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-compbio.data.*</FONT></TH>\r
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-<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-<TH ALIGN="left" COLSPAN="3">compbio.data.msa.<A HREF="compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A></TH>\r
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-<TD ALIGN="left"><CODE><A HREF="compbio/data/msa/JABAService.html#V2_SERVICE_NAMESPACE">V2_SERVICE_NAMESPACE</A></CODE></TD>\r
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-<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="3">compbio.data.sequence.<A HREF="compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A></TH>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<A NAME="compbio.data.sequence.ClustalAlignmentUtil.gapchar"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
-<CODE>public static final char</CODE></FONT></TD>\r
-<TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/ClustalAlignmentUtil.html#gapchar">gapchar</A></CODE></TD>\r
-<TD ALIGN="right"><CODE>45</CODE></TD>\r
-</TR>\r
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-\r
-<P>\r
-\r
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-\r
-<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-<TH ALIGN="left" COLSPAN="3">compbio.data.sequence.<A HREF="compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<A NAME="compbio.data.sequence.ScoreManager.SINGLE_ENTRY_KEY"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
-<CODE>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></CODE></FONT></TD>\r
-<TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/ScoreManager.html#SINGLE_ENTRY_KEY">SINGLE_ENTRY_KEY</A></CODE></TD>\r
-<TD ALIGN="right"><CODE>"Alignment"</CODE></TD>\r
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-</TABLE>\r
-\r
-<P>\r
-\r
-<P>\r
-\r
-<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="3">compbio.data.sequence.<A HREF="compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<A NAME="compbio.data.sequence.SMERFSConstraints.DEFAULT_GAP_THRESHOLD"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
-<CODE>public static final double</CODE></FONT></TD>\r
-<TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/SMERFSConstraints.html#DEFAULT_GAP_THRESHOLD">DEFAULT_GAP_THRESHOLD</A></CODE></TD>\r
-<TD ALIGN="right"><CODE>0.1</CODE></TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<A NAME="compbio.data.sequence.SMERFSConstraints.DEFAULT_WINDOW_SIZE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
-<CODE>public static final int</CODE></FONT></TD>\r
-<TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/SMERFSConstraints.html#DEFAULT_WINDOW_SIZE">DEFAULT_WINDOW_SIZE</A></CODE></TD>\r
-<TD ALIGN="right"><CODE>7</CODE></TD>\r
-</TR>\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-\r
-<P>\r
-<A NAME="compbio.metadata"><!-- --></A>\r
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-<TH ALIGN="left"><FONT SIZE="+2">\r
-compbio.metadata.*</FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-\r
-<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="3">compbio.metadata.<A HREF="compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>></TH>\r
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-<A NAME="compbio.metadata.PresetManager.LOCAL_ENGINE_LIMIT_PRESET"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
-<CODE>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></CODE></FONT></TD>\r
-<TD ALIGN="left"><CODE><A HREF="compbio/metadata/PresetManager.html#LOCAL_ENGINE_LIMIT_PRESET">LOCAL_ENGINE_LIMIT_PRESET</A></CODE></TD>\r
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