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5 <!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->
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7 Uses of Class compbio.metadata.Preset
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10 <META NAME="date" CONTENT="2010-02-17">
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18 parent.document.title="Uses of Class compbio.metadata.Preset";
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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> </TD>
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62 <A HREF="Preset.html" target="_top"><B>NO FRAMES</B></A>
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63 <SCRIPT type="text/javascript">
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66 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
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79 <!-- ========= END OF TOP NAVBAR ========= -->
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84 <B>Uses of Class<br>compbio.metadata.Preset</B></H2>
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87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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88 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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90 Packages that use <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></TH>
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92 <TR BGCOLOR="white" CLASS="TableRowColor">
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93 <TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>
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94 <TD> </TD>
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96 <TR BGCOLOR="white" CLASS="TableRowColor">
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97 <TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>
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98 <TD> </TD>
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100 <TR BGCOLOR="white" CLASS="TableRowColor">
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101 <TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>
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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. </TD>
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105 <TR BGCOLOR="white" CLASS="TableRowColor">
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106 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>
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107 <TD> </TD>
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112 <A NAME="compbio.data.msa"><!-- --></A>
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113 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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114 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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115 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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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>
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122 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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123 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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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>
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126 <TR BGCOLOR="white" CLASS="TableRowColor">
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127 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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128 <CODE> java.lang.String</CODE></FONT></TD>
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129 <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<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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130 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>> preset)</CODE>
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133 Align a list of sequences with preset.</TD>
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138 <A NAME="compbio.data.msa.jaxws"><!-- --></A>
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139 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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140 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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141 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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142 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>
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148 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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149 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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150 <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>
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152 <TR BGCOLOR="white" CLASS="TableRowColor">
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153 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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154 <CODE> <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></CODE></FONT></TD>
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155 <TD><CODE><B>PresetAlign.</B><B><A HREF="../../../compbio/data/msa/jaxws/PresetAlign.html#getPreset()">getPreset</A></B>()</CODE>
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158 </TD>
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164 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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165 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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166 <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>
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168 <TR BGCOLOR="white" CLASS="TableRowColor">
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169 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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170 <CODE> void</CODE></FONT></TD>
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171 <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> preset)</CODE>
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174 </TD>
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179 <A NAME="compbio.metadata"><!-- --></A>
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180 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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181 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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182 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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183 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>
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189 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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190 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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191 <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>
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193 <TR BGCOLOR="white" CLASS="TableRowColor">
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194 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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195 <CODE> <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>></CODE></FONT></TD>
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196 <TD><CODE><B>PresetManager.</B><B><A HREF="../../../compbio/metadata/PresetManager.html#getPresetByName(java.lang.String)">getPresetByName</A></B>(java.lang.String presetName)</CODE>
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199 </TD>
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205 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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206 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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207 <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>
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209 <TR BGCOLOR="white" CLASS="TableRowColor">
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210 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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211 <CODE> java.util.List<<A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>>></CODE></FONT></TD>
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212 <TD><CODE><B>PresetManager.</B><B><A HREF="../../../compbio/metadata/PresetManager.html#getPresets()">getPresets</A></B>()</CODE>
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215 </TD>
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221 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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222 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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223 <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>
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225 <TR BGCOLOR="white" CLASS="TableRowColor">
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226 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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227 <CODE> void</CODE></FONT></TD>
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228 <TD><CODE><B>PresetManager.</B><B><A HREF="../../../compbio/metadata/PresetManager.html#setPresets(java.util.List)">setPresets</A></B>(java.util.List<<A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>>> presets)</CODE>
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231 </TD>
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236 <A NAME="compbio.ws.server"><!-- --></A>
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237 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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238 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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239 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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240 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>
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246 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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247 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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248 <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>
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250 <TR BGCOLOR="white" CLASS="TableRowColor">
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251 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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252 <CODE> java.lang.String</CODE></FONT></TD>
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253 <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<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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254 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>> preset)</CODE>
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257 </TD>
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259 <TR BGCOLOR="white" CLASS="TableRowColor">
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260 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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261 <CODE> java.lang.String</CODE></FONT></TD>
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262 <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<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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263 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>> preset)</CODE>
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266 </TD>
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268 <TR BGCOLOR="white" CLASS="TableRowColor">
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269 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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270 <CODE> java.lang.String</CODE></FONT></TD>
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271 <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<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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272 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>> preset)</CODE>
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275 </TD>
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277 <TR BGCOLOR="white" CLASS="TableRowColor">
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278 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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279 <CODE> java.lang.String</CODE></FONT></TD>
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280 <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<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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281 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>> preset)</CODE>
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284 </TD>
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286 <TR BGCOLOR="white" CLASS="TableRowColor">
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287 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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288 <CODE> java.lang.String</CODE></FONT></TD>
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289 <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<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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290 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>> preset)</CODE>
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293 </TD>
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301 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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302 <A NAME="navbar_bottom"><!-- --></A>
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303 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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304 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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306 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
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307 <A NAME="navbar_bottom_firstrow"><!-- --></A>
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308 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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309 <TR ALIGN="center" VALIGN="top">
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310 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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311 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
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312 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
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313 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
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314 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
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315 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
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316 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
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317 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
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321 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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327 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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329 NEXT</FONT></TD>
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330 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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331 <A HREF="../../../index.html?compbio/metadata/\class-usePreset.html" target="_top"><B>FRAMES</B></A>
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332 <A HREF="Preset.html" target="_top"><B>NO FRAMES</B></A>
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333 <SCRIPT type="text/javascript">
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336 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
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341 <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
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348 <A NAME="skip-navbar_bottom"></A>
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