Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PairwiseAlignPanel	43	126	50	0.5051020450.5%	Show methods

Class PairwiseAlignPanel

Class PairwiseAlignPanel	Line # 43	Total Statements 126	Complexity 50	TOTAL Coverage 0.5051020450.5%
PairwiseAlignPanel(AlignmentViewport)   PairwiseAlignPanel(AlignmentViewport)	106106	1.01	1.01	1.0 1.0100%
PairwiseAlignPanel(AlignmentViewport,ScoreMatrix)   PairwiseAlignPanel(AlignmentViewport,ScoreMatrix)	112112	1.01	1.01	0.0 0.00%
PairwiseAlignPanel(AlignmentViewport,boolean,int,int)   PairwiseAlignPanel(AlignmentViewport,boolean,int,int)	118118	1.01	1.01	0.0 0.00%
PairwiseAlignPanel(AlignmentViewport,SequenceGroup,boolean,int,int,boolean,ScoreMatrix)   PairwiseAlignPanel(AlignmentViewport,SequenceGroup,boolean,int,int,boolean,ScoreMatrix)	136136	11.011	2.02	0.9230769 0.923076992.3%
calculate() : void   calculate() : void	155155	1.01	1.01	1.0 1.0100%
calculate(ScoreMatrix) : void   calculate(ScoreMatrix) : void	160160	77.077	19.019	0.7570093 0.757009375.7%
hasEta() : boolean   hasEta() : boolean	302302	1.01	1.01	0.0 0.00%
getEta() : double   getEta() : double	306306	1.01	1.01	0.0 0.00%
cancel() : void   cancel() : void	313313	1.01	1.01	0.0 0.00%
getScores() : float[][]   getScores() : float[][]	318318	1.01	1.01	0.0 0.00%
getAlignmentScores() : float[][]   getAlignmentScores() : float[][]	323323	1.01	1.01	0.0 0.00%
getAlignmentOutput() : String   getAlignmentOutput() : String	328328	1.01	1.01	0.0 0.00%
printScoreMatrix(SequenceI[],float[][],double) : void   printScoreMatrix(SequenceI[],float[][],double) : void	340340	13.013	5.05	0.0 0.00%
getPairwiseSimscoresAsString() : String   getPairwiseSimscoresAsString() : String	378378	1.01	3.03	0.0 0.00%
viewInEditorButton_actionPerformed(ActionEvent) : void   viewInEditorButton_actionPerformed(ActionEvent) : void	393393	5.05	2.02	0.0 0.00%
getTotal() : long   getTotal() : long	411411	1.01	1.01	0.0 0.00%
getProgress() : long   getProgress() : long	416416	1.01	1.01	0.0 0.00%
getInputSequences() : SequenceI[]   getInputSequences() : SequenceI[]	421421	1.01	1.01	0.0 0.00%
setQuiet(boolean) : void   setQuiet(boolean) : void	431431	1.01	1.01	0.0 0.00%
isQuiet() : boolean   isQuiet() : boolean	439439	1.01	1.01	0.0 0.00%
setDiscardAlignments(boolean) : void   setDiscardAlignments(boolean) : void	449449	1.01	1.01	0.0 0.00%
isDiscardAlignments() : boolean   isDiscardAlignments() : boolean	458458	1.01	1.01	0.0 0.00%
isCancelled() : boolean   isCancelled() : boolean	467467	1.01	1.01	0.0 0.00%
updateProgress(String,String) : void   updateProgress(String,String) : void	477477	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.49489796	jalview.gui.PairwiseAlignmentPanelTest.testConstructor_withSelectionGroupjalview.gui.PairwiseAlignmentPanelTest.testConstructor_withSelectionGroup	1PASS
	0.49489796	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.datamodel.Alignment;
26		import jalview.datamodel.AlignmentView;
27		import jalview.datamodel.SequenceGroup;
28		import jalview.datamodel.SequenceI;
29		import jalview.jbgui.GPairwiseAlignPanel;
30		import jalview.util.MessageManager;
31		import jalview.viewmodel.AlignmentViewport;
32		import jalview.math.MiscMath;
33
34		import java.awt.event.ActionEvent;
35		import java.util.Vector;
36
37		/**
38		* DOCUMENT ME!
