Merge remote-tracking branch 'origin/develop' into

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

diff --git a/src/jalview/analysis/scoremodels/FeatureScoreModel.java b/src/jalview/analysis/scoremodels/FeatureScoreModel.java
deleted file mode 100644 (file)
index 7c81912..0000000
--- a/src/jalview/analysis/scoremodels/FeatureScoreModel.java
+++ /dev/null
@@ -1,161 +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.api.analysis.ViewBasedAnalysisI;
-import jalview.datamodel.AlignmentView;
-import jalview.datamodel.SeqCigar;
-import jalview.datamodel.SequenceFeature;
-
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-
-public class FeatureScoreModel implements ScoreModelI, ViewBasedAnalysisI
-{
-  jalview.api.FeatureRenderer fr;
-
-  @Override
-  public boolean configureFromAlignmentView(
-          jalview.api.AlignmentViewPanel view)
-  {
-    fr = view.cloneFeatureRenderer();
-    return true;
-  }
-
-  @Override
-  public float[][] findDistances(AlignmentView seqData)
-  {
-    int nofeats = 0;
-    List<String> dft = fr.getDisplayedFeatureTypes();
-    nofeats = dft.size();
-    SeqCigar[] seqs = seqData.getSequences();
-    int noseqs = seqs.length;
-    int cpwidth = 0;// = seqData.getWidth();
-    float[][] distance = new float[noseqs][noseqs];
-    if (nofeats == 0)
-    {
-      for (float[] d : distance)
-      {
-        for (int i = 0; i < d.length; d[i++] = 0f)
-        {
-          ;
-        }
-      }
-      return distance;
-    }
-    // need to get real position for view position
-    int[] viscont = seqData.getVisibleContigs();
-    for (int vc = 0; vc < viscont.length; vc += 2)
-    {
-
-      for (int cpos = viscont[vc]; cpos <= viscont[vc + 1]; cpos++)
-      {
-        cpwidth++;
-        // get visible features at cpos under view's display settings and
-        // compare them
-        List<Hashtable<String, SequenceFeature>> sfap = new ArrayList<Hashtable<String, SequenceFeature>>();
-        for (int i = 0; i < noseqs; i++)
-        {
-          Hashtable<String, SequenceFeature> types = new Hashtable<String, SequenceFeature>();
-          int spos = seqs[i].findPosition(cpos);
-          if (spos != -1)
-          {
-            List<SequenceFeature> sfs = fr.findFeaturesAtRes(
-                    seqs[i].getRefSeq(), spos);
-            for (SequenceFeature sf : sfs)
-            {
-              types.put(sf.getType(), sf);
-            }
-          }
-          sfap.add(types);
-        }
-        for (int i = 0; i < (noseqs - 1); i++)
-        {
-          if (cpos == 0)
-          {
-            distance[i][i] = 0f;
-          }
-          for (int j = i + 1; j < noseqs; j++)
-          {
-            int sfcommon = 0;
-            // compare the two lists of features...
-            Hashtable<String, SequenceFeature> fi = sfap.get(i), fk, fj = sfap
-                    .get(j);
-            if (fi.size() > fj.size())
-            {
-              fk = fj;
-            }
-            else
-            {
-              fk = fi;
-              fi = fj;
-            }
-            for (String k : fi.keySet())
-            {
-              SequenceFeature sfj = fk.get(k);
-              if (sfj != null)
-              {
-                sfcommon++;
-              }
-            }
-            distance[i][j] += (fi.size() + fk.size() - 2f * sfcommon);
-            distance[j][i] += distance[i][j];
-          }
-        }
-      }
-    }
-    for (int i = 0; i < noseqs; i++)
-    {
-      for (int j = i + 1; j < noseqs; j++)
-      {
-        distance[i][j] /= cpwidth;
-        distance[j][i] = distance[i][j];
-      }
-    }
-    return distance;
-  }
-
-  @Override
-  public String getName()
-  {
-    return "Sequence Feature Similarity";
-  }
-
-  @Override
-  public boolean isDNA()
-  {
-    return true;
-  }
-
-  @Override
-  public boolean isProtein()
-  {
-    return true;
-  }
-
-  @Override
-  public String toString()
-  {
-    return "Score between sequences based on hamming distance between binary vectors marking features displayed at each column";
-  }
-}