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package jalview.util; |
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import java.util.ArrayList; |
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import java.util.BitSet; |
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import java.util.HashMap; |
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import java.util.HashSet; |
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import java.util.List; |
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import java.util.Locale; |
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import java.util.Map; |
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import com.stevesoft.pat.Regex; |
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import jalview.bin.Console; |
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import jalview.datamodel.DBRefEntry; |
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import jalview.datamodel.DBRefSource; |
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import jalview.datamodel.Mapping; |
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import jalview.datamodel.PDBEntry; |
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import jalview.datamodel.SequenceI; |
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| 0% |
Uncovered Elements: 331 (331) |
Complexity: 154 |
Complexity Density: 0.87 |
|
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public class DBRefUtils |
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{ |
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private static Map<String, String> canonicalSourceNameLookup = new HashMap<>(); |
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public final static int DB_SOURCE = 1; |
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public final static int DB_VERSION = 2; |
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public final static int DB_ID = 4; |
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public final static int DB_MAP = 8; |
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public final static int SEARCH_MODE_NO_MAP_NO_VERSION = DB_SOURCE | DB_ID; |
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public final static int SEARCH_MODE_FULL = DB_SOURCE | DB_VERSION | DB_ID |
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| DB_MAP; |
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| 0% |
Uncovered Elements: 10 (10) |
Complexity: 1 |
Complexity Density: 0.1 |
|
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static... |
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{ |
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canonicalSourceNameLookup.put("uniprotkb/swiss-prot", |
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DBRefSource.UNIPROT); |
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canonicalSourceNameLookup.put("uniprotkb/trembl", DBRefSource.UNIPROT); |
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canonicalSourceNameLookup.put("uniprot/sptrembl", DBRefSource.UNIPROT); |
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canonicalSourceNameLookup.put("uniprot/swissprot", DBRefSource.UNIPROT); |
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canonicalSourceNameLookup.put("pdb", DBRefSource.PDB); |
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canonicalSourceNameLookup.put("ensembl", DBRefSource.ENSEMBL); |
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canonicalSourceNameLookup.put("ensembl-tr", DBRefSource.ENSEMBL); |
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canonicalSourceNameLookup.put("ensembl-gn", DBRefSource.ENSEMBL); |
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for (String k : canonicalSourceNameLookup.keySet()) |
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{ |
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canonicalSourceNameLookup.put(k.toLowerCase(Locale.ROOT), |
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canonicalSourceNameLookup.get(k)); |
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} |
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} |
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@param |
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@param |
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@return |
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| 0% |
Uncovered Elements: 23 (23) |
Complexity: 6 |
Complexity Density: 0.4 |
|
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public static List<DBRefEntry> selectRefs(List<DBRefEntry> dbrefs,... |
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String[] sources) |
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{ |
