Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
RNAHelicesColour	42	44	27	0.00%	Show methods

Class RNAHelicesColour

Class RNAHelicesColour	Line # 42	Total Statements 44	Complexity 27	TOTAL Coverage 0.00%
RNAHelicesColour()   RNAHelicesColour()	6161	0.00	1.01	-1.0 -1.0 -
RNAHelicesColour(AlignmentAnnotation)   RNAHelicesColour(AlignmentAnnotation)	6969	4.04	1.01	0.0 0.00%
RNAHelicesColour(AnnotatedCollectionI)   RNAHelicesColour(AnnotatedCollectionI)	7777	3.03	1.01	0.0 0.00%
RNAHelicesColour(RNAHelicesColour)   RNAHelicesColour(RNAHelicesColour)	8989	3.03	1.01	0.0 0.00%
alignmentChanged(AnnotatedCollectionI,Map<SequenceI, SequenceCollectionI>) : void   alignmentChanged(AnnotatedCollectionI,Map<SequenceI, SequenceCollectionI>) : void	9696	8.08	6.06	0.0 0.00%
refresh() : void   refresh() : void	126126	11.011	7.07	0.0 0.00%
findColour(char) : Color   findColour(char) : Color	176176	1.01	1.01	0.0 0.00%
findColour(char,int,SequenceI) : Color   findColour(char,int,SequenceI) : Color	194194	7.07	2.02	0.0 0.00%
getInstance(AlignViewportI,AnnotatedCollectionI) : ColourSchemeI   getInstance(AlignViewportI,AnnotatedCollectionI) : ColourSchemeI	209209	1.01	1.01	0.0 0.00%
isNucleotideSpecific() : boolean   isNucleotideSpecific() : boolean	216216	1.01	1.01	0.0 0.00%
isApplicableTo(AnnotatedCollectionI) : boolean   isApplicableTo(AnnotatedCollectionI) : boolean	225225	3.03	3.03	0.0 0.00%
getSchemeName() : String   getSchemeName() : String	239239	1.01	1.01	0.0 0.00%
isSimple() : boolean   isSimple() : boolean	245245	1.01	1.01	0.0 0.00%

 

