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package jalview.datamodel; |
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import java.util.Locale; |
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import jalview.api.DBRefEntryI; |
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import jalview.util.DBRefUtils; |
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import jalview.util.MapList; |
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import java.util.List; |
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| 95.2% |
Uncovered Elements: 7 (146) |
Complexity: 70 |
Complexity Density: 1 |
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public class DBRefEntry implements DBRefEntryI |
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{ |
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String source = ""; |
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private String version = ""; |
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private String ucversion; |
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private String accessionId = ""; |
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int sourceKey = Integer.MIN_VALUE; |
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String canonicalSourceName; |
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boolean isCanonicalAccession = false; |
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Mapping map = null; |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
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public DBRefEntry()... |
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{ |
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} |
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@param |
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@param |
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@param |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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3004 |
public DBRefEntry(String source, String version, String accessionId)... |
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{ |
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3004 |
this(source, version, accessionId, null, false); |
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} |
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@param |
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@param |
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@param |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public DBRefEntry(String source, String version, String accessionId,... |
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Mapping map) |
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{ |
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this(source, version, accessionId, map, false); |
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} |
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@param |
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@param |
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@param |
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@param |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
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3215 |
public DBRefEntry(String source, String version, String accessionId,... |
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Mapping map, boolean isCanonical) |
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{ |
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3215 |
this.source = source.toUpperCase(Locale.ROOT); |
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setVersion(version); |
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this.accessionId = accessionId; |
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3215 |
this.map = map; |
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this.isCanonicalAccession = isCanonical; |
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} |
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| 66.7% |
Uncovered Elements: 3 (9) |
Complexity: 5 |
Complexity Density: 5 |
|
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public DBRefEntry(DBRefEntryI entry)... |
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{ |
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this((entry.getSource() == null ? "" : new String(entry.getSource())), |
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(entry.getVersion() == null ? "" |
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: new String(entry.getVersion())), |
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(entry.getAccessionId() == null ? "" |
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: new String(entry.getAccessionId())), |
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(entry.getMap() == null ? null : new Mapping(entry.getMap())), |
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entry.isCanonical()); |
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} |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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80 |
@Override... |
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public boolean equals(Object o) |
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{ |
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Mapping em; |
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return (o != null && o instanceof DBRefEntry && (o == this || equalRef( |
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(DBRefEntry) o) |
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&& (map == null) == ((em = ((DBRefEntry) o).map) == null) |
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&& (map == null || map.equals(em)))); |
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} |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (42) |
Complexity: 27 |
Complexity Density: 1.12 |
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68295 |
@Override... |
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public boolean updateFrom(DBRefEntryI other) |
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{ |
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68295 |
if (other == null) |
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{ |
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1 |
return false; |
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} |
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68294 |
if (other == this) |
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{ |
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return true; |
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} |
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68293 |
boolean improved = false; |
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68293 |
String otherSource = other.getSource(); |
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68293 |
if ((source == null && otherSource != null) |
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|| (source != null && otherSource == null) |
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|| (source != null && !source.equalsIgnoreCase(otherSource))) |
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{ |
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56124 |
return false; |
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} |
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12169 |
String otherAccession = other.getAccessionId(); |
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if ((accessionId == null && otherAccession != null) |
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|| (accessionId != null && otherAccession == null) |
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|| (accessionId != null |
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&& !accessionId.equalsIgnoreCase(otherAccession))) |
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{ |
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12118 |
return false; |
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} |
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if (!isCanonicalAccession && other.isCanonical()) |
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{ |
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isCanonicalAccession = true; |
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improved = true; |
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} |
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else |
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{ |
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if (isCanonicalAccession && !other.isCanonical()) |
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{ |
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3 |
return false; |
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} |
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} |
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48 |
String otherVersion = other.getVersion(); |
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if ((version == null || version.equals("0") || version.endsWith(":0")) |
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&& otherVersion != null) |
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{ |
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13 |
setVersion(otherVersion); |
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} |
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else |
227 |
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{ |
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35 |
if (version != null && (otherVersion == null |
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|| !version.equalsIgnoreCase(otherVersion))) |
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{ |
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4 |
return improved; |
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} |
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} |
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if (map == null) |
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{ |
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setMap(other.getMap()); |
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} |
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return true; |
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} |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (9) |
Complexity: 3 |
Complexity Density: 0.6 |
|
254 |
82 |
@Override... |
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public boolean equalRef(DBRefEntryI entry) |
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{ |
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if (entry == null) |
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{ |
