X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=511287bc2da6a2b8649d1cb7bd01b5edc5ccadc6;hb=d867cf856b9c0cdcb3d9732691f2c3afe861697c;hp=11e77d85a138ec545ddbd37c4287ce30ccdb0e7f;hpb=9a0e53e18ba1280658e1424c5e08b90e7beeebde;p=jalview.git
diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 11e77d8..511287b 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -21,14 +21,28 @@
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 = "";
+ String source = "";
- /**
+ private String version = "";
+
+ private String ucversion;
+
+ private String accessionId = "";
+
+ int sourceKey = Integer.MIN_VALUE;
+
+ String canonicalSourceName;
+
+ boolean isCanonicalAccession;
+
+ /*
* maps from associated sequence to the database sequence's coordinate system
*/
Mapping map = null;
@@ -38,40 +52,68 @@ public class DBRefEntry implements DBRefEntryI
}
+ /**
+ *
+ * @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
- * canonical source (uppercase only)
+ * may not be null
* @param version
- * (source dependent version string)
+ * may be null
* @param accessionId
- * (source dependent accession number string)
+ * may be null
+ */
+ public DBRefEntry(String source, String version, String accessionId, Mapping map)
+ {
+ this(source, version, accessionId, map,false);
+ }
+ /**
+ *
+ * @param source
+ * canonical source (turned to uppercase; cannot be null)
+ * @param version
+ * (source dependent version string or null)
+ * @param accessionId
+ * (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)
{
+
this.source = source.toUpperCase();
- this.version = version;
+ setVersion(version);
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() == 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.getVersion() == null ? ""
+ : new String(entry.getVersion())),
+ (entry.getAccessionId() == null ? ""
+ : new String(entry.getAccessionId())),
+ (entry.getMap() == null ? null : new Mapping(entry.getMap())),entry.isCanonical());
}
@Override
@@ -79,22 +121,28 @@ public class DBRefEntry implements DBRefEntryI
{
// 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;
}
/**
@@ -103,7 +151,8 @@ public class DBRefEntry implements DBRefEntryI
*
* - source and accession are identical (ignoring case)
* - 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
+ * "someSource:0", in which case the version for the other entry replaces
+ * it
* - mappings are not compared but if this entry has no mapping, replace
* with that for the other entry
*
@@ -123,6 +172,7 @@ public class DBRefEntry implements DBRefEntryI
return true;
}
+ boolean improved=false;
/*
* source must either match or be both null
*/
@@ -140,12 +190,25 @@ public class DBRefEntry implements DBRefEntryI
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;
}
+ 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
@@ -159,16 +222,18 @@ public class DBRefEntry implements DBRefEntryI
}
else
{
- if (version != null
- && (otherVersion == null || !version
- .equalsIgnoreCase(otherVersion)))
+ 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)
{
@@ -195,17 +260,17 @@ public class DBRefEntry implements DBRefEntryI
{
return true;
}
- 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())))
- {
- return true;
- }
- return false;
+
+ // 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())));
}
@Override
@@ -214,12 +279,23 @@ public class DBRefEntry implements DBRefEntryI
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()
{
@@ -229,19 +305,28 @@ public class DBRefEntry implements DBRefEntryI
@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
@@ -281,28 +366,32 @@ public class DBRefEntry implements DBRefEntryI
}
@Override
- public boolean isPrimary()
+ public boolean isPrimaryCandidate()
{
/*
* 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)
+ SequenceI mto = map.getTo();
+ if (mto != null)
+ {
+ return false;
+ }
+ MapList ml = map.getMap();
+ if (ml.getFromRatio() != ml.getToRatio()
+ || ml.getFromRatio() != 1)
{
return false;
}
- if (map.getMap().getFromRatio() != map.getMap().getToRatio()
- || map.getMap().getFromRatio() != 1)
+ // check map is between identical single contiguous ranges
+ List fromRanges, toRanges;
+ if ((fromRanges = ml.getFromRanges()).size() != 1 || (toRanges = ml.getToRanges()).size() != 1)
{
return false;
}
- // check map is really 1:1, no shifts allowed.
- if (map.getMap().getFromHighest() != map.getMap().getToHighest()
- && map.getMap().getFromLowest() != map.getMap().getToLowest()
- && !Arrays.equals(
- map.getMap().getFromRanges().toArray(new int[0][]),
- map.getMap().getToRanges().toArray(new int[0][])))
+ if (fromRanges.get(0)[0] != toRanges.get(0)[0]
+ || fromRanges.get(0)[1] != toRanges.get(0)[1])
{
return false;
}
@@ -312,20 +401,37 @@ public class DBRefEntry implements DBRefEntryI
// 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);
+ }
+
+ /**
+ *
+ * @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;
}
}