39		*
40		* @author $author$
41		* @version $Revision$
42		*/
		50.5% Uncovered Elements: 97 (196) Complexity: 50 Complexity Density: 0.4
43		public class PairwiseAlignPanel extends GPairwiseAlignPanel
44		{
45
46		private static final String DASHES = "---------------------\n";
47
48		private float[][] scores;
49
50		private float[][] alignmentScores; // scores used by PaSiMap
51
52		private int GAP_OPEN_COST;
53
54		private int GAP_EXTEND_COST;
55
56		AlignmentViewport av;
57
58		Vector<SequenceI> sequences;
59
60		private String alignmentOutput;
61
62		private boolean quiet;
63
64		private boolean discardAlignments;
65
66		private boolean endGaps;
67
68		// for listening
69		public static final String TOTAL = "total";
70
71		public static final String PROGRESS = "progress";
72
73		protected static final String ETA = "eta_in_minutes";
74
75		public static final String PROGRESSCOMPLETE = "finished_stop_progress";
76		public static final String PROGRESSMESSAGE = "message_in_progress";
77
78		private volatile boolean cancelled;
79
80		private long total;
81
82		private long progress;
83
84		private SequenceGroup selection;
85
86		/**
87		* input sequences
88		*/
89		private SequenceI[] seqs = null;
90
91		private ScoreMatrix scoreMatrix;
92
93		/**
94		* remaining time
95		*/
96		private double etime=Double.NaN;
97
98		/**
99		* Creates a new PairwiseAlignPanel object.
100		*
101		* @param viewport
102		* contains selected sequences to align
103		* @param endGaps
104		* ~ toggle gaps and the beginning and end of sequences
105		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
106	2	public PairwiseAlignPanel(AlignmentViewport viewport)...
107		{
108	2	this(viewport, null, false, 120, 20, true, null); // default penalties used
109		// in AlignSeq
110		}
111
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
112	0	public PairwiseAlignPanel(AlignmentViewport viewport, ScoreMatrix params)...
113		{
114	0	this(viewport, null, false, 120, 20, true, params); // default penalties
115		// used in AlignSeq
116		}
117
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
118	0	public PairwiseAlignPanel(AlignmentViewport viewport, boolean endGaps,...
119		int gapOpenCost, int gapExtendCost)
120		{
121	0	this(viewport, null, endGaps, gapOpenCost, gapExtendCost, true, null);
122		}
123
124		/**
125		* Create a new pairwise alignpanel with specified parameters and score model,
126		* and optionally start the calculation
127		*
128		* @param viewport
129		* @param selection
130		* @param endGaps
131		* @param gapOpenCost
132		* @param gapExtendCost
133		* @param run
134		* @param scoreMatrix
135		*/
		92.3% Uncovered Elements: 1 (13) Complexity: 2 Complexity Density: 0.18
136	2	public PairwiseAlignPanel(AlignmentViewport viewport,...
137		SequenceGroup selection, boolean endGaps, int gapOpenCost,
138		int gapExtendCost, boolean run, ScoreMatrix scoreMatrix)
139		{
140	2	super();
141	2	this.av = viewport;
142	2	this.GAP_OPEN_COST = gapOpenCost;
143	2	this.GAP_EXTEND_COST = gapExtendCost;
144	2	this.endGaps = endGaps;
145	2	this.selection = selection;
146	2	this.total = av.getAlignment().getHeight();
147	2	total = (total*total-total)/2;
148	2	this.scoreMatrix = scoreMatrix;
149	2	if (run)
150		{
151	2	calculate();
152		}
153		}
154
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
155	2	public void calculate()...
156		{
157	2	calculate(scoreMatrix);
158		}
159
		75.7% Uncovered Elements: 26 (107) Complexity: 19 Complexity Density: 0.25
160	2	public void calculate(ScoreMatrix sm)...
