Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
PairwiseAlignPanel	41	53	16	38	0.52552.5%	Show methods

Class PairwiseAlignPanel

Class PairwiseAlignPanel	Line # 41	Total Statements 53	Complexity 16	Uncovered Elements 38	TOTAL Coverage 0.52552.5%
PairwiseAlignPanel(AlignmentViewport)   PairwiseAlignPanel(AlignmentViewport)	5656	35.035	9.09	8.08	0.8367347 0.836734783.7%
printScoreMatrix(SequenceI[],float[][],double) : void   printScoreMatrix(SequenceI[],float[][],double) : void	135135	13.013	5.05	21.021	0.0 0.00%
viewInEditorButton_actionPerformed(ActionEvent) : void   viewInEditorButton_actionPerformed(ActionEvent) : void	179179	5.05	2.02	7.07	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.5	jalview.gui.PairwiseAlignmentPanelTest.testConstructor_withSelectionGroupjalview.gui.PairwiseAlignmentPanelTest.testConstructor_withSelectionGroup	1PASS
	0.5	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.datamodel.Alignment;
25		import jalview.datamodel.AlignmentView;
26		import jalview.datamodel.SequenceGroup;
27		import jalview.datamodel.SequenceI;
28		import jalview.jbgui.GPairwiseAlignPanel;
29		import jalview.util.MessageManager;
30		import jalview.viewmodel.AlignmentViewport;
31
32		import java.awt.event.ActionEvent;
33		import java.util.Vector;
34
35		/**
36		* DOCUMENT ME!
37		*
38		* @author $author$
39		* @version $Revision$
40		*/
		52.5% Uncovered Elements: 38 (80) Complexity: 16 Complexity Density: 0.3
41		public class PairwiseAlignPanel extends GPairwiseAlignPanel
42		{
43
44		private static final String DASHES = "---------------------\n";
45
46		AlignmentViewport av;
47
48		Vector<SequenceI> sequences;
49
50		/**
51		* Creates a new PairwiseAlignPanel object.
52		*
53		* @param viewport
54		* DOCUMENT ME!
55		*/
		83.7% Uncovered Elements: 8 (49) Complexity: 9 Complexity Density: 0.26
56	2	public PairwiseAlignPanel(AlignmentViewport viewport)...
57		{
58	2	super();
59	2	this.av = viewport;
60
61	2	sequences = new Vector<SequenceI>();
62
63	2	SequenceGroup selectionGroup = viewport.getSelectionGroup();
64	2	boolean isSelection = selectionGroup != null
65		&& selectionGroup.getSize() > 0;
66	2	AlignmentView view = viewport.getAlignmentView(isSelection);
67		// String[] seqStrings = viewport.getViewAsString(true);
68	2	String[] seqStrings = view.getSequenceStrings(viewport
69		.getGapCharacter());
70
71	2	SequenceI[] seqs;
72	2	if (isSelection)
73		{
74	1	seqs = (SequenceI[]) view.getAlignmentAndHiddenColumns(viewport
75		.getGapCharacter())[0];
76		}
77		else
78		{
79	1	seqs = av.getAlignment().getSequencesArray();
80		}
81
82	2	String type = (viewport.getAlignment().isNucleotide()) ? AlignSeq.DNA
83		: AlignSeq.PEP;
84
85	2	float[][] scores = new float[seqs.length][seqs.length];
86	2	double totscore = 0D;
87	2	int count = seqs.length;
88	2	boolean first = true;
89
90	4	for (int i = 1; i < count; i++)
91		{
92	4	for (int j = 0; j < i; j++)
93		{
94	2	AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
95		seqStrings[j], type);
96
97	2	if (as.s1str.length() == 0 || as.s2str.length() == 0)
98		{
99	0	continue;
100		}
101
102	2	as.calcScoreMatrix();
103	2	as.traceAlignment();
104
105	2	if (!first)
106		{
107	0	System.out.println(DASHES);
108	0	textarea.append(DASHES);
109		}
110	2	first = false;
111	2	as.printAlignment(System.out);
112	2	scores[i][j] = as.getMaxScore()
113		/ as.getASeq1().length;
114	2	totscore = totscore + scores[i][j];
115
116	2	textarea.append(as.getOutput());
117	2	sequences.add(as.getAlignedSeq1());
118	2	sequences.add(as.getAlignedSeq2());
119		}
120		}
121
122	2	if (count > 2)
123		{
124	0	printScoreMatrix(seqs, scores, totscore);
125		}
126		}
127
128		/**
129		* Prints a matrix of seqi-seqj pairwise alignment scores to sysout
130		*
131		* @param seqs
132		* @param scores
133		* @param totscore
134		*/
		0% Uncovered Elements: 21 (21) Complexity: 5 Complexity Density: 0.38
135	0	protected void printScoreMatrix(SequenceI[] seqs, float[][] scores,...
136		double totscore)
137		{
138	0	System.out
139		.println("Pairwise alignment scaled similarity score matrix\n");
140
141	0	for (int i = 0; i < seqs.length; i++)
142		{
143	0	System.out.println(String.format("%3d %s", i + 1,
144		seqs[i].getDisplayId(true)));
145		}
146
147		/*
148		* table heading columns for sequences 1, 2, 3...
149		*/
150	0	System.out.print("\n ");
151	0	for (int i = 0; i < seqs.length; i++)
152		{
153	0	System.out.print(String.format("%7d", i + 1));
154		}
155	0	System.out.println();
156
157	0	for (int i = 0; i < seqs.length; i++)
158		{
159	0	System.out.print(String.format("%3d", i + 1));
160	0	for (int j = 0; j < i; j++)
161		{
162		/*
163		* as a fraction of tot score, outputs are 0 <= score <= 1
164		*/
165	0	System.out.print(String.format("%7.3f", scores[i][j] / totscore));
166		}
167	0	System.out.println();
168		}
169
170	0	System.out.println("\n");
171		}
172
173		/**
174		* DOCUMENT ME!
175		*
176		* @param e
177		* DOCUMENT ME!
178		*/
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
179	0	@Override...
180		protected void viewInEditorButton_actionPerformed(ActionEvent e)
181		{
182	0	SequenceI[] seq = new SequenceI[sequences.size()];
183
184	0	for (int i = 0; i < sequences.size(); i++)
185		{
186	0	seq[i] = sequences.elementAt(i);
187		}
188
189	0	AlignFrame af = new AlignFrame(new Alignment(seq),
190		AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
191
192	0	Desktop.addInternalFrame(af,
193		MessageManager.getString("label.pairwise_aligned_sequences"),
194		AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
195		}
196		}