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if (dbrefs == null || sources == null) |
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{ |
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return dbrefs; |
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} |
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HashSet<String> srcs = new HashSet<String>(); |
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for (String src : sources) |
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{ |
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srcs.add(src.toUpperCase(Locale.ROOT)); |
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} |
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int nrefs = dbrefs.size(); |
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List<DBRefEntry> res = new ArrayList<DBRefEntry>(); |
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for (int ib = 0; ib < nrefs; ib++) |
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{ |
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DBRefEntry dbr = dbrefs.get(ib); |
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String source = getCanonicalName(dbr.getSource()); |
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if (srcs.contains(source.toUpperCase(Locale.ROOT))) |
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{ |
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res.add(dbr); |
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} |
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} |
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if (res.size() > 0) |
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{ |
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return res; |
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} |
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return null; |
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} |
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| 0% |
Uncovered Elements: 13 (13) |
Complexity: 5 |
Complexity Density: 0.71 |
|
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0 |
private static boolean selectRefsBS(List<DBRefEntry> dbrefs,... |
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int sourceKeys, BitSet bsSelect) |
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{ |
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if (dbrefs == null || sourceKeys == 0) |
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{ |
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return false; |
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} |
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for (int i = 0, n = dbrefs.size(); i < n; i++) |
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{ |
143 |
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DBRefEntry dbr = dbrefs.get(i); |
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if ((dbr.getSourceKey() & sourceKeys) != 0) |
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{ |
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bsSelect.clear(i); |
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} |
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} |
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return !bsSelect.isEmpty(); |
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} |
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@param |
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@param |
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@param |
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@return |
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| 0% |
Uncovered Elements: 13 (13) |
Complexity: 5 |
Complexity Density: 0.71 |
|
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static List<DBRefEntry> searchRefs(DBRefEntry[] refs, DBRefEntry entry,... |
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DbRefComp comparator) |
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{ |
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List<DBRefEntry> rfs = new ArrayList<>(); |
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if (refs == null || entry == null) |
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{ |
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return rfs; |
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} |
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for (int i = 0; i < refs.length; i++) |
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{ |
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if (comparator.matches(entry, refs[i])) |
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{ |
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rfs.add(refs[i]); |
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} |
