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package jalview.io; |
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import java.io.IOException; |
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import jalview.datamodel.AlignmentI; |
26 |
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import jalview.datamodel.DBRefSource; |
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import jalview.datamodel.PDBEntry; |
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import jalview.ext.jmol.JmolParser; |
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import jalview.structure.StructureImportSettings; |
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|
|
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| 56.6% |
Uncovered Elements: 56 (129) |
Complexity: 60 |
Complexity Density: 0.88 |
|
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public enum FileFormat implements FileFormatI |
32 |
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{ |
33 |
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Fasta("Fasta", "fa,fasta,mfa,fastq", true, true) |
34 |
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{ |
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
35 |
255 |
@Override... |
36 |
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public AlignmentFileReaderI getReader(FileParse source) |
37 |
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throws IOException |
38 |
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{ |
39 |
255 |
return new FastaFile(source); |
40 |
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} |
41 |
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|
|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
42 |
7 |
@Override... |
43 |
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public AlignmentFileWriterI getWriter(AlignmentI al) |
44 |
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{ |
45 |
7 |
return new FastaFile(); |
46 |
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} |
47 |
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}, |
48 |
|
Pfam("PFAM", "pfam", true, true) |
49 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
50 |
6 |
@Override... |
51 |
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public AlignmentFileReaderI getReader(FileParse source) |
52 |
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throws IOException |
53 |
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{ |
54 |
6 |
return new PfamFile(source); |
55 |
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} |
56 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
57 |
1 |
@Override... |
58 |
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public AlignmentFileWriterI getWriter(AlignmentI al) |
59 |
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{ |
60 |
1 |
return new PfamFile(); |
61 |
|
} |
62 |
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}, |
63 |
|
Stockholm("Stockholm", "sto,stk", true, true) |
64 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
65 |
47 |
@Override... |
66 |
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public AlignmentFileReaderI getReader(FileParse source) |
67 |
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throws IOException |
68 |
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{ |
69 |
47 |
return new StockholmFile(source); |
70 |
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} |
71 |
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|
|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
72 |
56 |
@Override... |
73 |
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public AlignmentFileWriterI getWriter(AlignmentI al) |
74 |
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{ |
75 |
56 |
return new StockholmFile(al); |
76 |
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} |
77 |
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|
78 |
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}, |
79 |
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|
80 |
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PIR("PIR", "pir", true, true) |
81 |
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{ |
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
82 |
1 |
@Override... |
83 |
|
public AlignmentFileReaderI getReader(FileParse source) |
84 |
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throws IOException |
85 |
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{ |
86 |
1 |
return new PIRFile(source); |
87 |
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} |
88 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
89 |
1 |
@Override... |
90 |
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public AlignmentFileWriterI getWriter(AlignmentI al) |
91 |
|
{ |
92 |
1 |
return new PIRFile(); |
93 |
|
} |
94 |
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}, |
95 |
|
BLC("BLC", "blc", true, true) |
96 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
97 |
1 |
@Override... |
98 |
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public AlignmentFileReaderI getReader(FileParse source) |
