \r
 173 <BR>\r
 174 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Analyse the sequences according to the preset settings.</TD>\r
 175 </TR>\r
 176 </TABLE>\r
 177 &nbsp;\r
 178 <P>\r
 179 <A NAME="compbio.data.sequence"><!-- --></A>\r
 180 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 181 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 182 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 183 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
 184 </TR>\r
 185 </TABLE>\r
 186 &nbsp;\r
 187 <P>\r
 188 \r
 189 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 190 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 191 <TH ALIGN="left" COLSPAN="2">Subclasses 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
 192 </TR>\r
 193 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 194 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 195 <CODE>&nbsp;class</CODE></FONT></TD>\r
 196 <TD><CODE><B><A HREF="../../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A></B></CODE>\r
 197 \r
 198 <BR>\r
 199 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 200 </TR>\r
 201 </TABLE>\r
 202 &nbsp;\r
 203 <P>\r
 204 \r
 205 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 206 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 207 <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
 208 </TR>\r
 209 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 210 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 211 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
 212 <TD><CODE><B>Alignment.</B><B><A HREF="../../../../compbio/data/sequence/Alignment.html#getSequences()">getSequences</A></B>()</CODE>\r
 213 \r
 214 <BR>\r
 215 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 216 </TR>\r
 217 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 218 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 219 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
 220 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)">readFasta</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A>&nbsp;inStream)</CODE>\r
 221 \r
 222 <BR>\r
 223 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads fasta sequences from inStream into the list of FastaSequence
 224  objects</TD>\r
 225 </TR>\r
 226 </TABLE>\r
 227 &nbsp;\r
 228 <P>\r
 229 \r
 230 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 231 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 232 <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
 233 </TR>\r
 234 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 235 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 236 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
 237 <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
 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 \r
 246 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 247 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 248 <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
 249 </TR>\r
 250 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 251 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 252 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 253 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List)">writeFasta</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A>&nbsp;os,\r
 254            <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 255 \r
 256 <BR>\r
 257 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Writes FastaSequence in the file, each sequence will take one line only</TD>\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>static&nbsp;void</CODE></FONT></TD>\r
 262 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List, int)">writeFasta</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A>&nbsp;outstream,\r
 263            <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 264            int&nbsp;width)</CODE>\r
 265 \r
 266 <BR>\r
 267 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Writes list of FastaSequeces into the outstream formatting the sequence
 268  so that it contains width chars on each line</TD>\r
 269 </TR>\r
 270 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 271 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 272 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 273 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#writeFastaKeepTheStream(java.io.OutputStream, java.util.List, int)">writeFastaKeepTheStream</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A>&nbsp;outstream,\r
 274                         <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 275                         int&nbsp;width)</CODE>\r
 276 \r
 277 <BR>\r
 278 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 279 </TR>\r
 280 </TABLE>\r
 281 &nbsp;\r
 282 <P>\r
 283 \r
 284 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 285 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 286 <TH ALIGN="left" COLSPAN="2">Constructors 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
 287 </TR>\r
 288 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 289 <TD><CODE><B><A HREF="../../../../compbio/data/sequence/AnnotatedSequence.html#AnnotatedSequence(compbio.data.sequence.FastaSequence, float[])">AnnotatedSequence</A></B>(<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&nbsp;fsequence,\r
 290                   float[]&nbsp;annotation)</CODE>\r
 291 \r
 292 <BR>\r
 293 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 294 </TR>\r
 295 </TABLE>\r
 296 &nbsp;\r
 297 <P>\r
 298 \r
 299 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 300 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 301 <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
 302 </TR>\r
 303 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 304 <TD><CODE><B><A HREF="../../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)">Alignment</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 305           <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>&nbsp;metadata)</CODE>\r
 306 \r
 307 <BR>\r
 308 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 309 </TR>\r
 310 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 311 <TD><CODE><B><A HREF="../../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)">Alignment</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 312           <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&nbsp;program,\r
 313           char&nbsp;gapchar)</CODE>\r
 314 \r
 315 <BR>\r
 316 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 317 </TR>\r
 318 </TABLE>\r
 319 &nbsp;\r
 320 <P>\r
 321 <A NAME="compbio.metadata"><!-- --></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 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
 326 </TR>\r
 327 </TABLE>\r
 328 &nbsp;\r
 329 <P>\r
 330 \r
 331 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 332 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 333 <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
 334 </TR>\r
 335 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 336 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 337 <CODE>static&nbsp;int</CODE></FONT></TD>\r
 338 <TD><CODE><B>Limit.</B><B><A HREF="../../../../compbio/metadata/Limit.html#getAvgSequenceLength(java.util.List)">getAvgSequenceLength</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;data)</CODE>\r
 339 \r
 340 <BR>\r
 341 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Calculates an average sequence length of the dataset</TD>\r
 342 </TR>\r
 343 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 344 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 345 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 346 <TD><CODE><B>Limit.</B><B><A HREF="../../../../compbio/metadata/Limit.html#isExceeded(java.util.List)">isExceeded</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;data)</CODE>\r
 347 \r
 348 <BR>\r
 349 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Checks if the number of sequences or their average length in the dataset
 350  exceeds this limit.</TD>\r
 351 </TR>\r
 352 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 353 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 354 <CODE>static&nbsp;<A HREF="../../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE></FONT></TD>\r
 355 <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
 356                  <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;seqs)</CODE>\r
 357 \r
 358 <BR>\r
 359 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 360 </TR>\r
 361 </TABLE>\r
 362 &nbsp;\r
 363 <P>\r
 364 <HR>\r
 365 \r
 366 \r
 367 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 368 <A NAME="navbar_bottom"><!-- --></A>\r
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 373 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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 376   <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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 396 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 397   <A HREF="../../../../index.html?compbio/data/sequence/\class-useFastaSequence.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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