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.PCA;
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;
32 import java.util.Vector;
39 private final AlignmentView seqstrings;
41 private final SequenceI[] seqs;
43 private final SimilarityParamsI similarityParams;
46 * options - score model, nucleotide / protein
48 private ScoreModelI scoreModel;
50 private boolean nucleotide = false;
59 private Vector<SequencePoint> points;
62 * Constructor given sequence data, score model and score calculation
71 public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
72 ScoreModelI modelName, SimilarityParamsI params)
77 scoreModel = modelName;
78 similarityParams = params;
82 * Performs the PCA calculation (in the same thread) and extracts result data
83 * needed for visualisation by PCAPanel
85 public void calculate()
87 pca = new PCA(seqstrings, scoreModel, similarityParams);
88 pca.run(); // executes in same thread, wait for completion
90 // Now find the component coordinates
93 while ((ii < seqs.length) && (seqs[ii] != null))
98 int height = pca.getHeight();
99 // top = pca.getM().height() - 1;
102 points = new Vector<>();
103 Point[] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
105 for (int i = 0; i < height; i++)
107 SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
108 points.addElement(sp);
112 public void updateRc(RotatableCanvasI rc)
114 rc.setPoints(points, pca.getHeight());
117 public boolean isNucleotide()
122 public void setNucleotide(boolean nucleotide)
124 this.nucleotide = nucleotide;
130 * @return index of principle dimension of PCA
138 * update the 2d coordinates for the list of points to the given dimensions
139 * Principal dimension is getTop(). Next greatest eigenvector is getTop()-1.
140 * Note - pca.getComponents starts counting the spectrum from rank-2 to zero,
141 * rather than rank-1, so getComponents(dimN ...) == updateRcView(dimN+1 ..)
147 public void updateRcView(int dim1, int dim2, int dim3)
149 // note: actual indices for components are dim1-1, etc (patch for JAL-1123)
150 Point[] scores = pca.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 100);
152 for (int i = 0; i < pca.getHeight(); i++)
154 points.elementAt(i).coord = scores[i];
158 public String getDetails()
160 return pca.getDetails();
163 public AlignmentView getSeqtrings()
168 public String getPointsasCsv(boolean transformed, int xdim, int ydim,
171 StringBuffer csv = new StringBuffer();
172 csv.append("\"Sequence\"");
184 for (int d = 1, dmax = pca.component(1).length; d <= dmax; d++)
190 for (int s = 0; s < seqs.length; s++)
192 csv.append("\"" + seqs[s].getName() + "\"");
196 // output pca in correct order
197 fl = pca.component(s);
198 for (int d = fl.length - 1; d >= 0; d--)
206 Point p = points.elementAt(s).coord;
207 csv.append(",").append(p.x);
208 csv.append(",").append(p.y);
209 csv.append(",").append(p.z);
213 return csv.toString();
218 * @return x,y,z positions of point s (index into points) under current
221 public double[] getPointPosition(int s)
223 double pts[] = new double[3];
224 Point p = points.elementAt(s).coord;
231 public String getScoreModelName()
233 return scoreModel == null ? "" : scoreModel.getName();
236 public void setScoreModel(ScoreModelI sm)
238 this.scoreModel = sm;