JAL-1473 refactor score matrices and tree score calculations to interface/api and...

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

diff --git a/src/jalview/analysis/scoremodels/SWScoreModel.java b/src/jalview/analysis/scoremodels/SWScoreModel.java
new file mode 100644 (file)
index 0000000..d8c6230
--- /dev/null
+++ b/src/jalview/analysis/scoremodels/SWScoreModel.java
@@ -0,0 +1,54 @@
+package jalview.analysis.scoremodels;
+
+import jalview.analysis.AlignSeq;
+import jalview.api.analysis.ScoreModelI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+
+public class SWScoreModel implements ScoreModelI
+{
+
+  @Override
+  public float[][] findDistances(AlignmentView seqData)
+  {
+    SequenceI[] sequenceString = seqData
+            .getVisibleAlignment(Comparison.GapChars.charAt(0)).getSequencesArray();
+    int noseqs = sequenceString.length;
+    float[][] distance = new float[noseqs][noseqs];
+    
+     float 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);
+      distance[i][j] = (float) as.maxscore;
+      
+      if (max < distance[i][j]) { max = distance[i][j]; } } }
+     
+      for (int i = 0; i < (noseqs - 1); i++) { for (int j = i; j < noseqs; j++)
+      { distance[i][j] = max - distance[i][j]; distance[j][i] = distance[i][j];
+      } } 
+     
+    return distance;
+  }
+
+  @Override
+  public String getName()
+  {
+    return "Smith Waterman Score";
+  }
+  @Override
+  public boolean isDNA()
+  {
+    return true;
+  }
+  @Override
+  public boolean isProtein()
+  {
+    return true;
+  }
+  public String toString() {
+    return "Score between two sequences aligned with Smith Waterman with default Peptide/Nucleotide matrix";
+  }
+}