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} |
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return rfs; |
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} |
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@param |
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@return |
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| 0% |
Uncovered Elements: 8 (8) |
Complexity: 3 |
Complexity Density: 0.75 |
|
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0 |
public static String getCanonicalName(String source)... |
191 |
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{ |
192 |
0 |
if (source == null) |
193 |
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{ |
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return null; |
195 |
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} |
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String canonical = canonicalSourceNameLookup |
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.get(source.toLowerCase(Locale.ROOT)); |
198 |
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return canonical == null ? source : canonical; |
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} |
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@param |
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@param |
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214 |
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@param |
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@return |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
218 |
0 |
public static List<DBRefEntry> searchRefs(List<DBRefEntry> ref,... |
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DBRefEntry entry, int mode) |
220 |
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{ |
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return searchRefs(ref, entry, |
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matchDbAndIdAndEitherMapOrEquivalentMapList, mode); |
223 |
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} |
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@param |
234 |
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235 |
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@param |
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@return |
238 |
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| 0% |
Uncovered Elements: 14 (14) |
Complexity: 5 |
Complexity Density: 0.62 |
|
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0 |
public static List<DBRefEntry> searchRefs(List<DBRefEntry> refs,... |
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String accId) |
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{ |
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List<DBRefEntry> rfs = new ArrayList<DBRefEntry>(); |
243 |
0 |
if (refs == null || accId == null) |
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{ |
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return rfs; |
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} |
247 |
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for (int i = 0, n = refs.size(); i < n; i++) |
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{ |
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DBRefEntry e = refs.get(i); |
250 |
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if (accId.equals(e.getAccessionId())) |
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{ |
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rfs.add(e); |
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} |
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} |
255 |
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return rfs; |
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257 |
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258 |
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} |
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@param |
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@param |
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268 |
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@param |
269 |
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@param |
270 |
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@return |
272 |
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| 0% |
Uncovered Elements: 14 (14) |
Complexity: 5 |
Complexity Density: 0.62 |
|
273 |
0 |
static List<DBRefEntry> searchRefs(List<DBRefEntry> refs,... |
274 |
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DBRefEntry entry, DbRefComp comparator, int mode) |
275 |
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{ |
276 |
0 |
List<DBRefEntry> rfs = new ArrayList<DBRefEntry>(); |
277 |
0 |
if (refs == null || entry == null) |
278 |
