*/
package jalview.datamodel;
+import java.util.Locale;
+
import jalview.api.DBRefEntryI;
import jalview.util.DBRefUtils;
import jalview.util.MapList;
-import java.util.Arrays;
import java.util.List;
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";
-
String source = "";
- String version = "", ucversion;
+ private String version = "";
+
+ private String ucversion;
- String accessionId = "";
+ private String accessionId = "";
- String sourceKey;
+ 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
+ */
public DBRefEntry(String source, String version, String accessionId)
{
- this(source, version, accessionId, null);
+ this(source, version, accessionId, null,false);
}
/**
*
* @param source
- * canonical source (uppercase only)
+ * may not be null
* @param version
- * (source dependent version string)
+ * may be null
* @param accessionId
- * (source dependent accession number string)
+ * may be null
+ */
+ public DBRefEntry(String source, String version, String accessionId, Mapping map)
+ {
+ this(source, version, accessionId, map,false);
+ }
+ /**
+ *
+ * @param source
+ * canonical source (turned to uppercase; cannot be null)
+ * @param version
+ * (source dependent version string or null)
+ * @param accessionId
+ * (source dependent accession number string or null)
* @param map
* (mapping from local sequence numbering to source accession
- * numbering)
+ * numbering or null)
*/
public DBRefEntry(String source, String version, String accessionId,
- Mapping map)
+ Mapping map,boolean isCanonical)
{
- // BH 2019.01.25 made these always non-null.
- // Is there a difference between "" and null for version?
- // evidence is that source CANNOT be null.
- setSource(source);
+
+ this.source = source.toUpperCase(Locale.ROOT);
setVersion(version);
- setAccessionId(accessionId);
+ this.accessionId = accessionId;
this.map = map;
+ this.isCanonicalAccession=isCanonical;
}
+ /**
+ * Clone an entry, this time not allowing any null fields except map.
+ *
+ */
public DBRefEntry(DBRefEntryI entry)
{
- this(entry.getSource(), entry.getVersion(), entry.getAccessionId(), entry.getMap() == null ? null : new Mapping(entry.getMap()));
-// this((entry.getSource() == null ? "" : new String(entry.getSource())),
-// (entry.getVersion() == null ? ""
-// : new String(entry.getVersion())),
-// (entry.getAccessionId() == null ? ""
-// : new String(entry.getAccessionId())),
-// (entry.getMap() == null ? null : new Mapping(entry.getMap())));
+ this((entry.getSource() == null ? "" : new String(entry.getSource())),
+ (entry.getVersion() == null ? ""
+ : new String(entry.getVersion())),
+ (entry.getAccessionId() == null ? ""
+ : new String(entry.getAccessionId())),
+ (entry.getMap() == null ? null : new Mapping(entry.getMap())),entry.isCanonical());
}
@Override
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 source, accessionId, and version cannot be null.
+ // BH 2019.01.25/2019.02.04 source cannot/should not be null.
// for example, StructureChooser has dbRef.getSource().equalsIgnoreCase...
- if (entry != null
+ return (entry != null
&& (source != null && entry.getSource() != null
&& source.equalsIgnoreCase(entry.getSource()))
&& (accessionId != null && entry.getAccessionId() != null
&& accessionId.equalsIgnoreCase(entry.getAccessionId()))
&& (version != null && entry.getVersion() != null
- && version.equalsIgnoreCase(entry.getVersion())))
- {
- return true;
- }
- return false;
+ && version.equalsIgnoreCase(entry.getVersion())));
}
@Override
return source;
}
- public String getSourceKey()
+ public int getSourceKey()
{
- return sourceKey;
+ return (sourceKey == Integer.MIN_VALUE ? (sourceKey = DBRefSource.getSourceKey(getCanonicalSourceName())) : sourceKey);
}
+ /**
+ * can be null
+ */
@Override
public String getVersion()
{
return version;
}
+ /**
+ * can be null
+ */
@Override
public String getAccessionId()
{
@Override
public void setAccessionId(String accessionId)
{
- this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase();
+ this.accessionId = accessionId;
+// this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase(Locale.ROOT);
}
+ /**
+ * CAUTION! allows setting source null or not uppercase!
+ */
@Override
public void setSource(String source)
{
- this.source = (source == null ? "" : source).toUpperCase();
- this.canonicalSourceName = DBRefUtils.getCanonicalName(this.source);
- this.sourceKey = ";" + 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 == null ? "" : version);
- this.ucversion = this.version.toUpperCase();
+ this.version = version;
+ this.ucversion = (version == null ? null : version.toUpperCase(Locale.ROOT));
}
@Override
return false;
}
}
- if (version == null || version == "")
+ if (version == null)
{
// no version string implies the reference has not been verified at all.
return false;
}
- // tricky - this test really needs to search the sequence's set of dbrefs to
- // see if there is a primary reference that derived this reference.
- String[] sources = DBRefSource.allSources();
- for (int i = sources.length; --i >= 0;)
- {
- if (ucversion.startsWith(sources[i])) // BH 2019.01.25 .toUpperCase() unnecessary here for allSources
- {
- // by convention, many secondary references inherit the primary
- // reference's
- // source string as a prefix for any version information from the
- // secondary reference.
- return false;
- }
- }
- return true;
+
+ 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()
- {
- return accessionId != null && accessionId.startsWith(CHROMOSOME + ":");
+ public String getCanonicalSourceName() {
+ return (canonicalSourceName == null ? (canonicalSourceName = DBRefUtils.getCanonicalName(this.source)) : canonicalSourceName);
}
- public Object getCanonicalSourceName() {
- return canonicalSourceName;
+ /**
+ *
+ * @param canonical
+ */
+ 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;
}
-
-
}
git://source.jalview.org / jalview.git / blobdiff