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package jalview.datamodel; |
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import java.util.Collections; |
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import java.util.Enumeration; |
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import java.util.Hashtable; |
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import jalview.io.StructureFile; |
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import jalview.util.CaseInsensitiveString; |
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| 82.8% |
Uncovered Elements: 39 (227) |
Complexity: 95 |
Complexity Density: 0.81 |
|
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public class PDBEntry |
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{ |
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private static final String CHAIN_ID = "chain_code"; |
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private Hashtable<String, Object> properties; |
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private static final int PDB_ID_LENGTH = 4; |
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private static final String FAKED_ID = "faked_pdbid"; |
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private static final String AUTHORITATIVE_ID = "authoritative_pdbid"; |
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private String file; |
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private String type; |
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private String id; |
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private StructureFile sf = null; |
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| 75% |
Uncovered Elements: 4 (16) |
Complexity: 6 |
Complexity Density: 0.67 |
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public enum Type |
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{ |
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PDB("pdb", "pdb"), MMCIF("mmcif", "cif"), BCIF("bcif", "bcif"), |
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FILE("?", "?"); |
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@see |
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String ext; |
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@see |
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String format; |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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220 |
private Type(String fmt, String ex)... |
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{ |
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format = fmt; |
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ext = ex; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
public String getFormat()... |
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{ |
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0 |
return format; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
public String getExtension()... |
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{ |
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return ext; |
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} |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
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public static Type getType(String value)... |
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{ |
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for (Type t : Type.values()) |
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{ |
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if (t.toString().equalsIgnoreCase(value)) |
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{ |
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return t; |
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} |
112 |
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} |
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1 |
return null; |
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} |
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118 |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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4 |
public boolean matches(String t)... |
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{ |
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return (this.toString().equalsIgnoreCase(t)); |
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} |
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} |
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| 100% |
Uncovered Elements: 0 (17) |
Complexity: 7 |
Complexity Density: 0.64 |
|
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17542 |
@Override... |
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public boolean equals(Object obj) |
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{ |
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17542 |
if (obj == null || !(obj instanceof PDBEntry)) |
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{ |
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2 |
return false; |
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} |
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17540 |
if (obj == this) |
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{ |
