JAL-2403 SWDistanceModel now SmithWatermanModel - a similarity model

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

diff --git a/src/jalview/analysis/scoremodels/SmithWatermanModel.java b/src/jalview/analysis/scoremodels/SmithWatermanModel.java
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+++ b/src/jalview/analysis/scoremodels/SmithWatermanModel.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.analysis.scoremodels;
+
+import jalview.analysis.AlignSeq;
+import jalview.api.analysis.SimilarityParamsI;
+import jalview.api.analysis.SimilarityScoreModelI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SequenceI;
+import jalview.math.Matrix;
+import jalview.math.MatrixI;
+import jalview.util.Comparison;
+
+/**
+ * A class that computes pairwise similarity scores using the Smith-Waterman
+ * alignment algorithm
+ */
+public class SmithWatermanModel implements SimilarityScoreModelI
+{
+  private static final String NAME = "Smith Waterman Score";
+
+  @Override
+  public MatrixI findSimilarities(AlignmentView seqData,
+          SimilarityParamsI options)
+  {
+    SequenceI[] sequenceString = seqData.getVisibleAlignment(
+            Comparison.GAP_SPACE).getSequencesArray();
+    int noseqs = sequenceString.length;
+    double[][] distances = new double[noseqs][noseqs];
+
+    double max = -1;
+
+    for (int i = 0; i < (noseqs - 1); i++)
+    {
+      for (int j = i; j < noseqs; j++)
+      {
+        AlignSeq as = new AlignSeq(sequenceString[i], sequenceString[j],
+                seqData.isNa() ? "dna" : "pep");
+        as.calcScoreMatrix();
+        as.traceAlignment();
+        as.printAlignment(System.out);
+        distances[i][j] = as.maxscore;
+
+        if (max < distances[i][j])
+        {
+          max = distances[i][j];
+        }
+      }
+    }
+
+    return new Matrix(distances);
+  }
+
+  @Override
+  public String getName()
+  {
+    return NAME;
+  }
+
+  @Override
+  public boolean isDNA()
+  {
+    return true;
+  }
+
+  @Override
+  public boolean isProtein()
+  {
+    return true;
+  }
+
+  @Override
+  public String toString()
+  {
+    return "Score between two sequences aligned with Smith Waterman with default Peptide/Nucleotide matrix";
+  }
+}