website/full_javadoc/compbio/runner/msa/class-use/Muscle.html

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   7 Uses of Class compbio.runner.msa.Muscle\r
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  84 <B>Uses of Class<br>compbio.runner.msa.Muscle</B></H2>\r
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  89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
  90 Packages that use <A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></FONT></TH>\r
  91 </TR>\r
  92 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  93 <TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
  94 <TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
  95 </TR>\r
  96 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  97 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
  98 <TD>&nbsp;&nbsp;</TD>\r
  99 </TR>\r
 100 </TABLE>\r
 101 &nbsp;\r
 102 <P>\r
 103 <A NAME="compbio.runner.msa"><!-- --></A>\r
 104 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 105 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 106 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 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>\r
 108 </TR>\r
 109 </TABLE>\r
 110 &nbsp;\r
 111 <P>\r
 112 \r
 113 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 114 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 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>\r
 116 </TR>\r
 117 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 118 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 119 <CODE>&nbsp;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></CODE></FONT></TD>\r
 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>&nbsp;inFile)</CODE>\r
 121 \r
 122 <BR>\r
 123 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 124 </TR>\r
 125 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 126 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 127 <CODE>&nbsp;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></CODE></FONT></TD>\r
 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>&nbsp;outFile)</CODE>\r
 129 \r
 130 <BR>\r
 131 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 132 </TR>\r
 133 </TABLE>\r
 134 &nbsp;\r
 135 <P>\r
 136 \r
 137 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 138 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 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>\r
 140 </TR>\r
 141 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 142 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 143 <CODE>&nbsp;<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>&lt;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
 144 <TD><CODE><B>Muscle.</B><B><A HREF="../../../../compbio/runner/msa/Muscle.html#getType()">getType</A></B>()</CODE>\r
 145 \r
 146 <BR>\r
 147 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 148 </TR>\r
 149 </TABLE>\r
 150 &nbsp;\r
 151 <P>\r
 152 <A NAME="compbio.ws.server"><!-- --></A>\r
 153 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 154 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 155 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 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>\r
 157 </TR>\r
 158 </TABLE>\r
 159 &nbsp;\r
 160 <P>\r
 161 \r
 162 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 163 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 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>\r
 165 </TR>\r
 166 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 167 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 168 <CODE>&nbsp;<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
 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>&nbsp;presetName)</CODE>\r
 170 \r
 171 <BR>\r
 172 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 173 </TR>\r
 174 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 175 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 176 <CODE>&nbsp;<A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
 177 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#getLimits()">getLimits</A></B>()</CODE>\r
 178 \r
 179 <BR>\r
 180 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 181 </TR>\r
 182 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 183 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 184 <CODE>&nbsp;<A HREF="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
 185 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#getPresets()">getPresets</A></B>()</CODE>\r
 186 \r
 187 <BR>\r
 188 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 189 </TR>\r
 190 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 191 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 192 <CODE>&nbsp;<A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
 193 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
 194 \r
 195 <BR>\r
 196 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 197 </TR>\r
 198 </TABLE>\r
 199 &nbsp;\r
 200 <P>\r
 201 \r
 202 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 203 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 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>\r
 205 </TR>\r
 206 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 207 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 208 <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
 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>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 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>&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&gt;&nbsp;options)</CODE>\r
 211 \r
 212 <BR>\r
 213 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 214 </TR>\r
 215 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 216 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 217 <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
 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>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 219             <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
 220 \r
 221 <BR>\r
 222 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 223 </TR>\r
 224 </TABLE>\r
 225 &nbsp;\r
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