/*
* 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 .
* 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.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import java.util.ArrayList;
import java.util.Arrays;
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 dft = Arrays.asList(fr.getDisplayedFeatureTypes());
if (dft != null)
{
nofeats = dft.size();
}
SequenceI[] sequenceString = seqData.getVisibleAlignment(
Comparison.GapChars.charAt(0)).getSequencesArray();
int noseqs = sequenceString.length;
int cpwidth = 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;
}
float max = 0;
for (int cpos = 0; cpos < cpwidth; cpos++)
{
// get visible features at cpos under view's display settings and compare
// them
List> sfap = new ArrayList>();
for (int i = 0; i < noseqs; i++)
{
Hashtable types = new Hashtable();
List sfs = fr.findFeaturesAtRes(sequenceString[i],
sequenceString[i].findPosition(cpos));
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 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;
}
public String toString()
{
return "Score between sequences based on hamming distance between binary vectors marking features displayed at each column";
}
}