2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.analysis.scoremodels;
23 import jalview.api.analysis.ScoreModelI;
24 import jalview.api.analysis.ViewBasedAnalysisI;
25 import jalview.datamodel.AlignmentView;
26 import jalview.datamodel.SequenceFeature;
27 import jalview.datamodel.SequenceI;
28 import jalview.util.Comparison;
30 import java.util.ArrayList;
31 import java.util.Hashtable;
32 import java.util.List;
34 public class FeatureScoreModel implements ScoreModelI, ViewBasedAnalysisI
36 jalview.api.FeatureRenderer fr;
39 public boolean configureFromAlignmentView(
40 jalview.api.AlignmentViewPanel view)
42 fr = view.cloneFeatureRenderer();
47 public float[][] findDistances(AlignmentView seqData)
50 List<String> dft = fr.getDisplayedFeatureTypes();
54 SequenceI[] sequenceString = seqData.getVisibleAlignment(
55 Comparison.GapChars.charAt(0)).getSequencesArray();
56 int noseqs = sequenceString.length;
57 int cpwidth = seqData.getWidth();
58 float[][] distance = new float[noseqs][noseqs];
61 for (float[] d : distance)
63 for (int i = 0; i < d.length; d[i++] = 0f)
71 for (int cpos = 0; cpos < cpwidth; cpos++)
73 // get visible features at cpos under view's display settings and compare
75 List<Hashtable<String, SequenceFeature>> sfap = new ArrayList<Hashtable<String, SequenceFeature>>();
76 for (int i = 0; i < noseqs; i++)
78 Hashtable<String, SequenceFeature> types = new Hashtable<String, SequenceFeature>();
79 List<SequenceFeature> sfs = fr.findFeaturesAtRes(sequenceString[i],
80 sequenceString[i].findPosition(cpos));
81 for (SequenceFeature sf : sfs)
83 types.put(sf.getType(), sf);
87 for (int i = 0; i < (noseqs - 1); i++)
93 for (int j = i + 1; j < noseqs; j++)
96 // compare the two lists of features...
97 Hashtable<String, SequenceFeature> fi = sfap.get(i), fk, fj = sfap
99 if (fi.size() > fj.size())
108 for (String k : fi.keySet())
110 SequenceFeature sfj = fk.get(k);
116 distance[i][j] += (fi.size() + fk.size() - 2f * sfcommon);
117 distance[j][i] += distance[i][j];
121 for (int i = 0; i < noseqs; i++)
123 for (int j = i + 1; j < noseqs; j++)
125 distance[i][j] /= cpwidth;
126 distance[j][i] = distance[i][j];
133 public String getName()
135 return "Sequence Feature Similarity";
139 public boolean isDNA()
145 public boolean isProtein()
151 public String toString()
153 return "Score between sequences based on hamming distance between binary vectors marking features displayed at each column";