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jalviewX

  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.io

File FileFormats.java

 

Coverage histogram

../../img/srcFileCovDistChart10.png
0% of files have more coverage

Code metrics

10
29
11
1
190
91
18
0.62
2.64
11
1.64

Classes

Class Line # Actions
FileFormats 39 29 18 0
1.0100%
 

Contributing tests

This file is covered by 132 tests. .

Source view

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.ArrayList;
24    import java.util.HashSet;
25    import java.util.LinkedHashMap;
26    import java.util.List;
27    import java.util.Map;
28    import java.util.Set;
29   
30    /**
31    * A singleton registry of alignment file formats known to Jalview. On startup,
32    * the 'built-in' formats are added (from the FileFormat enum). Additional
33    * formats can be registered (or formats deregistered) programmatically, for
34    * example with a Groovy script.
35    *
36    * @author gmcarstairs
37    *
38    */
 
39    public class FileFormats
40    {
41    private static FileFormats instance = new FileFormats();
42   
43    /*
44    * A lookup map of file formats by upper-cased name
45    */
46    private static Map<String, FileFormatI> formats;
47   
48    /*
49    * Formats in this set are capable of being identified by IdentifyFile
50    */
51    private static Set<FileFormatI> identifiable;
52   
 
53  1421 toggle public static FileFormats getInstance()
54    {
55  1421 return instance;
56    }
57   
58    /**
59    * Private constructor registers Jalview's built-in file formats
60    */
 
61  1 toggle private FileFormats()
62    {
63  1 reset();
64    }
65   
66    /**
67    * Reset to just the built-in file formats packaged with Jalview. These are
68    * added (and will be shown in menus) in the order of their declaration in the
69    * FileFormat enum.
70    */
 
71  15 toggle public synchronized void reset()
72    {
73  15 formats = new LinkedHashMap<String, FileFormatI>();
74  15 identifiable = new HashSet<FileFormatI>();
75  15 for (FileFormat format : FileFormat.values())
76    {
77  285 registerFileFormat(format, format.isIdentifiable());
78    }
79    }
80   
81    /**
82    * Answers true if the format is one that can be identified by IdentifyFile.
83    * Answers false for a null value.
84    */
 
85  8 toggle public boolean isIdentifiable(FileFormatI f)
86    {
87  8 return identifiable.contains(f);
88    }
89   
90    /**
91    * Registers a file format for case-insensitive lookup by name
92    *
93    * @param format
94    */
 
95  4 toggle public void registerFileFormat(FileFormatI format)
96    {
97  4 boolean isIdentifiable = format instanceof FileFormat
98    && ((FileFormat) format).isIdentifiable();
99  4 registerFileFormat(format, isIdentifiable);
100    }
101   
 
102  289 toggle protected void registerFileFormat(FileFormatI format,
103    boolean isIdentifiable)
104    {
105  289 String name = format.getName().toUpperCase();
106  289 if (formats.containsKey(name))
107    {
108  1 System.err.println("Overwriting file format: " + format.getName());
109    }
110  289 formats.put(name, format);
111  289 if (isIdentifiable)
112    {
113  274 identifiable.add(format);
114    }
115    }
116   
117    /**
118    * Deregisters a file format so it is no longer shown in menus
119    *
120    * @param name
121    */
 
122  4 toggle public void deregisterFileFormat(String name)
123    {
124  4 FileFormatI ff = formats.remove(name.toUpperCase());
125  4 identifiable.remove(ff);
126    }
127   
128    /**
129    * Answers a list of writeable file formats (as strings, corresponding to the
130    * getName() and forName() methods)
131    *
132    * @param textOnly
133    * if true, only text (not binary) formats are included
134    * @return
135    */
 
136  216 toggle public List<String> getWritableFormats(boolean textOnly)
137    {
138  216 List<String> l = new ArrayList<String>();
139  216 for (FileFormatI ff : formats.values())
140    {
141  4103 if (ff.isWritable() && (!textOnly || ff.isTextFormat()))
142    {
143  2376 l.add(ff.getName());
144    }
145    }
146  216 return l;
147    }
148   
149    /**
150    * Answers a list of readable file formats (as strings, corresponding to the
151    * getName() and forName() methods)
152    *
153    * @return
154    */
 
155  73 toggle public List<String> getReadableFormats()
156    {
157  73 List<String> l = new ArrayList<String>();
158  73 for (FileFormatI ff : formats.values())
159    {
160  1386 if (ff.isReadable())
161    {
162  1240 l.add(ff.getName());
163    }
164    }
165  73 return l;
166    }
167   
168    /**
169    * Returns the file format with the given name, or null if format is null or
170    * invalid. This is not case-sensitive.
171    *
172    * @param format
173    * @return
174    */
 
175  70 toggle public FileFormatI forName(String format)
176    {
177  70 return format == null ? null : formats.get(format.toUpperCase());
178    }
179   
180    /**
181    * Returns an iterable collection of registered file formats (in the order in
182    * which they were registered)
183    *
184    * @return
185    */
 
186  1122 toggle public Iterable<FileFormatI> getFormats()
187    {
188  1122 return formats.values();
189    }
190    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.