*/
package jalview.datamodel;
+import java.util.Locale;
+
import jalview.api.DBRefEntryI;
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";
-
String source = "";
- String version = "";
-
+ private String version = "";
+
private String ucversion;
- String accessionId = "";
-
- String sourceKey;
+ 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
+ */
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);
}
/**
*
* @param source
- * canonical source (uppercase only)
+ * canonical source (turned to uppercase; cannot be null)
* @param version
- * (source dependent version string)
+ * (source dependent version string or null)
* @param accessionId
- * (source dependent accession number string)
+ * (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
{
// 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 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;
}
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;
}
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;
- }
- /**
- * Mappings to chromosome are held with accessionId as "chromosome:id"
- *
- * @return
- */
- public boolean isChromosome()
- {
- return accessionId != null && accessionId.startsWith(CHROMOSOME + ":");
+ return DBRefSource.isPrimaryCandidate(ucversion);
}
/**
*
* @return
*/
- public Object getCanonicalSourceName() {
- return canonicalSourceName;
+ public String getCanonicalSourceName()
+ {
+ return (canonicalSourceName == null
+ ? (canonicalSourceName = DBRefUtils
+ .getCanonicalName(this.source))
+ : 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