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1 |
return false; |
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} |
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81 |
if (entry == this) |
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{ |
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1 |
return true; |
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} |
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80 |
return (entry != null |
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&& (source != null && entry.getSource() != null |
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&& source.equalsIgnoreCase(entry.getSource())) |
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&& (accessionId != null && entry.getAccessionId() != null |
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&& accessionId.equalsIgnoreCase(entry.getAccessionId())) |
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&& (version != null && entry.getVersion() != null |
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&& version.equalsIgnoreCase(entry.getVersion()))); |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
279 |
501052 |
@Override... |
280 |
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public String getSource() |
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{ |
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501052 |
return source; |
283 |
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} |
284 |
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
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325 |
public int getSourceKey()... |
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{ |
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return (sourceKey == Integer.MIN_VALUE |
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? (sourceKey = DBRefSource |
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.getSourceKey(getCanonicalSourceName())) |
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: sourceKey); |
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} |
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295 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
296 |
484 |
@Override... |
297 |
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public String getVersion() |
298 |
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{ |
299 |
484 |
return version; |
300 |
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} |
301 |
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302 |
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303 |
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304 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
305 |
49941 |
@Override... |
306 |
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public String getAccessionId() |
307 |
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{ |
308 |
49941 |
return accessionId; |
309 |
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} |
310 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
311 |
387 |
@Override... |
312 |
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public void setAccessionId(String accessionId) |
313 |
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{ |
314 |
387 |
this.accessionId = accessionId; |
315 |
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316 |
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317 |
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} |
318 |
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319 |
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320 |
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321 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
322 |
310 |
@Override... |
323 |
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public void setSource(String source) |
324 |
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{ |
325 |
310 |
this.source = source; |
326 |
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327 |
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328 |
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329 |
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330 |
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} |
331 |
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| 100% |
Uncovered Elements: 0 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
332 |
3550 |
@Override... |
333 |
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public void setVersion(String version) |
334 |
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{ |
335 |
3550 |
this.version = version; |
336 |
3550 |
this.ucversion = (version == null ? null |
337 |
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: version.toUpperCase(Locale.ROOT)); |
338 |
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} |
339 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
340 |
2488 |
@Override... |
341 |
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public Mapping getMap() |
342 |
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{ |
343 |
2488 |
return map; |
344 |
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} |
345 |
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346 |
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347 |
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@param |
348 |
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|
349 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
350 |
207 |
public void setMap(Mapping map)... |
351 |
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{ |
352 |
207 |
this.map = map; |
353 |
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} |
354 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
355 |
641 |
public boolean hasMap()... |
356 |
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{ |
357 |
641 |
return map != null; |
358 |
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} |
359 |
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|
360 |
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|
361 |
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362 |
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@return |
363 |
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| 60% |
Uncovered Elements: 2 (5) |
Complexity: 3 |
Complexity Density: 3 |
|
364 |
7 |
public String getSrcAccString()... |
365 |
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{ |
366 |
7 |
return ((source != null) ? source : "") + ":" |
367 |
7 |
+ ((accessionId != null) ? accessionId : ""); |
368 |
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} |
369 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
370 |
7 |
@Override... |
371 |
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public String toString() |
372 |
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{ |
373 |
7 |
return getSrcAccString(); |
374 |
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} |
375 |
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|
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| 92.6% |
Uncovered Elements: 2 (27) |
Complexity: 10 |
Complexity Density: 0.67 |
|
376 |
880 |
@Override... |
377 |
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public boolean isPrimaryCandidate() |
378 |
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{ |
379 |
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|
380 |
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|
381 |
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|
382 |
880 |
if (map != null) |
383 |
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{ |
384 |
51 |
SequenceI mto = map.getTo(); |
385 |
51 |
if (mto != null) |
386 |
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{ |
387 |
25 |
return false; |
388 |
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} |
389 |
26 |
MapList ml = map.getMap(); |
390 |
26 |
if (ml.getFromRatio() != ml.getToRatio() || ml.getFromRatio() != 1) |
391 |
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{ |
392 |
4 |
return false; |
393 |
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} |
394 |
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|
395 |
22 |
List<int[]> fromRanges, toRanges; |
396 |
? |
if ((fromRanges = ml.getFromRanges()).size() != 1 |
397 |
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|| (toRanges = ml.getToRanges()).size() != 1) |
398 |
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{ |
399 |
13 |
return false; |
400 |
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} |
401 |
9 |
if (fromRanges.get(0)[0] != toRanges.get(0)[0] |
402 |
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|| fromRanges.get(0)[1] != toRanges.get(0)[1]) |
403 |
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{ |
404 |
3 |
return false; |
405 |
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} |
406 |
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} |
407 |
835 |
if (version == null) |
408 |
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{ |
409 |
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|
410 |
1 |
return false; |
411 |
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} |
412 |
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|
413 |
834 |
return DBRefSource.isPrimaryCandidate(ucversion); |
414 |
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} |
415 |
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416 |
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417 |
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418 |
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419 |
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|
420 |
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@author |
421 |
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|
422 |
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@return |
423 |
|
|
|
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
424 |
358 |
public String getCanonicalSourceName()... |
425 |
|
{ |
426 |
358 |
return (canonicalSourceName == null |
427 |
|
? (canonicalSourceName = DBRefUtils |
428 |
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.getCanonicalName(this.source)) |
429 |
|
: canonicalSourceName); |
430 |
|
} |
431 |
|
|
432 |
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|
433 |
|
|
434 |
|
@param |
435 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
436 |
1104 |
public void setCanonical(boolean canonical)... |
437 |
|
{ |
438 |
1104 |
isCanonicalAccession = canonical; |
439 |
|
} |
440 |
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|
441 |
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|
442 |
|
|
443 |
|
@return |
444 |
|
|
445 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
446 |
411 |
public boolean isCanonical()... |
447 |
|
{ |
448 |
|
|
449 |
411 |
return isCanonicalAccession; |
450 |
|
} |
451 |
|
} |