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  1. Project Clover database Mon Nov 11 2024 16:01:40 GMT
  2. Package jalview.analysis

File PaSiMap.java

 

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59% of files have more coverage

Code metrics

10
68
22
1
382
186
29
0.43
3.09
22
1.32

Classes

Class Line # Actions
PaSiMap 44 68 29
0.00%
 

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.analysis;
22   
23    import jalview.api.analysis.ScoreModelI;
24    import jalview.api.analysis.SimilarityParamsI;
25    import jalview.analysis.scoremodels.ScoreMatrix;
26    import jalview.analysis.scoremodels.ScoreModels;
27    import jalview.bin.Console;
28    import jalview.datamodel.Point;
29    import jalview.datamodel.SequenceI;
30    import jalview.datamodel.SequenceGroup;
31    import jalview.gui.PairwiseAlignPanel;
32    import jalview.math.Matrix;
33    import jalview.math.MatrixI;
34    import jalview.viewmodel.AlignmentViewport;
35   
36    import java.io.PrintStream;
37    import java.util.Hashtable;
38   
39    /**
40    * Performs Principal Component Analysis on given sequences
41    *
42    * @AUTHOR MorellThomas
43    */
 
44    public class PaSiMap implements Runnable
45    {
46    /*
47    * inputs
48    */
49    final private AlignmentViewport seqs;
50   
51    final private ScoreMatrix scoreMatrix;
52   
53    final private byte dim = 8;
54   
55    final private int openCost = 100;
56   
57    final private int extendCost = 5;
58   
59    /*
60    * outputs
61    */
62    final private PairwiseAlignPanel alignment;
63   
64    private boolean cancelled=false;
65   
66    private MatrixI pairwiseScores;
67   
68    private MatrixI eigenMatrix;
69   
70    private volatile boolean canCancel;
71   
72    /**
73    * Constructor given the sequences to compute for, the similarity model to
74    * use, and a set of parameters for sequence comparison
75    *
76    * @param sequences
77    * @param sm
78    * @param options
79    */
 
80  0 toggle public PaSiMap(AlignmentViewport sequences, ScoreModelI sm,
81    PairwiseAlignPanel pap)
82    {
83  0 this.seqs = sequences;
84   
85  0 if (sm != null && sm instanceof ScoreMatrix)
86    {
87  0 this.scoreMatrix = ((ScoreMatrix) sm);
88    }
89    else
90    {
91  0 this.scoreMatrix = null;
92    }
93   
94  0 this.alignment = pap;
95    }
96   
97    /**
98    * Returns Eigenvalue
99    *
100    * @param i
101    * Index of diagonal within matrix
102    *
103    * @return Returns value of diagonal from matrix
104    */
 
105  0 toggle public double getEigenvalue(int i)
106    {
107  0 return eigenMatrix.getD()[i];
108    }
109   
110    /**
111    * Returns coordinates for each datapoint
112    *
113    * @param l
114    * DOCUMENT ME!
115    * @param n
116    * DOCUMENT ME!
117    * @param mm
118    * DOCUMENT ME!
119    * @param factor
120    * ~ is 1
121    *
122    * @return DOCUMENT ME!
123    */
 
124  0 toggle public Point[] getComponents(int l, int n, int mm, float factor)
125    {
126  0 Point[] out = new Point[getHeight()];
127   
128  0 for (int i = 0; i < out.length; i++)
129    {
130  0 float x = (float) component(i, l) * factor;
131  0 float y = (float) component(i, n) * factor;
132  0 float z = (float) component(i, mm) * factor;
133  0 out[i] = new Point(x, y, z);
134    }
135   
136  0 return out;
137    }
138   
139    /**
140    * DOCUMENT ME!
141    *
142    * @param n
143    * DOCUMENT ME!
144    *
145    * @return DOCUMENT ME!
146    */
 
147  0 toggle public double[] component(int n)
148    {
149    // n = index of eigenvector
150  0 double[] out = new double[getWidth()];
151   
152  0 for (int i = 0; i < out.length; i++)
153    {
154  0 out[i] = component(n, i);
155    }
156   
157  0 return out;
158    }
159   
160    /**
161    * DOCUMENT ME!
162    *
163    * @param row
164    * DOCUMENT ME!
165    * @param n
166    * DOCUMENT ME!
167    *
168    * @return DOCUMENT ME!
169    */
 
170  0 toggle double component(int row, int n)
171    {
172  0 return eigenMatrix.getValue(row, n);
173    }
174   
175    /**
176    * Answers a formatted text report of the PaSiMap calculation results
177    * (matrices and eigenvalues) suitable for display
178    *
179    * @return
180    */
 
