Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
OrderCommand	33	10	7	0.666666766.7%	Show methods

Class OrderCommand

Class OrderCommand	Line # 33	Total Statements 10	Complexity 7	TOTAL Coverage 0.666666766.7%
OrderCommand(String,SequenceI[],AlignmentI)   OrderCommand(String,SequenceI[],AlignmentI)	6363	5.05	1.01	1.0 1.0100%
getDescription() : String   getDescription() : String	7272	1.01	1.01	1.0 1.0100%
getSize() : int   getSize() : int	7777	1.01	1.01	1.0 1.0100%
doCommand(AlignmentI[]) : void   doCommand(AlignmentI[]) : void	8282	1.01	1.01	1.0 1.0100%
undoCommand(AlignmentI[]) : void   undoCommand(AlignmentI[]) : void	8787	1.01	1.01	0.0 0.00%
getSequenceOrder(boolean) : SequenceI[]   getSequenceOrder(boolean) : SequenceI[]	9898	1.01	2.02	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.analysis.AlignmentSorter;
24		import jalview.datamodel.AlignmentI;
25		import jalview.datamodel.SequenceI;
26
27		/**
28		* An undoable command to reorder the sequences in an alignment.
29		*
30		* @author gmcarstairs
31		*
32		*/
		66.7% Uncovered Elements: 6 (18) Complexity: 7 Complexity Density: 0.7
33		public class OrderCommand implements CommandI
34		{
35		String description;
36
37		/*
38		* The sequence order before sorting (target order for an undo)
39		*/
40		SequenceI[] seqs;
41
42		/*
43		* The sequence order specified by this command
44		*/
45		SequenceI[] seqs2;
46
47		/*
48		* The alignment the command acts on
49		*/
50		AlignmentI al;
51
52		/**
53		* Constructor given the 'undo' sequence order, and the (already) sorted
54		* alignment.
55		*
56		* @param description
57		* a text label for the 'undo' menu option
58		* @param seqs
59		* the sequence order for undo
60		* @param al
61		* the alignment as ordered by this command
62		*/
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2
63	1	public OrderCommand(String description, SequenceI[] seqs, AlignmentI al)...
64		{
65	1	this.description = description;
66	1	this.seqs = seqs;
67	1	this.seqs2 = al.getSequencesArray();
68	1	this.al = al;
69	1	doCommand(null);
70		}
71
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
72	2	public String getDescription()...
73		{
74	2	return description;
75		}
76
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
77	1	public int getSize()...
78		{
79	1	return 1;
80		}
81
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
82	1	public void doCommand(AlignmentI[] views)...
83		{
84	1	AlignmentSorter.setOrder(al, seqs2);
85		}
86
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
87	0	public void undoCommand(AlignmentI[] views)...
88		{
89	0	AlignmentSorter.setOrder(al, seqs);
90		}
91
92		/**
93		* Returns the sequence order used to sort, or before sorting if undo=true.
94		*
95		* @param undo
96		* @return
97		*/
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
98	0	public SequenceI[] getSequenceOrder(boolean undo)...
99		{
100	0	return undo ? seqs : seqs2;
101		}
102		}