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1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
2 <!--NewPage-->\r
3 <HTML>\r
4 <HEAD>\r
5 <!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:36 BST 2011 -->\r
6 <TITLE>\r
7 Uses of Class compbio.metadata.Preset\r
8 </TITLE>\r
9 \r
10 <META NAME="date" CONTENT="2011-08-12">\r
11 \r
12 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
13 \r
14 <SCRIPT type="text/javascript">\r
15 function windowTitle()\r
16 {\r
17     if (location.href.indexOf('is-external=true') == -1) {\r
18         parent.document.title="Uses of Class compbio.metadata.Preset";\r
19     }\r
20 }\r
21 </SCRIPT>\r
22 <NOSCRIPT>\r
23 </NOSCRIPT>\r
24 \r
25 </HEAD>\r
26 \r
27 <BODY BGCOLOR="white" onload="windowTitle();">\r
28 <HR>\r
29 \r
30 \r
31 <!-- ========= START OF TOP NAVBAR ======= -->\r
32 <A NAME="navbar_top"><!-- --></A>\r
33 <A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
34 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
35 <TR>\r
36 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
37 <A NAME="navbar_top_firstrow"><!-- --></A>\r
38 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
39   <TR ALIGN="center" VALIGN="top">\r
40   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
41   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
42   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
43   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
44   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
45   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
46   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
47   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
48   </TR>\r
49 </TABLE>\r
50 </TD>\r
51 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
52 </EM>\r
53 </TD>\r
54 </TR>\r
55 \r
56 <TR>\r
57 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
58 &nbsp;PREV&nbsp;\r
59 &nbsp;NEXT</FONT></TD>\r
60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
61   <A HREF="../../../index.html?compbio/metadata/\class-usePreset.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
62 &nbsp;<A HREF="Preset.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
63 &nbsp;<SCRIPT type="text/javascript">\r
64   <!--\r
65   if(window==top) {\r
66     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
67   }\r
68   //-->\r
69 </SCRIPT>\r
70 <NOSCRIPT>\r
71   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
72 </NOSCRIPT>\r
73 \r
74 \r
75 </FONT></TD>\r
76 </TR>\r
77 </TABLE>\r
78 <A NAME="skip-navbar_top"></A>\r
79 <!-- ========= END OF TOP NAVBAR ========= -->\r
80 \r
81 <HR>\r
82 <CENTER>\r
83 <H2>\r
84 <B>Uses of Class<br>compbio.metadata.Preset</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/metadata/Preset.html" title="class in compbio.metadata">Preset</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.metadata"><B>compbio.metadata</B></A></TD>\r
102 <TD>A meta-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.ws.server"><B>compbio.ws.server</B></A></TD>\r
107 <TD>&nbsp;&nbsp;</TD>\r
108 </TR>\r
109 </TABLE>\r
110 &nbsp;\r
111 <P>\r
112 <A NAME="compbio.data.msa"><!-- --></A>\r
113 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
114 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
115 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
116 Uses of <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
117 </TR>\r
118 </TABLE>\r
119 &nbsp;\r
120 <P>\r
121 \r
122 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
123 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
124 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> with parameters of type <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></TH>\r
125 </TR>\r
126 <TR BGCOLOR="white" CLASS="TableRowColor">\r
127 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
128 <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
129 <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
130             <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
131 \r
132 <BR>\r
133 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with preset.</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#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
139               <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
140 \r
141 <BR>\r
142 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Analyse the sequences according to the preset settings.</TD>\r
143 </TR>\r
144 </TABLE>\r
145 &nbsp;\r
146 <P>\r
147 <A NAME="compbio.data.msa.jaxws"><!-- --></A>\r
148 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
149 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
150 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
151 Uses of <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A> in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>\r
152 </TR>\r
153 </TABLE>\r
154 &nbsp;\r
155 <P>\r
156 \r
157 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
158 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
159 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> that return <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></TH>\r
160 </TR>\r
161 <TR BGCOLOR="white" CLASS="TableRowColor">\r
162 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
163 <CODE>&nbsp;<A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></CODE></FONT></TD>\r
164 <TD><CODE><B>PresetAnalize.</B><B><A HREF="../../../compbio/data/msa/jaxws/PresetAnalize.html#getPreset()">getPreset</A></B>()</CODE>\r
165 \r
166 <BR>\r
167 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
168 </TR>\r
169 <TR BGCOLOR="white" CLASS="TableRowColor">\r
170 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
171 <CODE>&nbsp;<A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></CODE></FONT></TD>\r
172 <TD><CODE><B>PresetAlign.</B><B><A HREF="../../../compbio/data/msa/jaxws/PresetAlign.html#getPreset()">getPreset</A></B>()</CODE>\r
173 \r
174 <BR>\r
175 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
176 </TR>\r
177 </TABLE>\r
178 &nbsp;\r
179 <P>\r
180 \r
181 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
182 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
183 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> with parameters of type <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></TH>\r
184 </TR>\r
185 <TR BGCOLOR="white" CLASS="TableRowColor">\r
186 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
187 <CODE>&nbsp;void</CODE></FONT></TD>\r
188 <TD><CODE><B>PresetAnalize.</B><B><A HREF="../../../compbio/data/msa/jaxws/PresetAnalize.html#setPreset(compbio.metadata.Preset)">setPreset</A></B>(<A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&nbsp;preset)</CODE>\r
189 \r
190 <BR>\r
191 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\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;void</CODE></FONT></TD>\r
196 <TD><CODE><B>PresetAlign.</B><B><A HREF="../../../compbio/data/msa/jaxws/PresetAlign.html#setPreset(compbio.metadata.Preset)">setPreset</A></B>(<A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&nbsp;preset)</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 <A NAME="compbio.metadata"><!-- --></A>\r
205 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
206 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
207 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
