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7 Uses of Class compbio.data.sequence.FastaSequence\r
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79 <!-- ========= END OF TOP NAVBAR ========= -->\r
80 \r
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82 <CENTER>\r
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>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 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
118 </TR>\r
119 </TABLE>\r
120 &nbsp;\r
121 <P>\r
122 \r
123 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
124 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
125 <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
126 </TR>\r
127 <TR BGCOLOR="white" CLASS="TableRowColor">\r
128 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
129 <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
130 <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
131 \r
132 <BR>\r
133 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with default settings.</TD>\r
134 </TR>\r
135 <TR BGCOLOR="white" CLASS="TableRowColor">\r
136 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
137 <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
138 <TD><CODE><B>SequenceAnnotation.</B><B><A HREF="../../../../compbio/data/msa/SequenceAnnotation.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
139 \r
140 <BR>\r
141 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Analyse the sequences.</TD>\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;<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
146 <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
147             <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
148 \r
149 <BR>\r
150 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with options.</TD>\r
151 </TR>\r
152 <TR BGCOLOR="white" CLASS="TableRowColor">\r
153 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
154 <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
155 <TD><CODE><B>SequenceAnnotation.</B><B><A HREF="../../../../compbio/data/msa/SequenceAnnotation.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
156               <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/SequenceAnnotation.html" title="type parameter in SequenceAnnotation">T</A>&gt;&gt;&nbsp;options)</CODE>\r
157 \r
158 <BR>\r
159 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Analyse the sequences according to custom settings defined in options
160  list.</TD>\r
161 </TR>\r
162 <TR BGCOLOR="white" CLASS="TableRowColor">\r
163 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
164 <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
165 <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
166             <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
167 \r
168 <BR>\r
169 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with preset.</TD>\r
170 </TR>\r
171 <TR BGCOLOR="white" CLASS="TableRowColor">\r
172 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
173 <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
174 <TD><CODE><B>SequenceAnnotation.</B><B><A HREF="../../../../compbio/data/msa/SequenceAnnotation.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
175               <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../../compbio/data/msa/SequenceAnnotation.html" title="type parameter in SequenceAnnotation">T</A>&gt;&nbsp;preset)</CODE>\r
176 \r
177 <BR>\r
178 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Analyse the sequences according to the preset settings.</TD>\r
179 </TR>\r
180 </TABLE>\r
181 &nbsp;\r
182 <P>\r
183 <A NAME="compbio.data.msa.jaxws"><!-- --></A>\r
184 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
185 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
186 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
187 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
188 </TR>\r
189 </TABLE>\r
190 &nbsp;\r
191 <P>\r
192 \r
193 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
194 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
195 <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
196 </TR>\r
197 <TR BGCOLOR="white" CLASS="TableRowColor">\r
198 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
199 <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
200 <TD><CODE><B>PresetAnalize.</B><B><A HREF="../../../../compbio/data/msa/jaxws/PresetAnalize.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>\r
201 \r
202 <BR>\r
203 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
204 </TR>\r
205 <TR BGCOLOR="white" CLASS="TableRowColor">\r
206 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
207 <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
208 <TD><CODE><B>PresetAlign.</B><B><A HREF="../../../../compbio/data/msa/jaxws/PresetAlign.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>\r
209 \r
210 <BR>\r
211 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
212 </TR>\r
213 <TR BGCOLOR="white" CLASS="TableRowColor">\r
214 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
215 <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
216 <TD><CODE><B>CustomAnalize.</B><B><A HREF="../../../../compbio/data/msa/jaxws/CustomAnalize.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>\r
217 \r
218 <BR>\r
219 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
220 </TR>\r
221 <TR BGCOLOR="white" CLASS="TableRowColor">\r
222 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
223 <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
224 <TD><CODE><B>CustomAlign.</B><B><A HREF="../../../../compbio/data/msa/jaxws/CustomAlign.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>\r
225 \r
226 <BR>\r
227 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
228 </TR>\r
229 <TR BGCOLOR="white" CLASS="TableRowColor">\r
230 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
231 <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
