Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ColourSchemeLoader	36	33	7	0.00%	Show methods

Class ColourSchemeLoader

Class ColourSchemeLoader	Line # 36	Total Statements 33	Complexity 7	TOTAL Coverage 0.00%
loadColourScheme(String) : UserColourScheme   loadColourScheme(String) : UserColourScheme	4848	33.033	7.07	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 java.awt.Color;
24		import java.io.File;
25		import java.io.FileInputStream;
26		import java.io.InputStreamReader;
27		import java.util.Locale;
28
29		import javax.xml.bind.JAXBContext;
30		import javax.xml.bind.JAXBElement;
31		import javax.xml.stream.XMLInputFactory;
32		import javax.xml.stream.XMLStreamReader;
33
34		import jalview.xml.binding.jalview.JalviewUserColours;
35
		0% Uncovered Elements: 44 (44) Complexity: 7 Complexity Density: 0.21
36		public class ColourSchemeLoader
37		{
38
39		/**
40		* Loads a user defined colour scheme from file. The file should contain a
41		* definition of residue colours in XML format as defined in
42		* JalviewUserColours.xsd.
43		*
44		* @param filePath
45		*
46		* @return
47		*/
		0% Uncovered Elements: 43 (43) Complexity: 7 Complexity Density: 0.21
48	0	public static UserColourScheme loadColourScheme(String filePath)...
49		{
50	0	UserColourScheme ucs = null;
51	0	Color[] newColours = null;
52	0	File file = new File(filePath);
53	0	try
54		{
55	0	InputStreamReader in = new InputStreamReader(
56		new FileInputStream(file), "UTF-8");
57
58	0	JAXBContext jc = JAXBContext.class.getDeclaredConstructor()
59		.newInstance("jalview.xml.binding.jalview");
60	0	javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
61	0	XMLStreamReader streamReader = XMLInputFactory.class
62		.getDeclaredConstructor().newInstance()
63		.createXMLStreamReader(in);
64	0	JAXBElement<JalviewUserColours> jbe = um.unmarshal(streamReader,
65		JalviewUserColours.class);
66	0	JalviewUserColours jucs = jbe.getValue();
67
68		/*
69		* non-case-sensitive colours are for 20 amino acid codes,
70		* B, Z, X and Gap
71		* optionally, lower-case alternatives for all except Gap
72		*/
73	0	newColours = new Color[24];
74	0	Color[] lowerCase = new Color[23];
75	0	boolean caseSensitive = false;
76
77	0	String name;
78	0	int index;
79	0	for (int i = 0; i < jucs.getColour().size(); i++)
80		{
81	0	name = jucs.getColour().get(i).getName();
82	0	if (ResidueProperties.aa3Hash.containsKey(name))
83		{
84	0	index = ResidueProperties.aa3Hash.get(name).intValue();
85		}
86		else
87		{
88	0	index = ResidueProperties.aaIndex[name.charAt(0)];
89		}
90	0	if (index == -1)
91		{
92	0	continue;
93		}
94
95	0	Color color = new Color(
96		Integer.parseInt(jucs.getColour().get(i).getRGB(), 16));
97	0	if (name.toLowerCase(Locale.ROOT).equals(name))
98		{
99	0	caseSensitive = true;
100	0	lowerCase[index] = color;
101		}
102		else
103		{
104	0	newColours[index] = color;
105		}
106		}
107
108		/*
109		* instantiate the colour scheme
110		*/
111	0	ucs = new UserColourScheme(newColours);
112	0	ucs.setName(jucs.getSchemeName());
113	0	if (caseSensitive)
114		{
115	0	ucs.setLowerCaseColours(lowerCase);
116		}
117		} catch (Exception ex)
118		{
119		// used to try to parse a V1 Castor generated colours file
120	0	jalview.bin.Console.errPrintln("Failed to read colour scheme from "
121		+ filePath + " : " + ex.toString());
122		}
123
124	0	return ucs;
125		}
126
127		}