Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ColourSchemeProperty	41	20	11	0.00%	Show methods

Class ColourSchemeProperty

Class ColourSchemeProperty	Line # 41	Total Statements 20	Complexity 11	TOTAL Coverage 0.00%
getColourScheme(AlignViewportI,AnnotatedCollectionI,String) : ColourSchemeI   getColourScheme(AlignViewportI,AnnotatedCollectionI,String) : ColourSchemeI	7979	7.07	3.03	0.0 0.00%
initRnaHelicesShading(int) : void   initRnaHelicesShading(int) : void	112112	11.011	5.05	0.0 0.00%
resetRnaHelicesShading() : void   resetRnaHelicesShading() : void	140140	1.01	1.01	0.0 0.00%
getColourName(ColourSchemeI) : String   getColourName(ColourSchemeI) : String	151151	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.schemes;
22
23		import jalview.api.AlignViewportI;
24		import jalview.datamodel.AnnotatedCollectionI;
25		import jalview.util.ColorUtils;
26
27		import java.awt.Color;
28
29		/**
30		* ColourSchemeProperty binds names to hardwired colourschemes and tries to deal
31		* intelligently with mapping unknown names to user defined colourschemes (that
32		* exist or can be created from the string representation of the colourscheme
33		* name - either a hex RGB triplet or a named colour under java.awt.color ). The
34		* values of the colourscheme constants is important for callers of
35		* getColourName(int i), since it can be used to enumerate the set of built in
36		* colours. The FIRST_COLOUR and LAST_COLOUR symbols are provided for this.
37		*
38		* @author $author$
39		* @version $Revision$
40		*/
		0% Uncovered Elements: 36 (36) Complexity: 11 Complexity Density: 0.55
41		public class ColourSchemeProperty
42		{
43
44		/**
45		* Returns a colour scheme for the given name, with which the given data may
46		* be coloured. The name is not case-sensitive, and may be one of
47		* <ul>
48		* <li>any currently registered colour scheme; Jalview by default
49		* provides</li>
50		* <ul>
51		* <li>Clustal</li>
52		* <li>Blosum62</li>
53		* <li>% Identity</li>
54		* <li>Hydrophobic</li>
55		* <li>Zappo</li>
56		* <li>Taylor</li>
57		* <li>Helix Propensity</li>
58		* <li>Strand Propensity</li>
59		* <li>Turn Propensity</li>
60		* <li>Buried Index</li>
61		* <li>Nucleotide</li>
62		* <li>Purine/Pyrimidine</li>
63		* <li>T-Coffee Scores</li>
64		* <li>RNA Helices</li>
65		* </ul>
66		* <li>the name of a programmatically added colour scheme</li>
67		* <li>an AWT colour name e.g. red</li>
68		* <li>an AWT hex rgb colour e.g. ff2288</li>
69		* <li>residue colours list e.g. D,E=red;K,R,H=0022FF;c=yellow</li>
70		* </ul>
71		*
72		* If none of these formats is matched, the string is converted to a colour
73		* using a hashing algorithm. For name "None", returns null.
74		*
75		* @param forData
76		* @param name
77		* @return
78		*/
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.43
79	0	public static ColourSchemeI getColourScheme(AlignViewportI view,...
80		AnnotatedCollectionI forData, String name)
81		{
82	0	if (ResidueColourScheme.NONE.equalsIgnoreCase(name))
83		{
84	0	return null;
85
86		}
87
88		/*
89		* if this is the name of a registered colour scheme, just
90		* create a new instance of it
91		*/
92	0	ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(name,
93		view, forData, null);
94	0	if (scheme != null)
95		{
96	0	return scheme;
97		}
98
99		/*
100		* try to parse the string as a residues colour scheme
101		* e.g. A=red;T,G=blue etc
102		* else parse the name as a colour specification
103		* e.g. "red" or "ff00ed",
104		* or failing that hash the name to a colour
105		*/
106	0	UserColourScheme ucs = new UserColourScheme(name);
107	0	return ucs;
108		}
109
110		public static Color rnaHelices[] = null;
111
		0% Uncovered Elements: 17 (17) Complexity: 5 Complexity Density: 0.45
112	0	public static void initRnaHelicesShading(int n)...
113		{
114	0	int j = 0;
115	0	if (rnaHelices == null)
116		{
117	0	rnaHelices = new Color[n + 1];
118		}
119	0	else if (rnaHelices != null && rnaHelices.length <= n)
120		{
121	0	Color[] t = new Color[n + 1];
122	0	System.arraycopy(rnaHelices, 0, t, 0, rnaHelices.length);
123	0	j = rnaHelices.length;
124	0	rnaHelices = t;
125		}
126		else
127		{
128	0	return;
129		}
130		// Generate random colors and store
131	0	for (; j <= n; j++)
132		{
133	0	rnaHelices[j] = ColorUtils.generateRandomColor(Color.white);
134		}
135		}
136
137		/**
138		* delete the existing cached RNA helices colours
139		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
140	0	public static void resetRnaHelicesShading()...
141		{
142	0	rnaHelices = null;
143		}
144
145		/**
146		* Returns the name of the colour scheme (or "None" if it is null)
147		*
148		* @param cs
149		* @return
150		*/
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
151	0	public static String getColourName(ColourSchemeI cs)...
152		{
153	0	return cs == null ? ResidueColourScheme.NONE : cs.getSchemeName();
154		}
155
156		}