JAL-838 first version of PID parameters model

[jalview.git] / src / jalview / analysis / scoremodels / SimilarityParams.java

diff --git a/src/jalview/analysis/scoremodels/SimilarityParams.java b/src/jalview/analysis/scoremodels/SimilarityParams.java
new file mode 100644 (file)
index 0000000..8b6b7d0
--- /dev/null
+++ b/src/jalview/analysis/scoremodels/SimilarityParams.java
@@ -0,0 +1,73 @@
+package jalview.analysis.scoremodels;
+
+import jalview.api.analysis.SimilarityParamsI;
+
+public class SimilarityParams implements SimilarityParamsI
+{
+  public static final SimilarityParamsI Jalview = new SimilarityParams(
+          true, true, true, true);
+
+  public static final SimilarityParamsI PID1 = new SimilarityParams(false,
+          false, true, false);
+
+  public static final SimilarityParamsI PID2 = new SimilarityParams(false,
+          false, false, false);
+
+  public static final SimilarityParamsI PID3 = new SimilarityParams(false,
+          false, false, true);
+
+  public static final SimilarityParamsI PID4 = new SimilarityParams(false,
+          false, true, true);
+
+  private boolean includeGappedColumns;
+
+  private boolean matchGaps;
+
+  private boolean denominatorIncludesGaps;
+
+  private boolean denominateByShortestLength;
+
+  /**
+   * Constructor
+   * 
+   * @param includeGapGap
+   * @param matchGap
+   * @param includeGaps
+   *          if true, gapped positions are counted in the PID denominator
+   * @param shortestLength
+   *          if true, the denominator is the shorter sequence length (possibly
+   *          including gaps)
+   */
+  SimilarityParams(boolean includeGapGap, boolean matchGap,
+          boolean includeGaps, boolean shortestLength)
+  {
+    includeGappedColumns = includeGapGap;
+    matchGaps = matchGap;
+    denominatorIncludesGaps = includeGaps;
+    denominateByShortestLength = shortestLength;
+  }
+
+  @Override
+  public boolean denominatorIncludesGaps()
+  {
+    return denominatorIncludesGaps;
+  }
+
+  @Override
+  public boolean denominateByShortestLength()
+  {
+    return denominateByShortestLength;
+  }
+
+  @Override
+  public boolean includeGappedColumns()
+  {
+    return includeGappedColumns;
+  }
+
+  @Override
+  public boolean matchGaps()
+  {
+    return matchGaps;
+  }
+}