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17 if (location.href.indexOf('is-external=true') == -1) {
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18 parent.document.title="Mafft";
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27 <BODY BGCOLOR="white" onload="windowTitle();">
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31 <!-- ========= START OF TOP NAVBAR ======= -->
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42 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
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58 <A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa"><B>PREV CLASS</B></A>
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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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95 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>
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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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>>
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97 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.msa.Mafft</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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>>, <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></DD>
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104 <DT><PRE>public class <B>Mafft</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>><DT>implements <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></DL>
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109 <DT><B>Author:</B></DT>
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115 <!-- ======== NESTED CLASS SUMMARY ======== -->
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117 <A NAME="nested_class_summary"><!-- --></A>
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118 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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119 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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120 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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121 <B>Nested Class Summary</B></FONT></TH>
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124 <A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>
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125 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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126 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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127 <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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129 <TR BGCOLOR="white" CLASS="TableRowColor">
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130 <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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134 <!-- =========== FIELD SUMMARY =========== -->
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136 <A NAME="field_summary"><!-- --></A>
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137 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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138 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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139 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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140 <B>Field Summary</B></FONT></TH>
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142 <TR BGCOLOR="white" CLASS="TableRowColor">
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143 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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144 <CODE>static <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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145 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Mafft.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></B></CODE>
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148 </TD>
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151 <A NAME="fields_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>
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152 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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153 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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154 <TH ALIGN="left"><B>Fields 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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156 <TR BGCOLOR="white" CLASS="TableRowColor">
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157 <TD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#ERROR">ERROR</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#INPUT">INPUT</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#OUTPUT">OUTPUT</A></CODE></TD>
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161 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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163 <A NAME="constructor_summary"><!-- --></A>
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164 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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165 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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166 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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167 <B>Constructor Summary</B></FONT></TH>
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169 <TR BGCOLOR="white" CLASS="TableRowColor">
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170 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Mafft.html#Mafft()">Mafft</A></B>()</CODE>
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173 </TD>
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177 <!-- ========== METHOD SUMMARY =========== -->
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179 <A NAME="method_summary"><!-- --></A>
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180 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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181 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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182 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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183 <B>Method Summary</B></FONT></TH>
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185 <TR BGCOLOR="white" CLASS="TableRowColor">
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186 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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187 <CODE> <A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></CODE></FONT></TD>
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188 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Mafft.html#addParameters(java.util.List)">addParameters</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="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> parameters)</CODE>
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191 Mafft input must always be the last parameter!</TD>
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193 <TR BGCOLOR="white" CLASS="TableRowColor">
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194 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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195 <CODE> <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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196 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Mafft.html#getResults(java.lang.String)">getResults</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> workDirectory)</CODE>
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199 </TD>
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201 <TR BGCOLOR="white" CLASS="TableRowColor">
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202 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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203 <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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></CODE></FONT></TD>
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204 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Mafft.html#getType()">getType</A></B>()</CODE>
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207 </TD>
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209 <TR BGCOLOR="white" CLASS="TableRowColor">
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210 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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211 <CODE> <A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></CODE></FONT></TD>
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212 <TD><CODE><B><A HREF="../../../compbio/runner/msa/Mafft.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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215 </TD>
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218 <A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>
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219 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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220 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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221 <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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223 <TR BGCOLOR="white" CLASS="TableRowColor">
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224 <TD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)">equals</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterCpuNum(java.lang.Class)">getClusterCpuNum</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterJobSettings()">getClusterJobSettings</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">getCreatedFiles</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#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getLimits()">getLimits</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#setOutput(java.lang.String)">setOutput</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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227 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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228 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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229 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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230 <TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>
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232 <TR BGCOLOR="white" CLASS="TableRowColor">
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233 <TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>
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236 <A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>
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237 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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238 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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239 <TH ALIGN="left"><B>Methods 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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241 <TR BGCOLOR="white" CLASS="TableRowColor">
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242 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getClusterJobSettings()">getClusterJobSettings</A>, <A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A>, <A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></CODE></TD>
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248 <!-- ============ FIELD DETAIL =========== -->
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250 <A NAME="field_detail"><!-- --></A>
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251 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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252 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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253 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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254 <B>Field Detail</B></FONT></TH>
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258 <A NAME="KEY_VALUE_SEPARATOR"><!-- --></A><H3>
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259 KEY_VALUE_SEPARATOR</H3>
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261 public static final <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> <B>KEY_VALUE_SEPARATOR</B></PRE>
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264 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.msa.Mafft.KEY_VALUE_SEPARATOR">Constant Field Values</A></DL>
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267 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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269 <A NAME="constructor_detail"><!-- --></A>
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270 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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271 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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272 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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273 <B>Constructor Detail</B></FONT></TH>
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277 <A NAME="Mafft()"><!-- --></A><H3>
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280 public <B>Mafft</B>()</PRE>
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284 <!-- ============ METHOD DETAIL ========== -->
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286 <A NAME="method_detail"><!-- --></A>
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287 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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288 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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289 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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290 <B>Method Detail</B></FONT></TH>
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294 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>
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297 public <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResults</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> workDirectory)
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298 throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
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301 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></CODE></DL>
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306 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>
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311 <A NAME="setInput(java.lang.String)"><!-- --></A><H3>
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314 public <A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A> <B>setInput</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)</PRE>
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317 <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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></CODE></DL>
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325 <A NAME="addParameters(java.util.List)"><!-- --></A><H3>
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328 public <A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A> <B>addParameters</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="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> parameters)</PRE>
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330 <DD>Mafft input must always be the last parameter!
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333 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)">addParameters</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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></CODE></DL>
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337 <DT><B>Returns:</B><DD>this Executable</DL>
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342 <A NAME="getType()"><!-- --></A><H3>
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345 public <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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>> <B>getType</B>()</PRE>
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348 <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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></CODE></DL>
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352 <DT><B>Returns:</B><DD>subclasses must return their type</DL>
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355 <!-- ========= END OF CLASS DATA ========= -->
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359 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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360 <A NAME="navbar_bottom"><!-- --></A>
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361 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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362 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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364 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
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365 <A NAME="navbar_bottom_firstrow"><!-- --></A>
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366 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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367 <TR ALIGN="center" VALIGN="top">
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368 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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369 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
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