1 package jalview.analysis.scoremodels;
3 import jalview.api.analysis.SimilarityParamsI;
5 public class SimilarityParams implements SimilarityParamsI
8 * Based on Jalview's Comparison.PID method, which includes gaps and counts
9 * them as matching; it counts over the length of the shorter sequence
11 public static final SimilarityParamsI Jalview = new SimilarityParams(
12 true, true, true, true);
15 * 'SeqSpace' mode PCA calculation includes gaps but does not count them as
16 * matching; it uses the longest sequence length
18 public static final SimilarityParamsI SeqSpace = new SimilarityParams(
19 true, false, true, true);
22 * as described in the Raghava-Barton paper; considers pairwise similarity
23 * only (excludes gap-gap) and does not match gaps
25 public static final SimilarityParamsI PID1 = new SimilarityParams(false,
29 * as described in the Raghava-Barton paper; considers pairwise similarity
30 * only (excludes gap-gap) and does not match gaps
32 public static final SimilarityParamsI PID2 = new SimilarityParams(false,
36 * as described in the Raghava-Barton paper; considers pairwise similarity
37 * only (excludes gap-gap) and does not match gaps
39 public static final SimilarityParamsI PID3 = new SimilarityParams(false,
43 * as described in the Raghava-Barton paper; considers pairwise similarity
44 * only (excludes gap-gap) and does not match gaps
46 public static final SimilarityParamsI PID4 = new SimilarityParams(false,
49 private boolean includeGappedColumns;
51 private boolean matchGaps;
53 private boolean denominatorIncludesGaps;
55 private boolean denominateByShortestLength;
60 * @param includeGapGap
63 * if true, gapped positions are counted in the PID denominator
64 * @param shortestLength
65 * if true, the denominator is the shorter sequence length (possibly
68 public SimilarityParams(boolean includeGapGap, boolean matchGap,
69 boolean includeGaps, boolean shortestLength)
71 includeGappedColumns = includeGapGap;
73 denominatorIncludesGaps = includeGaps;
74 denominateByShortestLength = shortestLength;
78 public boolean includesGaps()
80 return denominatorIncludesGaps;
84 public boolean denominateByShortestLength()
86 return denominateByShortestLength;
90 public boolean includeGappedColumns()
92 return includeGappedColumns;
96 public boolean matchGaps()