Merge branch 'bug/JAL-3120restoreFeatureColour' into merge/JAL-3120

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

diff --git a/src/jalview/analysis/scoremodels/PIDModel.java b/src/jalview/analysis/scoremodels/PIDModel.java
index 50c4a71..c1e8b42 100644 (file)
--- a/src/jalview/analysis/scoremodels/PIDModel.java
+++ b/src/jalview/analysis/scoremodels/PIDModel.java
@@ -1,24 +1,65 @@
+/*
+ * 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.analysis.scoremodels;
 
+import jalview.api.AlignmentViewPanel;
 import jalview.api.analysis.PairwiseScoreModelI;
+import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
-import jalview.api.analysis.SimilarityScoreModelI;
 import jalview.datamodel.AlignmentView;
 import jalview.math.Matrix;
 import jalview.math.MatrixI;
 import jalview.util.Comparison;
 
 /**
- * A class to provide sequence pairwise similarity based on residue identity
+ * A class to provide sequence pairwise similarity based on residue identity.
+ * Instances of this class are immutable and thread-safe, so the same object is
+ * returned from calls to getInstance().
  */
-public class PIDModel implements SimilarityScoreModelI,
-        PairwiseScoreModelI
+public class PIDModel extends SimilarityScoreModel
+        implements PairwiseScoreModelI
 {
+  private static final String NAME = "PID";
+
+  /**
+   * Constructor
+   */
+  public PIDModel()
+  {
+  }
 
   @Override
   public String getName()
   {
-    return "% Identity (PID)";
+    return NAME;
+  }
+
+  /**
+   * Answers null for description. If a display name is needed, use getName() or
+   * an internationalized string built from the name.
+   */
+  @Override
+  public String getDescription()
+  {
+    return null;
   }
 
   @Override
@@ -61,12 +102,43 @@ public class PIDModel implements SimilarityScoreModelI,
     return c;
   }
 
+  /**
+   * Computes similarity scores based on pairwise percentage identity of
+   * sequences. For consistency with Jalview 2.10.1's SeqSpace mode PCA
+   * calculation, the percentage scores are rescaled to the width of the
+   * sequences (as if counts of identical residues). This method is thread-safe.
+   */
   @Override
   public MatrixI findSimilarities(AlignmentView seqData,
           SimilarityParamsI options)
   {
-    String[] seqs = seqData.getSequenceStrings(' ');
-    return findSimilarities(seqs, options);
+    String[] seqs = seqData.getSequenceStrings(Comparison.GAP_DASH);
+
+    MatrixI result = findSimilarities(seqs, options);
+
+    result.multiply(seqData.getWidth() / 100d);
+
+    return result;
+  }
+
+  /**
+   * A distance score is computed in the usual way (by reversing the range of
+   * the similarity score results), and then rescaled to percentage values
+   * (reversing the rescaling to count values done in findSimilarities). This
+   * method is thread-safe.
+   */
+  @Override
+  public MatrixI findDistances(AlignmentView seqData,
+          SimilarityParamsI options)
+  {
+    MatrixI result = super.findDistances(seqData, options);
+
+    if (seqData.getWidth() != 0)
+    {
+      result.multiply(100d / seqData.getWidth());
+    }
+
+    return result;
   }
 
   /**
@@ -103,7 +175,7 @@ public class PIDModel implements SimilarityScoreModelI,
    * @param options
    * @return
    */
-  protected static double computePID(String seq1, String seq2,
+  public static double computePID(String seq1, String seq2,
           SimilarityParamsI options)
   {
     int len1 = seq1.length();
@@ -124,7 +196,7 @@ public class PIDModel implements SimilarityScoreModelI,
         {
           break;
         }
-        if (options.includesGaps())
+        if (options.includeGaps())
         {
           divideBy++;
         }
@@ -159,7 +231,7 @@ public class PIDModel implements SimilarityScoreModelI,
          * gap-residue: include if options say so, 
          * count as match if options say so
          */
-        if (options.includesGaps())
+        if (options.includeGaps())
         {
           divideBy++;
         }
@@ -182,4 +254,10 @@ public class PIDModel implements SimilarityScoreModelI,
 
     return divideBy == 0 ? 0D : 100D * total / divideBy;
   }
+
+  @Override
+  public ScoreModelI getInstance(AlignmentViewPanel avp)
+  {
+    return this;
+  }
 }