Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PairwiseAlignPanel	46	128	51	0.50550.5%	Show methods

Class PairwiseAlignPanel

Class PairwiseAlignPanel	Line # 46	Total Statements 128	Complexity 51	TOTAL Coverage 0.50550.5%
PairwiseAlignPanel(AlignViewportI)   PairwiseAlignPanel(AlignViewportI)	110110	1.01	1.01	1.0 1.0100%
PairwiseAlignPanel(AlignViewportI,ScoreMatrix)   PairwiseAlignPanel(AlignViewportI,ScoreMatrix)	116116	1.01	1.01	0.0 0.00%
PairwiseAlignPanel(AlignViewportI,boolean,int,int)   PairwiseAlignPanel(AlignViewportI,boolean,int,int)	122122	1.01	1.01	0.0 0.00%
PairwiseAlignPanel(AlignViewportI,SequenceGroup,boolean,int,int,boolean,ScoreMatrix)   PairwiseAlignPanel(AlignViewportI,SequenceGroup,boolean,int,int,boolean,ScoreMatrix)	140140	11.011	2.02	0.9230769 0.923076992.3%
calculate() : void   calculate() : void	159159	1.01	1.01	1.0 1.0100%
calculate(ScoreMatrix) : void   calculate(ScoreMatrix) : void	164164	79.079	20.020	0.7477477 0.747747774.8%
hasEta() : boolean   hasEta() : boolean	309309	1.01	1.01	0.0 0.00%
getEta() : double   getEta() : double	313313	1.01	1.01	0.0 0.00%
cancel() : void   cancel() : void	320320	1.01	1.01	0.0 0.00%
getScores() : float[][]   getScores() : float[][]	325325	1.01	1.01	0.0 0.00%
getAlignmentScores() : float[][]   getAlignmentScores() : float[][]	330330	1.01	1.01	0.0 0.00%
getAlignmentOutput() : String   getAlignmentOutput() : String	335335	1.01	1.01	0.0 0.00%
printScoreMatrix(SequenceI[],float[][],double) : void   printScoreMatrix(SequenceI[],float[][],double) : void	347347	13.013	5.05	0.0 0.00%
getPairwiseSimscoresAsString() : String   getPairwiseSimscoresAsString() : String	385385	1.01	3.03	0.0 0.00%
viewInEditorButton_actionPerformed(ActionEvent) : void   viewInEditorButton_actionPerformed(ActionEvent) : void	400400	5.05	2.02	0.0 0.00%
getTotal() : long   getTotal() : long	418418	1.01	1.01	0.0 0.00%
getProgress() : long   getProgress() : long	423423	1.01	1.01	0.0 0.00%
getInputSequences() : SequenceI[]   getInputSequences() : SequenceI[]	428428	1.01	1.01	0.0 0.00%
setQuiet(boolean) : void   setQuiet(boolean) : void	438438	1.01	1.01	0.0 0.00%
isQuiet() : boolean   isQuiet() : boolean	446446	1.01	1.01	0.0 0.00%
setDiscardAlignments(boolean) : void   setDiscardAlignments(boolean) : void	456456	1.01	1.01	0.0 0.00%
isDiscardAlignments() : boolean   isDiscardAlignments() : boolean	465465	1.01	1.01	0.0 0.00%
isCancelled() : boolean   isCancelled() : boolean	474474	1.01	1.01	0.0 0.00%
updateProgress(String,String) : void   updateProgress(String,String) : void	484484	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.495	jalview.gui.PairwiseAlignmentPanelTest.testConstructor_withSelectionGroupjalview.gui.PairwiseAlignmentPanelTest.testConstructor_withSelectionGroup	1PASS
	0.495	jalview.gui.PairwiseAlignmentPanelTest.testConstructor_noSelectionGroupjalview.gui.PairwiseAlignmentPanelTest.testConstructor_noSelectionGroup	1PASS

 

Source view

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.gui;
22
23		import jalview.analysis.AlignSeq;
24		import jalview.analysis.scoremodels.ScoreMatrix;
25		import jalview.api.analysis.ScoreModelI;
26		import jalview.api.analysis.SimilarityParamsI;
27		import jalview.api.AlignViewportI;
28		import jalview.datamodel.Alignment;
29		import jalview.datamodel.AlignmentView;
30		import jalview.datamodel.SequenceGroup;
31		import jalview.datamodel.SequenceI;
32		import jalview.jbgui.GPairwiseAlignPanel;
33		import jalview.util.MessageManager;
34		import jalview.viewmodel.AlignmentViewport;
35		import jalview.math.MiscMath;
36
37		import java.awt.event.ActionEvent;
38		import java.util.Vector;
39
40		/**
41		* DOCUMENT ME!
