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5 <!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:30:42 GMT 2011 -->
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7 Uses of Class compbio.runner.msa.Muscle
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18 parent.document.title="Uses of Class compbio.runner.msa.Muscle";
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42 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
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84 <B>Uses of Class<br>compbio.runner.msa.Muscle</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/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></FONT></TH>
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92 <TR BGCOLOR="white" CLASS="TableRowColor">
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93 <TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>
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94 <TD>Wrappers for native executables for multiple sequence alignment (msa) </TD>
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96 <TR BGCOLOR="white" CLASS="TableRowColor">
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97 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>
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98 <TD> </TD>
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103 <A NAME="compbio.runner.msa"><!-- --></A>
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104 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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105 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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106 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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107 Uses of <A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>
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113 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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114 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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115 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return <A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></FONT></TH>
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117 <TR BGCOLOR="white" CLASS="TableRowColor">
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118 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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119 <CODE> <A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></CODE></FONT></TD>
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120 <TD><CODE><B>Muscle.</B><B><A HREF="../../../../compbio/runner/msa/Muscle.html#setInput(java.lang.String)">setInput</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> inFile)</CODE>
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123 </TD>
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125 <TR BGCOLOR="white" CLASS="TableRowColor">
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126 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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127 <CODE> <A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></CODE></FONT></TD>
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128 <TD><CODE><B>Muscle.</B><B><A HREF="../../../../compbio/runner/msa/Muscle.html#setOutput(java.lang.String)">setOutput</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> outFile)</CODE>
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131 </TD>
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137 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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138 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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139 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return types with arguments of type <A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></FONT></TH>
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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/Class.html?is-external=true" title="class or interface in java.lang">Class</A><<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>></CODE></FONT></TD>
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144 <TD><CODE><B>Muscle.</B><B><A HREF="../../../../compbio/runner/msa/Muscle.html#getType()">getType</A></B>()</CODE>
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147 </TD>
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152 <A NAME="compbio.ws.server"><!-- --></A>
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153 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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154 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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155 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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156 Uses of <A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A> in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>
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162 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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163 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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164 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that return types with arguments of type <A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></FONT></TH>
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166 <TR BGCOLOR="white" CLASS="TableRowColor">
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167 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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168 <CODE> <A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>></CODE></FONT></TD>
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169 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#getLimit(java.lang.String)">getLimit</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> presetName)</CODE>
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172 </TD>
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174 <TR BGCOLOR="white" CLASS="TableRowColor">
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175 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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176 <CODE> <A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>></CODE></FONT></TD>
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177 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#getLimits()">getLimits</A></B>()</CODE>
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180 </TD>
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182 <TR BGCOLOR="white" CLASS="TableRowColor">
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183 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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184 <CODE> <A HREF="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>></CODE></FONT></TD>
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185 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#getPresets()">getPresets</A></B>()</CODE>
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188 </TD>
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190 <TR BGCOLOR="white" CLASS="TableRowColor">
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191 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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192 <CODE> <A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>></CODE></FONT></TD>
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193 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>
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196 </TD>
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202 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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203 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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204 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> with type arguments of type <A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></FONT></TH>
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206 <TR BGCOLOR="white" CLASS="TableRowColor">
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207 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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208 <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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209 <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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210 <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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213 </TD>
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215 <TR BGCOLOR="white" CLASS="TableRowColor">
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216 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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217 <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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218 <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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219 <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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