Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
ColourSchemeLoader	32	42	10	57	0.00%	Show methods

Class ColourSchemeLoader

Class ColourSchemeLoader	Line # 32	Total Statements 42	Complexity 10	Uncovered Elements 57	TOTAL Coverage 0.00%
loadColourScheme(String) : UserColourScheme   loadColourScheme(String) : UserColourScheme	4444	42.042	10.010	56.056	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.binding.JalviewUserColours;
24
25		import java.awt.Color;
26		import java.io.File;
27		import java.io.FileInputStream;
28		import java.io.InputStreamReader;
29
30		import org.exolab.castor.xml.Unmarshaller;
31
		0% Uncovered Elements: 57 (57) Complexity: 10 Complexity Density: 0.24
32		public class ColourSchemeLoader
33		{
34
35		/**
36		* Loads a user defined colour scheme from file. The file should contain a
37		* definition of residue colours in XML format as defined in
38		* JalviewUserColours.xsd.
39		*
40		* @param filePath
41		*
42		* @return
43		*/
		0% Uncovered Elements: 56 (56) Complexity: 10 Complexity Density: 0.24
44	0	public static UserColourScheme loadColourScheme(String filePath)...
45		{
46	0	UserColourScheme ucs = null;
47	0	Color[] newColours = null;
48	0	File file = new File(filePath);
49	0	try
50		{
51	0	InputStreamReader in = new InputStreamReader(
52		new FileInputStream(file), "UTF-8");
53
54	0	jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
55
56	0	org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
57		jucs);
58	0	jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar
59		.unmarshal(in);
60
61		/*
62		* non-case-sensitive colours are for 20 amino acid codes,
63		* B, Z, X and Gap
64		* optionally, lower-case alternatives for all except Gap
65		*/
66	0	newColours = new Color[24];
67	0	Color[] lowerCase = new Color[23];
68	0	boolean caseSensitive = false;
69
70	0	String name;
71	0	int index;
72	0	for (int i = 0; i < jucs.getColourCount(); i++)
73		{
74	0	name = jucs.getColour(i).getName();
75	0	if (ResidueProperties.aa3Hash.containsKey(name))
76		{
77	0	index = ResidueProperties.aa3Hash.get(name).intValue();
78		}
79		else
80		{
81	0	index = ResidueProperties.aaIndex[name.charAt(0)];
82		}
83	0	if (index == -1)
84		{
85	0	continue;
86		}
87
88	0	Color color = new Color(
89		Integer.parseInt(jucs.getColour(i).getRGB(), 16));
90	0	if (name.toLowerCase().equals(name))
91		{
92	0	caseSensitive = true;
93	0	lowerCase[index] = color;
94		}
95		else
96		{
97	0	newColours[index] = color;
98		}
99		}
100
101		/*
102		* instantiate the colour scheme
103		*/
104	0	ucs = new UserColourScheme(newColours);
105	0	ucs.setName(jucs.getSchemeName());
106	0	if (caseSensitive)
107		{
108	0	ucs.setLowerCaseColours(lowerCase);
109		}
110		} catch (Exception ex)
111		{
112		// Could be old Jalview Archive format
113	0	try
114		{
115	0	InputStreamReader in = new InputStreamReader(
116		new FileInputStream(file), "UTF-8");
117
118	0	jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
119
120	0	jucs = JalviewUserColours.unmarshal(in);
121
122	0	newColours = new Color[jucs.getColourCount()];
123
124	0	for (int i = 0; i < 24; i++)
125		{
126	0	newColours[i] = new Color(
127		Integer.parseInt(jucs.getColour(i).getRGB(), 16));
128		}
129	0	ucs = new UserColourScheme(newColours);
130	0	ucs.setName(jucs.getSchemeName());
131		} catch (Exception ex2)
132		{
133	0	ex2.printStackTrace();
134		}
135
136	0	if (newColours == null)
137		{
138	0	System.out.println("Error loading User ColourFile\n" + ex);
139		}
140		}
141
142	0	return ucs;
143		}
144
145		}