181  0 toggle public String getDetails()
182    {
183  0 StringBuilder sb = new StringBuilder(1024);
184  0 sb.append("PaSiMap calculation using ").append(scoreMatrix.getName())
185    .append(" sequence similarity matrix\n========\n\n");
186  0 PrintStream ps = wrapOutputBuffer(sb);
187   
188    /*
189    * coordinates matrix, with D vector
190    */
191  0 sb.append(" --- Pairwise correlation coefficients ---\n");
192  0 pairwiseScores.print(ps, "%8.6f ");
193  0 ps.println();
194   
195  0 sb.append(" --- Eigenvalues ---\n");
196  0 eigenMatrix.printD(ps, "%15.4e");
197  0 ps.println();
198   
199  0 sb.append(" --- Coordinates ---\n");
200  0 eigenMatrix.print(ps, "%8.6f ");
201  0 ps.println();
202   
203  0 return sb.toString();
204    }
205   
206    /**
207    * Performs the PaSiMap calculation
208    *
209    * creates a new gui/PairwiseAlignPanel with the input sequences
210    * (AlignmentViewport)
211    *
212    * uses analysis/AlignSeq to creatue the pairwise alignments and calculate the
213    * AlignmentScores (float for each pair)
214    *
215    * gets all float[][] scores from the gui/PairwiseAlignPanel
216    *
217    * checks the connections for each sequence with AlignmentViewport
218    * seqs.calculateConnectivity(float[][] scores, int dim) (from
219    * analysis/Connectivity) -- throws an Exception if insufficient
220    *
221    * creates a math/MatrixI pairwiseScores of the float[][] scores
222    *
223    * copys the scores and fills the diagonal to create a symmetric matrix using
224    * math/Matrix.fillDiagonal()
225    *
226    * performs the analysis/ccAnalysis with the symmetric matrix
227    *
228    * gets the eigenmatrix and the eigenvalues using math/Matrix.tqli()
229    */
 
230  0 toggle @Override
231    public void run()
232    {
233  0 canCancel=true;
234  0 try
235    {
236    // alignment = new PairwiseAlignPanel(seqs, true, 100, 5);
237  0 alignment.calculate(scoreMatrix);
238  0 if (alignment.isCancelled())
239    {
240  0 cancel();
241  0 return;
242    }
243    //alignment.setProgressMessage("Preparing to calculate pasimap...");
244  0 float[][] scores = alignment.getAlignmentScores(); // bigger index first
245    // -- eg scores[14][13]
246  0 SequenceI[] iseqs = alignment.getInputSequences();
247  0 Connectivity.getConnectivity(iseqs, scores, dim);
248   
249  0 canCancel=false;
250  0 alignment.updateProgress(PairwiseAlignPanel.PROGRESSMESSAGE, "Creating the PaSiMap");
251  0 pairwiseScores = new Matrix(scores);
252  0 pairwiseScores.fillDiagonal();
253   
254  0 eigenMatrix = pairwiseScores.copy();
255   
256  0 ccAnalysis cc = new ccAnalysis(pairwiseScores, dim);
257  0 eigenMatrix = cc.run().mirrorCol();
258  0 alignment.updateProgress(PairwiseAlignPanel.PROGRESSCOMPLETE, "Finished PaSiMap.");
259   
260    } catch (Exception q)
261    {
262  0 Console.error("Error computing PaSiMap: " + q.getMessage());
263  0 q.printStackTrace();
264    }
265    }
266   
267   
268   
 
269  0 toggle public void cancel()
270    {
271  0 if (alignment!=null)
272    {
273  0 alignment.cancel();
274    }
275  0 cancelled=true;
276    }
277   
 
278  0 toggle public boolean isCancelled()
279    {
280  0 return cancelled;
281    }
282   
283    /**
284    * Returns a PrintStream that wraps (appends its output to) the given
285    * StringBuilder
286    *
287    * @param sb
288    * @return
289    */
 
290  0 toggle protected PrintStream wrapOutputBuffer(StringBuilder sb)
291    {
292  0 PrintStream ps = new PrintStream(System.out)
293    {
 
294  0 toggle @Override
295    public void print(String x)
296    {
297  0 sb.append(x);
298    }
299   
 
300  0 toggle @Override
301    public void println()
302    {
303  0 sb.append("\n");
304    }
305    };
306  0 return ps;
307    }
308   
309    /**
310    * Answers the N dimensions of the NxM PaSiMap matrix. This is the number of
311    * sequences involved in the pairwise score calculation.
312    *
313    * @return
314    */
 
315  0 toggle public int getHeight()
316    {
317    // TODO can any of seqs[] be null?
318  0 return eigenMatrix.height();// seqs.getSequences().length;
319    }
320   
321    /**
322    * Answers the M dimensions of the NxM PaSiMap matrix. This is the number of
323    * sequences involved in the pairwise score calculation.
324    *
325    * @return
326    */
 
327  0 toggle public int getWidth()
328    {
329    // TODO can any of seqs[] be null?
330  0 return eigenMatrix.width();// seqs.getSequences().length;
331    }
332   
333    /**
334    * Answers the sequence pairwise similarity scores which were the first step
335    * of the PaSiMap calculation
336    *
337    * @return
338    */
 
339  0 toggle public MatrixI getPairwiseScores()
340    {
341  0 return pairwiseScores;
342    }
343   
 
344  0 toggle public void setPairwiseScores(MatrixI m)
345    {
346  0 pairwiseScores = m;
347    }
348   
 
349  0 toggle public MatrixI getEigenmatrix()
350    {
351  0 return eigenMatrix;
352    }
353   
 
354  0 toggle public void setEigenmatrix(MatrixI m)
355    {
356  0 eigenMatrix = m;
357    }
358   
 
359  0 toggle public PairwiseAlignPanel getAlignments()
360    {
361  0 return alignment;
362    }
363   
 
364  0 toggle public String getAlignmentOutput()
365    {
366  0 return alignment.getAlignmentOutput();
367    }
368   
 
369  0 toggle public byte getDim()
370    {
371  0 return dim;
372    }
373   
374    /**
375    *
376    * @return true if pasimap calculation can (still) be interrupted
377    */
 
378  0 toggle public boolean isCancellable()
379    {
380  0 return canCancel;
381    }
382    }