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11 |
return true; |
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} |
143 |
17529 |
PDBEntry o = (PDBEntry) obj; |
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17529 |
boolean idMatches = id == o.id |
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|| (id != null && id.equalsIgnoreCase(o.id)); |
152 |
17529 |
boolean fileMatches = file == o.file |
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|| (file != null && file.equals(o.file)); |
154 |
17529 |
boolean typeMatches = type == o.type |
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|| (type != null && type.equals(o.type)); |
156 |
17529 |
if (idMatches && fileMatches && typeMatches) |
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{ |
158 |
379 |
return properties == o.properties |
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|| (properties != null && properties.equals(o.properties)); |
160 |
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} |
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17150 |
return false; |
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} |
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166 |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
167 |
738 |
public PDBEntry()... |
168 |
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{ |
169 |
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} |
170 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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90 |
public PDBEntry(String pdbId, String chain, PDBEntry.Type type,... |
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String filePath) |
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{ |
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init(pdbId, chain, type, filePath); |
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} |
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@param |
179 |
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@param |
180 |
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@param |
181 |
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@param |
182 |
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| 100% |
Uncovered Elements: 0 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
183 |
302 |
void init(String pdbId, String chain, PDBEntry.Type entryType,... |
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String filePath) |
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{ |
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302 |
this.id = pdbId; |
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302 |
this.type = entryType == null ? null : entryType.toString(); |
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302 |
this.file = filePath; |
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302 |
setChainCode(chain); |
190 |
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} |
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192 |
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193 |
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194 |
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195 |
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@param |
196 |
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| 100% |
Uncovered Elements: 0 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
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146 |
public PDBEntry(PDBEntry entry)... |
198 |
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{ |
199 |
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file = entry.file; |
200 |
146 |
type = entry.type; |
201 |
146 |
id = entry.id; |
202 |
146 |
if (entry.properties != null) |
203 |
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{ |
204 |
6 |
properties = (Hashtable<String, Object>) entry.properties.clone(); |
205 |
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} |
206 |
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} |
207 |
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208 |
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209 |
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210 |
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211 |
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212 |
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213 |
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@param |
214 |
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| 100% |
Uncovered Elements: 0 (16) |
Complexity: 7 |
Complexity Density: 0.7 |
|
215 |
213 |
public PDBEntry(DBRefEntry dbr)... |
216 |
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{ |
217 |
213 |
if (!DBRefSource.PDB.equals(dbr.getSource())) |
218 |
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{ |
219 |
1 |
throw new IllegalArgumentException( |
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"Invalid source: " + dbr.getSource()); |
221 |
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} |
222 |
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223 |
212 |
String pdbId = dbr.getAccessionId(); |
224 |
212 |
String chainCode = null; |
225 |
212 |
if (pdbId.length() == PDB_ID_LENGTH + 1) |
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{ |
227 |
17 |
char chain = pdbId.charAt(PDB_ID_LENGTH); |
228 |
17 |
