*/
package jalview.datamodel;
+import java.util.Locale;
+
import jalview.api.DBRefEntryI;
-import jalview.io.vamsas.Dbref;
import jalview.util.DBRefUtils;
import jalview.util.MapList;
public class DBRefEntry implements DBRefEntryI
{
- /*
- * the mapping to chromosome (genome) is held as an instance with
- * source = speciesId
- * version = assemblyId
- * accessionId = "chromosome:" + chromosomeId
- * map = mapping from sequence to reference assembly
- */
- public static final String CHROMOSOME = "chromosome";
-
- private String source = "";
+ String source = "";
private String version = "";
-
+
private String ucversion;
private String accessionId = "";
-
+
int sourceKey = Integer.MIN_VALUE;
String canonicalSourceName;
+ boolean isCanonicalAccession = false;
- /**
+ /*
* maps from associated sequence to the database sequence's coordinate system
*/
Mapping map = null;
{
}
-/**
- *
- * @param source may not be null
- * @param version may be null
- * @param accessionId may be null
- */
+
+ /**
+ *
+ * @param source
+ * may not be null
+ * @param version
+ * may be null
+ * @param accessionId
+ * may be null
+ */
public DBRefEntry(String source, String version, String accessionId)
{
- this(source, version, accessionId, null);
+ this(source, version, accessionId, null, false);
+ }
+
+ /**
+ *
+ * @param source
+ * may not be null
+ * @param version
+ * may be null
+ * @param accessionId
+ * may be null
+ */
+ public DBRefEntry(String source, String version, String accessionId,
+ Mapping map)
+ {
+ this(source, version, accessionId, map, false);
}
/**
* numbering or null)
*/
public DBRefEntry(String source, String version, String accessionId,
- Mapping map)
+ Mapping map, boolean isCanonical)
{
-
- this.source = source.toUpperCase();
+
+ this.source = source.toUpperCase(Locale.ROOT);
setVersion(version);
this.accessionId = accessionId;
this.map = map;
+ this.isCanonicalAccession = isCanonical;
}
/**
: new String(entry.getVersion())),
(entry.getAccessionId() == null ? ""
: new String(entry.getAccessionId())),
- (entry.getMap() == null ? null : new Mapping(entry.getMap())));
+ (entry.getMap() == null ? null : new Mapping(entry.getMap())),
+ entry.isCanonical());
}
@Override
{
// TODO should also override hashCode to ensure equal objects have equal
// hashcodes
-
-
-// if (o == null || !(o instanceof DBRefEntry))
-// {
-// return false;
-// }
-// DBRefEntry entry = (DBRefEntry) o;
-// if (entry == this)
-// {
-// return true;
-// }
+
+ // if (o == null || !(o instanceof DBRefEntry))
+ // {
+ // return false;
+ // }
+ // DBRefEntry entry = (DBRefEntry) o;
+ // if (entry == this)
+ // {
+ // return true;
+ // }
Mapping em;
- return (o != null && o instanceof DBRefEntry
- && (o == this
- || equalRef((DBRefEntry) o)
- && (map == null) == ((em = ((DBRefEntry) o).map) == null)
- && (map == null || map.equals(em))));
-//
-// {
-// return true;
-// }
-// return false;
+ return (o != null && o instanceof DBRefEntry && (o == this || equalRef(
+ (DBRefEntry) o)
+ && (map == null) == ((em = ((DBRefEntry) o).map) == null)
+ && (map == null || map.equals(em))));
+ //
+ // {
+ // return true;
+ // }
+ // return false;
}
/**
return true;
}
+ boolean improved = false;
/*
* source must either match or be both null
*/
return false;
}
+ if (!isCanonicalAccession && other.isCanonical())
+ {
+ isCanonicalAccession = true;
+ improved = true;
+ }
+ else
+ {
+ if (isCanonicalAccession && !other.isCanonical())
+ {
+ // other is not an authoritative source of canonical accessions
+ return false;
+ }
+ }
/*
* if my version is null, "0" or "source:0" then replace with other version,
* otherwise the versions have to match
if (version != null && (otherVersion == null
|| !version.equalsIgnoreCase(otherVersion)))
{
- return false;
+ // FIXME: there may be a problem with old version strings not allowing
+ // updating of dbrefentries
+ return improved;
}
}
/*
- * if I have no mapping, take that of the other dbref
+ * if I have no mapping, take that of the other dbref
+ * - providing it had a version and so do I
*/
if (map == null)
{
{
return true;
}
-
- // BH 2019.01.25/2019.02.04 source cannot/should not be null.
