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17 if (location.href.indexOf('is-external=true') == -1) {
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18 parent.document.title="ClustalW";
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78 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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79 SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
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80 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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81 DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
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84 <A NAME="skip-navbar_top"></A>
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85 <!-- ========= END OF TOP NAVBAR ========= -->
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88 <!-- ======== START OF CLASS DATA ======== -->
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91 compbio.runner.msa</FONT>
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96 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">compbio.engine.client.SkeletalExecutable</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>>
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97 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.msa.ClustalW</B>
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100 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></DD>
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104 <DT><PRE>public class <B>ClustalW</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></DL>
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111 <!-- ======== NESTED CLASS SUMMARY ======== -->
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115 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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116 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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117 <B>Nested Class Summary</B></FONT></TH>
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120 <A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>
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121 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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122 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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123 <TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>
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125 <TR BGCOLOR="white" CLASS="TableRowColor">
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126 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>
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130 <!-- =========== FIELD SUMMARY =========== -->
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132 <A NAME="field_summary"><!-- --></A>
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133 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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134 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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135 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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136 <B>Field Summary</B></FONT></TH>
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138 <TR BGCOLOR="white" CLASS="TableRowColor">
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139 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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140 <CODE>static java.lang.String</CODE></FONT></TD>
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141 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></B></CODE>
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144 </TD>
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148 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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150 <A NAME="constructor_summary"><!-- --></A>
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151 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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152 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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153 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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154 <B>Constructor Summary</B></FONT></TH>
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156 <TR BGCOLOR="white" CLASS="TableRowColor">
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157 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#ClustalW()">ClustalW</A></B>()</CODE>
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160 </TD>
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164 <!-- ========== METHOD SUMMARY =========== -->
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166 <A NAME="method_summary"><!-- --></A>
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167 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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168 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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169 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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170 <B>Method Summary</B></FONT></TH>
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172 <TR BGCOLOR="white" CLASS="TableRowColor">
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173 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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174 <CODE> java.util.List<java.lang.String></CODE></FONT></TD>
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175 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>
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178 This method cannot really tell whether the files has actually been
179 created or not.</TD>
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181 <TR BGCOLOR="white" CLASS="TableRowColor">
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182 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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183 <CODE> <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></FONT></TD>
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184 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String presetName)</CODE>
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187 </TD>
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189 <TR BGCOLOR="white" CLASS="TableRowColor">
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190 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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191 <CODE> <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></FONT></TD>
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192 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#getLimits()">getLimits</A></B>()</CODE>
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195 </TD>
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197 <TR BGCOLOR="white" CLASS="TableRowColor">
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198 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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199 <CODE> <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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200 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String workDirectory)</CODE>
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203 </TD>
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205 <TR BGCOLOR="white" CLASS="TableRowColor">
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206 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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207 <CODE>static java.lang.String</CODE></FONT></TD>
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208 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#getStatFile()">getStatFile</A></B>()</CODE>
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211 </TD>
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213 <TR BGCOLOR="white" CLASS="TableRowColor">
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214 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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215 <CODE> java.lang.Class<? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>></CODE></FONT></TD>
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216 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#getType()">getType</A></B>()</CODE>
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219 </TD>
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221 <TR BGCOLOR="white" CLASS="TableRowColor">
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222 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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223 <CODE> <A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></CODE></FONT></TD>
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224 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#setInput(java.lang.String)">setInput</A></B>(java.lang.String inFile)</CODE>
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227 </TD>
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229 <TR BGCOLOR="white" CLASS="TableRowColor">
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230 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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231 <CODE> <A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></CODE></FONT></TD>
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232 <TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#setOutput(java.lang.String)">setOutput</A></B>(java.lang.String outFile)</CODE>
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235 </TD>
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238 <A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>
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239 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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240 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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241 <TH ALIGN="left"><B>Methods inherited from class compbio.engine.client.<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A></B></TH>
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243 <TR BGCOLOR="white" CLASS="TableRowColor">
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244 <TD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)">equals</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterSettings()">getClusterSettings</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#hashCode()">hashCode</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)">setError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)">setParameter</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#toString()">toString</A></CODE></TD>
