Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FeatureColourI	27	0	0	-1.0 -	Show methods

Class FeatureColourI

Class FeatureColourI	Line # 27	Total Statements 0	Complexity 0	TOTAL Coverage -1.0 -

 

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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.api;
22
23		import jalview.datamodel.SequenceFeature;
24
25		import java.awt.Color;
26
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
27		public interface FeatureColourI
28		{
29
30		/**
31		* Answers true when the feature colour varies across the score range
32		*
33		* @return
34		*/
35		boolean isGraduatedColour();
36
37		/**
38		* Returns the feature colour (when isGraduatedColour answers false)
39		*
40		* @return
41		*/
42		Color getColour();
43
44		/**
45		* Returns the minimum colour (when isGraduatedColour answers true)
46		*
47		* @return
48		*/
49		Color getMinColour();
50
51		/**
52		* Returns the maximum colour (when isGraduatedColour answers true)
53		*
54		* @return
55		*/
56		Color getMaxColour();
57
58		/**
59		* Returns the 'no value' colour (used when a feature lacks score, or the
60		* attribute, being used for colouring)
61		*
62		* @return
63		*/
64		Color getNoColour();
65
66		/**
67		* Answers true if the feature has a single colour, i.e. if isColourByLabel()
68		* and isGraduatedColour() both answer false
69		*
70		* @return
71		*/
72		boolean isSimpleColour();
73
74		/**
75		* Answers true if the feature is coloured by label (description) or by text
76		* value of an attribute
77		*
78		* @return
79		*/
80		boolean isColourByLabel();
81
82		void setColourByLabel(boolean b);
83
84		/**
85		* Answers true if the feature is coloured below a threshold value; only
86		* applicable when isGraduatedColour answers true
87		*
88		* @return
89		*/
90		boolean isBelowThreshold();
91
92		void setBelowThreshold(boolean b);
93
94		/**
95		* Answers true if the feature is coloured above a threshold value; only
96		* applicable when isGraduatedColour answers true
97		*
98		* @return
99		*/
100		boolean isAboveThreshold();
101
102		void setAboveThreshold(boolean b);
103
104		/**
105		* Returns the threshold value (if any), else zero
106		*
107		* @return
108		*/
109		float getThreshold();
110
111		void setThreshold(float f);
112
113		/**
114		* Answers true if the colour varies between the actual minimum and maximum
115		* score values of the feature, or false if between absolute minimum and
116		* maximum values (or if not a graduated colour).
117		*
118		* @return
119		*/
120		boolean isAutoScaled();
121
122		void setAutoScaled(boolean b);
123
124		/**
125		* Returns the maximum score of the graduated colour range
126		*
127		* @return
128		*/
129		float getMax();
130
131		/**
132		* Returns the minimum score of the graduated colour range
133		*
134		* @return
135		*/
136		float getMin();
137
138		/**
139		* Answers true if either isAboveThreshold or isBelowThreshold answers true
140		*
141		* @return
142		*/
143		boolean hasThreshold();
144
145		/**
146		* Returns the computed colour for the given sequence feature. Answers null if
147		* the score of this feature instance is outside the range to render (if any),
148		* i.e. lies below or above a configured threshold.
149		*
150		* @param feature
151		* @return
152		*/
153		Color getColor(SequenceFeature feature);
154
155		/**
156		* Update the min-max range for a graduated colour scheme. Note that the
157		* colour scheme may be configured to colour by feature score, or a
158		* (numeric-valued) attribute - the caller should ensure that the correct
159		* range is being set.
160		*
161		* @param min
162		* @param max
163		*/
164		void updateBounds(float min, float max);
165
166		/**
167		* Returns the colour in Jalview features file format
168		*
169		* @return
170		*/
171		String toJalviewFormat(String featureType);
172
173		/**
174		* Answers true if colour is by attribute text or numerical value
175		*
176		* @return
177		*/
178		boolean isColourByAttribute();
179
180		/**
181		* Answers the name of the attribute (and optional sub-attribute...) used for
182		* colouring if any, or null
183		*
184		* @return
185		*/
186		String[] getAttributeName();
187
188		/**
189		* Sets the name of the attribute (and optional sub-attribute...) used for
190		* colouring if any, or null to remove this property
191		*
192		* @return
193		*/
194		void setAttributeName(String... name);
195
196		/**
197		* Answers true if colour has a threshold set, and the feature score (or other
198		* attribute selected for colouring) is outwith the threshold.
199		* <p>
200		* Answers false if not a graduated colour, or no threshold is set, or value
201		* is not outwith the threshold, or value is null or non-numeric.
202		*
203		* @param sf
204		* @return
205		*/
206		boolean isOutwithThreshold(SequenceFeature sf);
207
208		/**
209		* Answers a human-readable text description of the colour, suitable for
210		* display as a tooltip, possibly internationalised for the user's locale.
211		*
212		* @return
213		*/
214		String getDescription();
215		}