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package jalview.datamodel; |
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import jalview.api.DBRefEntryI; |
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import java.util.Arrays; |
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import java.util.List; |
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| 95% |
Uncovered Elements: 7 (141) |
Complexity: 79 |
Complexity Density: 1.14 |
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public class DBRefEntry implements DBRefEntryI |
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{ |
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public static final String CHROMOSOME = "chromosome"; |
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String source = ""; |
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String version = ""; |
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String accessionId = ""; |
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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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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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2231 |
public DBRefEntry(String source, String version, String accessionId)... |
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{ |
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this(source, version, accessionId, null); |
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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 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
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4793 |
public DBRefEntry(String source, String version, String accessionId,... |
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Mapping map) |
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{ |
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this.source = source.toUpperCase(); |
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this.version = version; |
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this.accessionId = accessionId; |
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this.map = map; |
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} |
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| 66.7% |
Uncovered Elements: 3 (9) |
Complexity: 5 |
Complexity Density: 5 |
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2514 |
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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} |
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| 85.7% |
Uncovered Elements: 2 (14) |
Complexity: 10 |
Complexity Density: 1.25 |
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872 |
@Override... |
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public boolean equals(Object o) |
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{ |
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if (o == null || !(o instanceof DBRefEntry)) |
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{ |
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return false; |
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} |
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872 |
DBRefEntry entry = (DBRefEntry) o; |
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if (entry == this) |
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{ |
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return true; |
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} |
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if (equalRef(entry) && ((map == null && entry.map == null) |
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|| (map != null && entry.map != null && map.equals(entry.map)))) |
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{ |
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return true; |
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} |
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return false; |
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} |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (32) |
Complexity: 23 |
Complexity Density: 1.28 |
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2261 |
@Override... |
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public boolean updateFrom(DBRefEntryI other) |
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{ |
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2261 |
if (other == null) |
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{ |
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1 |
return false; |
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} |
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2260 |
if (other == this) |
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{ |
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1 |
return true; |
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} |
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2259 |
String otherSource = other.getSource(); |
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2259 |
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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2118 |
return false; |
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} |
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141 |
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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return false; |
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} |
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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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4 |
setVersion(otherVersion); |
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} |
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else |
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{ |
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24 |
if (version != null && (otherVersion == null |
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|| !version.equalsIgnoreCase(otherVersion))) |
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{ |
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6 |
return false; |
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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 (13) |
Complexity: 13 |
Complexity Density: 1.86 |
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165 |
@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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return false; |
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} |
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if (entry == this) |
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{ |
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1 |
return true; |
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} |
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if (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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return true; |
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} |
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145 |
return false; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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20774 |
@Override... |
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public String getSource() |
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{ |
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20774 |
return source; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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5403 |
@Override... |
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public String getVersion() |
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{ |
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5403 |
return version; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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7075 |
@Override... |
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public String getAccessionId() |
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{ |
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7075 |
return accessionId; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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190 |
@Override... |
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public void setAccessionId(String accessionId) |
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{ |
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this.accessionId = accessionId; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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180 |
@Override... |
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public void setSource(String source) |
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{ |
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this.source = source; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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2688 |
@Override... |
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public void setVersion(String version) |
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{ |
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2688 |
this.version = version; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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3738 |
@Override... |
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public Mapping getMap() |
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{ |
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3738 |
return map; |
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} |
265 |
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266 |
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@param |
268 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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2583 |
public void setMap(Mapping map)... |
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{ |
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this.map = map; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
275 |
2270 |
public boolean hasMap()... |
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{ |
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2270 |
return map != null; |
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} |
279 |
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280 |
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@return |
283 |
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| 60% |
Uncovered Elements: 2 (5) |
Complexity: 3 |
Complexity Density: 3 |
|
284 |
3 |
public String getSrcAccString()... |
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{ |
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3 |
return ((source != null) ? source : "") + ":" |
287 |
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+ ((accessionId != null) ? accessionId : ""); |
288 |
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} |
289 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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1 |
@Override... |
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public String toString() |
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{ |
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1 |
return getSrcAccString(); |
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} |
295 |
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| 100% |
Uncovered Elements: 0 (32) |
Complexity: 11 |
Complexity Density: 0.61 |
|
296 |
4737 |
@Override... |
297 |
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public boolean isPrimaryCandidate() |
298 |
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{ |
299 |
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300 |
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301 |
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302 |
4737 |
if (map != null) |
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{ |
304 |
213 |
if (map.getTo() != null) |
305 |
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{ |
306 |
97 |
return false; |
307 |
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} |
308 |
116 |
if (map.getMap().getFromRatio() != map.getMap().getToRatio() |
309 |
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|| map.getMap().getFromRatio() != 1) |
310 |
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{ |
311 |
29 |
return false; |
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} |
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List<int[]> fromRanges = map.getMap().getFromRanges(); |
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List<int[]> toRanges = map.getMap().getToRanges(); |
316 |
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if (fromRanges.size() != 1 || toRanges.size() != 1) |
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{ |
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return false; |
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} |
320 |
61 |
if (fromRanges.get(0)[0] != toRanges.get(0)[0] |
321 |
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|| fromRanges.get(0)[1] != toRanges.get(0)[1]) |
322 |
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{ |
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22 |
return false; |
324 |
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} |
325 |
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} |
326 |
4563 |
if (version == null) |
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{ |
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1 |
return false; |
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} |
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4562 |
String ucv = version.toUpperCase(); |
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4562 |
for (String primsrc : Arrays.asList(DBRefSource.allSources())) |
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{ |
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45024 |
if (ucv.startsWith(primsrc.toUpperCase())) |
337 |
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{ |
338 |
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339 |
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340 |
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341 |
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342 |
2599 |
return false; |
343 |
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} |
344 |
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} |
345 |
1963 |
return true; |
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} |
347 |
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348 |
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349 |
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350 |
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351 |
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@return |
352 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
353 |
320 |
public boolean isChromosome()... |
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{ |
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return accessionId != null && accessionId.startsWith(CHROMOSOME + ":"); |
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} |
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} |