X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fapi%2Fanalysis%2FSimilarityParamsI.java;fp=src%2Fjalview%2Fapi%2Fanalysis%2FSimilarityParamsI.java;h=581449fb617332f21c2e7be7ecba3fe3b7caf70e;hp=0000000000000000000000000000000000000000;hb=e67e5f3a5b922e8a7729a0e9e9b174f46b11456c;hpb=8356850ec2f6043a65d3d892f9ebd405f23893e2

diff --git a/src/jalview/api/analysis/SimilarityParamsI.java b/src/jalview/api/analysis/SimilarityParamsI.java
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+++ b/src/jalview/api/analysis/SimilarityParamsI.java
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+package jalview.api.analysis;
+
+/**
+ * A description of options when computing percentage identity of two aligned
+ * sequences
+ */
+public interface SimilarityParamsI
+{
+  /**
+   * Answers true if gap-gap aligned positions should be included in the
+   * calculation
+   * 
+   * @return
+   */
+  boolean includeGappedColumns();
+
+  /**
+   * Answers true if gap-residue alignment is considered a match
+   * 
+   * @return
+   */
+  // TODO is this specific to a PID score only?
+  // score matrix will compute whatever is configured for gap-residue
+  boolean matchGaps();
+
+  /**
+   * Answers true if gaps are included in the calculation. This may affect the
+   * calculated score, the denominator (normalisation factor) of the score, or
+   * both. Gap-gap positions are included if this and includeGappedColumns both
+   * answer true.
+   * 
+   * @return
+   */
+  boolean includeGaps();
+
+  /**
+   * Answers true if only the shortest sequence length is used to divide the
+   * total score, false if the longest sequence length
+   * 
+   * @return
+   */
+  boolean denominateByShortestLength();
+}