42		*
43		* @author $author$
44		* @version $Revision$
45		*/
		50.5% Uncovered Elements: 99 (200) Complexity: 51 Complexity Density: 0.4
46		public class PairwiseAlignPanel extends GPairwiseAlignPanel
47		{
48
49		private static final String DASHES = "---------------------\n";
50
51		private float[][] scores;
52
53		private float[][] alignmentScores; // scores used by PaSiMap
54
55		private int GAP_OPEN_COST;
56
57		private int GAP_EXTEND_COST;
58
59		// TODO JAL-4107 can we make this AlignViewportI ?
60		AlignViewportI av;
61
62		Vector<SequenceI> sequences;
63
64		private String alignmentOutput;
65
66		private boolean quiet;
67
68		private boolean discardAlignments;
69
70		private boolean endGaps;
71
72		// for listening
73		public static final String TOTAL = "total";
74
75		public static final String PROGRESS = "progress";
76
77		protected static final String ETA = "eta_in_minutes";
78
79		public static final String PROGRESSCOMPLETE = "finished_stop_progress";
80		public static final String PROGRESSMESSAGE = "message_in_progress";
81
82		private volatile boolean cancelled;
83
84		private long total;
85
86		private long progress;
87
88		private SequenceGroup selection;
89
90		/**
91		* input sequences
92		*/
93		private SequenceI[] seqs = null;
94
95		private ScoreMatrix scoreMatrix;
96
97		/**
98		* remaining time
99		*/
100		private double etime=Double.NaN;
101
102		/**
103		* Creates a new PairwiseAlignPanel object.
104		*
105		* @param viewport
106		* contains selected sequences to align
107		* @param endGaps
108		* ~ toggle gaps and the beginning and end of sequences
109		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
110	2	public PairwiseAlignPanel(AlignViewportI viewport)...
111		{
112	2	this(viewport, null, false, 120, 20, true, null); // default penalties used
113		// in AlignSeq
114		}
115
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
116	0	public PairwiseAlignPanel(AlignViewportI viewport, ScoreMatrix params)...
117		{
118	0	this(viewport, null, false, 120, 20, true, params); // default penalties
119		// used in AlignSeq
120		}
121
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
122	0	public PairwiseAlignPanel(AlignViewportI viewport, boolean endGaps,...
123		int gapOpenCost, int gapExtendCost)
124		{
125	0	this(viewport, null, endGaps, gapOpenCost, gapExtendCost, true, null);
126		}
127
128		/**
129		* Create a new pairwise alignpanel with specified parameters and score model,
130		* and optionally start the calculation
131		*
132		* @param viewport
133		* @param selection
134		* @param endGaps
135		* @param gapOpenCost
136		* @param gapExtendCost
137		* @param run
138		* @param scoreMatrix
139		*/
		92.3% Uncovered Elements: 1 (13) Complexity: 2 Complexity Density: 0.18
140	2	public PairwiseAlignPanel(AlignViewportI viewport,...
141		SequenceGroup selection, boolean endGaps, int gapOpenCost,
142		int gapExtendCost, boolean run, ScoreMatrix scoreMatrix)
143		{
144	2	super();
145	2	this.av = viewport;
146	2	this.GAP_OPEN_COST = gapOpenCost;
147	2	this.GAP_EXTEND_COST = gapExtendCost;
148	2	this.endGaps = endGaps;
149	2	this.selection = selection;
150	2	this.total = av.getAlignment().getHeight();
151	2	total = (total*total-total)/2;
152	2	this.scoreMatrix = scoreMatrix;
153	2	if (run)
154		{
155	2	calculate();
156		}
157		}
158
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
159	2	public void calculate()...
160		{
161	2	calculate(scoreMatrix);
162		}
163
		74.8% Uncovered Elements: 28 (111) Complexity: 20 Complexity Density: 0.25
164	2	public void calculate(ScoreMatrix sm)...
