From f3fde43f69bd21759da2273418b4a1a6fb7186fa Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 27 Mar 2017 10:09:22 +0100
Subject: [PATCH] JAL-2403 PIDDistanceModel deleted as superseded by PIDModel

---
 .../analysis/scoremodels/PIDDistanceModel.java     |   88 --------------------
 1 file changed, 88 deletions(-)
 delete mode 100644 src/jalview/analysis/scoremodels/PIDDistanceModel.java

diff --git a/src/jalview/analysis/scoremodels/PIDDistanceModel.java b/src/jalview/analysis/scoremodels/PIDDistanceModel.java
deleted file mode 100644
index bb9d834..0000000
--- a/src/jalview/analysis/scoremodels/PIDDistanceModel.java
+++ /dev/null
@@ -1,88 +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.DistanceScoreModelI;
-import jalview.api.analysis.SimilarityParamsI;
-import jalview.datamodel.AlignmentView;
-import jalview.math.Matrix;
-import jalview.math.MatrixI;
-import jalview.util.Comparison;
-
-/**
- * @deprecated superseded by PIDModel
- */
-@Deprecated
-public class PIDDistanceModel implements DistanceScoreModelI
-{
-
-  @Override
-  public MatrixI findDistances(AlignmentView seqData,
-          SimilarityParamsI options)
-  {
-    String[] sequenceString = seqData
-            .getSequenceStrings(Comparison.GAP_SPACE);
-    int noseqs = sequenceString.length;
-    double[][] distance = new double[noseqs][noseqs];
-    for (int i = 0; i < (noseqs - 1); i++)
-    {
-      for (int j = i; j < noseqs; j++)
-      {
-        if (j == i)
-        {
-          distance[i][i] = 0;
-        }
-        else
-        {
-          distance[i][j] = 100 - Comparison.PID(sequenceString[i],
-                  sequenceString[j]);
-
-          distance[j][i] = distance[i][j];
-        }
-      }
-    }
-    return new Matrix(distance);
-  }
-
-  @Override
-  public String getName()
-  {
-    return "PID";
-  }
-
-  @Override
-  public boolean isDNA()
-  {
-    return true;
-  }
-
-  @Override
-  public boolean isProtein()
-  {
-    return true;
-  }
-
-  @Override
-  public String toString()
-  {
-    return "Percentage identity of sequences";
-  }
-}
-- 
1.7.10.2