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Merge branch 'develop' into features/JAL-2393customMatrices
[jalview.git]
/
src
/
jalview
/
api
/
analysis
/
DistanceScoreModelI.java
diff --git
a/src/jalview/api/analysis/DistanceScoreModelI.java
b/src/jalview/api/analysis/DistanceScoreModelI.java
index
27003e8
..
0a39c0b
100644
(file)
--- a/
src/jalview/api/analysis/DistanceScoreModelI.java
+++ b/
src/jalview/api/analysis/DistanceScoreModelI.java
@@
-5,7
+5,8
@@
import jalview.math.MatrixI;
/**
* A sequence distance score models, that provides a method to compute distances
/**
* A sequence distance score models, that provides a method to compute distances
- * between pairs of sequences
+ * between pairs of sequences. The options parameter provides configuration
+ * choices for how the similarity score is calculated.
*
* @author gmcarstairs
*
*
* @author gmcarstairs
*
@@
-18,7
+19,8
@@
public interface DistanceScoreModelI extends ScoreModelI
* measure
*
* @param seqData
* measure
*
* @param seqData
+ * @param options
* @return
*/
* @return
*/
- MatrixI findDistances(AlignmentView seqData);
+ MatrixI findDistances(AlignmentView seqData, SimilarityParamsI options);
}
}