165		{
166	2	cancelled=false;
167	2	StringBuilder sb = new StringBuilder(1024);
168
169	2	sequences = new Vector<SequenceI>();
170	2	String[] seqStrings;
171	2	seqs = null;
172
173	2	if (selection != null)
174		{
175		// given a set of sequences to compare
176	0	seqs = selection.getSelectionAsNewSequences(av.getAlignment());
177	0	seqStrings = new String[seqs.length];
178	0	int s = 0;
179	0	for (SequenceI seq : seqs)
180		{
181	0	seqStrings[s++] = seq.getSequenceAsString();
182		}
183		}
184		else
185		{
186	2	SequenceGroup selectionGroup = av.getSelectionGroup();
187	2	boolean isSelection = selectionGroup != null
188		&& selectionGroup.getSize() > 0;
189	2	AlignmentView view = av.getAlignmentView(isSelection);
190	2	seqStrings = view.getSequenceStrings(av.getGapCharacter());
191	2	if (isSelection)
192		{
193	1	seqs = (SequenceI[]) view
194		.getAlignmentAndHiddenColumns(av.getGapCharacter())[0];
195		}
196		else
197		{
198	1	seqs = av.getAlignment().getSequencesArray();
199		}
200		}
201
202	2	String type = (av.getAlignment().isNucleotide()) ? AlignSeq.DNA
203		: AlignSeq.PEP;
204
205	2	float[][] scores = new float[seqs.length][seqs.length];
206	2	float[][] alignmentScores = new float[seqs.length][seqs.length];
207	2	double totscore = 0D;
208	2	int count = seqs.length;
209	2	int fracprogress=0;
210	2	boolean first = true;
211	2	long time=System.currentTimeMillis();
212	2	long fprogress = 0;
213	2	firePropertyChange(TOTAL, 0, 500);
214
215	4	for (int i = 1; i < count; i++)
216		{
217		// fill diagonal alignmentScores with Float.NaN
218	2	alignmentScores[i - 1][i - 1] = Float.NaN;
219	4	for (int j = 0; j < i; j++)
220		{
221	2	if (cancelled)
222		{
223	0	alignmentOutput = "Alignment was cancelled.";
224	0	return;
225		}
226	2	AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
227		seqStrings[j], type, GAP_OPEN_COST, GAP_EXTEND_COST);
228
229	2	if (sm != null)
230		{
231	0	as.setScoreMatrix(sm);
232		}
233
234	2	if (as.s1str.length() == 0 || as.s2str.length() == 0)
235		{
236	0	continue;
237		}
238	2	if (sm!=null)
239		{
240	0	as.setScoreMatrix(sm);
241		}
242	2	as.calcScoreMatrix();
243	2	if (endGaps)
244		{
245	0	as.traceAlignmentWithEndGaps();
246		}
247		else
248		{
249	2	as.traceAlignment();
250		}
251	2	as.scoreAlignment();
252
253	2	if (!first && !quiet)
254		{
255	0	jalview.bin.Console.outPrintln(DASHES);
256	0	textarea.append(DASHES);
257	0	sb.append(DASHES);
258		}
259	2	first = false;
260	2	if (!discardAlignments)
261		{
262	2	as.printAlignment(System.out);
263		}
264	2	scores[i][j] = as.getMaxScore() / as.getASeq1().length;
265	2	alignmentScores[i][j] = as.getAlignmentScore();
266	2	totscore = totscore + scores[i][j];
267	2	if (!quiet)
268		{
269	2	textarea.append(as.getOutput());
270	2	sb.append(as.getOutput());
271		}
272	2	if (!discardAlignments)
273		{
274	2	sequences.add(as.getAlignedSeq1());
275	2	sequences.add(as.getAlignedSeq2());
276		}
277	2	++fprogress;
278		}
279	2	if (i<count)
280		{
281	2	int newfracprogress=(int) Math.floor((500.0*(double)fprogress)/((double)total));
282		// need to fake a different starting value until we have an ETA calculated
283	2	firePropertyChange(PROGRESS, fracprogress, newfracprogress);
284	2	fracprogress = newfracprogress;
285	2	progress=fprogress;
286		// remaining time in minutes ~ is remaining*(elapsed time)/progress;
287	2	double lasteta=etime;
288	2	double rate = ((double)(System.currentTimeMillis()-time))/(double)progress;
289	2	etime = rate*(total-progress)/60000;
290	2	firePropertyChange(ETA, lasteta,etime);
291		}
292		}
293	2	alignmentScores[count - 1][count - 1] = Float.NaN;
294		// done - mark progress as indeterminate again
295	2	firePropertyChange(TOTAL, -1, -2);
296
297
298	2	this.scores = scores;
299	2	this.alignmentScores = alignmentScores;
300
301	2	if (count > 2 && !quiet)
302		{
303	0	printScoreMatrix(seqs, scores, totscore);
304		}
305
306	2	alignmentOutput = sb.toString();
307		}
308
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
309	0	public boolean hasEta()...
310		{
311	0	return etime>0;
312		}
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
313	0	public double getEta()...
314		{
315	0	return etime;
316		}
317		/**
318		* stops the run() loop ASAP
319		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
320	0	public void cancel()...
321		{
322	0	cancelled=true;
323		}
324
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
325	0	public float[][] getScores()...
