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 height = pasimap.getHeight();
105 // top = pasimap.getM().height() - 1;
108 points = new Vector<>();
109 Point[] scores = pasimap.getComponents(top - 1, top - 2, top - 3, 100);
111 for (int i = 0; i < height; i++)
113 SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
118 public void updateRc(RotatableCanvasI rc)
120 rc.setPoints(points, pasimap.getHeight());
123 public boolean isNucleotide()
128 public void setNucleotide(boolean nucleotide)
130 this.nucleotide = nucleotide;
134 * Answers the index of the principal dimension of the PaSiMap
143 public void setTop(int t)
149 * Updates the 3D coordinates for the list of points to the given dimensions.
150 * Principal dimension is getTop(). Next greatest eigenvector is getTop()-1.
151 * Note - pasimap.getComponents starts counting the spectrum from rank-2 to zero,
152 * rather than rank-1, so getComponents(dimN ...) == updateRcView(dimN+1 ..)
158 public void updateRcView(int dim1, int dim2, int dim3)
160 // note: actual indices for components are dim1-1, etc (patch for JAL-1123)
161 Point[] scores = pasimap.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 100);
163 for (int i = 0; i < pasimap.getHeight(); i++)
165 points.get(i).coord = scores[i];
169 public String getDetails()
171 return pasimap.getDetails();
175 //public AlignmentView getInputData()
176 public AlignmentViewport getInputData()
182 //public void setInputData(AlignmentView data)
183 public void setInputData(AlignmentViewport data)
188 public String getPointsasCsv(boolean transformed, int xdim, int ydim,
191 StringBuffer csv = new StringBuffer();
192 csv.append("\"Sequence\"");
204 for (int d = 1, dmax = pasimap.component(1).length; d <= dmax; d++)
210 for (int s = 0; s < seqs.length; s++)
212 csv.append("\"" + seqs[s].getName() + "\"");
216 // output pasimap in correct order
217 fl = pasimap.component(s);
218 for (int d = fl.length - 1; d >= 0; d--)
226 Point p = points.get(s).coord;
227 csv.append(",").append(p.x);
228 csv.append(",").append(p.y);
229 csv.append(",").append(p.z);
233 return csv.toString();
236 public String getScoreModelName()
238 return scoreModel == null ? "" : scoreModel.getName();
241 public void setScoreModel(ScoreModelI sm)
243 this.scoreModel = sm;
247 * Answers the parameters configured for pairwise similarity calculations
251 public SimilarityParamsI getSimilarityParameters()
253 return similarityParams;
256 public List<SequencePoint> getSequencePoints()
261 public void setSequencePoints(List<SequencePoint> sp)
267 * Answers the object holding the values of the computed PaSiMap
271 public PaSiMap getPasimapData()
276 public void setPaSiMap(PaSiMap data)