232 <TD><CODE><B>Analize.</B><B><A HREF="../../../../compbio/data/msa/jaxws/Analize.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>\r
233 \r
234 <BR>\r
235 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
236 </TR>\r
237 <TR BGCOLOR="white" CLASS="TableRowColor">\r
238 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
239 <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
240 <TD><CODE><B>Align.</B><B><A HREF="../../../../compbio/data/msa/jaxws/Align.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>\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 \r
249 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
250 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
251 <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
252 </TR>\r
253 <TR BGCOLOR="white" CLASS="TableRowColor">\r
254 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
255 <CODE>&nbsp;void</CODE></FONT></TD>\r
256 <TD><CODE><B>PresetAnalize.</B><B><A HREF="../../../../compbio/data/msa/jaxws/PresetAnalize.html#setFastaSequences(java.util.List)">setFastaSequences</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;fastaSequences)</CODE>\r
257 \r
258 <BR>\r
259 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
260 </TR>\r
261 <TR BGCOLOR="white" CLASS="TableRowColor">\r
262 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
263 <CODE>&nbsp;void</CODE></FONT></TD>\r
264 <TD><CODE><B>PresetAlign.</B><B><A HREF="../../../../compbio/data/msa/jaxws/PresetAlign.html#setFastaSequences(java.util.List)">setFastaSequences</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;fastaSequences)</CODE>\r
265 \r
266 <BR>\r
267 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
268 </TR>\r
269 <TR BGCOLOR="white" CLASS="TableRowColor">\r
270 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
271 <CODE>&nbsp;void</CODE></FONT></TD>\r
272 <TD><CODE><B>CustomAnalize.</B><B><A HREF="../../../../compbio/data/msa/jaxws/CustomAnalize.html#setFastaSequences(java.util.List)">setFastaSequences</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;fastaSequences)</CODE>\r
273 \r
274 <BR>\r
275 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
276 </TR>\r
277 <TR BGCOLOR="white" CLASS="TableRowColor">\r
278 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
279 <CODE>&nbsp;void</CODE></FONT></TD>\r
280 <TD><CODE><B>CustomAlign.</B><B><A HREF="../../../../compbio/data/msa/jaxws/CustomAlign.html#setFastaSequences(java.util.List)">setFastaSequences</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;fastaSequences)</CODE>\r
281 \r
282 <BR>\r
283 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
284 </TR>\r
285 <TR BGCOLOR="white" CLASS="TableRowColor">\r
286 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
287 <CODE>&nbsp;void</CODE></FONT></TD>\r
288 <TD><CODE><B>Analize.</B><B><A HREF="../../../../compbio/data/msa/jaxws/Analize.html#setFastaSequences(java.util.List)">setFastaSequences</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;fastaSequences)</CODE>\r
289 \r
290 <BR>\r
291 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
292 </TR>\r
293 <TR BGCOLOR="white" CLASS="TableRowColor">\r
294 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
295 <CODE>&nbsp;void</CODE></FONT></TD>\r
296 <TD><CODE><B>Align.</B><B><A HREF="../../../../compbio/data/msa/jaxws/Align.html#setFastaSequences(java.util.List)">setFastaSequences</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;fastaSequences)</CODE>\r
297 \r
298 <BR>\r
299 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
300 </TR>\r
301 </TABLE>\r
302 &nbsp;\r
303 <P>\r
304 <A NAME="compbio.data.sequence"><!-- --></A>\r
305 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
306 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
307 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
308 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
309 </TR>\r
310 </TABLE>\r
311 &nbsp;\r
312 <P>\r
313 \r
314 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
315 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
316 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
317 </TR>\r
318 <TR BGCOLOR="white" CLASS="TableRowColor">\r
319 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
320 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></CODE></FONT></TD>\r
321 <TD><CODE><B>FastaReader.</B><B><A HREF="../../../../compbio/data/sequence/FastaReader.html#next()">next</A></B>()</CODE>\r
322 \r
323 <BR>\r
324 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads the next FastaSequence from the input</TD>\r
325 </TR>\r
326 </TABLE>\r
327 &nbsp;\r
328 <P>\r
329 \r
330 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
331 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
332 <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
333 </TR>\r
334 <TR BGCOLOR="white" CLASS="TableRowColor">\r
335 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
336 <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
337 <TD><CODE><B>Alignment.</B><B><A HREF="../../../../compbio/data/sequence/Alignment.html#getSequences()">getSequences</A></B>()</CODE>\r
338 \r
339 <BR>\r
340 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
341 </TR>\r
342 <TR BGCOLOR="white" CLASS="TableRowColor">\r
343 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
344 <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
345 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#openInputStream(java.lang.String)">openInputStream</A></B>(<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>&nbsp;inFilePath)</CODE>\r
346 \r
347 <BR>\r
348 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads and parses Fasta or Clustal formatted file into a list of
349  FastaSequence objects</TD>\r
350 </TR>\r
351 <TR BGCOLOR="white" CLASS="TableRowColor">\r
352 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