if (('a' <= chain && chain <= 'z') || ('A' <= chain && chain <= 'Z')) |
229 |
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{ |
230 |
15 |
pdbId = pdbId.substring(0, PDB_ID_LENGTH); |
231 |
15 |
chainCode = String.valueOf(chain); |
232 |
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} |
233 |
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} |
234 |
212 |
init(pdbId, chainCode, null, null); |
235 |
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} |
236 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
237 |
475 |
public void setFile(String f)... |
238 |
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{ |
239 |
475 |
this.file = f; |
240 |
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} |
241 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
242 |
18985 |
public String getFile()... |
243 |
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{ |
244 |
18985 |
return file; |
245 |
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} |
246 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
247 |
313 |
public void setType(String t)... |
248 |
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{ |
249 |
313 |
this.type = t; |
250 |
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} |
251 |
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| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
252 |
120 |
public void setType(PDBEntry.Type type)... |
253 |
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{ |
254 |
120 |
this.type = type == null ? null : type.toString(); |
255 |
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} |
256 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
257 |
361 |
public String getType()... |
258 |
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{ |
259 |
361 |
return type; |
260 |
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} |
261 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
262 |
738 |
public void setId(String id)... |
263 |
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{ |
264 |
738 |
this.id = id; |
265 |
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} |
266 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
267 |
52034 |
public String getId()... |
268 |
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{ |
269 |
52034 |
return id; |
270 |
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} |
271 |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
272 |
637 |
public void setProperty(String key, Object value)... |
273 |
|
{ |
274 |
637 |
if (this.properties == null) |
275 |
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{ |
276 |
496 |
this.properties = new Hashtable<String, Object>(); |
277 |
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} |
278 |
637 |
properties.put(key, value); |
279 |
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} |
280 |
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
281 |
329 |
public Object getProperty(String key)... |
282 |
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{ |
283 |
329 |
return properties == null ? null : properties.get(key); |
284 |
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} |
285 |
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286 |
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287 |
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288 |
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289 |
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290 |
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@return |
291 |
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|
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|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
292 |
203 |
public Enumeration<String> getProperties()... |
293 |
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{ |
294 |
203 |
if (properties == null) |
295 |
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{ |
296 |
114 |
return Collections.emptyEnumeration(); |
297 |
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} |
298 |
89 |
return properties.keys(); |
299 |
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} |
300 |
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|
301 |
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|
302 |
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|
303 |
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@return |
304 |
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|
|
|
| 100% |
Uncovered Elements: 0 (3) |
Complexity: 3 |
Complexity Density: 3 |
|
305 |
386 |
public String getChainCode()... |
306 |
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{ |
307 |
386 |
return (properties == null || properties.get(CHAIN_ID) == null) ? null |
308 |
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: properties.get(CHAIN_ID).toString(); |
309 |
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} |
310 |
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311 |
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312 |
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|
313 |
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|
314 |
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|
315 |
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|
316 |
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@param |