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{ |
279 |
0 |
return rfs; |
280 |
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} |
281 |
0 |
for (int i = 0, n = refs.size(); i < n; i++) |
282 |
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{ |
283 |
0 |
DBRefEntry e = refs.get(i); |
284 |
0 |
if (comparator.matches(entry, e, SEARCH_MODE_FULL)) |
285 |
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{ |
286 |
0 |
rfs.add(e); |
287 |
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} |
288 |
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} |
289 |
0 |
return rfs; |
290 |
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} |
291 |
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| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 1 |
|
292 |
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interface DbRefComp |
293 |
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{ |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
294 |
0 |
default public boolean matches(DBRefEntry refa, DBRefEntry refb)... |
295 |
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{ |
296 |
0 |
return matches(refa, refb, SEARCH_MODE_FULL); |
297 |
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}; |
298 |
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|
299 |
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public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode); |
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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305 |
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306 |
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public static DbRefComp matchNonNullonA = new DbRefComp() |
307 |
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{ |
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| 0% |
Uncovered Elements: 14 (14) |
Complexity: 14 |
Complexity Density: 2.33 |
|
308 |
0 |
@Override... |
309 |
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public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) |
310 |
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{ |
311 |
0 |
if ((mode & DB_SOURCE) != 0 && (refa.getSource() == null |
312 |
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|| DBRefUtils.getCanonicalName(refb.getSource()).equals( |
313 |
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DBRefUtils.getCanonicalName(refa.getSource())))) |
314 |
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{ |
315 |
0 |
if ((mode & DB_VERSION) != 0 && (refa.getVersion() == null |
316 |
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|| refb.getVersion().equals(refa.getVersion()))) |
317 |
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{ |
318 |
0 |
if ((mode & DB_ID) != 0 && (refa.getAccessionId() == null |
319 |
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|| refb.getAccessionId().equals(refa.getAccessionId()))) |
320 |
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{ |
321 |
0 |
if ((mode & DB_MAP) != 0 |
322 |
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&& (refa.getMap() == null || (refb.getMap() != null |
323 |
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&& refb.getMap().equals(refa.getMap())))) |
324 |
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{ |
325 |
0 |
return true; |
326 |
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} |
327 |
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} |
328 |
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} |
329 |
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} |
330 |
0 |
return false; |
331 |
|
} |
332 |
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}; |
333 |
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334 |
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335 |
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336 |
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337 |
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338 |
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339 |
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public static DbRefComp matchEitherNonNull = new DbRefComp() |
340 |
|
{ |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 5 |
Complexity Density: 1.67 |
|
341 |
0 |
@Override... |
342 |
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public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) |
343 |
|
{ |
344 |
0 |
if (nullOrEqualSource(refa.getSource(), refb.getSource()) |
345 |
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&& nullOrEqual(refa.getVersion(), refb.getVersion()) |
346 |
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&& nullOrEqual(refa.getAccessionId(), refb.getAccessionId()) |
347 |
