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.SeqCigar;
27 import jalview.datamodel.SequenceFeature;
29 import java.util.ArrayList;
30 import java.util.Hashtable;
31 import java.util.List;
33 public class FeatureScoreModel implements ScoreModelI, ViewBasedAnalysisI
35 jalview.api.FeatureRenderer fr;
38 public boolean configureFromAlignmentView(
39 jalview.api.AlignmentViewPanel view)
41 fr = view.cloneFeatureRenderer();
46 public float[][] findDistances(AlignmentView seqData)
49 List<String> dft = fr.getDisplayedFeatureTypes();
51 SeqCigar[] seqs = seqData.getSequences();
52 int noseqs = seqs.length;
53 int cpwidth = 0;// = seqData.getWidth();
54 float[][] distance = new float[noseqs][noseqs];
57 for (float[] d : distance)
59 for (int i = 0; i < d.length; d[i++] = 0f)
66 // need to get real position for view position
67 int[] viscont = seqData.getVisibleContigs();
68 for (int vc = 0; vc < viscont.length; vc += 2)
71 for (int cpos = viscont[vc]; cpos <= viscont[vc + 1]; cpos++)
74 // get visible features at cpos under view's display settings and
76 List<Hashtable<String, SequenceFeature>> sfap = new ArrayList<Hashtable<String, SequenceFeature>>();
77 for (int i = 0; i < noseqs; i++)
79 Hashtable<String, SequenceFeature> types = new Hashtable<String, SequenceFeature>();
80 int spos = seqs[i].findPosition(cpos);
83 List<SequenceFeature> sfs = fr.findFeaturesAtRes(
84 seqs[i].getRefSeq(), spos);
85 for (SequenceFeature sf : sfs)
87 types.put(sf.getType(), sf);
92 for (int i = 0; i < (noseqs - 1); i++)
98 for (int j = i + 1; j < noseqs; j++)
101 // compare the two lists of features...
102 Hashtable<String, SequenceFeature> fi = sfap.get(i), fk, fj = sfap
104 if (fi.size() > fj.size())
113 for (String k : fi.keySet())
115 SequenceFeature sfj = fk.get(k);
121 distance[i][j] += (fi.size() + fk.size() - 2f * sfcommon);
122 distance[j][i] += distance[i][j];
127 for (int i = 0; i < noseqs; i++)
129 for (int j = i + 1; j < noseqs; j++)
131 distance[i][j] /= cpwidth;
132 distance[j][i] = distance[i][j];
139 public String getName()
141 return "Sequence Feature Similarity";
145 public boolean isDNA()
151 public boolean isProtein()
157 public String toString()
159 return "Score between sequences based on hamming distance between binary vectors marking features displayed at each column";