317 |
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|
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|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
318 |
652 |
public void setChainCode(String chainCode)... |
319 |
|
{ |
320 |
652 |
if (chainCode == null) |
321 |
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{ |
322 |
227 |
deleteProperty(CHAIN_ID); |
323 |
|
} |
324 |
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else |
325 |
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{ |
326 |
425 |
setProperty(CHAIN_ID, new CaseInsensitiveString(chainCode)); |
327 |
|
} |
328 |
|
} |
329 |
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|
330 |
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|
331 |
|
|
332 |
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|
333 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
334 |
227 |
Object deleteProperty(String key)... |
335 |
|
{ |
336 |
227 |
Object result = null; |
337 |
227 |
if (properties != null) |
338 |
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{ |
339 |
1 |
result = properties.remove(key); |
340 |
|
} |
341 |
227 |
return result; |
342 |
|
} |
343 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
344 |
26 |
@Override... |
345 |
|
public String toString() |
346 |
|
{ |
347 |
26 |
return id; |
348 |
|
} |
349 |
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|
350 |
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|
351 |
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|
352 |
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|
353 |
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|
354 |
|
@deprecated |
355 |
|
@see |
356 |
|
@see |
357 |
|
@see |
358 |
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@return |
359 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
360 |
0 |
@Deprecated... |
361 |
|
public Hashtable<String, Object> getProps() |
362 |
|
{ |
363 |
0 |
return properties; |
364 |
|
} |
365 |
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|
366 |
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|
367 |
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|
368 |
|
|
369 |
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|
370 |
|
@deprecated |
371 |
|
@return |
372 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
373 |
0 |
@Deprecated... |
374 |
|
public void setProps(Hashtable<String, Object> props) |
375 |
|
{ |
376 |
0 |
properties = props; |
377 |
|
} |
378 |
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|
379 |
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|
380 |
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|
381 |
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|
382 |
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|
383 |
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|
384 |
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|
385 |
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|
386 |
|
|
387 |
|
@param |
388 |
|
@return |
389 |
|
|
|
|
| 93.7% |
Uncovered Elements: 4 (63) |
Complexity: 27 |
Complexity Density: 0.77 |
|
390 |
17500 |
public boolean updateFrom(PDBEntry newEntry)... |
391 |
|
{ |
392 |
17500 |
if (this.equals(newEntry)) |
393 |
|
{ |
394 |
329 |
return true; |
395 |
|
} |
396 |
|
|
397 |
17171 |
String newId = newEntry.getId(); |
398 |
17171 |
if (newId == null || getId() == null) |
399 |
|
{ |
400 |
0 |
return false; |
401 |
|
} |
402 |
|
|
403 |
17171 |
boolean idMatches = getId().equalsIgnoreCase(newId); |
404 |
|
|
405 |
|
|
406 |
|
|
407 |
|
|
408 |
17171 |
String newFile = newEntry.getFile(); |
409 |
17171 |
if (newFile != null && getFile() != null) |
410 |
|
{ |
411 |
179 |
if (!newFile.equals(getFile())) |
412 |
|
{ |
413 |
103 |
return false; |
414 |
|
} |
415 |
|
else |
416 |
|
{ |
417 |
|
|
418 |
76 |
if (!idMatches) |
419 |
|
{ |
420 |
|
|
421 |
|
|
422 |
|
|
423 |
2 |
if (!newEntry.fakedPDBId() && !isAuthoritative()) |
424 |
|
{ |
425 |
0 |
return false; |
426 |
|
} |
427 |
|
} |
428 |
|
} |
429 |
|
} |
430 |
|
else |
431 |
|
{ |
432 |
|
|
433 |
16992 |
if (!idMatches) |
434 |
|
{ |
435 |
16919 |
return false; |
436 |
|
} |
437 |
|
} |
438 |
|
|
439 |
|
|
440 |
|
|
441 |
|
|
442 |
149 |
String newChain = newEntry.getChainCode(); |
443 |
149 |
if (newChain != null && newChain.length() > 0 && getChainCode() != null |
444 |
|
&& getChainCode().length() > 0 |
445 |
|
&& !getChainCode().equalsIgnoreCase(newChain)) |
446 |
|
{ |
447 |
8 |
return false; |
448 |
|
} |
449 |
|
|
450 |
|
|
451 |
|
|
452 |
|
|
453 |
141 |
String newType = newEntry.getType(); |
454 |
141 |
if (getFile() == null && newFile != null) |
455 |
|
{ |
456 |
3 |
setFile(newFile); |
457 |
3 |
setType(newType); |
458 |
|
} |
459 |
|
|
460 |
|
|
461 |
|
|
462 |
|
|
463 |
|
|
464 |
141 |
if (getType() == null && newType != null) |
465 |
|
{ |
466 |
7 |
setType(newType); |
467 |
|
} |
468 |
|
|
469 |
|
|
470 |
|
|
471 |
|
|
472 |
|
|
473 |
141 |
if (newChain != null && newChain.length() > 0 |
474 |
|
&& !newChain.equalsIgnoreCase(getChainCode())) |
475 |
|
{ |
476 |
18 |
setChainCode(newChain); |
477 |
|
} |
478 |
|
|
479 |
|
|
480 |
|
|
481 |
|
|
482 |
141 |
Enumeration<String> newProps = newEntry.getProperties(); |
483 |
186 |
while (newProps.hasMoreElements()) |
484 |
