Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
RemoveGapsCommand	26	36	15	0.00%	Show methods

Class RemoveGapsCommand

Class RemoveGapsCommand	Line # 26	Total Statements 36	Complexity 15	TOTAL Coverage 0.00%
RemoveGapsCommand(String,SequenceI[],AlignmentI)   RemoveGapsCommand(String,SequenceI[],AlignmentI)	2828	6.06	3.03	0.0 0.00%
RemoveGapsCommand(String,SequenceI[],int,int,AlignmentI)   RemoveGapsCommand(String,SequenceI[],int,int,AlignmentI)	4444	2.02	1.01	0.0 0.00%
findGaps(SequenceI[],int,int,AlignmentI) : void   findGaps(SequenceI[],int,int,AlignmentI) : void	5151	28.028	11.011	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.commands;
22
23		import jalview.datamodel.AlignmentI;
24		import jalview.datamodel.SequenceI;
25
		0% Uncovered Elements: 57 (57) Complexity: 15 Complexity Density: 0.42
26		public class RemoveGapsCommand extends EditCommand
27		{
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
28	0	public RemoveGapsCommand(String description, SequenceI[] seqs,...
29		AlignmentI al)
30		{
31	0	this.description = description;
32	0	int width = 0;
33	0	for (int i = 0; i < seqs.length; i++)
34		{
35	0	if (seqs[i].getLength() > width)
36		{
37	0	width = seqs[i].getLength();
38		}
39		}
40
41	0	findGaps(seqs, 0, width, al);
42		}
43
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
44	0	public RemoveGapsCommand(String description, SequenceI[] seqs, int start,...
45		int end, AlignmentI al)
46		{
47	0	this.description = description;
48	0	findGaps(seqs, start, end, al);
49		}
50
		0% Uncovered Elements: 42 (42) Complexity: 11 Complexity Density: 0.39
51	0	void findGaps(SequenceI[] seqs, int start, int end, AlignmentI al)...
52		{
53
54	0	int startCol = -1, endCol = -1;
55	0	int deletedCols = 0;
56
57	0	int j, jSize;
58
59	0	clearEdits();
60
61	0	boolean delete = true;
62	0	char[] sequence;
63
64	0	for (int s = 0; s < seqs.length; s++)
65		{
66	0	deletedCols = 0;
67	0	startCol = -1;
68	0	endCol = -1;
69	0	sequence = seqs[s].getSequence(start, end + 1);
70
71	0	jSize = sequence.length;
72	0	for (j = 0; j < jSize; j++)
73		{
74	0	delete = true;
75
76	0	if (!jalview.util.Comparison.isGap(sequence[j]))
77		{
78	0	if (delete)
79		{
80	0	endCol = j;
81		}
82
83	0	delete = false;
84		}
85
86	0	if (delete && startCol == -1)
87		{
88	0	startCol = j;
89		}
90
91	0	if (!delete && startCol > -1)
92		{
93	0	this.appendEdit(
94		Action.DELETE_GAP, new SequenceI[]
95		{ seqs[s] }, start + startCol - deletedCols,
96		endCol - startCol, al, false, null);
97
98	0	deletedCols += (endCol - startCol);
99	0	startCol = -1;
100	0	endCol = -1;
101		}
102		}
103	0	if (delete && startCol > -1)
104		{
105	0	this.appendEdit(
106		Action.DELETE_GAP, new SequenceI[]
107		{ seqs[s] }, start + startCol - deletedCols,
108		jSize - startCol, al, false, null);
109		}
110
111		}
112
113	0	performEdit(0, null);
114		}
115
116		}