208 Uses of <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\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">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</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;<A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt;</CODE></FONT></TD>\r
221 <TD><CODE><B>PresetManager.</B><B><A HREF="../../../compbio/metadata/PresetManager.html#getPresetByName(java.lang.String)">getPresetByName</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;presetName)</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 </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/metadata/package-summary.html">compbio.metadata</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</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>&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/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt;&gt;</CODE></FONT></TD>\r
237 <TD><CODE><B>PresetManager.</B><B><A HREF="../../../compbio/metadata/PresetManager.html#getPresets()">getPresets</A></B>()</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/metadata/package-summary.html">compbio.metadata</A> with type arguments of type <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</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>&nbsp;void</CODE></FONT></TD>\r
253 <TD><CODE><B>PresetManager.</B><B><A HREF="../../../compbio/metadata/PresetManager.html#setPresets(java.util.List)">setPresets</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/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt;&gt;&nbsp;presets)</CODE>\r
254 \r
255 <BR>\r
256 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
257 </TR>\r
258 </TABLE>\r
259 &nbsp;\r
260 <P>\r
261 <A NAME="compbio.ws.server"><!-- --></A>\r
262 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
263 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
264 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
265 Uses of <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A> in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
266 </TR>\r
267 </TABLE>\r
268 &nbsp;\r
269 <P>\r
270 \r
271 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
272 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
273 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> with parameters of type <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></TH>\r
274 </TR>\r
275 <TR BGCOLOR="white" CLASS="TableRowColor">\r
276 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
277 <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
278 <TD><CODE><B>ClustalOWS.</B><B><A HREF="../../../compbio/ws/server/ClustalOWS.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
279             <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>&gt;&nbsp;preset)</CODE>\r
280 \r
281 <BR>\r
282 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\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>&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
287 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.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
288             <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
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;<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
296 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.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
297             <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
298 \r
299 <BR>\r
300 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
301 </TR>\r
302 <TR BGCOLOR="white" CLASS="TableRowColor">\r
303 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
304 <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
305 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.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
306             <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
307 \r
308 <BR>\r
309 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
310 </TR>\r
311 <TR BGCOLOR="white" CLASS="TableRowColor">\r
312 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
313 <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
314 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.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
315             <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
316 \r
317 <BR>\r
318 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
319 </TR>\r
320 <TR BGCOLOR="white" CLASS="TableRowColor">\r
321 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
322 <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
323 <TD><CODE><B>_MsaService.</B><B><A HREF="../../../compbio/ws/server/_MsaService.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
324             <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/ws/server/_MsaService.html" title="type parameter in _MsaService">T</A>&gt;&nbsp;preset)</CODE>\r
325 \r
326 <BR>\r
327 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
328 </TR>\r
329 <TR BGCOLOR="white" CLASS="TableRowColor">\r
330 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
331 <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
332 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.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
333             <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
334 \r
335 <BR>\r
336 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
337 </TR>\r
338 <TR BGCOLOR="white" CLASS="TableRowColor">\r
339 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
340 <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
341 <TD><CODE><B>DisemblWS.</B><B><A HREF="../../../compbio/ws/server/DisemblWS.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
342               <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;&nbsp;preset)</CODE>\r
343 \r
344 <BR>\r
345 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
346 </TR>\r
347 <TR BGCOLOR="white" CLASS="TableRowColor">\r
348 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
349 <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
350 <TD><CODE><B>GlobPlotWS.</B><B><A HREF="../../../compbio/ws/server/GlobPlotWS.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
351               <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>&gt;&nbsp;preset)</CODE>\r
352 \r
353 <BR>\r
354 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
355 </TR>\r
356 <TR BGCOLOR="white" CLASS="TableRowColor">\r
357 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
358 <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
359 <TD><CODE><B>IUPredWS.</B><B><A HREF="../../../compbio/ws/server/IUPredWS.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
360               <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>&gt;&nbsp;preset)</CODE>\r
361 \r
362 <BR>\r
363 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
364 </TR>\r
365 <TR BGCOLOR="white" CLASS="TableRowColor">\r
366 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
367 <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
368 <TD><CODE><B>SequenceAnnotationService.</B><B><A HREF="../../../compbio/ws/server/SequenceAnnotationService.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
369               <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/ws/server/SequenceAnnotationService.html" title="type parameter in SequenceAnnotationService">T</A>&gt;&nbsp;preset)</CODE>\r
370 \r
371 <BR>\r
372 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
373 </TR>\r
374 </TABLE>\r
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