-<CODE> <A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></CODE></FONT></TD>\r
-<TD><CODE><B>Mafft.</B><B><A HREF="../../../../compbio/runner/msa/Mafft.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String presetName)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></CODE></FONT></TD>\r
-<TD><CODE><B>Mafft.</B><B><A HREF="../../../../compbio/runner/msa/Mafft.html#getLimits()">getLimits</A></B>()</CODE>\r
+<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>\r
+<TD><CODE><B>Mafft.</B><B><A HREF="../../../../compbio/runner/msa/Mafft.html#getType()">getType</A></B>()</CODE>\r