+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 java.awt.Color;
-
-import jalview.analysis.AlignSeq;
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;
-public class FeatureScoreModel implements ScoreModelI,ViewBasedAnalysisI
+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)
+
+ @Override
+ public boolean configureFromAlignmentView(
+ jalview.api.AlignmentViewPanel view)
{
fr = view.cloneFeatureRenderer();
return true;
@Override
public float[][] findDistances(AlignmentView seqData)
{
-
- SequenceI[] sequenceString = seqData
- .getVisibleAlignment(Comparison.GapChars.charAt(0)).getSequencesArray();
+ int nofeats = 0;
+ List<String> 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];
- float max=0;
- for (int cpos = 0;cpos<cpwidth;cpos++)
+ 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
+ // 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>();
+ List<SequenceFeature> 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++)
{
- SequenceFeature[] sf = fr.getVisible(sequenceString[i],cpos);
- for (int j=i+1;j<noseqs;j++)
+ if (cpos == 0)
{
- SequenceFeature[] jsf = fr.getVisible(sequenceString[i],cpos);
-
-
- if (max < distance[i][j])
+ 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
public boolean isDNA()
{
return true;
}
+
@Override
public boolean isProtein()
{
return true;
}
- public String toString() {
- return "Score between two sequences aligned with Smith Waterman with default Peptide/Nucleotide matrix";
+
+ public String toString()
+ {
+ return "Score between sequences based on hamming distance between binary vectors marking features displayed at each column";
}
}
git://source.jalview.org / jalview.git / blobdiff