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&& nullOrEqual(refa.getMap(), refb.getMap())) |
348 |
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{ |
349 |
0 |
return true; |
350 |
|
} |
351 |
0 |
return false; |
352 |
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} |
353 |
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|
354 |
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}; |
355 |
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356 |
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357 |
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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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363 |
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@param |
364 |
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@param |
365 |
|
@param |
366 |
|
@param |
367 |
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|
368 |
|
@return |
369 |
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|
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| 0% |
Uncovered Elements: 35 (35) |
Complexity: 7 |
Complexity Density: 0.3 |
|
370 |
0 |
public static DBRefEntry parseToDbRef(SequenceI seq, String dbname,... |
371 |
|
String version, String acn) |
372 |
|
{ |
373 |
0 |
DBRefEntry ref = null; |
374 |
0 |
if (dbname != null) |
375 |
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{ |
376 |
0 |
String locsrc = DBRefUtils.getCanonicalName(dbname); |
377 |
0 |
if (locsrc.equals(DBRefSource.PDB)) |
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 |
0 |
Regex r = new com.stevesoft.pat.Regex( |
384 |
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"([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)"); |
385 |
0 |
if (r.search(acn.trim())) |
386 |
|
{ |
387 |
0 |
String pdbid = r.stringMatched(1); |
388 |
0 |
String chaincode = r.stringMatched(2); |
389 |
0 |
if (chaincode == null) |
390 |
|
{ |
391 |
0 |
chaincode = " "; |
392 |
|
} |
393 |
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|
394 |
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|
395 |
0 |
if (chaincode.equals(" ")) |
396 |
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{ |
397 |
0 |
chaincode = "_"; |
398 |
|
} |
399 |
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|
400 |
0 |
ref = new DBRefEntry(locsrc, version, pdbid + chaincode); |
401 |
0 |
PDBEntry pdbr = new PDBEntry(); |
402 |
0 |
pdbr.setId(pdbid); |
403 |
0 |
pdbr.setType(PDBEntry.Type.PDB); |
404 |
0 |
pdbr.setChainCode(chaincode); |
405 |
0 |
seq.addPDBId(pdbr); |
406 |
|
} |
407 |
|
else |
408 |
|
{ |
409 |
0 |
jalview.bin.Console.errPrintln("Malformed PDB DR line:" + acn); |
410 |
|
} |
411 |
|
} |
412 |
|
else |
413 |
|
{ |
414 |
|
|
415 |
0 |
ref = new DBRefEntry(locsrc, version, acn.trim()); |
416 |
|
} |
417 |
|
} |
418 |
0 |
if (ref != null) |
419 |
|
{ |
420 |
0 |
seq.addDBRef(ref); |
421 |
|
} |
422 |
0 |
return ref; |
423 |
|
} |
424 |
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|
425 |
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426 |
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|
427 |
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|
428 |
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|
429 |
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|
430 |
|
public static DbRefComp matchDbAndIdAndEitherMap = new DbRefComp() |
431 |
|
{ |
|
|
| 0% |
Uncovered Elements: 11 (11) |
Complexity: 12 |
Complexity Density: 2.4 |
|
432 |
0 |
@Override... |
433 |
|
public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) |
434 |
|
{ |
435 |
0 |
if (refa.getSource() != null && refb.getSource() != null |
436 |
|
&& DBRefUtils.getCanonicalName(refb.getSource()).equals( |
437 |
|
DBRefUtils.getCanonicalName(refa.getSource()))) |
438 |
|
{ |
439 |
|
|
440 |
0 |
if (refa.getAccessionId() != null && refb.getAccessionId() != null |
441 |
|
|
442 |
|
|| refb.getAccessionId().equals(refa.getAccessionId())) |
443 |
|
{ |
444 |
0 |
if ((refa.getMap() == null || refb.getMap() == null) |
445 |
|
|| (refa.getMap() != null && refb.getMap() != null |
446 |
|
&& refb.getMap().equals(refa.getMap()))) |
447 |
|
{ |
448 |
0 |
return true; |
449 |
|
} |
450 |
|
} |
451 |
|
} |
452 |
0 |
return false; |
453 |
|
} |
454 |
|
}; |
455 |
|
|
456 |
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|
457 |
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|
458 |
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|
459 |
|
|
460 |
|
|
461 |
|
|
462 |
|
public static DbRefComp matchDbAndIdAndComplementaryMapList = new DbRefComp() |
463 |
|
{ |
|
|
| 0% |
Uncovered Elements: 14 (14) |
Complexity: 16 |
Complexity Density: 2.67 |
|
464 |
0 |
@Override... |
465 |
|
public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) |
