Merge branch 'develop' into features/JAL-250_hideredundantseqs

[jalview.git] / src / jalview / api / analysis / SimilarityParamsI.java

diff --git a/src/jalview/api/analysis/SimilarityParamsI.java b/src/jalview/api/analysis/SimilarityParamsI.java
new file mode 100644 (file)
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+++ b/src/jalview/api/analysis/SimilarityParamsI.java
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+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+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();
+}