-<DT><A HREF="../compbio/metadata/Option.html#defaultValue"><B>defaultValue</B></A> - \r
-Variable in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#description"><B>description</B></A> - \r
-Variable in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD> \r
+<DT><A HREF="../compbio/data/sequence/SMERFSConstraints.html#DEFAULT_COLUMN_SCORE"><B>DEFAULT_COLUMN_SCORE</B></A> - \r
+Static variable in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A>\r
+<DD>Default column scoring schema\r
+<DT><A HREF="../compbio/data/sequence/SMERFSConstraints.html#DEFAULT_GAP_THRESHOLD"><B>DEFAULT_GAP_THRESHOLD</B></A> - \r
+Static variable in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A>\r
+<DD>Default gap threshold value for SMERFS algorithm\r
+<DT><A HREF="../compbio/data/sequence/SMERFSConstraints.html#DEFAULT_WINDOW_SIZE"><B>DEFAULT_WINDOW_SIZE</B></A> - \r
+Static variable in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A>\r
+<DD>Default window size value for SMERFS algorithm\r