466 |
|
{ |
467 |
0 |
if (refa.getSource() != null && refb.getSource() != null |
468 |
|
&& DBRefUtils.getCanonicalName(refb.getSource()).equals( |
469 |
|
DBRefUtils.getCanonicalName(refa.getSource()))) |
470 |
|
{ |
471 |
|
|
472 |
0 |
if (refa.getAccessionId() != null && refb.getAccessionId() != null |
473 |
|
|| refb.getAccessionId().equals(refa.getAccessionId())) |
474 |
|
{ |
475 |
0 |
if ((refa.getMap() == null && refb.getMap() == null) |
476 |
|
|| (refa.getMap() != null && refb.getMap() != null)) |
477 |
|
{ |
478 |
0 |
if ((refb.getMap().getMap() == null |
479 |
|
&& refa.getMap().getMap() == null) |
480 |
|
|| (refb.getMap().getMap() != null |
481 |
|
&& refa.getMap().getMap() != null |
482 |
|
&& refb.getMap().getMap().getInverse() |
483 |
|
.equals(refa.getMap().getMap()))) |
484 |
|
{ |
485 |
0 |
return true; |
486 |
|
} |
487 |
|
} |
488 |
|
} |
489 |
|
} |
490 |
0 |
return false; |
491 |
|
} |
492 |
|
}; |
493 |
|
|
494 |
|
|
495 |
|
|
496 |
|
|
497 |
|
|
498 |
|
|
499 |
|
|
500 |
|
public static DbRefComp matchDbAndIdAndEquivalentMapList = new DbRefComp() |
501 |
|
{ |
|
|
| 0% |
Uncovered Elements: 15 (15) |
Complexity: 16 |
Complexity Density: 2.29 |
|
502 |
0 |
@Override... |
503 |
|
public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) |
504 |
|
{ |
505 |
0 |
if (refa.getSource() != null && refb.getSource() != null |
506 |
|
&& DBRefUtils.getCanonicalName(refb.getSource()).equals( |
507 |
|
DBRefUtils.getCanonicalName(refa.getSource()))) |
508 |
|
{ |
509 |
|
|
510 |
|
|
511 |
|
|
512 |
|
|
513 |
0 |
if (refa.getAccessionId() != null && refb.getAccessionId() != null |
514 |
|
|| refb.getAccessionId().equals(refa.getAccessionId())) |
515 |
|
{ |
516 |
0 |
if (refa.getMap() == null && refb.getMap() == null) |
517 |
|
{ |
518 |
0 |
return true; |
519 |
|
} |
520 |
0 |
if (refa.getMap() != null && refb.getMap() != null |
521 |
|
&& ((refb.getMap().getMap() == null |
522 |
|
&& refa.getMap().getMap() == null) |
523 |
|
|| (refb.getMap().getMap() != null |
524 |
|
&& refa.getMap().getMap() != null |
525 |
|
&& refb.getMap().getMap() |
526 |
|
.equals(refa.getMap().getMap())))) |
527 |
|
{ |
528 |
0 |
return true; |
529 |
|
} |
530 |
|
} |
531 |
|
} |
532 |
0 |
return false; |
533 |
|
} |
534 |
|
}; |
535 |
|
|
536 |
|
|
537 |
|
|
538 |
|
|
539 |
|
|
540 |
|
|
541 |
|
public static DbRefComp matchDbAndIdAndEitherMapOrEquivalentMapList = new DbRefComp() |
542 |
|
{ |
|
|
| 0% |
Uncovered Elements: 15 (15) |
Complexity: 15 |
Complexity Density: 2.14 |
|
543 |
0 |
@Override... |
544 |
|
public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) |
545 |
|
{ |
546 |
0 |
if (refa.getSource() != null && refb.getSource() != null |
547 |
|
&& DBRefUtils.getCanonicalName(refb.getSource()).equals( |
548 |
|
DBRefUtils.getCanonicalName(refa.getSource()))) |
549 |
|
{ |
550 |
|
|
551 |
0 |
if (refa.getAccessionId() == null |
552 |
|
|| refa.getAccessionId().equals(refb.getAccessionId())) |
553 |
|
{ |
554 |
0 |
if (refa.getMap() == null || refb.getMap() == null) |
555 |
|
{ |
556 |
0 |
return true; |
557 |
|
} |
558 |
0 |
if ((refa.getMap() != null && refb.getMap() != null) |
559 |
|
&& (refb.getMap().getMap() == null |
560 |
|
&& refa.getMap().getMap() == null) |
561 |
|
|| (refb.getMap().getMap() != null |
562 |
|
&& refa.getMap().getMap() != null |
563 |
|
&& (refb.getMap().getMap() |
564 |
|
.equals(refa.getMap().getMap())))) |
565 |
|
{ |
566 |
0 |
return true; |
567 |
|
} |
568 |
|
} |
569 |
|
} |
570 |
0 |
return false; |
571 |
|
} |
572 |
|
}; |
573 |
|
|
574 |
|
|
575 |
|
|
576 |
|
|
577 |
|
|
578 |
|
@param |
579 |
|
@param |
580 |
|
@return |
581 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 4 |
Complexity Density: 0.67 |
|
582 |
0 |
public static List<DBRefEntry> searchRefsForSource(DBRefEntry[] dbRefs,... |
583 |
|
String source) |
584 |
|
{ |
585 |
0 |
List<DBRefEntry> matches = new ArrayList<>(); |
586 |
0 |
if (dbRefs != null && source != null) |
587 |
|
{ |
588 |
0 |
for (DBRefEntry dbref : dbRefs) |
589 |
|
{ |
590 |
0 |
if (source.equalsIgnoreCase(dbref.getSource())) |
591 |
|
{ |
592 |
0 |
matches.add(dbref); |
593 |
|
} |
594 |
|
} |
595 |
|
} |
596 |
0 |
return matches; |
597 |
|
} |
598 |
|
|
599 |
|
|
600 |
|
|
601 |
|
|
602 |
|
@param |
603 |
|
@param |
604 |
|
@return |
605 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
606 |
0 |
public static boolean nullOrEqual(Object o1, Object o2)... |
607 |
|
{ |
608 |
0 |
if (o1 == null || o2 == null) |
609 |
|
{ |
610 |
0 |
return true; |
611 |
|
} |
612 |
0 |
return o1.equals(o2); |
613 |
|
} |
614 |
|
|
615 |
|
|
616 |
|
|
617 |
|
|
618 |
|
@param |
619 |
|
|
620 |
|
@param |
621 |
|
|
622 |
|
@return |
623 |
|
|
624 |
|
|
625 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