326		{
327	0	return this.scores;
328		}
329
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
330	0	public float[][] getAlignmentScores()...
331		{
332	0	return this.alignmentScores;
333		}
334
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
335	0	public String getAlignmentOutput()...
336		{
337	0	return this.alignmentOutput;
338		}
339
340		/**
341		* Prints a matrix of seqi-seqj pairwise alignment scores to sysout
342		*
343		* @param seqs
344		* @param scores
345		* @param totscore
346		*/
		0% Uncovered Elements: 21 (21) Complexity: 5 Complexity Density: 0.38
347	0	protected void printScoreMatrix(SequenceI[] seqs, float[][] scores,...
348		double totscore)
349		{
350	0	System.out
351		.println("Pairwise alignment scaled similarity score matrix "+getPairwiseSimscoresAsString()+"\n");
352
353	0	for (int i = 0; i < seqs.length; i++)
354		{
355	0	jalview.bin.Console.outPrintln(
356		String.format("%3d %s", i + 1, seqs[i].getDisplayId(true)));
357		}
358
359		/*
360		* table heading columns for sequences 1, 2, 3...
361		*/
362	0	System.out.print("\n ");
363	0	for (int i = 0; i < seqs.length; i++)
364		{
365	0	System.out.print(String.format("%7d", i + 1));
366		}
367	0	jalview.bin.Console.outPrintln();
368
369	0	for (int i = 0; i < seqs.length; i++)
370		{
371	0	System.out.print(String.format("%3d", i + 1));
372	0	for (int j = 0; j < i; j++)
373		{
374		/*
375		* as a fraction of tot score, outputs are 0 <= score <= 1
376		*/
377	0	System.out.print(String.format("%7.3f", scores[i][j] / totscore));
378		}
379	0	jalview.bin.Console.outPrintln();
380		}
381
382	0	jalview.bin.Console.outPrintln("\n");
383		}
384
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 3
385	0	public String getPairwiseSimscoresAsString()...
386		{
387	0	return (scoreMatrix != null
388		? " (" + scoreMatrix.getName() + ", open=" + GAP_OPEN_COST
389		+ ", extend=" + GAP_EXTEND_COST
390	0	+ (endGaps ? ", with endGaps" : ", no endGaps") + ")"
391		: "");
392		}
393
394		/**
395		* DOCUMENT ME!
396		*
397		* @param e
398		* DOCUMENT ME!
399		*/
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
400	0	@Override...
401		protected void viewInEditorButton_actionPerformed(ActionEvent e)
402		{
403	0	SequenceI[] seq = new SequenceI[sequences.size()];
404
405	0	for (int i = 0; i < sequences.size(); i++)
406		{
407	0	seq[i] = sequences.elementAt(i);
408		}
409
410	0	AlignFrame af = new AlignFrame(new Alignment(seq),
411		AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
412
413	0	Desktop.addInternalFrame(af,
414		MessageManager.getString("label.pairwise_aligned_sequences")+" "+getPairwiseSimscoresAsString(),
415		AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
416		}
417
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
418	0	public long getTotal()...
419		{
420	0	return total;
421		}
422
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
423	0	public long getProgress()...
424		{
425	0	return progress;
426		}
427
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
428	0	public SequenceI[] getInputSequences()...
429		{
430	0	return seqs;
431		}
432
433		/**
434		* Set to true to suppress output of progress to Console.stdout or GUI
435		*
436		* @param quiet
437		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
438	0	public void setQuiet(boolean quiet)...
439		{
440	0	this.quiet = quiet;
441		}
442
443		/**
444		* @return true if no textual alignment report was generated
445		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
446	0	public boolean isQuiet()...
447		{
448	0	return quiet;
449		}
450
451		/**
452		* set this if you are only interested in final alignment scores
453		*
454		* @param discard
455		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
456	0	public void setDiscardAlignments(boolean discard)...
457		{
458	0	discardAlignments = discard;
459		}
460
461		/**
462		* @return true if no alignments were saved
463		* @return
464		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
465	0	public boolean isDiscardAlignments()...
466		{
467	0	return discardAlignments;
468		}
469
470		/**
471		*
472		* @return true if the calculation was cancelled before completion
473		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
474	0	public boolean isCancelled()...
475		{
476	0	return cancelled;
477		}
478
479		/**
480		* sends status updates to the progress bar for this panel
481		* @param type - PROGRESSMESSAGE or PROGRESSCOMPLETE
482		* @param message - the message (may be internationalised key)
483		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
484	0	public void updateProgress(String type, String message)...
485		{
486	0	firePropertyChange(type, "", MessageManager.getStringOrReturn("progress", message));
487		}
488		}