161		{
162	2	cancelled=false;
163	2	StringBuilder sb = new StringBuilder(1024);
164
165	2	sequences = new Vector<SequenceI>();
166	2	String[] seqStrings;
167	2	seqs = null;
168
169	2	if (selection != null)
170		{
171		// given a set of sequences to compare
172	0	seqs = selection.getSelectionAsNewSequences(av.getAlignment());
173	0	seqStrings = new String[seqs.length];
174	0	int s = 0;
175	0	for (SequenceI seq : seqs)
176		{
177	0	seqStrings[s++] = seq.getSequenceAsString();
178		}
179		}
180		else
181		{
182	2	SequenceGroup selectionGroup = av.getSelectionGroup();
183	2	boolean isSelection = selectionGroup != null
184		&& selectionGroup.getSize() > 0;
185	2	AlignmentView view = av.getAlignmentView(isSelection);
186	2	seqStrings = view.getSequenceStrings(av.getGapCharacter());
187	2	if (isSelection)
188		{
189	1	seqs = (SequenceI[]) view
190		.getAlignmentAndHiddenColumns(av.getGapCharacter())[0];
191		}
192		else
193		{
194	1	seqs = av.getAlignment().getSequencesArray();
195		}
196		}
197
198	2	String type = (av.getAlignment().isNucleotide()) ? AlignSeq.DNA
199		: AlignSeq.PEP;
200
201	2	float[][] scores = new float[seqs.length][seqs.length];
202	2	float[][] alignmentScores = new float[seqs.length][seqs.length];
203	2	double totscore = 0D;
204	2	int count = seqs.length;
205	2	int fracprogress=0;
206	2	boolean first = true;
207	2	long time=System.currentTimeMillis();
208	2	long fprogress = 0;
209	2	firePropertyChange(TOTAL, 0, 500);
210
211	4	for (int i = 1; i < count; i++)
212		{
213		// fill diagonal alignmentScores with Float.NaN
214	2	alignmentScores[i - 1][i - 1] = Float.NaN;
215	4	for (int j = 0; j < i; j++)
216		{
217	2	if (cancelled)
218		{
219	0	alignmentOutput = "Alignment was cancelled.";
220	0	return;
221		}
222	2	AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
223		seqStrings[j], type, GAP_OPEN_COST, GAP_EXTEND_COST);
224
225	2	if (sm != null)
226		{
227	0	as.setScoreMatrix(sm);
228		}
229
230	2	if (as.s1str.length() == 0 || as.s2str.length() == 0)
231		{
232	0	continue;
233		}
234
235	2	as.calcScoreMatrix();
236	2	if (endGaps)
237		{
238	0	as.traceAlignmentWithEndGaps();
239		}
240		else
241		{
242	2	as.traceAlignment();
243		}
244	2	as.scoreAlignment();
245
246	2	if (!first && !quiet)
247		{
248	0	jalview.bin.Console.outPrintln(DASHES);
249	0	textarea.append(DASHES);
250	0	sb.append(DASHES);
251		}
252	2	first = false;
253	2	if (!discardAlignments)
254		{
255	2	as.printAlignment(System.out);
256		}
257	2	scores[i][j] = as.getMaxScore() / as.getASeq1().length;
258	2	alignmentScores[i][j] = as.getAlignmentScore();
259	2	totscore = totscore + scores[i][j];
260	2	if (!quiet)
261		{
262	2	textarea.append(as.getOutput());
263	2	sb.append(as.getOutput());
264		}
265	2	if (!discardAlignments)
266		{
267	2	sequences.add(as.getAlignedSeq1());
268	2	sequences.add(as.getAlignedSeq2());
269		}
270	2	++fprogress;
271		}
272	2	if (i<count)
273		{
274	2	int newfracprogress=(int) Math.floor((500.0*(double)fprogress)/((double)total));
275		// need to fake a different starting value until we have an ETA calculated
276	2	firePropertyChange(PROGRESS, fracprogress, newfracprogress);
277	2	fracprogress = newfracprogress;
278	2	progress=fprogress;
279		// remaining time in minutes ~ is remaining*(elapsed time)/progress;
280	2	double lasteta=etime;
281	2	double rate = ((double)(System.currentTimeMillis()-time))/(double)progress;
282	2	etime = rate*(total-progress)/60000;
283	2	firePropertyChange(ETA, lasteta,etime);
284		}
285		}
286	2	alignmentScores[count - 1][count - 1] = Float.NaN;
287		// done - mark progress as indeterminate again
288	2	firePropertyChange(TOTAL, -1, -2);
289
290
291	2	this.scores = scores;
292	2	this.alignmentScores = alignmentScores;
293
294	2	if (count > 2 && !quiet)
295		{
296	0	printScoreMatrix(seqs, scores, totscore);
297		}
298
299	2	alignmentOutput = sb.toString();
300		}
301
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
302	0	public boolean hasEta()...
303		{
304	0	return etime>0;
305		}
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
306	0	public double getEta()...
307		{
308	0	return etime;
309		}
310		/**
311		* stops the run() loop ASAP
312		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
313	0	public void cancel()...
314		{
315	0	cancelled=true;
316		}
317
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
318	0	public float[][] getScores()...
319		{
320	0	return this.scores;
321		}
322
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
323	0	public float[][] getAlignmentScores()...
324		{
325	0	return this.alignmentScores;
326		}
327
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
328	0	public String getAlignmentOutput()...