99 |
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throws IOException |
100 |
|
{ |
101 |
1 |
return new BLCFile(source); |
102 |
|
} |
103 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
104 |
1 |
@Override... |
105 |
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public AlignmentFileWriterI getWriter(AlignmentI al) |
106 |
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{ |
107 |
1 |
return new BLCFile(); |
108 |
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} |
109 |
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}, |
110 |
|
AMSA("AMSA", "amsa", true, true) |
111 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
112 |
1 |
@Override... |
113 |
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public AlignmentFileReaderI getReader(FileParse source) |
114 |
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throws IOException |
115 |
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{ |
116 |
1 |
return new AMSAFile(source); |
117 |
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} |
118 |
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|
|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
119 |
1 |
@Override... |
120 |
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public AlignmentFileWriterI getWriter(AlignmentI al) |
121 |
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{ |
122 |
1 |
return new AMSAFile(al); |
123 |
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} |
124 |
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}, |
125 |
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Html("HTML", "html", true, false) |
126 |
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{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
127 |
0 |
@Override... |
128 |
|
public AlignmentFileReaderI getReader(FileParse source) |
129 |
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throws IOException |
130 |
|
{ |
131 |
0 |
return new HtmlFile(source); |
132 |
|
} |
133 |
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|
|
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
134 |
0 |
@Override... |
135 |
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public AlignmentFileWriterI getWriter(AlignmentI al) |
136 |
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{ |
137 |
0 |
return new HtmlFile(); |
138 |
|
} |
139 |
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|
|
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
140 |
0 |
@Override... |
141 |
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public boolean isComplexAlignFile() |
142 |
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{ |
143 |
0 |
return true; |
144 |
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} |
145 |
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|
146 |
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}, |
147 |
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Rnaml("RNAML", "xml,rnaml", true, false) |
148 |
|
{ |
|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
149 |
1 |
@Override... |
150 |
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public AlignmentFileReaderI getReader(FileParse source) |
151 |
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throws IOException |
152 |
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{ |
153 |
1 |
return new RnamlFile(source); |
154 |
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} |
155 |
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|
|
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
156 |
0 |
@Override... |
157 |
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public AlignmentFileWriterI getWriter(AlignmentI al) |
158 |
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{ |
159 |
0 |
return new RnamlFile(); |
160 |
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} |
161 |
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|
162 |
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}, |
163 |
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Json("JSON", "json", true, true) |
164 |
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{ |
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
165 |
6 |
@Override... |
166 |
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public AlignmentFileReaderI getReader(FileParse source) |
167 |
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throws IOException |
168 |
|
{ |
169 |
6 |
return new JSONFile(source); |
170 |
|
} |
171 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
172 |
4 |
@Override... |
173 |
|
public AlignmentFileWriterI getWriter(AlignmentI al) |
174 |
|
{ |
175 |
4 |
return new JSONFile(); |
176 |
|
} |
177 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
178 |
0 |
@Override... |
179 |
|
public boolean isComplexAlignFile() |
180 |
|
{ |
181 |
0 |
return true; |
182 |
|
} |
183 |
|
|
184 |
|
}, |
185 |
|
Pileup("PileUp", "pileup", true, true) |
186 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
187 |
1 |
@Override... |
188 |
|
public AlignmentFileReaderI getReader(FileParse source) |
189 |
|
throws IOException |
190 |
|
{ |
