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7 Uses of Class compbio.metadata.WrongParameterException
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84 <B>Uses of Class<br>compbio.metadata.WrongParameterException</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/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</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>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>
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96 <TR BGCOLOR="white" CLASS="TableRowColor">
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97 <TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>
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98 <TD>A meta-data model for multiple sequence alignment web services
99 Classes in this package have no dependencies to other sources in the project. </TD>
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101 <TR BGCOLOR="white" CLASS="TableRowColor">
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102 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>
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103 <TD> </TD>
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108 <A NAME="compbio.data.msa"><!-- --></A>
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109 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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110 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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111 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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112 Uses of <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>
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118 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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119 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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120 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that throw <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></FONT></TH>
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122 <TR BGCOLOR="white" CLASS="TableRowColor">
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123 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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124 <CODE> <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>
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125 <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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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126 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>>> options)</CODE>
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129 Align a list of sequences with options.</TD>
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131 <TR BGCOLOR="white" CLASS="TableRowColor">
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132 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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133 <CODE> <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>
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134 <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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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135 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/data/msa/SequenceAnnotation.html" title="type parameter in SequenceAnnotation">T</A>>> options)</CODE>
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138 Analyse the sequences according to custom settings defined in options
141 <TR BGCOLOR="white" CLASS="TableRowColor">
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142 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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143 <CODE> <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>
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144 <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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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145 <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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148 Align a list of sequences with preset.</TD>
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150 <TR BGCOLOR="white" CLASS="TableRowColor">
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151 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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152 <CODE> <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>
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153 <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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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154 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/data/msa/SequenceAnnotation.html" title="type parameter in SequenceAnnotation">T</A>> preset)</CODE>
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157 Analyse the sequences according to the preset settings.</TD>
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162 <A NAME="compbio.metadata"><!-- --></A>
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163 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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164 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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165 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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166 Uses of <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>
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172 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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173 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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174 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that throw <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></FONT></TH>
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176 <TR BGCOLOR="white" CLASS="TableRowColor">
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177 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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178 <CODE> <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>>></CODE></FONT></TD>
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179 <TD><CODE><B>Preset.</B><B><A HREF="../../../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)">getArguments</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>> rconfig)</CODE>
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182 Converts list of options as String to type Option</TD>
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184 <TR BGCOLOR="white" CLASS="TableRowColor">
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185 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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186 <CODE> void</CODE></FONT></TD>
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187 <TD><CODE><B>Parameter.</B><B><A HREF="../../../compbio/metadata/Parameter.html#setDefaultValue(java.lang.String)">setDefaultValue</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> defaultVal)</CODE>
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190 </TD>
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192 <TR BGCOLOR="white" CLASS="TableRowColor">
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193 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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194 <CODE> void</CODE></FONT></TD>
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195 <TD><CODE><B>Option.</B><B><A HREF="../../../compbio/metadata/Option.html#setDefaultValue(java.lang.String)">setDefaultValue</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> defaultVal)</CODE>
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198 Sets one of the values defined in optionList as default.</TD>
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200 <TR BGCOLOR="white" CLASS="TableRowColor">
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201 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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202 <CODE> void</CODE></FONT></TD>
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203 <TD><CODE><B>Argument.</B><B><A HREF="../../../compbio/metadata/Argument.html#setValue(java.lang.String)">setValue</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> defaultValue)</CODE>
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206 Set default values for the parameter or an option</TD>
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208 <TR BGCOLOR="white" CLASS="TableRowColor">
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209 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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210 <CODE> void</CODE></FONT></TD>
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211 <TD><CODE><B>Option.</B><B><A HREF="../../../compbio/metadata/Option.html#setValue(java.lang.String)">setValue</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> dValue)</CODE>
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214 </TD>
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219 <A NAME="compbio.ws.server"><!-- --></A>
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220 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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221 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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222 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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223 Uses of <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A> in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>
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229 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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230 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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231 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that throw <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></FONT></TH>
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233 <TR BGCOLOR="white" CLASS="TableRowColor">
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234 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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235 <CODE> <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>
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236 <TD><CODE><B>ClustalOWS.</B><B><A HREF="../../../compbio/ws/server/ClustalOWS.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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237 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>>> options)</CODE>
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240 </TD>
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242 <TR BGCOLOR="white" CLASS="TableRowColor">
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243 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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244 <CODE> <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>
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245 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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246 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>>> options)</CODE>
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249 </TD>
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251 <TR BGCOLOR="white" CLASS="TableRowColor">
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252 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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253 <CODE> <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>
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254 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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255 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>>> options)</CODE>
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258 </TD>
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260 <TR BGCOLOR="white" CLASS="TableRowColor">
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261 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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262 <CODE> <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>
