JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix delegate of

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

diff --git a/src/jalview/analysis/scoremodels/SWScoreModel.java b/src/jalview/analysis/scoremodels/SWScoreModel.java
deleted file mode 100644 (file)
index d5d998e..0000000
--- a/src/jalview/analysis/scoremodels/SWScoreModel.java
+++ /dev/null
@@ -1,94 +0,0 @@
-/*
- * 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.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";
-  }
-}