Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PairwiseAlignPanel	38	53	17	0.00%	Show methods

Class PairwiseAlignPanel

Class PairwiseAlignPanel	Line # 38	Total Statements 53	Complexity 17	TOTAL Coverage 0.00%
PairwiseAlignPanel(AlignmentPanel)   PairwiseAlignPanel(AlignmentPanel)	4444	37.037	12.012	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	129129	2.02	2.02	0.0 0.00%
viewInEditorButton_actionPerformed() : void   viewInEditorButton_actionPerformed() : void	137137	4.04	2.02	0.0 0.00%
jbInit() : void   jbInit() : void	162162	10.010	1.01	0.0 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.appletgui;
22
23		import jalview.analysis.AlignSeq;
24		import jalview.datamodel.Alignment;
25		import jalview.datamodel.Sequence;
26		import jalview.datamodel.SequenceI;
27		import jalview.util.MessageManager;
28
29		import java.awt.BorderLayout;
30		import java.awt.Button;
31		import java.awt.Panel;
32		import java.awt.ScrollPane;
33		import java.awt.TextArea;
34		import java.awt.event.ActionEvent;
35		import java.awt.event.ActionListener;
36		import java.util.Vector;
37
		0% Uncovered Elements: 79 (79) Complexity: 17 Complexity Density: 0.32
38		public class PairwiseAlignPanel extends Panel implements ActionListener
39		{
40		Vector sequences = new Vector();
41
42		AlignmentPanel ap;
43
		0% Uncovered Elements: 55 (55) Complexity: 12 Complexity Density: 0.32
44	0	public PairwiseAlignPanel(AlignmentPanel ap)...
45		{
46	0	try
47		{
48	0	jbInit();
49		} catch (Exception e)
50		{
51	0	e.printStackTrace();
52		}
53	0	this.ap = ap;
54	0	sequences = new Vector();
55
56	0	SequenceI[] seqs;
57	0	String[] seqStrings = ap.av.getViewAsString(true);
58
59	0	if (ap.av.getSelectionGroup() == null)
60		{
61	0	seqs = ap.av.getAlignment().getSequencesArray();
62		}
63		else
64		{
65	0	seqs = ap.av.getSelectionGroup()
66		.getSequencesInOrder(ap.av.getAlignment());
67		}
68
69	0	float scores[][] = new float[seqs.length][seqs.length];
70	0	double totscore = 0;
71	0	int count = ap.av.getSelectionGroup().getSize();
72	0	String type = (ap.av.getAlignment().isNucleotide()) ? AlignSeq.DNA
73		: AlignSeq.PEP;
74	0	Sequence seq;
75
76	0	for (int i = 1; i < count; i++)
77		{
78	0	for (int j = 0; j < i; j++)
79		{
80
81	0	AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
82		seqStrings[j], type);
83
84	0	if (as.s1str.length() == 0 || as.s2str.length() == 0)
85		{
86	0	continue;
87		}
88
89	0	as.calcScoreMatrix();
90	0	as.traceAlignment();
91
92	0	as.printAlignment(System.out);
93	0	scores[i][j] = (float) as.getMaxScore()
94		/ (float) as.getASeq1().length;
95	0	totscore = totscore + scores[i][j];
96
97	0	textarea.append(as.getOutput());
98	0	sequences.add(as.getAlignedSeq1());
99	0	sequences.add(as.getAlignedSeq1());
100		}
101		}
102
103	0	if (count > 2)
104		{
105	0	System.out.println(
106		"Pairwise alignment scaled similarity score matrix\n");
107
108	0	for (int i = 0; i < count; i++)
109		{
110	0	jalview.util.Format.print(System.out, "%s \n",
111		("" + i) + " " + seqs[i].getName());
112		}
113
114	0	System.out.println("\n");
115
116	0	for (int i = 0; i < count; i++)
117		{
118	0	for (int j = 0; j < i; j++)
119		{
120	0	jalview.util.Format.print(System.out, "%7.3f",
121		scores[i][j] / totscore);
122		}
123		}
124
125	0	System.out.println("\n");
126		}
127		}
128
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
129	0	public void actionPerformed(ActionEvent evt)...
130		{
131	0	if (evt.getSource() == viewInEditorButton)
132		{
133	0	viewInEditorButton_actionPerformed();
134		}
135		}
136
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
137	0	protected void viewInEditorButton_actionPerformed()...
138		{
139
140	0	Sequence[] seq = new Sequence[sequences.size()];
141
142	0	for (int i = 0; i < sequences.size(); i++)
143		{
144	0	seq[i] = (Sequence) sequences.elementAt(i);
145		}
146
147	0	new AlignFrame(new Alignment(seq), ap.av.applet,
148		"Pairwise Aligned Sequences", false);
149
150		}
151
152		protected ScrollPane scrollPane = new ScrollPane();
153
154		protected TextArea textarea = new TextArea();
155
156		protected Button viewInEditorButton = new Button();
157
158		Panel jPanel1 = new Panel();
159
160		BorderLayout borderLayout1 = new BorderLayout();
161
		0% Uncovered Elements: 10 (10) Complexity: 1 Complexity Density: 0.1
162	0	private void jbInit() throws Exception...
163		{
164	0	this.setLayout(borderLayout1);
165	0	textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
166	0	textarea.setText("");
167	0	viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
168	0	viewInEditorButton.setLabel(
169		MessageManager.getString("label.view_alignment_editor"));
170	0	viewInEditorButton.addActionListener(this);
171	0	this.add(scrollPane, BorderLayout.CENTER);
172	0	scrollPane.add(textarea);
173	0	this.add(jPanel1, BorderLayout.SOUTH);
174	0	jPanel1.add(viewInEditorButton, null);
175		}
176
177		}