{
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);
this.map = map;
}
- public DBRefEntry(DBRefEntry entry)
+ public DBRefEntry(DBRefEntryI entry)
{
- this(
- (entry.source == null ? "" : new String(entry.source)),
- (entry.version == null ? "" : new String(entry.version)),
- (entry.accessionId == null ? "" : new String(entry.accessionId)),
- (entry.map == null ? null : new Mapping(entry.map)));
+ 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
}
/**
+ * Answers true if this object is either equivalent to, or can be 'improved'
+ * by, the given entry. Specifically, answers true if
+ * <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>
+ * <li>mappings are not compared but if this entry has no mapping, replace
+ * with that for the other entry</li>
+ * </ul>
+ *
+ * @param other
+ * @return
+ */
+ @Override
+ public boolean updateFrom(DBRefEntryI other)
+ {
+ if (other == null)
+ {
+ return false;
+ }
+ if (other == this)
+ {
+ return true;
+ }
+
+ /*
+ * source must either match or be both null
+ */
+ String otherSource = other.getSource();
+ if ((source == null && otherSource != null)
+ || (source != null && otherSource == null)
+ || (source != null && !source.equalsIgnoreCase(otherSource)))
+ {
+ return false;
+ }
+
+ /*
+ * accession id must either match or be both null
+ */
+ String otherAccession = other.getAccessionId();
+ if ((accessionId == null && otherAccession != null)
+ || (accessionId != null && otherAccession == null)
+ || (accessionId != null && !accessionId.equalsIgnoreCase(otherAccession)))
+ {
+ return false;
+ }
+
+ /*
+ * if my version is null, "0" or "source:0" then replace with other version,
+ * otherwise the versions have to match
+ */
+ String otherVersion = other.getVersion();
+
+ if ((version == null || version.equals("0") || version.endsWith(":0"))
+ && otherVersion != null)
+ {
+ setVersion(otherVersion);
+ }
+ else
+ {
+ if (version != null
+ && (otherVersion == null || !version
+ .equalsIgnoreCase(otherVersion)))
+ {
+ return false;
+ }
+ }
+
+ /*
+ * if I have no mapping, take that of the other dbref
+ */
+ if (map == null)
+ {
+ setMap(other.getMap());
+ }
+ return true;
+ }
+
+ /**
* test for similar DBRef attributes, except for the map object.
*
* @param entry
@Override
public boolean equalRef(DBRefEntryI entry)
{
+ // TODO is this method and equals() not needed?
if (entry == null)
{
return false;
return accessionId;
}
- /**
- * @param accessionId
- * the accessionId to set
- */
+
@Override
public void setAccessionId(String accessionId)
{
this.accessionId = accessionId;
}
- /**
- * @param source
- * the source to set
- */
+
@Override
public void setSource(String source)
{
this.source = source;
}
- /**
- * @param version
- * the version to set
- */
+
@Override
public void setVersion(String version)
{
this.version = version;
}
- /**
- * @return the map
- */
+
+ @Override
public Mapping getMap()
{
return map;
{
return getSrcAccString();
}
+
+ @Override
+ public int getStartRes()
+ {
+ return startRes;
+ }
+
+ @Override
+ public void setStartRes(int startRes)
+ {
+ this.startRes = startRes;
+ }
+
+ @Override
+ public int getEndRes()
+ {
+ return endRes;
+ }
+
+ @Override
+ public void setEndRes(int endRes)
+ {
+ this.endRes = endRes;
+ }
}