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.gui.PairwiseAlignPanel;
32 import jalview.viewmodel.AlignmentViewport;
34 import java.util.List;
35 import java.util.Vector;
37 public class PaSiMapModel
42 private AlignmentViewport inputData;
44 private final SequenceI[] seqs;
47 * options - score model, nucleotide / protein
49 private ScoreModelI scoreModel;
51 private boolean nucleotide = false;
56 private PaSiMap pasimap;
60 private List<SequencePoint> points;
63 * Constructor given sequence data, score model and score calculation
72 public PaSiMapModel(AlignmentViewport seqData, SequenceI[] sqs, boolean nuc,
73 ScoreModelI modelName)
78 scoreModel = modelName;
82 * Performs the PaSiMap calculation (in the same thread) and extracts result data
83 * needed for visualisation by PaSiMapPanel
85 public void calculate(PairwiseAlignPanel pap)
87 pasimap = new PaSiMap(inputData, scoreModel, pap);
88 pasimap.run(); // executes in same thread, wait for completion
90 // Now find the component coordinates
93 while ((ii < seqs.length) && (seqs[ii] != null))
98 int width = pasimap.getWidth();
99 int height = pasimap.getHeight();
102 points = new Vector<>();
103 Point[] scores = pasimap.getComponents(width - 1, width - 2, width - 3, 1);
105 for (int i = 0; i < height; i++)
107 SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
112 public void updateRc(RotatableCanvasI rc)
114 rc.setPoints(points, pasimap.getHeight());
117 public boolean isNucleotide()
122 public void setNucleotide(boolean nucleotide)
124 this.nucleotide = nucleotide;
128 * Answers the index of the principal dimension of the PaSiMap
137 public void setTop(int t)
143 * Updates the 3D coordinates for the list of points to the given dimensions.
144 * Principal dimension is getTop(). Next greatest eigenvector is getTop()-1.
145 * Note - pasimap.getComponents starts counting the spectrum from rank-2 to zero,
146 * rather than rank-1, so getComponents(dimN ...) == updateRcView(dimN+1 ..)
152 public void updateRcView(int dim1, int dim2, int dim3)
154 // note: actual indices for components are dim1-1, etc (patch for JAL-1123)
155 Point[] scores = pasimap.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 1);
157 for (int i = 0; i < pasimap.getHeight(); i++)
159 points.get(i).coord = scores[i];
163 public String getDetails()
165 return pasimap.getDetails();
168 public String getAlignmentOutput()
170 return pasimap.getAlignmentOutput();
173 public AlignmentViewport getInputData()
178 public void setInputData(AlignmentViewport data)
183 public String getPointsasCsv(boolean transformed, int xdim, int ydim,
186 StringBuffer csv = new StringBuffer();
187 csv.append("\"Sequence\"");
199 for (int d = 1, dmax = (int) pasimap.getDim(); d <= dmax; d++)
205 for (int s = 0; s < seqs.length; s++)
207 csv.append("\"" + seqs[s].getName() + "\"");
210 double[] fl = pasimap.component(s);
211 for (int d = fl.length - 1; d >= 0; d--)
217 Point p = points.get(s).coord;
218 csv.append(",").append(p.x);
219 csv.append(",").append(p.y);
220 csv.append(",").append(p.z);
224 return csv.toString();
227 public String getScoreModelName()
229 return scoreModel == null ? "" : scoreModel.getName();
232 public void setScoreModel(ScoreModelI sm)
234 this.scoreModel = sm;
237 public List<SequencePoint> getSequencePoints()
242 public void setSequencePoints(List<SequencePoint> sp)
248 * Answers the object holding the values of the computed PaSiMap
252 public PaSiMap getPasimapData()
257 public void setPaSiMap(PaSiMap data)