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 = "";
- String version = "";
+ private String version = "";
+
+ private String ucversion;
- String accessionId = "";
+ private String accessionId = "";
+
+ int sourceKey = Integer.MIN_VALUE;
- /**
+ String canonicalSourceName;
+
+ /*
* 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);
/**
*
* @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)
{
+
this.source = source.toUpperCase();
- this.version = version;
+ setVersion(version);
this.accessionId = accessionId;
this.map = map;
}
+ /**
+ * Clone an entry, this time not allowing any null fields except map.
+ *
+ */
public DBRefEntry(DBRefEntryI entry)
{
this((entry.getSource() == null ? "" : new String(entry.getSource())),
{
// 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;
}
/**
{
return true;
}
- if (entry != null
+
+ // BH 2019.01.25/2019.02.04 source cannot/should not be null.
+ // for example, StructureChooser has dbRef.getSource().equalsIgnoreCase...
+
+ 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 int getSourceKey()
+ {
+ 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;
+ this.accessionId = accessionId;
+// this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase();
}
+ /**
+ * CAUTION! allows setting source null or not uppercase!
+ */
@Override
public void setSource(String source)
{
- this.source = source;
+ this.source = source;
+
+// this.source = (source == null ? "" : source).toUpperCase();
+// this.canonicalSourceName = DBRefUtils.getCanonicalName(this.source);
+// this.sourceKey = DBRefSource.getSourceKey(this.canonicalSourceName);
}
@Override
public void setVersion(String version)
{
this.version = version;
+ this.ucversion = (version == null ? null : version.toUpperCase());
}
@Override
*/
if (map != null)
{
- if (map.getTo() != null)
+ SequenceI mto = map.getTo();
+ if (mto != null)
{
return false;
}
- if (map.getMap().getFromRatio() != map.getMap().getToRatio()
- || map.getMap().getFromRatio() != 1)
+ 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 = map.getMap().getFromRanges();
- List<int[]> toRanges = map.getMap().getToRanges();
- if (fromRanges.size() != 1 || toRanges.size() != 1)
+ List<int[]> fromRanges, toRanges;
+ if ((fromRanges = ml.getFromRanges()).size() != 1 || (toRanges = ml.getToRanges()).size() != 1)
{
return false;
}
// 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;
+
+ return DBRefSource.isPrimaryCandidate(ucversion);
+ }
+
+ /**
+ * stores the upper-case canonical name of the source for use in
+ * Sequence.getPrimaryDBRefs().
+ *
+ * @author Bob Hanson
+ *
+ * @return
+ */
+ public String getCanonicalSourceName() {
+ return (canonicalSourceName == null ? (canonicalSourceName = DBRefUtils.getCanonicalName(this.source)) : canonicalSourceName);
}
}
git://source.jalview.org / jalview.git / blobdiff