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263 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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264 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>>> options)</CODE>
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267 </TD>
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269 <TR BGCOLOR="white" CLASS="TableRowColor">
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270 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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271 <CODE> <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>
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272 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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273 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>>> options)</CODE>
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276 </TD>
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278 <TR BGCOLOR="white" CLASS="TableRowColor">
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279 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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280 <CODE> <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>
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281 <TD><CODE><B>_MsaService.</B><B><A HREF="../../../compbio/ws/server/_MsaService.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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282 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/ws/server/_MsaService.html" title="type parameter in _MsaService">T</A>>> options)</CODE>
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285 </TD>
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287 <TR BGCOLOR="white" CLASS="TableRowColor">
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288 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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289 <CODE> <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>
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290 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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291 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>>> options)</CODE>
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294 </TD>
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296 <TR BGCOLOR="white" CLASS="TableRowColor">
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297 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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298 <CODE> <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>
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299 <TD><CODE><B>DisemblWS.</B><B><A HREF="../../../compbio/ws/server/DisemblWS.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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300 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>>> options)</CODE>
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303 </TD>
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305 <TR BGCOLOR="white" CLASS="TableRowColor">
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306 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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307 <CODE> <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>
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308 <TD><CODE><B>GlobPlotWS.</B><B><A HREF="../../../compbio/ws/server/GlobPlotWS.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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309 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>>> options)</CODE>
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312 </TD>
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314 <TR BGCOLOR="white" CLASS="TableRowColor">
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315 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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316 <CODE> <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>
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317 <TD><CODE><B>SequenceAnnotationService.</B><B><A HREF="../../../compbio/ws/server/SequenceAnnotationService.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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318 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/ws/server/SequenceAnnotationService.html" title="type parameter in SequenceAnnotationService">T</A>>> options)</CODE>
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321 </TD>
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323 <TR BGCOLOR="white" CLASS="TableRowColor">
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324 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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325 <CODE> <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>
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326 <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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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327 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>> preset)</CODE>
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330 </TD>
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332 <TR BGCOLOR="white" CLASS="TableRowColor">
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333 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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334 <CODE> <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>
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335 <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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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336 <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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339 </TD>
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341 <TR BGCOLOR="white" CLASS="TableRowColor">
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342 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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343 <CODE> <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>
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344 <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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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345 <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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348 </TD>
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350 <TR BGCOLOR="white" CLASS="TableRowColor">
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351 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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352 <CODE> <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>
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353 <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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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354 <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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357 </TD>
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359 <TR BGCOLOR="white" CLASS="TableRowColor">
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360 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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361 <CODE> <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>
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362 <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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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363 <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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366 </TD>
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368 <TR BGCOLOR="white" CLASS="TableRowColor">
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369 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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370 <CODE> <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>
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371 <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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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372 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/ws/server/_MsaService.html" title="type parameter in _MsaService">T</A>> preset)</CODE>
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375 </TD>
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377 <TR BGCOLOR="white" CLASS="TableRowColor">
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378 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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379 <CODE> <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>
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380 <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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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381 <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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384 </TD>
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386 <TR BGCOLOR="white" CLASS="TableRowColor">
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387 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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388 <CODE> <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>
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389 <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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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390 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>> preset)</CODE>
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393 </TD>
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395 <TR BGCOLOR="white" CLASS="TableRowColor">
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396 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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397 <CODE> <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>
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398 <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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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399 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>> preset)</CODE>
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402 </TD>
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404 <TR BGCOLOR="white" CLASS="TableRowColor">
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405 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
406 <CODE> <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>
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407 <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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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408 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>> preset)</CODE>
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411 </TD>
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413 <TR BGCOLOR="white" CLASS="TableRowColor">
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414 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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415 <CODE> <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>
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416 <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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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417 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/ws/server/SequenceAnnotationService.html" title="type parameter in SequenceAnnotationService">T</A>> preset)</CODE>
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420 </TD>
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428 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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429 <A NAME="navbar_bottom"><!-- --></A>
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430 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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