329		{
330	0	return this.alignmentOutput;
331		}
332
333		/**
334		* Prints a matrix of seqi-seqj pairwise alignment scores to sysout
335		*
336		* @param seqs
337		* @param scores
338		* @param totscore
339		*/
		0% Uncovered Elements: 21 (21) Complexity: 5 Complexity Density: 0.38
340	0	protected void printScoreMatrix(SequenceI[] seqs, float[][] scores,...
341		double totscore)
342		{
343	0	System.out
344		.println("Pairwise alignment scaled similarity score matrix "+getPairwiseSimscoresAsString()+"\n");
345
346	0	for (int i = 0; i < seqs.length; i++)
347		{
348	0	jalview.bin.Console.outPrintln(
349		String.format("%3d %s", i + 1, seqs[i].getDisplayId(true)));
350		}
351
352		/*
353		* table heading columns for sequences 1, 2, 3...
354		*/
355	0	System.out.print("\n ");
356	0	for (int i = 0; i < seqs.length; i++)
357		{
358	0	System.out.print(String.format("%7d", i + 1));
359		}
360	0	jalview.bin.Console.outPrintln();
361
362	0	for (int i = 0; i < seqs.length; i++)
363		{
364	0	System.out.print(String.format("%3d", i + 1));
365	0	for (int j = 0; j < i; j++)
366		{
367		/*
368		* as a fraction of tot score, outputs are 0 <= score <= 1
369		*/
370	0	System.out.print(String.format("%7.3f", scores[i][j] / totscore));
371		}
372	0	jalview.bin.Console.outPrintln();
373		}
374
375	0	jalview.bin.Console.outPrintln("\n");
376		}
377
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 3
378	0	public String getPairwiseSimscoresAsString()...
379		{
380	0	return (scoreMatrix != null
381		? " (" + scoreMatrix.getName() + ", open=" + GAP_OPEN_COST
382		+ ", extend=" + GAP_EXTEND_COST
383	0	+ (endGaps ? ", with endGaps" : ", no endGaps") + ")"
384		: "");
385		}
386
387		/**
388		* DOCUMENT ME!
389		*
390		* @param e
391		* DOCUMENT ME!
392		*/
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
393	0	@Override...
394		protected void viewInEditorButton_actionPerformed(ActionEvent e)
395		{
396	0	SequenceI[] seq = new SequenceI[sequences.size()];
397
398	0	for (int i = 0; i < sequences.size(); i++)
399		{
400	0	seq[i] = sequences.elementAt(i);
401		}
402
403	0	AlignFrame af = new AlignFrame(new Alignment(seq),
404		AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
405
406	0	Desktop.addInternalFrame(af,
407		MessageManager.getString("label.pairwise_aligned_sequences")+" "+getPairwiseSimscoresAsString(),
408		AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
409		}
410
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
411	0	public long getTotal()...
412		{
413	0	return total;
414		}
415
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
416	0	public long getProgress()...
417		{
418	0	return progress;
419		}
420
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
421	0	public SequenceI[] getInputSequences()...
422		{
423	0	return seqs;
424		}
425
426		/**
427		* Set to true to suppress output of progress to Console.stdout or GUI
428		*
429		* @param quiet
430		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
431	0	public void setQuiet(boolean quiet)...
432		{
433	0	this.quiet = quiet;
434		}
435
436		/**
437		* @return true if no textual alignment report was generated
438		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
439	0	public boolean isQuiet()...
440		{
441	0	return quiet;
442		}
443
444		/**
445		* set this if you are only interested in final alignment scores
446		*
447		* @param discard
448		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
449	0	public void setDiscardAlignments(boolean discard)...
450		{
451	0	discardAlignments = discard;
452		}
453
454		/**
455		* @return true if no alignments were saved
456		* @return
457		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
458	0	public boolean isDiscardAlignments()...
459		{
460	0	return discardAlignments;
461		}
462
463		/**
464		*
465		* @return true if the calculation was cancelled before completion
466		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
467	0	public boolean isCancelled()...
468		{
469	0	return cancelled;
470		}
471
472		/**
473		* sends status updates to the progress bar for this panel
474		* @param type - PROGRESSMESSAGE or PROGRESSCOMPLETE
475		* @param message - the message (may be internationalised key)
476		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
477	0	public void updateProgress(String type, String message)...
478		{
479	0	firePropertyChange(type, "", MessageManager.getStringOrReturn("progress", message));
480		}
481		}