191 |
1 |
return new PileUpfile(source); |
192 |
|
} |
193 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
194 |
1 |
@Override... |
195 |
|
public AlignmentFileWriterI getWriter(AlignmentI al) |
196 |
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{ |
197 |
1 |
return new PileUpfile(); |
198 |
|
} |
199 |
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|
200 |
|
}, |
201 |
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MSF("MSF", "msf", true, true) |
202 |
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{ |
|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
203 |
1 |
@Override... |
204 |
|
public AlignmentFileReaderI getReader(FileParse source) |
205 |
|
throws IOException |
206 |
|
{ |
207 |
1 |
return new MSFfile(source); |
208 |
|
} |
209 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
210 |
1 |
@Override... |
211 |
|
public AlignmentFileWriterI getWriter(AlignmentI al) |
212 |
|
{ |
213 |
1 |
return new MSFfile(); |
214 |
|
} |
215 |
|
|
216 |
|
}, |
217 |
|
Clustal("Clustal", "aln", true, true) |
218 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
219 |
1 |
@Override... |
220 |
|
public AlignmentFileReaderI getReader(FileParse source) |
221 |
|
throws IOException |
222 |
|
{ |
223 |
1 |
return new ClustalFile(source); |
224 |
|
} |
225 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
226 |
34 |
@Override... |
227 |
|
public AlignmentFileWriterI getWriter(AlignmentI al) |
228 |
|
{ |
229 |
34 |
return new ClustalFile(); |
230 |
|
} |
231 |
|
}, |
232 |
|
Phylip("PHYLIP", "phy", true, true) |
233 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
234 |
7 |
@Override... |
235 |
|
public AlignmentFileReaderI getReader(FileParse source) |
236 |
|
throws IOException |
237 |
|
{ |
238 |
7 |
return new PhylipFile(source); |
239 |
|
} |
240 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
241 |
3 |
@Override... |
242 |
|
public AlignmentFileWriterI getWriter(AlignmentI al) |
243 |
|
{ |
244 |
3 |
return new PhylipFile(); |
245 |
|
} |
246 |
|
}, |
247 |
|
GenBank("GenBank Flatfile", "gb,gbk", true, false) |
248 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
249 |
0 |
@Override... |
250 |
|
public AlignmentFileReaderI getReader(FileParse source) |
251 |
|
throws IOException |
252 |
|
{ |
253 |
0 |
return new GenBankFile(source, "GenBank"); |
254 |
|
} |
255 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
256 |
0 |
@Override... |
257 |
|
public AlignmentFileWriterI getWriter(AlignmentI al) |
258 |
|
{ |
259 |
0 |
return null; |
260 |
|
} |
261 |
|
}, |
262 |
|
Embl("ENA Flatfile", "txt", true, false) |
263 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
264 |
0 |
@Override... |
265 |
|
public AlignmentFileReaderI getReader(FileParse source) |
266 |
|
throws IOException |
267 |
|
{ |
268 |
|
|
269 |
0 |
return new EmblFlatFile(source, DBRefSource.EMBL); |
270 |
|
} |
271 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
272 |
0 |
@Override... |
273 |
|
public AlignmentFileWriterI getWriter(AlignmentI al) |
274 |
|
{ |
275 |
0 |
return null; |
276 |
|
} |
277 |
|
}, |
278 |
|
Jnet("JnetFile", "", false, false) |
279 |
|
{ |
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
280 |
0 |
@Override... |
281 |
|
public AlignmentFileReaderI getReader(FileParse source) |
282 |
|
throws IOException |
283 |
|
{ |
284 |
0 |
JPredFile af = new JPredFile(source); |
285 |
0 |
af.removeNonSequences(); |
286 |
0 |
return af; |
287 |
|
} |
288 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
289 |
0 |
@Override... |
290 |
|
public AlignmentFileWriterI getWriter(AlignmentI al) |
291 |
|
{ |
292 |
0 |
return null; |
293 |
|
} |
294 |
|
|
295 |
|
}, |
296 |
|
Features("GFF or Jalview features", "gff2,gff3", true, false) |
297 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
298 |
0 |
@Override... |
299 |
|
public AlignmentFileReaderI getReader(FileParse source) |
300 |
|
throws IOException |
301 |
|
{ |
302 |
0 |
return new FeaturesFile(source); |
303 |
|
} |
304 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
305 |
0 |
@Override... |
306 |
|
public AlignmentFileWriterI getWriter(AlignmentI al) |
307 |
|
{ |
308 |
0 |
return new FeaturesFile(); |
309 |
|
} |
310 |
|
}, |
311 |
|
FeatureSettings("Jalview Feature Settings File", "fc", false, false) |
312 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
313 |
0 |
@Override... |
314 |
|
public AlignmentFileReaderI getReader(FileParse source) |
315 |
|
throws IOException |
316 |
|
{ |
317 |
0 |
return null; |
318 |
|
} |
319 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
320 |
0 |
@Override... |
321 |
|
public AlignmentFileWriterI getWriter(AlignmentI al) |
322 |
|
{ |
323 |
0 |
return null; |
324 |
|
} |
325 |
|
}, |
326 |
|
ScoreMatrix("Substitution matrix", "", false, false) |
327 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
328 |
0 |
@Override... |
329 |
|
public AlignmentFileReaderI getReader(FileParse source) |
330 |
|
throws IOException |
331 |
|
{ |
332 |
0 |
return new ScoreMatrixFile(source); |
333 |
|
} |
334 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
335 |
