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.analysis.scoremodels.ScoreModels;
25 import jalview.api.RotatableCanvasI;
26 import jalview.api.analysis.ScoreModelI;
27 import jalview.datamodel.AlignmentView;
28 import jalview.datamodel.SequenceI;
29 import jalview.datamodel.SequencePoint;
31 import java.util.Vector;
35 private volatile PCA pca;
39 AlignmentView seqstrings;
44 * Score model used to calculate PCA
46 ScoreModelI scoreModel;
48 private boolean nucleotide = false;
50 private Vector<SequencePoint> points;
52 private boolean jvCalcMode = true;
54 public PCAModel(AlignmentView seqstrings2, SequenceI[] seqs2,
57 seqstrings = seqstrings2;
59 nucleotide = nucleotide2;
60 scoreModel = ScoreModels.getInstance().getDefaultModel(!nucleotide);
63 public boolean isJvCalcMode()
70 pca = new PCA(seqstrings, scoreModel);
71 pca.setJvCalcMode(jvCalcMode);
74 // Now find the component coordinates
77 while ((ii < seqs.length) && (seqs[ii] != null))
82 int height = pca.getHeight();
83 // top = pca.getM().height() - 1;
86 points = new Vector<SequencePoint>();
87 float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
89 for (int i = 0; i < height; i++)
91 SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
92 points.addElement(sp);
96 public void updateRc(RotatableCanvasI rc)
98 rc.setPoints(points, pca.getHeight());
101 public boolean isNucleotide()
106 public void setNucleotide(boolean nucleotide)
108 this.nucleotide = nucleotide;
114 * @return index of principle dimension of PCA
122 * update the 2d coordinates for the list of points to the given dimensions
123 * Principal dimension is getTop(). Next greatest eigenvector is getTop()-1.
124 * Note - pca.getComponents starts counting the spectrum from rank-2 to zero,
125 * rather than rank-1, so getComponents(dimN ...) == updateRcView(dimN+1 ..)
131 public void updateRcView(int dim1, int dim2, int dim3)
133 // note: actual indices for components are dim1-1, etc (patch for JAL-1123)
134 float[][] scores = pca.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 100);
136 for (int i = 0; i < pca.getHeight(); i++)
138 points.elementAt(i).coord = scores[i];
142 public String getDetails()
144 return pca.getDetails();
147 public AlignmentView getSeqtrings()
152 public String getPointsasCsv(boolean transformed, int xdim, int ydim,
155 StringBuffer csv = new StringBuffer();
156 csv.append("\"Sequence\"");
168 for (int d = 1, dmax = pca.component(1).length; d <= dmax; d++)
174 for (int s = 0; s < seqs.length; s++)
176 csv.append("\"" + seqs[s].getName() + "\"");
180 // output pca in correct order
181 fl = pca.component(s);
182 for (int d = fl.length - 1; d >= 0; d--)
190 // output current x,y,z coords for points
191 fl = getPointPosition(s);
192 for (int d = 0; d < fl.length; d++)
200 return csv.toString();
205 * @return x,y,z positions of point s (index into points) under current
208 public double[] getPointPosition(int s)
210 double pts[] = new double[3];
211 float[] p = points.elementAt(s).coord;
218 public void setJvCalcMode(boolean state)
223 public String getScoreModelName()
225 return scoreModel == null ? "" : scoreModel.getName();
228 public void setScoreModel(ScoreModelI sm)
230 this.scoreModel = sm;