import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
-import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import java.util.Set;
/*
* lookup from lower-case form of a name to its canonical (standardised) form
*/
- private static Map<String, String> canonicalSourceNameLookup = new HashMap<String, String>();
+ private static Map<String, String> canonicalSourceNameLookup = new HashMap<>();
- private static Map<String, String> dasCoordinateSystemsLookup = new HashMap<String, String>();
static
{
canonicalSourceNameLookup.get(k));
}
- dasCoordinateSystemsLookup.put("pdbresnum", DBRefSource.PDB);
- dasCoordinateSystemsLookup.put("uniprot", DBRefSource.UNIPROT);
- dasCoordinateSystemsLookup.put("embl", DBRefSource.EMBL);
- // dasCoordinateSystemsLookup.put("embl", DBRefSource.EMBLCDS);
}
/**
{
return dbrefs;
}
- HashSet<String> srcs = new HashSet<String>();
+ HashSet<String> srcs = new HashSet<>();
for (String src : sources)
{
- srcs.add(src);
+ srcs.add(src.toUpperCase());
}
- List<DBRefEntry> res = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> res = new ArrayList<>();
for (DBRefEntry dbr : dbrefs)
{
String source = getCanonicalName(dbr.getSource());
- if (srcs.contains(source))
+ if (srcs.contains(source.toUpperCase()))
{
res.add(dbr);
}
}
/**
- * isDasCoordinateSystem
- *
- * @param string
- * String
- * @param dBRefEntry
- * DBRefEntry
- * @return boolean true if Source DBRefEntry is compatible with DAS
- * CoordinateSystem name
- */
-
- public static boolean isDasCoordinateSystem(String string,
- DBRefEntry dBRefEntry)
- {
- if (string == null || dBRefEntry == null)
- {
- return false;
- }
- String coordsys = dasCoordinateSystemsLookup.get(string.toLowerCase());
- return coordsys == null ? false : coordsys.equals(dBRefEntry
- .getSource());
- }
-
- /**
* look up source in an internal list of database reference sources and return
* the canonical jalview name for the source, or the original string if it has
* no canonical form.
static List<DBRefEntry> searchRefs(DBRefEntry[] refs, DBRefEntry entry,
DbRefComp comparator)
{
- List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> rfs = new ArrayList<>();
if (refs == null || entry == null)
{
return rfs;
if (refa.getAccessionId() == null
|| refb.getAccessionId().equals(refa.getAccessionId()))
{
- if (refa.getMap() == null
- || (refb.getMap() != null && refb.getMap().equals(
- refa.getMap())))
+ if (refa.getMap() == null || (refb.getMap() != null
+ && refb.getMap().equals(refa.getMap())))
{
return true;
}
@Override
public boolean matches(DBRefEntry refa, DBRefEntry refb)
{
- if (refa.getSource() != null
- && refb.getSource() != null
+ if (refa.getSource() != null && refb.getSource() != null
&& DBRefUtils.getCanonicalName(refb.getSource()).equals(
DBRefUtils.getCanonicalName(refa.getSource())))
{
// We dont care about version
if (refa.getAccessionId() != null && refb.getAccessionId() != null
- // FIXME should be && not || here?
+ // FIXME should be && not || here?
|| refb.getAccessionId().equals(refa.getAccessionId()))
{
if ((refa.getMap() == null || refb.getMap() == null)
- || (refa.getMap() != null && refb.getMap() != null && refb
- .getMap().equals(refa.getMap())))
+ || (refa.getMap() != null && refb.getMap() != null
+ && refb.getMap().equals(refa.getMap())))
{
return true;
}
@Override
public boolean matches(DBRefEntry refa, DBRefEntry refb)
{
- if (refa.getSource() != null
- && refb.getSource() != null
+ if (refa.getSource() != null && refb.getSource() != null
&& DBRefUtils.getCanonicalName(refb.getSource()).equals(
DBRefUtils.getCanonicalName(refa.getSource())))
{
if ((refa.getMap() == null && refb.getMap() == null)
|| (refa.getMap() != null && refb.getMap() != null))
{
- if ((refb.getMap().getMap() == null && refa.getMap().getMap() == null)
+ if ((refb.getMap().getMap() == null
+ && refa.getMap().getMap() == null)
|| (refb.getMap().getMap() != null
- && refa.getMap().getMap() != null && refb
- .getMap().getMap().getInverse()
- .equals(refa.getMap().getMap())))
+ && refa.getMap().getMap() != null
+ && refb.getMap().getMap().getInverse()
+ .equals(refa.getMap().getMap())))
{
return true;
}
@Override
public boolean matches(DBRefEntry refa, DBRefEntry refb)
{
- if (refa.getSource() != null
