Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JustifyLeftOrRightCommand	30	24	10	0.00%	Show methods

Class JustifyLeftOrRightCommand

Class JustifyLeftOrRightCommand	Line # 30	Total Statements 24	Complexity 10	TOTAL Coverage 0.00%
JustifyLeftOrRightCommand(String,boolean,List<SequenceI>,int,int,AlignmentI)   JustifyLeftOrRightCommand(String,boolean,List<SequenceI>,int,int,AlignmentI)	4949	24.024	10.010	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 java.util.List;
24
25		import jalview.datamodel.AlignmentI;
26		import jalview.datamodel.ContiguousI;
27		import jalview.datamodel.SequenceI;
28		import jalview.util.Comparison;
29
		0% Uncovered Elements: 39 (39) Complexity: 10 Complexity Density: 0.42
30		public class JustifyLeftOrRightCommand extends EditCommand
31		{
32		/**
33		* Constructs and performs a trim alignment command
34		*
35		* @param description
36		* (to show in Undo/Redo menu)
37		* @param justifyLeft
38		* if true left justify, otherwise right
39		* @param seqs
40		* the sequences to justify
41		* @param start
42		* - leftmost column (base 0) to justify
43		*
44		* @param end
45		* - rightmost column (base 0) to justify
46		*
47		* @param al
48		*/
		0% Uncovered Elements: 38 (38) Complexity: 10 Complexity Density: 0.42
49	0	public JustifyLeftOrRightCommand(String description, boolean left,...
50		List<SequenceI> seqs, int from, int to, AlignmentI al)
51		{
52	0	this.description = description;
53
54	0	for (SequenceI seq : seqs)
55		{
56	0	ContiguousI cont = seq.findPositions(from + 1, to + 1);
57	0	if (cont == null)
58		{
59	0	continue;
60		}
61	0	char[] range = seq.getSequence(from, to + 1);
62	0	if (range == null || range.length == 0)
63		{
64	0	continue;
65		}
66	0	int dsstart = seq.getDatasetSequence().getStart();
67	0	char[] sqchar = seq.getDatasetSequence().getSequence(
68		-dsstart + cont.getBegin(), -dsstart + cont.getEnd() + 1);
69		// debug
70		// println sqchar;
71	0	char[] alseq = new char[to - from + 1];
72	0	int sqstart = left ? 0 : alseq.length - sqchar.length;
73	0	int gaps = alseq.length - sqchar.length;
74	0	int gapstart = left ? sqchar.length : 0;
75	0	char gc = al.getGapCharacter();
76	0	for (int gp = 0; gp < gaps; gp++)
77		{
78	0	alseq[gapstart + gp] = gc;
79		}
80
81	0	for (int sqp = 0, insp = 0; sqp < alseq.length; sqp++)
82		{
83	0	if (sqp < range.length && !Comparison.isGap(range[sqp]))
84		{
85	0	alseq[insp++ + sqstart] = range[sqp];
86		}
87		}
88	0	SequenceI[] sqa = new SequenceI[1];
89	0	sqa[0] = seq;
90
91	0	addEdit(new jalview.commands.EditCommand.Edit(
92		jalview.commands.EditCommand.Action.REPLACE, sqa, from,
93		to + 1, al, new String(alseq)));
94		}
95
96	0	performEdit(0, null);
97		}
98		}