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.analysis;
23 import jalview.api.analysis.ScoreModelI;
24 import jalview.api.analysis.SimilarityParamsI;
25 import jalview.bin.Console;
26 import jalview.datamodel.AlignmentView;
27 import jalview.datamodel.Point;
28 import jalview.datamodel.SequenceI;
29 import jalview.gui.PairwiseAlignPanel;
30 import jalview.gui.PaSiMapPanel;
31 import jalview.math.Matrix;
32 import jalview.math.MatrixI;
33 import jalview.viewmodel.AlignmentViewport;
36 import java.io.PrintStream;
37 import java.util.Hashtable;
38 import java.util.Enumeration;
41 * Performs Principal Component Analysis on given sequences
42 * @AUTHOR MorellThomas
44 public class PaSiMap implements Runnable
49 final private AlignmentViewport seqs;
51 final private ScoreModelI scoreModel;
53 final private SimilarityParamsI similarityParams;
55 final private byte dim = 3;
60 private MatrixI pairwiseScores;
62 private MatrixI eigenMatrix;
65 * Constructor given the sequences to compute for, the similarity model to
66 * use, and a set of parameters for sequence comparison
72 public PaSiMap(AlignmentViewport sequences, ScoreModelI sm,
73 SimilarityParamsI options)
75 this.seqs = sequences;
77 this.similarityParams = options;
84 * Index of diagonal within matrix
86 * @return Returns value of diagonal from matrix
88 public double getEigenvalue(int i)
90 return eigenMatrix.getD()[i];
94 * Returns coordinates for each datapoint
102 * @param factor ~ is 1
104 * @return DOCUMENT ME!
106 public Point[] getComponents(int l, int n, int mm, float factor)
108 Point[] out = new Point[getHeight()];
110 for (int i = 0; i < out.length; i++)
112 float x = (float) component(i, l) * factor;
113 float y = (float) component(i, n) * factor;
114 float z = (float) component(i, mm) * factor;
115 out[i] = new Point(x, y, z);
118 System.out.println("Points:");
119 for (Point point : out)
121 System.out.println(point.toString());
133 * @return DOCUMENT ME!
135 public double[] component(int n)
137 // n = index of eigenvector
138 double[] out = new double[getHeight()];
140 for (int i = 0; i < out.length; i++)
142 out[i] = component(i, n);
156 * @return DOCUMENT ME!
158 double component(int row, int n)
160 return eigenMatrix.getValue(row, n);
164 * Answers a formatted text report of the PaSiMap calculation results (matrices
165 * and eigenvalues) suitable for display
169 public String getDetails()
171 StringBuilder sb = new StringBuilder(1024);
172 sb.append("PaSiMap calculation using ").append(scoreModel.getName())
173 .append(" sequence similarity matrix\n========\n\n");
174 PrintStream ps = wrapOutputBuffer(sb);
177 * pairwise similarity scores
179 sb.append(" --- OrigT * Orig ---- \n");
180 pairwiseScores.print(ps, "%8.2f");
183 * eigenvalues matrix, with D vector
185 sb.append(" --- New diagonalization matrix ---\n");
186 eigenMatrix.print(ps, "%8.2f");
187 sb.append(" --- Eigenvalues ---\n");
188 eigenMatrix.printD(ps, "%15.4e");
191 return sb.toString();
195 * Performs the PaSiMap calculation
197 * creates a new gui/PairwiseAlignPanel with the input sequences (AlignmentViewport)
198 * uses analysis/AlignSeq to creatue the pairwise alignments and calculate the AlignmentScores (float for each pair)
199 * gets all float[][] scores from the gui/PairwiseAlignPanel
200 * checks the connections for each sequence with AlignmentViewport seqs.calculateConnectivity(float[][] scores, int dim) (from analysis/Connectivity) -- throws an Exception if insufficient
201 * creates a math/MatrixI pairwiseScores of the float[][] scores
202 * copys the scores and fills the diagonal to create a symmetric matrix using math/Matrix.fillDiagonal()
203 * performs the analysis/ccAnalysis with the symmetric matrix
204 * gets the eigenmatrix and the eigenvalues using math/Matrix.tqli()
211 PairwiseAlignPanel alignment = new PairwiseAlignPanel(seqs, true);
212 float[][] scores = alignment.getAlignmentScores(); //bigger index first -- eg scores[14][13]
214 Hashtable<SequenceI, Integer> connectivity = seqs.calculateConnectivity(scores, dim);
216 pairwiseScores = new Matrix(scores);
217 pairwiseScores.fillDiagonal();
219 ccAnalysis cc = new ccAnalysis(pairwiseScores, dim);
220 pairwiseScores = cc.run();
222 /** perform the eigendecomposition for the plot */
223 eigenMatrix = pairwiseScores.copy();
224 eigenMatrix.setD(pairwiseScores.getD());
225 System.out.println(getDetails());
228 } catch (Exception q)
230 Console.error("Error computing PaSiMap: " + q.getMessage());
236 * Returns a PrintStream that wraps (appends its output to) the given
242 protected PrintStream wrapOutputBuffer(StringBuilder sb)
244 PrintStream ps = new PrintStream(System.out)
247 public void print(String x)
253 public void println()
262 * Answers the N dimensions of the NxM PaSiMap matrix. This is the number of
263 * sequences involved in the pairwise score calculation.
267 public int getHeight()
269 // TODO can any of seqs[] be null?
270 return pairwiseScores.height();// seqs.getSequences().length;
274 * Answers the M dimensions of the NxM PaSiMap matrix. This is the number of
275 * sequences involved in the pairwise score calculation.
279 public int getWidth()
281 // TODO can any of seqs[] be null?
282 return pairwiseScores.width();// seqs.getSequences().length;
286 * Answers the sequence pairwise similarity scores which were the first step
287 * of the PaSiMap calculation
291 public MatrixI getPairwiseScores()
293 return pairwiseScores;
296 public void setPairwiseScores(MatrixI m)
301 public MatrixI getEigenmatrix()
306 public void setEigenmatrix(MatrixI m)