- && refb.getSource() != null
+ if (refa.getSource() != null && refb.getSource() != null
&& DBRefUtils.getCanonicalName(refb.getSource()).equals(
DBRefUtils.getCanonicalName(refa.getSource())))
{
{
return true;
}
- if (refa.getMap() != null
- && refb.getMap() != null
- && ((refb.getMap().getMap() == null && refa.getMap()
- .getMap() == null) || (refb.getMap().getMap() != null
- && refa.getMap().getMap() != null && refb
- .getMap().getMap().equals(refa.getMap().getMap()))))
+ if (refa.getMap() != null && refb.getMap() != null
+ && ((refb.getMap().getMap() == null
+ && refa.getMap().getMap() == null)
+ || (refb.getMap().getMap() != null
+ && refa.getMap().getMap() != null
+ && refb.getMap().getMap()
+ .equals(refa.getMap().getMap()))))
{
return true;
}
@Override
public boolean matches(DBRefEntry refa, DBRefEntry refb)
{
- if (refa.getSource() != null
- && refb.getSource() != null
+ if (refa.getSource() != null && refb.getSource() != null
&& DBRefUtils.getCanonicalName(refb.getSource()).equals(
DBRefUtils.getCanonicalName(refa.getSource())))
{
return true;
}
if ((refa.getMap() != null && refb.getMap() != null)
- && (refb.getMap().getMap() == null && refa.getMap()
- .getMap() == null)
+ && (refb.getMap().getMap() == null
+ && refa.getMap().getMap() == null)
|| (refb.getMap().getMap() != null
- && refa.getMap().getMap() != null && (refb
- .getMap().getMap().equals(refa.getMap().getMap()))))
+ && refa.getMap().getMap() != null
+ && (refb.getMap().getMap()
+ .equals(refa.getMap().getMap()))))
{
return true;
}
PDBEntry pdbr = new PDBEntry();
pdbr.setId(pdbid);
pdbr.setType(PDBEntry.Type.PDB);
- pdbr.setProperty(new Hashtable());
pdbr.setChainCode(chaincode);
- // pdbr.getProperty().put("CHAIN", chaincode);
seq.addPDBId(pdbr);
}
else
{
return true;
}
- return DBRefUtils.getCanonicalName(o1).equals(
- DBRefUtils.getCanonicalName(o2));
+ return DBRefUtils.getCanonicalName(o1)
+ .equals(DBRefUtils.getCanonicalName(o2));
}
/**
public static DBRefEntry[] selectDbRefs(boolean selectDna,
DBRefEntry[] refs)
{
- return selectRefs(refs, selectDna ? DBRefSource.DNACODINGDBS
- : DBRefSource.PROTEINDBS);
+ return selectRefs(refs,
+ selectDna ? DBRefSource.DNACODINGDBS : DBRefSource.PROTEINDBS);
// could attempt to find other cross
// refs here - ie PDB xrefs
// (not dna, not protein seq)
public static List<DBRefEntry> searchRefsForSource(DBRefEntry[] dbRefs,
String source)
{
- List<DBRefEntry> matches = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> matches = new ArrayList<>();
if (dbRefs != null && source != null)
{
for (DBRefEntry dbref : dbRefs)
* sequences if they have an appropriate primary ref
* <table>
* <tr>
- * <td>Seq Type</td>
- * <td>Primary DB</td>
- * <td>Direct which will be promoted</td>
+ * <th>Seq Type</th>
+ * <th>Primary DB</th>
+ * <th>Direct which will be promoted</th>
* </tr>
- * <tr>
+ * <tr align=center>
* <td>peptides</td>
* <td>Ensembl</td>
* <td>Uniprot</td>
* </tr>
- * <tr>
+ * <tr align=center>
* <td>peptides</td>
* <td>Ensembl</td>
* <td>Uniprot</td>
* </tr>
- * <tr>
+ * <tr align=center>
* <td>dna</td>
* <td>Ensembl</td>
* <td>ENA</td>
// nothing to do
return;
}
- List<DBRefEntry> selfs = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> selfs = new ArrayList<>();
{
DBRefEntry[] selfArray = selectDbRefs(!sequence.isProtein(),
sequence.getDBRefs());
selfs.remove(p);
}
}
- List<DBRefEntry> toPromote = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> toPromote = new ArrayList<>();
for (DBRefEntry p : pr)
{
- List<String> promType = new ArrayList<String>();
+ List<String> promType = new ArrayList<>();
if (sequence.isProtein())
{
switch (getCanonicalName(p.getSource()))
}
// collate candidates and promote them
- DBRefEntry[] candidates = selectRefs(
- selfs.toArray(new DBRefEntry[0]),
+ DBRefEntry[] candidates = selectRefs(selfs.toArray(new DBRefEntry[0]),
promType.toArray(new String[0]));
if (candidates != null)
{
toPromote.add(cand);
if (!cand.isPrimaryCandidate())
{
- System.out.println("Warning: Couldn't promote dbref "
- + cand.toString() + " for sequence "
- + sequence.toString());
+ System.out.println(
+ "Warning: Couldn't promote dbref " + cand.toString()
+ + " for sequence " + sequence.toString());
}
}
}