Merge remote-tracking branch 'origin/develop' into

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

diff --git a/src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java b/src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java
deleted file mode 100644 (file)
index 2ff2518..0000000
--- a/src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java
+++ /dev/null
@@ -1,80 +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.api.analysis.ScoreModelI;
-import jalview.datamodel.AlignmentView;
-import jalview.util.Comparison;
-
-public abstract class PairwiseSeqScoreModel implements ScoreModelI
-{
-  abstract public int getPairwiseScore(char c, char d);
-
-  public float[][] findDistances(AlignmentView seqData)
-  {
-    String[] sequenceString = seqData
-            .getSequenceStrings(Comparison.GapChars.charAt(0));
-    int noseqs = sequenceString.length;
-    float[][] distance = new float[noseqs][noseqs];
-
-    int maxscore = 0;
-    int end = sequenceString[0].length();
-    for (int i = 0; i < (noseqs - 1); i++)
-    {
-      for (int j = i; j < noseqs; j++)
-      {
-        int score = 0;
-
-        for (int k = 0; k < end; k++)
-        {
-          try
-          {
-            score += getPairwiseScore(sequenceString[i].charAt(k),
-                    sequenceString[j].charAt(k));
-          } catch (Exception ex)
-          {
-            System.err.println("err creating " + getName() + " tree");
-            ex.printStackTrace();
-          }
-        }
-
-        distance[i][j] = (float) score;
-
-        if (score > maxscore)
-        {
-          maxscore = score;
-        }
-      }
-    }
-
-    for (int i = 0; i < (noseqs - 1); i++)
-    {
-      for (int j = i; j < noseqs; j++)
-      {
-        distance[i][j] = (float) maxscore - distance[i][j];
-        distance[j][i] = distance[i][j];
-      }
-    }
-    return distance;
-  }
-
-  abstract public int[][] getMatrix();
-}