Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Annotation	31	46	18	0.00%	Show methods

Class Annotation

Class Annotation	Line # 31	Total Statements 46	Complexity 18	TOTAL Coverage 0.00%
Annotation(String,String,char,float)   Annotation(String,String,char,float)	7474	4.04	1.01	0.0 0.00%
Annotation(String,String,char,float,Color)   Annotation(String,String,char,float,Color)	9797	2.02	1.01	0.0 0.00%
Annotation(Annotation)   Annotation(Annotation)	111111	9.09	5.05	0.0 0.00%
Annotation(float)   Annotation(float)	137137	1.01	1.01	0.0 0.00%
toString() : String   toString() : String	151151	29.029	9.09	0.0 0.00%
isWhitespace() : boolean   isWhitespace() : boolean	208208	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.datamodel;
22
23		import java.awt.Color;
24
25		/**
26		* Holds all annotation values for a position in an AlignmentAnnotation row
27		*
28		* @author $author$
29		* @version $Revision$
30		*/
		0% Uncovered Elements: 70 (70) Complexity: 18 Complexity Density: 0.39
31		public class Annotation
32		{
33		/**
34		* the empty annotation - proxy for null entries in annotation row
35		*/
36		public static final Annotation EMPTY_ANNOTATION = new Annotation("", "",
37		' ', 0f);
38
39		/** Character label - also shown below histogram */
40		public String displayCharacter = "";
41
42		/**
43		* Text label for position: shown in mouse over and displayed on secondary
44		* structure glyphs
45		*/
46		public String description = "";
47
48		/**
49		* Secondary structure symbol: Protein symbols are H, E and S(?), RNA are
50		* WUSS/Vienna plus extended pseudoknot symbols
51		*/
52		public char secondaryStructure = ' ';
53
54		/**
55		* Score for the position - used in histograms, line graphs and for shading
56		*/
57		public float value;
58
59		/** Colour for position */
60		public Color colour;
61
62		/**
63		* Creates a new Annotation object.
64		*
65		* @param displayChar
66		* DOCUMENT ME!
67		* @param desc
68		* DOCUMENT ME!
69		* @param ss
70		* DOCUMENT ME!
71		* @param val
72		* DOCUMENT ME!
73		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
74	0	public Annotation(String displayChar, String desc, char ss, float val)...
75		{
76	0	displayCharacter = displayChar;
77	0	description = desc;
78	0	secondaryStructure = ss;
79	0	value = val;
80
81		}
82
83		/**
84		* Creates a new Annotation object.
85		*
86		* @param displayChar
87		* DOCUMENT ME!
88		* @param desc
89		* DOCUMENT ME!
90		* @param ss
91		* DOCUMENT ME!
92		* @param val
93		* DOCUMENT ME!
94		* @param colour
95		* DOCUMENT ME!
96		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
97	0	public Annotation(String displayChar, String desc, char ss, float val,...
98		Color colour)
99		{
100	0	this(displayChar, desc, ss, val);
101	0	this.colour = colour;
102		}
103
104		/**
105		* Copy constructor New annotation takes on the same (or duplicated)
106		* attributes as the given template
107		*
108		* @param that
109		* template annotation
110		*/
		0% Uncovered Elements: 15 (15) Complexity: 5 Complexity Density: 0.56
111	0	public Annotation(Annotation that)...
112		{
113	0	if (that == null || this == that)
114		{
115	0	return;
116		}
117	0	if (that.displayCharacter != null)
118		{
119	0	displayCharacter = new String(that.displayCharacter);
120		}
121	0	if (that.description != null)
122		{
123	0	description = new String(that.description);
124		}
125	0	secondaryStructure = that.secondaryStructure;
126	0	value = that.value;
127	0	colour = that.colour;
128
129		}
130
131		/**
132		* Value only annotation.
133		*
134		* @param val
135		* value at this annotation position
136		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
137	0	public Annotation(float val)...
138		{
139	0	this(null, null, ' ', val, null);
140		}
141
142		/**
143		* human readable representation of an annotation row element.
144		*
145		* Format is 'display Char','secondary Structure
146		* Char',"description",score,[colourstring]
147		*
148		* fields may be missing if they are null, whitespace, or equivalent to
149		* Float.NaN
150		*/
		0% Uncovered Elements: 41 (41) Complexity: 9 Complexity Density: 0.31
151	0	@Override...
152		public String toString()
153		{
154	0	StringBuffer sb = new StringBuffer();
155	0	if (displayCharacter != null)
156		{
157	0	sb.append("\'");
158	0	sb.append(displayCharacter);
159	0	sb.append("\'");
160		}
161		{
162	0	sb.append(",");
163		}
164	0	if (secondaryStructure != 0
165		&& !("" + displayCharacter).equals("" + secondaryStructure))
166		{
167	0	sb.append("\'");
168	0	sb.append(secondaryStructure);
169	0	sb.append("\'");
170		}
171		{
172	0	sb.append(",");
173		}
174	0	if (description != null && description.length() > 0)
175		{
176	0	sb.append("\"");
177	0	sb.append(description);
178	0	sb.append("\"");
179		}
180		{
181	0	sb.append(",");
182		}
183	0	if (!Float.isNaN(value))
184		{
185	0	sb.append(value);
186		}
187	0	if (colour != null)
188		{
189	0	if (sb.length() > 0)
190		{
191	0	sb.append(",");
192		}
193	0	sb.append("[");
194	0	sb.append(colour.getRed());
195	0	sb.append(",");
196	0	sb.append(colour.getGreen());
197	0	sb.append(",");
198	0	sb.append(colour.getBlue());
199	0	sb.append("]");
200		}
201	0	return sb.toString();
202		}
203
204		/**
205		* @return true if annot is 'whitespace' annotation (zero score, whitespace or
206		* zero length display character, label, description
207		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
208	0	public boolean isWhitespace()...
209		{
210	0	return ((value == 0f)
211		&& ((description == null) || (description.trim().length() == 0))
212		&& ((displayCharacter == null)
213		|| (displayCharacter.trim().length() == 0)
214		|| (displayCharacter.equals(" ."))) // RNA Stockholm blank
215		// displayCharacter can
216		// end up like this
217		&& (secondaryStructure == '\0' || (secondaryStructure == ' '))
218		&& colour == null);
219		}
220		}