Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
RNAHelicesColourChooser	40	25	8	0.00%	Show methods

Class RNAHelicesColourChooser

Class RNAHelicesColourChooser	Line # 40	Total Statements 25	Complexity 8	TOTAL Coverage 0.00%
RNAHelicesColourChooser(AlignViewportI,AlignmentViewPanel)   RNAHelicesColourChooser(AlignViewportI,AlignmentViewPanel)	5555	20.020	6.06	0.0 0.00%
changeColour() : void   changeColour() : void	9797	5.05	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.schemes;
22
23		import jalview.api.AlignViewportI;
24		import jalview.api.AlignmentViewPanel;
25		import jalview.datamodel.AlignmentAnnotation;
26		import jalview.datamodel.SequenceGroup;
27
28		import java.util.Hashtable;
29		import java.util.Map;
30		import java.util.Vector;
31
32		/**
33		* Helps generate the colors for RNA secondary structure. Future: add option to
34		* change colors based on covariation.
35		*
36		* @author Lauren Michelle Lui
37		* @deprecated this seems to be unfinished - just use RNAHelicesColour
38		*/
39		@Deprecated
		0% Uncovered Elements: 39 (39) Complexity: 8 Complexity Density: 0.32
40		public class RNAHelicesColourChooser
41		{
42
43		AlignViewportI av;
44
45		AlignmentViewPanel ap;
46
47		ColourSchemeI oldcs;
48
49		Map<SequenceGroup, ColourSchemeI> oldgroupColours;
50
51		AlignmentAnnotation currentAnnotation;
52
53		boolean adjusting = false;
54
		0% Uncovered Elements: 30 (30) Complexity: 6 Complexity Density: 0.3
55	0	public RNAHelicesColourChooser(AlignViewportI av,...
56		final AlignmentViewPanel ap)
57		{
58	0	oldcs = av.getGlobalColourScheme();
59	0	if (av.getAlignment().getGroups() != null)
60		{
61	0	oldgroupColours = new Hashtable<>();
62	0	for (SequenceGroup sg : ap.getAlignment().getGroups())
63		{
64	0	if (sg.getColourScheme() != null)
65		{
66	0	oldgroupColours.put(sg, sg.getColourScheme());
67		}
68		}
69		}
70	0	this.av = av;
71	0	this.ap = ap;
72
73	0	adjusting = true;
74	0	Vector<String> list = new Vector<>();
75	0	int index = 1;
76	0	AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
77	0	if (anns != null)
78		{
79	0	for (int i = 0; i < anns.length; i++)
80		{
81	0	String label = anns[i].label;
82	0	if (!list.contains(label))
83		{
84	0	list.addElement(label);
85		}
86		else
87		{
88	0	list.addElement(label + "_" + (index++));
89		}
90		}
91		}
92
93	0	adjusting = false;
94	0	changeColour();
95		}
96
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
97	0	void changeColour()...
98		{
99		// Check if combobox is still adjusting
100	0	if (adjusting)
101		{
102	0	return;
103		}
104	0	RNAHelicesColour rhc = new RNAHelicesColour(av.getAlignment());
105
106	0	av.setGlobalColourScheme(rhc);
107
108	0	ap.paintAlignment(true, true);
109		}
110		}