import jalview.api.DBRefEntryI;
+import java.util.Arrays;
+import java.util.List;
+
public class DBRefEntry implements DBRefEntryI
{
String source = "", version = "", accessionId = "";
- 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);
* @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 accessionId;
}
-
@Override
public void setAccessionId(String accessionId)
{
this.accessionId = accessionId;
}
-
@Override
public void setSource(String source)
{
this.source = source;
}
-
@Override
public void setVersion(String version)
{
this.version = version;
}
-
@Override
public Mapping getMap()
{
}
@Override
- public int getStartRes()
- {
- return startRes;
- }
-
- @Override
- public void setStartRes(int startRes)
+ public boolean isPrimaryCandidate()
{
- this.startRes = startRes;
- }
-
- @Override
- public int getEndRes()
- {
- return endRes;
- }
-
- @Override
- public void setEndRes(int endRes)
- {
- this.endRes = endRes;
+ /*
+ * if a map is present, unless it is 1:1 and has no SequenceI mate, it cannot be a primary reference.
+ */
+ if (map != null)
+ {
+ if (map.getTo() != null)
+ {
+ return false;
+ }
+ if (map.getMap().getFromRatio() != map.getMap().getToRatio()
+ || map.getMap().getFromRatio() != 1)
+ {
+ return false;
+ }
+ // check map is between identical single contiguous ranges
+ List<int[]> fromRanges = map.getMap().getFromRanges();
+ List<int[]> toRanges = map.getMap().getToRanges();
+ if (fromRanges.size() != 1 || toRanges.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)
+ {
+ // 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 ucv = version.toUpperCase();
+ for (String primsrc : Arrays.asList(DBRefSource.allSources()))
+ {
+ if (ucv.startsWith(primsrc.toUpperCase()))
+ {
+ // 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;
}
}