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.viewmodel;
23 import jalview.analysis.PaSiMap;
24 import jalview.api.RotatableCanvasI;
25 import jalview.api.analysis.ScoreModelI;
26 import jalview.api.analysis.SimilarityParamsI;
27 import jalview.datamodel.AlignmentView;
28 import jalview.datamodel.Point;
29 import jalview.datamodel.SequenceI;
30 import jalview.datamodel.SequencePoint;
31 import jalview.viewmodel.AlignmentViewport;
33 import java.util.List;
34 import java.util.Vector;
36 public class PaSiMapModel
41 //private AlignmentView inputData;
43 private AlignmentViewport inputData;
45 private final SequenceI[] seqs;
47 private final SimilarityParamsI similarityParams;
50 * options - score model, nucleotide / protein
52 private ScoreModelI scoreModel;
54 private boolean nucleotide = false;
59 private PaSiMap pasimap;
63 private List<SequencePoint> points;
66 * Constructor given sequence data, score model and score calculation
75 //public PaSiMapModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
76 //&! viewport or panel?
77 public PaSiMapModel(AlignmentViewport seqData, SequenceI[] sqs, boolean nuc,
78 ScoreModelI modelName, SimilarityParamsI params)
83 scoreModel = modelName;
84 similarityParams = params;
88 * Performs the PaSiMap calculation (in the same thread) and extracts result data
89 * needed for visualisation by PaSiMapPanel
91 public void calculate()
93 pasimap = new PaSiMap(inputData, scoreModel, similarityParams);
94 pasimap.run(); // executes in same thread, wait for completion
96 // Now find the component coordinates
99 while ((ii < seqs.length) && (seqs[ii] != null))
104 int width = pasimap.getWidth();
105 int height = pasimap.getHeight();
106 // top = pasimap.getM().height() - 1;
111 points = new Vector<>();
113 //Point[] scores = pasimap.getComponents(top - 1, top - 2, top - 3, 100);
114 Point[] scores = pasimap.getComponents(width - 1, width - 2, width - 3, 1);
116 for (int i = 0; i < top; i++)
118 SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
123 public void updateRc(RotatableCanvasI rc)
125 rc.setPoints(points, pasimap.getHeight());
128 public boolean isNucleotide()
133 public void setNucleotide(boolean nucleotide)
135 this.nucleotide = nucleotide;
139 * Answers the index of the principal dimension of the PaSiMap
148 public void setTop(int t)
154 * Updates the 3D coordinates for the list of points to the given dimensions.
155 * Principal dimension is getTop(). Next greatest eigenvector is getTop()-1.
156 * Note - pasimap.getComponents starts counting the spectrum from rank-2 to zero,
157 * rather than rank-1, so getComponents(dimN ...) == updateRcView(dimN+1 ..)
163 public void updateRcView(int dim1, int dim2, int dim3)
165 // note: actual indices for components are dim1-1, etc (patch for JAL-1123)
167 //Point[] scores = pasimap.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 100);
168 Point[] scores = pasimap.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 1);
170 for (int i = 0; i < pasimap.getWidth(); i++)
172 points.get(i).coord = scores[i];
176 public String getDetails()
178 return pasimap.getDetails();
182 //public AlignmentView getInputData()
183 public AlignmentViewport getInputData()
189 //public void setInputData(AlignmentView data)
190 public void setInputData(AlignmentViewport data)
195 public String getPointsasCsv(boolean transformed, int xdim, int ydim,
198 StringBuffer csv = new StringBuffer();
199 csv.append("\"Sequence\"");
211 for (int d = 1, dmax = pasimap.component(1).length; d <= dmax; d++)
217 for (int s = 0; s < seqs.length; s++)
219 csv.append("\"" + seqs[s].getName() + "\"");
223 // output pasimap in correct order
224 fl = pasimap.component(s);
225 for (int d = fl.length - 1; d >= 0; d--)
233 Point p = points.get(s).coord;
234 csv.append(",").append(p.x);
235 csv.append(",").append(p.y);
236 csv.append(",").append(p.z);
240 return csv.toString();
243 public String getScoreModelName()
245 return scoreModel == null ? "" : scoreModel.getName();
248 public void setScoreModel(ScoreModelI sm)
250 this.scoreModel = sm;
254 * Answers the parameters configured for pairwise similarity calculations
258 public SimilarityParamsI getSimilarityParameters()
260 return similarityParams;
263 public List<SequencePoint> getSequencePoints()
268 public void setSequencePoints(List<SequencePoint> sp)
274 * Answers the object holding the values of the computed PaSiMap
278 public PaSiMap getPasimapData()
283 public void setPaSiMap(PaSiMap data)