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247 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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248 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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249 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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250 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>
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252 <TR BGCOLOR="white" CLASS="TableRowColor">
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253 <TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>
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259 <!-- ============ FIELD DETAIL =========== -->
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261 <A NAME="field_detail"><!-- --></A>
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262 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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263 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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264 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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265 <B>Field Detail</B></FONT></TH>
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269 <A NAME="KEY_VALUE_SEPARATOR"><!-- --></A><H3>
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270 KEY_VALUE_SEPARATOR</H3>
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272 public static final java.lang.String <B>KEY_VALUE_SEPARATOR</B></PRE>
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275 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.msa.ClustalW.KEY_VALUE_SEPARATOR">Constant Field Values</A></DL>
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278 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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280 <A NAME="constructor_detail"><!-- --></A>
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281 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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282 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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283 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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284 <B>Constructor Detail</B></FONT></TH>
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288 <A NAME="ClustalW()"><!-- --></A><H3>
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291 public <B>ClustalW</B>()</PRE>
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295 <!-- ============ METHOD DETAIL ========== -->
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297 <A NAME="method_detail"><!-- --></A>
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298 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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299 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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300 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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301 <B>Method Detail</B></FONT></TH>
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305 <A NAME="setOutput(java.lang.String)"><!-- --></A><H3>
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308 public <A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A> <B>setOutput</B>(java.lang.String outFile)</PRE>
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311 <DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)">setOutput</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>
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319 <A NAME="setInput(java.lang.String)"><!-- --></A><H3>
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322 public <A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A> <B>setInput</B>(java.lang.String inFile)</PRE>
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325 <DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)">setInput</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>
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333 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>
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336 public <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResults</B>(java.lang.String workDirectory)
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337 throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
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342 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>
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347 <A NAME="getCreatedFiles()"><!-- --></A><H3>
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348 getCreatedFiles</H3>
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350 public java.util.List<java.lang.String> <B>getCreatedFiles</B>()</PRE>
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352 <DD><B>Description copied from class: <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">SkeletalExecutable</A></CODE></B></DD>
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353 <DD>This method cannot really tell whether the files has actually been
354 created or not. It must be overridden as required.
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357 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">getCreatedFiles</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>
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360 <DT><B>See Also:</B><DD><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()"><CODE>Executable.getCreatedFiles()</CODE></A></DL>
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365 <A NAME="getStatFile()"><!-- --></A><H3>
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368 public static java.lang.String <B>getStatFile</B>()</PRE>
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376 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>
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379 public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>> <B>getLimit</B>(java.lang.String presetName)</PRE>
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387 <A NAME="getLimits()"><!-- --></A><H3>
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390 public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>> <B>getLimits</B>()</PRE>
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398 <A NAME="getType()"><!-- --></A><H3>
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401 public java.lang.Class<? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>> <B>getType</B>()</PRE>
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404 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getType()">getType</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>
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410 <!-- ========= END OF CLASS DATA ========= -->
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414 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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415 <A NAME="navbar_bottom"><!-- --></A>
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416 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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417 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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419 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
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420 <A NAME="navbar_bottom_firstrow"><!-- --></A>
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421 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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422 <TR ALIGN="center" VALIGN="top">
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423 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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424 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
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425 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
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426 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ClustalW.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
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427 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
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428 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
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429 <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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430 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
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434 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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440 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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441 PREV CLASS
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442 <A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa"><B>NEXT CLASS</B></A></FONT></TD>
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443 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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444 <A HREF="../../../index.html?compbio/runner/msa/ClustalW.html" target="_top"><B>FRAMES</B></A>
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445 <A HREF="ClustalW.html" target="_top"><B>NO FRAMES</B></A>
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446 <SCRIPT type="text/javascript">
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449 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
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454 <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
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461 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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462 SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
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463 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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464 DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
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467 <A NAME="skip-navbar_bottom"></A>
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468 <!-- ======== END OF BOTTOM NAVBAR ======= -->
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