0 |
@Override... |
336 |
|
public AlignmentFileWriterI getWriter(AlignmentI al) |
337 |
|
{ |
338 |
0 |
return null; |
339 |
|
} |
340 |
|
}, |
341 |
|
PDB("PDB", "pdb,ent", true, false) |
342 |
|
{ |
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
343 |
0 |
@Override... |
344 |
|
public AlignmentFileReaderI getReader(FileParse source) |
345 |
|
throws IOException |
346 |
|
{ |
347 |
0 |
boolean isParseWithJMOL = StructureImportSettings |
348 |
|
.getDefaultStructureFileFormat() != PDBEntry.Type.PDB; |
349 |
0 |
if (isParseWithJMOL) |
350 |
|
{ |
351 |
0 |
return new JmolParser(source); |
352 |
|
} |
353 |
|
else |
354 |
|
{ |
355 |
0 |
StructureImportSettings.setShowSeqFeatures(true); |
356 |
0 |
return new mc_view.PDBfile( |
357 |
|
StructureImportSettings.isVisibleChainAnnotation(), |
358 |
|
StructureImportSettings.isProcessSecondaryStructure(), |
359 |
|
StructureImportSettings.isExternalSecondaryStructure(), |
360 |
|
source); |
361 |
|
} |
362 |
|
} |
363 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
364 |
0 |
@Override... |
365 |
|
public AlignmentFileWriterI getWriter(AlignmentI al) |
366 |
|
{ |
367 |
0 |
return new JmolParser(); |
368 |
|
} |
369 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
370 |
25 |
@Override... |
371 |
|
public boolean isStructureFile() |
372 |
|
{ |
373 |
25 |
return true; |
374 |
|
} |
375 |
|
}, |
376 |
|
MMCif("mmCIF", "cif", true, false) |
377 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
378 |
0 |
@Override... |
379 |
|
public AlignmentFileReaderI getReader(FileParse source) |
380 |
|
throws IOException |
381 |
|
{ |
382 |
0 |
return new JmolParser(source); |
383 |
|
} |
384 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
385 |
0 |
@Override... |
386 |
|
public AlignmentFileWriterI getWriter(AlignmentI al) |
387 |
|
{ |
388 |
0 |
return new JmolParser(); |
389 |
|
} |
390 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
391 |
0 |
@Override... |
392 |
|
public boolean isStructureFile() |
393 |
|
{ |
394 |
0 |
return true; |
395 |
|
} |
396 |
|
}, |
397 |
|
Jalview("Jalview", "jvp,jar", true, true) |
398 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
399 |
0 |
@Override... |
400 |
|
public AlignmentFileReaderI getReader(FileParse source) |
401 |
|
throws IOException |
402 |
|
{ |
403 |
0 |
return null; |
404 |
|
} |
405 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
406 |
0 |
@Override... |
407 |
|
public AlignmentFileWriterI getWriter(AlignmentI al) |
408 |
|
{ |
409 |
0 |
return null; |
410 |
|
} |
411 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
412 |
231 |
@Override... |
413 |
|
public boolean isTextFormat() |
414 |
|
{ |
415 |
231 |
return false; |
416 |
|
} |
417 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
418 |
5 |
@Override... |
419 |
|
public boolean isIdentifiable() |
420 |
|
{ |
421 |
5 |
return true; |
422 |
|
} |
423 |
|
}; |
424 |
|
|
425 |
|
private boolean writable; |
426 |
|
|
427 |
|
private boolean readable; |
428 |
|
|
429 |
|
private String extensions; |
430 |
|
|
431 |
|
private String name; |
432 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
433 |
56 |
@Override... |
434 |
|
public boolean isComplexAlignFile() |
435 |
|
{ |
436 |
56 |
return false; |
437 |
|
} |
438 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
439 |
4906 |
@Override... |
440 |
|
public boolean isReadable() |
441 |
|
{ |
442 |
4906 |
return readable; |
443 |
|
} |
444 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
445 |
8323 |
@Override... |
446 |
|
public boolean isWritable() |
447 |
|
{ |
448 |
8323 |
return writable; |
449 |
|
} |
450 |
|
|
451 |
|
|
452 |
|
|
453 |
|
|
454 |
|
@param |
455 |
|
@param |
456 |
|
|
457 |
|
@param |
458 |
|
|
459 |
|
|
460 |
|
@param |
461 |
|
|
462 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
463 |
110 |
private FileFormat(String shortName, String extensions,... |
464 |
|
boolean isReadable, boolean isWritable) |
465 |
|
{ |
466 |
110 |
this.name = shortName; |
467 |
110 |
this.extensions = extensions; |
468 |
110 |
this.readable = isReadable; |
469 |
110 |
this.writable = isWritable; |
470 |
|
} |
471 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
472 |
1138 |
@Override... |
473 |
|
public String getExtensions() |
474 |
|
{ |
475 |
1138 |
return extensions; |
476 |
|
} |
477 |
|
|
478 |
|
|
479 |
|
|
480 |
|
|
481 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
482 |
10052 |
@Override... |
483 |
|
public String getName() |
484 |
|
{ |
485 |
10052 |
return name; |
486 |
|
} |
487 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
488 |
2541 |
@Override... |
489 |
|
public boolean isTextFormat() |
490 |
|
{ |
491 |
2541 |
return true; |
492 |
|
} |
493 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
494 |
562 |
@Override... |
495 |
|
public boolean isStructureFile() |
496 |
|
{ |
497 |
562 |
return false; |
498 |
|
} |
499 |
|
|
500 |
|
|
501 |
|
|
502 |
|
|
503 |
|
|
504 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
505 |
105 |
public boolean isIdentifiable()... |
506 |
|
{ |
507 |
105 |
return true; |
508 |
|
} |
509 |
|
} |