353 <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
354 <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
355 \r
356 <BR>\r
357 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads fasta sequences from inStream into the list of FastaSequence
358  objects</TD>\r
359 </TR>\r
360 </TABLE>\r
361 &nbsp;\r
362 <P>\r
363 \r
364 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
365 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
366 <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
367 </TR>\r
368 <TR BGCOLOR="white" CLASS="TableRowColor">\r
369 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
370 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
371 <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
372 \r
373 <BR>\r
374 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
375 </TR>\r
376 </TABLE>\r
377 &nbsp;\r
378 <P>\r
379 \r
380 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
381 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
382 <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
383 </TR>\r
384 <TR BGCOLOR="white" CLASS="TableRowColor">\r
385 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
386 <CODE>static&nbsp;void</CODE></FONT></TD>\r
387 <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
388            <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
389 \r
390 <BR>\r
391 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Writes FastaSequence in the file, each sequence will take one line only</TD>\r
392 </TR>\r
393 <TR BGCOLOR="white" CLASS="TableRowColor">\r
394 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
395 <CODE>static&nbsp;void</CODE></FONT></TD>\r
396 <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
397            <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
398            int&nbsp;width)</CODE>\r
399 \r
400 <BR>\r
401 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Writes list of FastaSequeces into the outstream formatting the sequence
402  so that it contains width chars on each line</TD>\r
403 </TR>\r
404 <TR BGCOLOR="white" CLASS="TableRowColor">\r
405 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
406 <CODE>static&nbsp;void</CODE></FONT></TD>\r
407 <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
408                         <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
409                         int&nbsp;width)</CODE>\r
410 \r
411 <BR>\r
412 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
413 </TR>\r
414 </TABLE>\r
415 &nbsp;\r
416 <P>\r
417 \r
418 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
419 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
420 <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
421 </TR>\r
422 <TR BGCOLOR="white" CLASS="TableRowColor">\r
423 <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
424           <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>&nbsp;metadata)</CODE>\r
425 \r
426 <BR>\r
427 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
428 </TR>\r
429 <TR BGCOLOR="white" CLASS="TableRowColor">\r
430 <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
431           <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&nbsp;program,\r
432           char&nbsp;gapchar)</CODE>\r
433 \r
434 <BR>\r
435 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
436 </TR>\r
437 </TABLE>\r
438 &nbsp;\r
439 <P>\r
440 <A NAME="compbio.metadata"><!-- --></A>\r
441 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
442 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
443 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
444 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
445 </TR>\r
446 </TABLE>\r
447 &nbsp;\r
448 <P>\r
449 \r
450 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
451 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
452 <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
453 </TR>\r
454 <TR BGCOLOR="white" CLASS="TableRowColor">\r
455 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
456 <CODE>static&nbsp;int</CODE></FONT></TD>\r
457 <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
458 \r
459 <BR>\r
460 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Calculates an average sequence length of the dataset</TD>\r
461 </TR>\r
462 <TR BGCOLOR="white" CLASS="TableRowColor">\r
463 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
464 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
465 <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
466 \r
467 <BR>\r
468 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Checks if the number of sequences or their average length in the dataset
469  exceeds this limit.</TD>\r
470 </TR>\r
471 <TR BGCOLOR="white" CLASS="TableRowColor">\r
472 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
473 <CODE>static&nbsp;<A HREF="../../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE></FONT></TD>\r
474 <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
475                  <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
476 \r
477 <BR>\r
478 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
479 </TR>\r
480 </TABLE>\r
481 &nbsp;\r
482 <P>\r
483 <HR>\r
484 \r
485 \r
486 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
487 <A NAME="navbar_bottom"><!-- --></A>\r
488 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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492 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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503   </TR>\r
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507 </EM>\r
508 </TD>\r
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510 \r
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516   <A HREF="../../../../index.html?compbio/data/sequence/\class-useFastaSequence.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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