+/*
+ * 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 jalview.datamodel.SequenceI;
-import jalview.util.Comparison;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.Hashtable;
import java.util.List;
@Override
public float[][] findDistances(AlignmentView seqData)
{
-
- SequenceI[] sequenceString = seqData.getVisibleAlignment(
- Comparison.GapChars.charAt(0)).getSequencesArray();
- int noseqs = sequenceString.length;
- int cpwidth = seqData.getWidth();
+ 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];
- float max = 0;
- for (int cpos = 0; cpos < cpwidth; cpos++)
+ if (nofeats == 0)
{
- // get visible features at cpos under view's display settings and compare
- // them
- for (int i = 0; i < (noseqs - 1); i++)
+ for (float[] d : distance)
{
- List<SequenceFeature> sf = fr.findFeaturesAtRes(sequenceString[i],
- cpos);
- for (int j = i + 1; j < noseqs; j++)
+ for (int i = 0; i < d.length; d[i++] = 0f)
{
- List<SequenceFeature> jsf = fr.findFeaturesAtRes(
- sequenceString[i], cpos);
- // compare the two lists of features...
+ ;
+ }
+ }
+ return distance;
+ }
+ // need to get real position for view position
+ int[] viscont = seqData.getVisibleContigs();
+ for (int vc = 0; vc < viscont.length; vc += 2)
+ {
- if (max < distance[i][j])
+ 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++)
{
- max = distance[i][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 - 1); i++)
+ for (int i = 0; i < noseqs; i++)
{
- for (int j = i; j < noseqs; j++)
+ for (int j = i + 1; j < noseqs; j++)
{
- distance[i][j] = max - distance[i][j];
+ distance[i][j] /= cpwidth;
distance[j][i] = distance[i][j];
}
}
-
return distance;
}
@Override
public String getName()
{
- return "Smith Waterman Score";
+ return "Sequence Feature Similarity";
}
@Override
return true;
}
+ @Override
public String toString()
{
- return "Score between two sequences aligned with Smith Waterman with default Peptide/Nucleotide matrix";
+ return "Score between sequences based on hamming distance between binary vectors marking features displayed at each column";
}
}