Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FileFormats	44	29	18	0.00%	Show methods

Class FileFormats

Class FileFormats	Line # 44	Total Statements 29	Complexity 18	TOTAL Coverage 0.00%
getInstance() : FileFormats   getInstance() : FileFormats	4646	1.01	1.01	0.0 0.00%
FileFormats()   FileFormats()	5454	1.01	1.01	0.0 0.00%
reset() : void   reset() : void	7575	4.04	1.01	0.0 0.00%
isIdentifiable(FileFormatI) : boolean   isIdentifiable(FileFormatI) : boolean	8989	1.01	1.01	0.0 0.00%
registerFileFormat(FileFormatI) : void   registerFileFormat(FileFormatI) : void	9999	2.02	1.01	0.0 0.00%
registerFileFormat(FileFormatI,boolean) : void   registerFileFormat(FileFormatI,boolean) : void	106106	6.06	3.03	0.0 0.00%
deregisterFileFormat(String) : void   deregisterFileFormat(String) : void	127127	2.02	1.01	0.0 0.00%
getWritableFormats(boolean) : List<String>   getWritableFormats(boolean) : List<String>	141141	5.05	4.04	0.0 0.00%
getReadableFormats() : List<String>   getReadableFormats() : List<String>	160160	5.05	2.02	0.0 0.00%
forName(String) : FileFormatI   forName(String) : FileFormatI	180180	1.01	2.02	0.0 0.00%
getFormats() : Iterable<FileFormatI>   getFormats() : Iterable<FileFormatI>	192192	1.01	1.01	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.io;
22
23		import java.util.Locale;
24
25		import java.util.ArrayList;
26		import java.util.HashSet;
27		import java.util.LinkedHashMap;
28		import java.util.List;
29		import java.util.Map;
30		import java.util.Set;
31
32		import jalview.bin.ApplicationSingletonProvider;
33		import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
34
35		/**
36		* A singleton registry of alignment file formats known to Jalview. On startup,
37		* the 'built-in' formats are added (from the FileFormat enum). Additional
38		* formats can be registered (or formats deregistered) programmatically, for
39		* example with a Groovy script.
40		*
41		* @author gmcarstairs
42		*
43		*/
		0% Uncovered Elements: 50 (50) Complexity: 18 Complexity Density: 0.62
44		public class FileFormats implements ApplicationSingletonI
45		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
46	0	public static FileFormats getInstance()...
47		{
48	0	return ApplicationSingletonProvider.getInstance(FileFormats.class);
49		}
50
51		/**
52		* Private constructor registers Jalview's built-in file formats
53		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
54	0	private FileFormats()...
55		{
56	0	reset();
57		}
58
59		/*
60		* A lookup map of file formats by upper-cased name
61		*/
62		private Map<String, FileFormatI> formats;
63
64		/*
65		* Formats in this set are capable of being identified by IdentifyFile
66		*/
67		private Set<FileFormatI> identifiable;
68
69
70		/**
71		* Reset to just the built-in file formats packaged with Jalview. These are
72		* added (and will be shown in menus) in the order of their declaration in the
73		* FileFormat enum.
74		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
75	0	public synchronized void reset()...
76		{
77	0	formats = new LinkedHashMap<String, FileFormatI>();
78	0	identifiable = new HashSet<FileFormatI>();
79	0	for (FileFormat format : FileFormat.values())
80		{
81	0	registerFileFormat(format, format.isIdentifiable());
82		}
83		}
84
85		/**
86		* Answers true if the format is one that can be identified by IdentifyFile.
87		* Answers false for a null value.
88		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
89	0	public boolean isIdentifiable(FileFormatI f)...
90		{
91	0	return identifiable.contains(f);
92		}
93
94		/**
95		* Registers a file format for case-insensitive lookup by name
96		*
97		* @param format
98		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
99	0	public void registerFileFormat(FileFormatI format)...
100		{
101	0	boolean isIdentifiable = format instanceof FileFormat
102		&& ((FileFormat) format).isIdentifiable();
103	0	registerFileFormat(format, isIdentifiable);
104		}
105
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
106	0	protected void registerFileFormat(FileFormatI format,...
107		boolean isIdentifiable)
108		{
109	0	String name = format.getName().toUpperCase(Locale.ROOT);
110	0	if (formats.containsKey(name))
111		{
112	0	jalview.bin.Console
113		.errPrintln("Overwriting file format: " + format.getName());
114		}
115	0	formats.put(name, format);
116	0	if (isIdentifiable)
117		{
118	0	identifiable.add(format);
119		}
120		}
121
122		/**
123		* Deregisters a file format so it is no longer shown in menus
124		*
125		* @param name
126		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
127	0	public void deregisterFileFormat(String name)...
128		{
129	0	FileFormatI ff = formats.remove(name.toUpperCase(Locale.ROOT));
130	0	identifiable.remove(ff);
131		}
132
133		/**
134		* Answers a list of writeable file formats (as strings, corresponding to the
135		* getName() and forName() methods)
136		*
137		* @param textOnly
138		* if true, only text (not binary) formats are included
139		* @return
140		*/
		0% Uncovered Elements: 7 (7) Complexity: 4 Complexity Density: 0.8
141	0	public List<String> getWritableFormats(boolean textOnly)...
142		{
143	0	List<String> l = new ArrayList<String>();
144	0	for (FileFormatI ff : formats.values())
145		{
146	0	if (ff.isWritable() && (!textOnly || ff.isTextFormat()))
147		{
148	0	l.add(ff.getName());
149		}
150		}
151	0	return l;
152		}
153
154		/**
155		* Answers a list of readable file formats (as strings, corresponding to the
156		* getName() and forName() methods)
157		*
158		* @return
159		*/
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
160	0	public List<String> getReadableFormats()...
161		{
162	0	List<String> l = new ArrayList<String>();
163	0	for (FileFormatI ff : formats.values())
164		{
165	0	if (ff.isReadable())
166		{
167	0	l.add(ff.getName());
168		}
169		}
170	0	return l;
171		}
172
173		/**
174		* Returns the file format with the given name, or null if format is null or
175		* invalid. This is not case-sensitive.
176		*
177		* @param format
178		* @return
179		*/
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
180	0	public FileFormatI forName(String format)...
181		{
182	0	return format == null ? null
183		: formats.get(format.toUpperCase(Locale.ROOT));
184		}
185
186		/**
187		* Returns an iterable collection of registered file formats (in the order in
188		* which they were registered)
189		*
190		* @return
191		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
192	0	public Iterable<FileFormatI> getFormats()...
193		{
194	0	return formats.values();
195		}
196		}