626 |
0 |
public static boolean nullOrEqualSource(String o1, String o2)... |
627 |
|
{ |
628 |
0 |
if (o1 == null || o2 == null) |
629 |
|
{ |
630 |
0 |
return true; |
631 |
|
} |
632 |
0 |
return DBRefUtils.getCanonicalName(o1) |
633 |
|
.equals(DBRefUtils.getCanonicalName(o2)); |
634 |
|
} |
635 |
|
|
636 |
|
|
637 |
|
|
638 |
|
|
639 |
|
@param |
640 |
|
|
641 |
|
|
642 |
|
@param |
643 |
|
|
644 |
|
@return |
645 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
646 |
0 |
public static List<DBRefEntry> selectDbRefs(boolean selectDna,... |
647 |
|
List<DBRefEntry> refs) |
648 |
|
{ |
649 |
0 |
return selectRefs(refs, |
650 |
0 |
selectDna ? DBRefSource.DNACODINGDBS : DBRefSource.PROTEINDBS); |
651 |
|
|
652 |
|
|
653 |
|
|
654 |
|
} |
655 |
|
|
656 |
|
|
657 |
|
|
658 |
|
|
659 |
|
|
660 |
|
@param |
661 |
|
@param |
662 |
|
@return |
663 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 4 |
Complexity Density: 0.67 |
|
664 |
0 |
public static List<DBRefEntry> searchRefsForSource(... |
665 |
|
List<DBRefEntry> dbRefs, String source) |
666 |
|
{ |
667 |
0 |
List<DBRefEntry> matches = new ArrayList<DBRefEntry>(); |
668 |
0 |
if (dbRefs != null && source != null) |
669 |
|
{ |
670 |
0 |
for (DBRefEntry dbref : dbRefs) |
671 |
|
{ |
672 |
0 |
if (source.equalsIgnoreCase(dbref.getSource())) |
673 |
|
{ |
674 |
0 |
matches.add(dbref); |
675 |
|
} |
676 |
|
} |
677 |
|
} |
678 |
0 |
return matches; |
679 |
|
} |
680 |
|
|
681 |
|
|
682 |
|
|
683 |
|
|
684 |
|
|
685 |
|
|
686 |
|
|
687 |
|
|
688 |
|
|
689 |
|
|
690 |
|
|
691 |
|
|
692 |
|
|
693 |
|
|
694 |
|
|
695 |
|
|
696 |
|
|
697 |
|
|
698 |
|
|
699 |
|
|
700 |
|
|
701 |
|
|
702 |
|
|
703 |
|
|
704 |
|
|
705 |
|
|
706 |
|
|
707 |
|
@param |
708 |
|
|
|
|
| 0% |
Uncovered Elements: 72 (72) |
Complexity: 22 |
Complexity Density: 0.52 |
|
709 |
0 |
public static void ensurePrimaries(SequenceI sequence,... |
710 |
|
List<DBRefEntry> pr) |
711 |
|
{ |
712 |
0 |
if (pr.size() == 0) |
713 |
|
{ |
714 |
|
|
715 |
0 |
return; |
716 |
|
} |
717 |
0 |
int sstart = sequence.getStart(); |
718 |
0 |
int send = sequence.getEnd(); |
719 |
0 |
boolean isProtein = sequence.isProtein(); |
720 |
0 |
BitSet bsSelect = new BitSet(); |
721 |
|
|
722 |
|
|
723 |
|
|
724 |
|
|
725 |
|
|
726 |
|
|
727 |
|
|
728 |
|
|
729 |
|
|
730 |
|
|
731 |
|
|
732 |
0 |
List<DBRefEntry> dbrefs = sequence.getDBRefs(); |
733 |
0 |
bsSelect.set(0, dbrefs.size()); |
734 |
|
|
735 |
0 |
if (!selectRefsBS(dbrefs, isProtein ? DBRefSource.PROTEIN_MASK |
736 |
|
: DBRefSource.DNA_CODING_MASK, bsSelect)) |
737 |
0 |
return; |
738 |
|
|
739 |
|
|
740 |
|
|
741 |
|
|
742 |
|
|
743 |
0 |
for (int ip = pr.size(); --ip >= 0;) |
744 |
|
{ |
745 |
0 |
DBRefEntry p = pr.get(ip); |
746 |
0 |
for (int i = bsSelect.nextSetBit(0); i >= 0; i = bsSelect |
747 |
|
.nextSetBit(i + 1)) |
748 |
|
{ |
749 |
0 |
if (dbrefs.get(i) == p) |
750 |
0 |
bsSelect.clear(i); |
751 |
|
} |
752 |
|
|
753 |
|
|
754 |
|
|
755 |
|
|
756 |
|
} |
757 |
|
|
758 |
|
|
759 |
0 |
for (int ip = pr.size(), keys = 0; --ip >= 0 |
760 |
|
&& keys != DBRefSource.PRIMARY_MASK;) |
761 |
|
{ |
762 |
0 |
DBRefEntry p = pr.get(ip); |
763 |
0 |
if (isProtein) |
764 |
|
{ |
765 |
0 |
switch (getCanonicalName(p.getSource())) |
766 |
|
{ |
767 |
0 |
case DBRefSource.UNIPROT: |
768 |
0 |
keys |= DBRefSource.UNIPROT_MASK; |
769 |
0 |
break; |
770 |
0 |
case DBRefSource.ENSEMBL: |
771 |
0 |
keys |= DBRefSource.ENSEMBL_MASK; |
772 |
0 |
break; |
773 |
|
} |
774 |
|
} |
775 |
|
else |
776 |
|
{ |
777 |
|
|
778 |
|
} |
779 |
0 |
if (keys == 0 || !selectRefsBS(dbrefs, keys, bsSelect)) |
780 |
0 |
return; |
781 |
|
|
782 |
|
{ |
783 |
0 |
for (int ic = bsSelect.nextSetBit(0); ic >= 0; ic = bsSelect |
784 |
|
.nextSetBit(ic + 1)) |
785 |
|
|
786 |
|
{ |
787 |
0 |
DBRefEntry cand = dbrefs.get(ic); |
788 |
0 |
if (cand.hasMap()) |
789 |
|
{ |
790 |
0 |
Mapping map = cand.getMap(); |
791 |
0 |
SequenceI cto = map.getTo(); |
792 |
0 |
if (cto != null && cto != sequence) |
793 |
|
{ |
794 |
|
|
795 |
0 |
continue; |
796 |
|
} |
797 |
0 |
MapList mlist = map.getMap(); |
798 |
0 |
if (mlist.getFromLowest() != sstart |
799 |
|
&& mlist.getFromHighest() != send) |
800 |
|
{ |
801 |
|
|
802 |
|
|
803 |
0 |
continue; |
804 |
|
} |
805 |
|
} |
806 |
|
|
807 |
|
|
808 |
0 |
cand.setVersion(cand.getVersion() + " (promoted)"); |
809 |
0 |
bsSelect.clear(ic); |
810 |
|
|
811 |
|
|
812 |
0 |
if (!cand.isPrimaryCandidate()) |
813 |
|
{ |
814 |
0 |
if (Console.isDebugEnabled()) |
815 |
|
{ |
816 |
0 |
Console.debug( |
817 |
|
"Warning: Couldn't promote dbref " + cand.toString() |
818 |
|
+ " for sequence " + sequence.toString()); |
819 |
|
} |
820 |
|
} |
821 |
|
} |
822 |
|
} |
823 |
|
} |
824 |
|
} |
825 |
|
|
826 |
|
} |