package jalview.datamodel;
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
{
- String source = "", version = "", accessionId = "";
+ /*
+ * 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;
+
+ String accessionId = "";
+
+ String sourceKey;
+
+ String canonicalSourceName;
+
- private int startRes, endRes;
/**
* maps from associated sequence to the database sequence's coordinate system
*/
}
-
public DBRefEntry(String source, String version, String accessionId)
{
this(source, version, accessionId, null);
public DBRefEntry(String source, String version, String accessionId,
Mapping map)
{
- this.source = source.toUpperCase();
- this.version = version;
- this.accessionId = accessionId;
+ // 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);
+ setVersion(version);
+ setAccessionId(accessionId);
this.map = map;
}
public DBRefEntry(DBRefEntryI entry)
{
- 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(), 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())));
}
@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 (equalRef(entry)
- && ((map == null && entry.map == null) || (map != null
- && entry.map != null && map.equals(entry.map))))
- {
- return true;
- }
- return false;
+
+
+// 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;
}
/**
* <ul>
* <li>source and accession are identical (ignoring case)</li>
* <li>version is identical (ignoring case), or this version is of the format
- * "someSource:0", in which case the version for the other entry replaces it</li>
+ * "someSource:0", in which case the version for the other entry replaces
+ * it</li>
* <li>mappings are not compared but if this entry has no mapping, replace
* with that for the other entry</li>
* </ul>
* @return
*/
@Override
- public boolean updateFrom(DBRefEntry other)
+ public boolean updateFrom(DBRefEntryI other)
{
if (other == null)
{
String otherAccession = other.getAccessionId();
if ((accessionId == null && otherAccession != null)
|| (accessionId != null && otherAccession == null)
- || (accessionId != null && !accessionId.equalsIgnoreCase(otherAccession)))
+ || (accessionId != null
+ && !accessionId.equalsIgnoreCase(otherAccession)))
{
return false;
}
* otherwise the versions have to match
*/
String otherVersion = other.getVersion();
+
if ((version == null || version.equals("0") || version.endsWith(":0"))
&& otherVersion != null)
{
}
else
{
- if (!version.equalsIgnoreCase(otherVersion))
+ if (version != null && (otherVersion == null
+ || !version.equalsIgnoreCase(otherVersion)))
{
return false;
}
{
return true;
}
+
+ // BH 2019.01.25 source, accessionId, and version cannot be null.
+ // for example, StructureChooser has dbRef.getSource().equalsIgnoreCase...
+
if (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())))
+ && (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 source;
}
+ public String getSourceKey()
+ {
+ return sourceKey;
+ }
+
@Override
public String getVersion()
{
return accessionId;
}
-
@Override
public void setAccessionId(String accessionId)
{
- this.accessionId = accessionId;
+ this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase();
}
-
@Override
public void setSource(String source)
{
- this.source = source;
+ this.source = (source == null ? "" : source).toUpperCase();
+ this.canonicalSourceName = DBRefUtils.getCanonicalName(this.source);
+ this.sourceKey = ";" + canonicalSourceName + ";";
}
-
@Override
public void setVersion(String version)
{
- this.version = version;
+ this.version = (version == null ? "" : version);
+ this.ucversion = this.version.toUpperCase();
}
-
@Override
public Mapping getMap()
{
}
@Override
- public int getStartRes()
+ public boolean isPrimaryCandidate()
{
- return startRes;
+ /*
+ * if a map is present, unless it is 1:1 and has no SequenceI mate, it cannot be a primary reference.
+ */
+ if (map != null)
+ {
+ SequenceI mto = map.getTo();
+ if (mto != null)
+ {
+ return false;
+ }
+ MapList ml = map.getMap();
+ 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)
+ {
+ return false;
+ }
+ if (fromRanges.get(0)[0] != toRanges.get(0)[0]
+ || fromRanges.get(0)[1] != toRanges.get(0)[1])
+ {
+ return false;
+ }
+ }
+ if (version == null || version == "")
+ {
+ // 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;
}
- @Override
- public void setStartRes(int startRes)
+ /**
+ * Mappings to chromosome are held with accessionId as "chromosome:id"
+ *
+ * @return
+ */
+ public boolean isChromosome()
{
- this.startRes = startRes;
+ return accessionId != null && accessionId.startsWith(CHROMOSOME + ":");
}
- @Override
- public int getEndRes()
- {
- return endRes;
+ public Object getCanonicalSourceName() {
+ return canonicalSourceName;
}
- @Override
- public void setEndRes(int endRes)
- {
- this.endRes = endRes;
- }
+
}
git://source.jalview.org / jalview.git / blobdiff