Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
RemoveGapColCommand	26	27	13	0.866666786.7%	Show methods

Class RemoveGapColCommand

Class RemoveGapColCommand	Line # 26	Total Statements 27	Complexity 13	TOTAL Coverage 0.866666786.7%
RemoveGapColCommand(String,SequenceI[],int,int,AlignmentI)   RemoveGapColCommand(String,SequenceI[],int,int,AlignmentI)	3030	26.026	12.012	0.9047619 0.904761990.5%
getSize() : int   getSize() : int	9494	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.8666667	jalview.analysis.AlignmentUtilsTests.testAlignAsSameSequencesjalview.analysis.AlignmentUtilsTests.testAlignAsSameSequences	1PASS
	0.8666667	jalview.analysis.AlignmentUtilsTests.testAlignAsSameSequencesMultipleSubSeqjalview.analysis.AlignmentUtilsTests.testAlignAsSameSequencesMultipleSubSeq	1PASS

 

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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
		86.7% Uncovered Elements: 6 (45) Complexity: 13 Complexity Density: 0.48
26		public class RemoveGapColCommand extends EditCommand
27		{
28		int columnsDeleted;
29
		90.5% Uncovered Elements: 4 (42) Complexity: 12 Complexity Density: 0.46
30	3	public RemoveGapColCommand(String description, SequenceI[] seqs,...
31		int start, int end, AlignmentI al)
32		{
33	3	this.description = description;
34
35	3	int j, jSize = seqs.length;
36
37	3	int startCol = -1, endCol = -1;
38	3	columnsDeleted = 0;
39
40	3	clearEdits();
41
42	3	boolean delete = true;
43	58	for (int i = start; i <= end; i++)
44		{
45	55	delete = true;
46
47	89	for (j = 0; j < jSize; j++)
48		{
49	81	if (seqs[j].getLength() > i)
50		{
51	72	if (!jalview.util.Comparison.isGap(seqs[j].getCharAt(i)))
52		{
53	47	if (delete)
54		{
55	47	endCol = i;
56		}
57
58	47	delete = false;
59	47	break;
60		}
61		}
62		}
63
64	55	if (delete && startCol == -1)
65		{
66	7	startCol = i;
67		}
68
69	55	if (!delete && startCol > -1)
70		{
71	7	this.appendEdit(Action.DELETE_GAP, seqs, startCol - columnsDeleted,
72		endCol - startCol, al, false, null);
73
74	7	columnsDeleted += (endCol - startCol);
75	7	startCol = -1;
76	7	endCol = -1;
77		}
78		}
79
80	3	if (delete && startCol > -1)
81		{
82		// This is for empty columns at the
83		// end of the alignment
84
85	0	this.appendEdit(Action.DELETE_GAP, seqs, startCol - columnsDeleted,
86		end - startCol + 1, al, false, null);
87
88	0	columnsDeleted += (end - startCol + 1);
89		}
90
91	3	performEdit(0, null);
92		}
93
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
94	0	@Override...
95		public int getSize()
96		{
97		// We're interested in the number of columns deleted,
98		// Not the number of sequence edits.
99	0	return columnsDeleted;
100		}
101
102		}