Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PaSiMap	44	68	29	0.00%	Show methods

Class PaSiMap

Class PaSiMap	Line # 44	Total Statements 68	Complexity 29	TOTAL Coverage 0.00%
PaSiMap(AlignmentViewport,ScoreModelI,PairwiseAlignPanel)   PaSiMap(AlignmentViewport,ScoreModelI,PairwiseAlignPanel)	8080	5.05	3.03	0.0 0.00%
getEigenvalue(int) : double   getEigenvalue(int) : double	105105	1.01	1.01	0.0 0.00%
getComponents(int,int,int,float) : Point[]   getComponents(int,int,int,float) : Point[]	124124	7.07	2.02	0.0 0.00%
component(int) : double[]   component(int) : double[]	147147	4.04	2.02	0.0 0.00%
component(int,int) : double   component(int,int) : double	170170	1.01	1.01	0.0 0.00%
getDetails() : String   getDetails() : String	181181	13.013	1.01	0.0 0.00%
run() : void   run() : void	230230	19.019	3.03	0.0 0.00%
cancel() : void   cancel() : void	269269	3.03	2.02	0.0 0.00%
isCancelled() : boolean   isCancelled() : boolean	278278	1.01	1.01	0.0 0.00%
print(String) : void   print(String) : void	294294	1.01	1.01	0.0 0.00%
println() : void   println() : void	300300	1.01	1.01	0.0 0.00%
wrapOutputBuffer(StringBuilder) : PrintStream   wrapOutputBuffer(StringBuilder) : PrintStream	290290	2.02	1.01	0.0 0.00%
getHeight() : int   getHeight() : int	315315	1.01	1.01	0.0 0.00%
getWidth() : int   getWidth() : int	327327	1.01	1.01	0.0 0.00%
getPairwiseScores() : MatrixI   getPairwiseScores() : MatrixI	339339	1.01	1.01	0.0 0.00%
setPairwiseScores(MatrixI) : void   setPairwiseScores(MatrixI) : void	344344	1.01	1.01	0.0 0.00%
getEigenmatrix() : MatrixI   getEigenmatrix() : MatrixI	349349	1.01	1.01	0.0 0.00%
setEigenmatrix(MatrixI) : void   setEigenmatrix(MatrixI) : void	354354	1.01	1.01	0.0 0.00%
getAlignments() : PairwiseAlignPanel   getAlignments() : PairwiseAlignPanel	359359	1.01	1.01	0.0 0.00%
getAlignmentOutput() : String   getAlignmentOutput() : String	364364	1.01	1.01	0.0 0.00%
getDim() : byte   getDim() : byte	369369	1.01	1.01	0.0 0.00%
isCancellable() : boolean   isCancellable() : boolean	378378	1.01	1.01	0.0 0.00%

 

Contributing tests

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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		*/
		0% Uncovered Elements: 100 (100) Complexity: 29 Complexity Density: 0.43
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		*/
		0% Uncovered Elements: 7 (7) Complexity: 3 Complexity Density: 0.6
80	0	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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
105	0	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		*/
		0% Uncovered Elements: 9 (9) Complexity: 2 Complexity Density: 0.29
124	0	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		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
147	0	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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
170	0	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		*/
		0% Uncovered Elements: 13 (13) Complexity: 1 Complexity Density: 0.08
181	0	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		*/
		0% Uncovered Elements: 21 (21) Complexity: 3 Complexity Density: 0.16
230	0	@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
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
269	0	public void cancel()...
270		{
271	0	if (alignment!=null)
272		{
273	0	alignment.cancel();
274		}
275	0	cancelled=true;
276		}
277
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
278	0	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		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
290	0	protected PrintStream wrapOutputBuffer(StringBuilder sb)...
291		{
292	0	PrintStream ps = new PrintStream(System.out)
293		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
294	0	@Override...
295		public void print(String x)
296		{
297	0	sb.append(x);
298		}
299
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
300	0	@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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
315	0	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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
327	0	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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
339	0	public MatrixI getPairwiseScores()...
340		{
341	0	return pairwiseScores;
342		}
343
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
344	0	public void setPairwiseScores(MatrixI m)...
345		{
346	0	pairwiseScores = m;
347		}
348
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
349	0	public MatrixI getEigenmatrix()...
350		{
351	0	return eigenMatrix;
352		}
353
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
354	0	public void setEigenmatrix(MatrixI m)...
355		{
356	0	eigenMatrix = m;
357		}
358
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
359	0	public PairwiseAlignPanel getAlignments()...
360		{
361	0	return alignment;
362		}
363
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
364	0	public String getAlignmentOutput()...
365		{
366	0	return alignment.getAlignmentOutput();
367		}
368
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
369	0	public byte getDim()...
370		{
371	0	return dim;
372		}
373
374		/**
375		*
376		* @return true if pasimap calculation can (still) be interrupted
377		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
378	0	public boolean isCancellable()...
379		{
380	0	return canCancel;
381		}
382		}