+
+ // BH 2019.01.25/2019.02.04 source cannot/should not be null.
// for example, StructureChooser has dbRef.getSource().equalsIgnoreCase...
-
+
return (entry != null
&& (source != null && entry.getSource() != null
&& source.equalsIgnoreCase(entry.getSource()))
return source;
}
- public int getSourceKey()
+ public int getSourceKey()
{
- return (sourceKey == Integer.MIN_VALUE ? (sourceKey = DBRefSource.getSourceKey(getCanonicalSourceName())) : sourceKey);
+ return (sourceKey == Integer.MIN_VALUE
+ ? (sourceKey = DBRefSource
+ .getSourceKey(getCanonicalSourceName()))
+ : sourceKey);
}
/**
@Override
public void setAccessionId(String accessionId)
{
- this.accessionId = accessionId;
-// this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase();
+ this.accessionId = accessionId;
+ // this.accessionId = (accessionId == null ? "" :
+ // accessionId).toUpperCase(Locale.ROOT);
}
/**
@Override
public void setSource(String source)
{
- this.source = source;
-
-// this.source = (source == null ? "" : source).toUpperCase();
-// this.canonicalSourceName = DBRefUtils.getCanonicalName(this.source);
-// this.sourceKey = DBRefSource.getSourceKey(this.canonicalSourceName);
+ this.source = source;
+
+ // this.source = (source == null ? "" : source).toUpperCase(Locale.ROOT);
+ // this.canonicalSourceName = DBRefUtils.getCanonicalName(this.source);
+ // this.sourceKey = DBRefSource.getSourceKey(this.canonicalSourceName);
}
@Override
public void setVersion(String version)
{
this.version = version;
- this.ucversion = (version == null ? null : version.toUpperCase());
+ this.ucversion = (version == null ? null
+ : version.toUpperCase(Locale.ROOT));
}
@Override
return false;
}
MapList ml = map.getMap();
- if (ml.getFromRatio() != ml.getToRatio()
- || ml.getFromRatio() != 1)
+ if (ml.getFromRatio() != ml.getToRatio() || ml.getFromRatio() != 1)
{
return false;
}
// check map is between identical single contiguous ranges
List<int[]> fromRanges, toRanges;
- if ((fromRanges = ml.getFromRanges()).size() != 1 || (toRanges = ml.getToRanges()).size() != 1)
+ if ((fromRanges = ml.getFromRanges()).size() != 1
+ || (toRanges = ml.getToRanges()).size() != 1)
{
return false;
}
// no version string implies the reference has not been verified at all.
return false;
}
-
+
return DBRefSource.isPrimaryCandidate(ucversion);
}
/**
- * Mappings to chromosome are held with accessionId as "chromosome:id"
+ * stores the upper-case canonical name of the source for use in
+ * Sequence.getPrimaryDBRefs().
+ *
+ * @author Bob Hanson
*
* @return
*/
- public boolean isChromosome()
+ public String getCanonicalSourceName()
{
- return accessionId != null && accessionId.startsWith(CHROMOSOME + ":");
+ return (canonicalSourceName == null
+ ? (canonicalSourceName = DBRefUtils
+ .getCanonicalName(this.source))
+ : canonicalSourceName);
}
/**
- * stores the upper-case canonical name of the source for use in
- * Sequence.getPrimaryDBRefs().
- *
- * @author Bob Hanson
*
- * @return
+ * @param canonical
*/
- public String getCanonicalSourceName() {
- return (canonicalSourceName == null ? (canonicalSourceName = DBRefUtils.getCanonicalName(this.source)) : canonicalSourceName);
+ public void setCanonical(boolean canonical)
+ {
+ isCanonicalAccession = canonical;
}
-
+ /**
+ *
+ * @return true if this is the primary canonical accession for the database
+ * source
+ */
+ public boolean isCanonical()
+ {
+ // TODO Auto-generated method stub
+ return isCanonicalAccession;
+ }
}