|
{ |
485 |
|
|
486 |
|
|
487 |
|
|
488 |
|
|
489 |
45 |
String key = newProps.nextElement(); |
490 |
45 |
Object value = newEntry.getProperty(key); |
491 |
45 |
if (FAKED_ID.equals(key) || AUTHORITATIVE_ID.equals(key)) |
492 |
|
{ |
493 |
|
|
494 |
1 |
continue; |
495 |
|
} |
496 |
44 |
if (!value.equals(getProperty(key))) |
497 |
|
{ |
498 |
11 |
setProperty(key, value); |
499 |
|
} |
500 |
|
} |
501 |
141 |
return true; |
502 |
|
} |
503 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
504 |
1 |
public void setAuthoritative(boolean isAuthoritative)... |
505 |
|
{ |
506 |
1 |
setProperty(AUTHORITATIVE_ID, Boolean.valueOf(isAuthoritative)); |
507 |
|
} |
508 |
|
|
509 |
|
|
510 |
|
|
511 |
|
@return |
512 |
|
|
513 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
514 |
3 |
public boolean isAuthoritative()... |
515 |
|
{ |
516 |
3 |
if (_hasProperty(AUTHORITATIVE_ID)) |
517 |
|
{ |
518 |
2 |
return ((Boolean) getProperty(AUTHORITATIVE_ID)); |
519 |
|
} |
520 |
1 |
return false; |
521 |
|
} |
522 |
|
|
523 |
|
|
524 |
|
|
525 |
|
|
526 |
|
@return |
527 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
528 |
4 |
public boolean fakedPDBId()... |
529 |
|
{ |
530 |
4 |
if (_hasProperty(FAKED_ID)) |
531 |
|
{ |
532 |
2 |
return true; |
533 |
|
} |
534 |
2 |
return false; |
535 |
|
} |
536 |
|
|
|
|
| 75% |
Uncovered Elements: 2 (8) |
Complexity: 3 |
Complexity Density: 0.75 |
|
537 |
304 |
public void setFakedPDBId(boolean faked)... |
538 |
|
{ |
539 |
304 |
if (faked) |
540 |
|
{ |
541 |
96 |
setProperty(FAKED_ID, Boolean.TRUE); |
542 |
|
} |
543 |
|
else |
544 |
|
{ |
545 |
208 |
if (properties != null) |
546 |
|
{ |
547 |
0 |
properties.remove(FAKED_ID); |
548 |
|
} |
549 |
|
} |
550 |
|
} |
551 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
552 |
7 |
private boolean _hasProperty(final String key)... |
553 |
|
{ |
554 |
7 |
return (properties != null && properties.containsKey(key)); |
555 |
|
} |
556 |
|
|
557 |
|
private static final String RETRIEVE_FROM = "RETRIEVE_FROM"; |
558 |
|
|
559 |
|
private static final String PROVIDER = "PROVIDER"; |
560 |
|
|
561 |
|
private static final String MODELPAGE = "PROVIDERPAGE"; |
562 |
|
|
563 |
|
private static final String PROVIDERCATEGORY = "PROVIDERCATEGORY"; |
564 |
|
|
565 |
|
|
566 |
|
|
567 |
|
|
568 |
|
@param |
569 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
570 |
0 |
public void setRetrievalUrl(String urlStr)... |
571 |
|
{ |
572 |
0 |
setProperty(RETRIEVE_FROM, urlStr); |
573 |
|
} |
574 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
575 |
0 |
public boolean hasRetrievalUrl()... |
576 |
|
{ |
577 |
0 |
return _hasProperty(RETRIEVE_FROM); |
578 |
|
} |
579 |
|
|
580 |
|
|
581 |
|
|
582 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
583 |
0 |
public String getRetrievalUrl()... |
584 |
|
{ |
585 |
0 |
return (String) getProperty(RETRIEVE_FROM); |
586 |
|
} |
587 |
|
|
588 |
|
|
589 |
|
|
590 |
|
|
591 |
|
@param |
592 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
593 |
0 |
public void setProvider(String provider)... |
594 |
|
{ |
595 |
0 |
setProperty(PROVIDER, provider); |
596 |
|
} |
597 |
|
|
598 |
|
|
599 |
|
|
600 |
|
|
601 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
602 |
0 |
public String getProvider()... |
603 |
|
{ |
604 |
0 |
return (String) getProperty(PROVIDER); |
605 |
|
} |
606 |
|
|
607 |
|
|
608 |
|
|
609 |
|
|
610 |
|
@param |
611 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
612 |
0 |
public void setProviderPage(String urlStr)... |
613 |
|
{ |
614 |
0 |
setProperty(MODELPAGE, urlStr); |
615 |
|
} |
616 |
|
|
617 |
|
|
618 |
|
|
619 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
620 |
0 |
public String getProviderPage()... |
621 |
|
{ |
622 |
0 |
return (String) getProperty(MODELPAGE); |
623 |
|
} |
624 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
625 |
0 |
public boolean hasProviderPage()... |
626 |
|
{ |
627 |
0 |
return _hasProperty(MODELPAGE); |
628 |
|
} |
629 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
630 |
0 |
public boolean hasProvider()... |
631 |
|
{ |
632 |
0 |
return _hasProperty(PROVIDER); |
633 |
|
} |
634 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
635 |
0 |
public StructureFile getStructureFile()... |
636 |
|
{ |
637 |
0 |
return sf; |
638 |
|
} |
639 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
640 |
55 |
public void setStructureFile(StructureFile f)... |
641 |
|
{ |
642 |
55 |
sf = f; |
643 |
|
} |
644 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
645 |
0 |
public boolean hasStructureFile()... |
646 |
|
{ |
647 |
0 |
return sf != null && sf.inFile != null && sf.inFile.exists(); |
648 |
|
} |
649 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
650 |
0 |
public void setProviderCategory(String providerCategory)... |
651 |
|
{ |
652 |
0 |
setProperty(PROVIDERCATEGORY, providerCategory); |
653 |
|
} |
654 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
655 |
0 |
public String getProviderCategory()... |
656 |
|
{ |
657 |
0 |
return (String) getProperty(PROVIDERCATEGORY); |
658 |
|
} |
659 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
660 |
0 |
public boolean hasProviderCategory()... |
661 |
|
{ |
662 |
0 |
return _hasProperty(PROVIDERCATEGORY); |
663 |
|
} |
664 |
|
|
665 |
|
} |