Contributing tests

Source view

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.datamodel.AlignmentAnnotation;
25		import jalview.datamodel.AlignmentI;
26		import jalview.datamodel.AnnotatedCollectionI;
27		import jalview.datamodel.SequenceCollectionI;
28		import jalview.datamodel.SequenceI;
29
30		import java.awt.Color;
31		import java.util.Hashtable;
32		import java.util.Map;
33
34		/**
35		* Looks at the information computed from an RNA Stockholm format file on the
36		* secondary structure of the alignment. Extracts the information on the
37		* positions of the helices present and assigns colors.
38		*
39		* @author Lauren Michelle Lui
40		* @version 2.5
41		*/
		0% Uncovered Elements: 73 (73) Complexity: 27 Complexity Density: 0.61
42		public class RNAHelicesColour extends ResidueColourScheme
43		{
44
45		/**
46		* Maps sequence positions to the RNA helix they belong to. Key: position,
47		* Value: helix TODO: Revise or drop in favour of annotation position numbers
48		*/
49		public Hashtable<Integer, String> positionsToHelix = new Hashtable<>();
50
51		/**
52		* Number of helices in the RNA secondary structure
53		*/
54		int numHelix = 0;
55
56		public AlignmentAnnotation annotation;
57
58		/**
59		* Default constructor (required for ColourSchemes cache)
60		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
61	0	public RNAHelicesColour()...
62		{
63
64		}
65
66		/**
67		* Creates a new RNAHelicesColour object.
68		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
69	0	public RNAHelicesColour(AlignmentAnnotation annotation)...
70		{
71	0	super(ResidueProperties.nucleotideIndex);
72	0	this.annotation = annotation;
73	0	ColourSchemeProperty.resetRnaHelicesShading();
74	0	refresh();
75		}
76
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
77	0	public RNAHelicesColour(AnnotatedCollectionI alignment)...
78		{
79	0	super(ResidueProperties.nucleotideIndex);
80	0	ColourSchemeProperty.resetRnaHelicesShading();
81	0	alignmentChanged(alignment, null);
82		}
83
84		/**
85		* clones colour settings and annotation row data
86		*
87		* @param rnaHelicesColour
88		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
89	0	public RNAHelicesColour(RNAHelicesColour rnaHelicesColour)...
90		{
91	0	super(ResidueProperties.nucleotideIndex);
92	0	annotation = rnaHelicesColour.annotation;
93	0	refresh();
94		}
95
		0% Uncovered Elements: 14 (14) Complexity: 6 Complexity Density: 0.75
96	0	@Override...
97		public void alignmentChanged(AnnotatedCollectionI alignment,
98		Map<SequenceI, SequenceCollectionI> hiddenReps)
99		{
100
101		// This loop will find the first rna structure annotation by which to colour
102		// the sequences.
103	0	AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation();
104	0	if (annotations == null)
105		{
106	0	return;
107		}
108	0	for (int i = 0; i < annotations.length; i++)
109		{
110
111		// is this a sensible way of determining type of annotation?
112	0	if (annotations[i].isForDisplay() && annotations[i].isRNA()
113		&& annotations[i].isValidStruc())
114		{
115	0	annotation = annotations[i];
116	0	break;
117		}
118		}
119
120	0	refresh();
121
122		}
123
124		private long lastrefresh = -1;
125
		0% Uncovered Elements: 17 (17) Complexity: 7 Complexity Density: 0.64
126	0	public void refresh()...
127		{
128
129	0	if (annotation != null && ((annotation._rnasecstr == null
130		|| lastrefresh != annotation._rnasecstr.hashCode())
131		&& annotation.isValidStruc()))
132		{
133	0	annotation.getRNAStruc();
134	0	lastrefresh = annotation._rnasecstr.hashCode();
135	0	numHelix = 0;
136	0	positionsToHelix = new Hashtable<>();
137
138		// Figure out number of helices
139		// Length of rnasecstr is the number of pairs of positions that base pair
140		// with each other in the secondary structure
141	0	for (int x = 0; x < this.annotation._rnasecstr.length; x++)
142		{
143
144		/*
145		* jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x] + " Begin" +
146		* this.annotation._rnasecstr[x].getBegin());
147		*/
148		// jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x].getFeatureGroup());
149
150	0	positionsToHelix.put(this.annotation._rnasecstr[x].getBegin(),
151		this.annotation._rnasecstr[x].getFeatureGroup());
152	0	positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
153		this.annotation._rnasecstr[x].getFeatureGroup());
154
155	0	if (Integer.parseInt(
156		this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
157		{
158	0	numHelix = Integer.parseInt(
159		this.annotation._rnasecstr[x].getFeatureGroup());
160		}
161
162		}
163	0	ColourSchemeProperty.initRnaHelicesShading(numHelix);
164		}
165		}
166
167		/**
168		* Returns default color base on purinepyrimidineIndex in
169		* jalview.schemes.ResidueProperties (Allows coloring in sequence logo)
170		*
171		* @param c
172		* Character in sequence
173		*
174		* @return color in RGB
175		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
176	0	@Override...
177		public Color findColour(char c)
178		{
179	0	return ResidueProperties.purinepyrimidine[ResidueProperties.purinepyrimidineIndex[c]];
180		// random colors for all positions
181		// jalview.util.ColorUtils.generateRandomColor(Color.white); If you want
182		}
183
184		/**
185		* Returns color based on helices
186		*
187		* @param c
188		* Character in sequence
189		* @param j
190		* position in sequence - used to locate helix
191		*
192		* @return Color in RGB
193		*/
		0% Uncovered Elements: 9 (9) Complexity: 2 Complexity Density: 0.29
194	0	@Override...
195		public Color findColour(char c, int j, SequenceI seq)
196		{
197	0	refresh();
198	0	Color currentColour = Color.white;
199	0	String currentHelix = null;
200	0	currentHelix = positionsToHelix.get(j);
201	0	if (currentHelix != null)
202		{
203	0	currentColour = ColourSchemeProperty.rnaHelices[Integer
204		.parseInt(currentHelix)];
205		}
206	0	return currentColour;
207		}
208
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
209	0	@Override...
210		public ColourSchemeI getInstance(AlignViewportI view,
211		AnnotatedCollectionI sg)
212		{
213	0	return new RNAHelicesColour(sg);
214		}
215
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
216	0	@Override...
217		public boolean isNucleotideSpecific()
218		{
219	0	return true;
220		}
221
222		/**
223		* Answers true if the data has RNA secondary structure annotation
224		*/
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
225	0	@Override...
226		public boolean isApplicableTo(AnnotatedCollectionI ac)
227		{
228	0	if (ac instanceof AlignmentI && ((AlignmentI) ac).hasRNAStructure())
229		{
230	0	return true;
231		}
232
233		/*
234		* not currently supporting this option for group annotation / colouring
235		*/
236	0	return false;
237		}
238
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
239	0	@Override...
240		public String getSchemeName()
241		{
242	0	return JalviewColourScheme.RNAHelices.toString();
243		}
244
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
245	0	@Override...
246		public boolean isSimple()
247		{
248	0	return false;
249		}
250		}