/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-public class DBRefEntry
+import jalview.api.DBRefEntryI;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
+
+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;
- public DBRefEntry() {
-
+ Mapping map = null;
+
+ public DBRefEntry()
+ {
+
}
+
+ /**
+ *
+ * @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);
}
- public DBRefEntry(String source, String version, String accessionId, Mapping map) {
- this.source = source;
- this.version = version;
+
+ /**
+ *
+ * @param source
+ * may not be null
+ * @param version
+ * may be null
+ * @param accessionId
+ * 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 or null)
+ */
+ public DBRefEntry(String source, String version, String accessionId,
+ Mapping map,boolean isCanonical)
+ {
+
+ this.source = source.toUpperCase();
+ setVersion(version);
this.accessionId = accessionId;
this.map = map;
+ this.isCanonicalAccession=isCanonical;
}
- public DBRefEntry(DBRefEntry entry)
+
+ /**
+ * 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.isCanonical());
+ }
+
+ @Override
+ public boolean equals(Object o)
{
- this(new String(entry.source), new String(entry.version), new String(entry.accessionId), new Mapping(entry.map));
+ // 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;
+// }
+ 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;
}
- public boolean equals(DBRefEntry entry) {
- if (entry==this)
- return true;
- if (entry==null)
- return false;
- if (equalRef(entry)
- &&
- ((map==null && entry.map==null) || (map!=null && entry.map!=null && map.equals(entry.map)))) {
- return true;
- }
+
+ /**
+ * 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
+ *
+ * @param entry
* @return true if source, accession and version are equal with those of entry
*/
- public boolean equalRef(DBRefEntry entry)
+ @Override
+ public boolean equalRef(DBRefEntryI entry)
{
- if (entry==null)
+ // TODO is this method and equals() not needed?
+ if (entry == null)
{
return false;
}
- if (entry==this)
- return true;
- if ((source!=null && entry.source!=null && source.equals(entry.source))
- &&
- (accessionId!=null && entry.accessionId!=null && accessionId.equalsIgnoreCase(entry.accessionId))
- &&
- (version!=null && entry.version!=null && version.equalsIgnoreCase(entry.version))
- )
+ if (entry == this)
{
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
public String getSource()
{
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()
{
return accessionId;
}
-/**
- * @param accessionId the accessionId to set
- */
-public void setAccessionId(String accessionId) {
- this.accessionId = accessionId;
-}
-/**
- * @param source the source to set
- */
-public void setSource(String source) {
- this.source = source;
-}
-/**
- * @param version the version to set
- */
-public void setVersion(String version) {
+
+ @Override
+ public void setAccessionId(String 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 == null ? "" : source).toUpperCase();
+// this.canonicalSourceName = DBRefUtils.getCanonicalName(this.source);
+// this.sourceKey = DBRefSource.getSourceKey(this.canonicalSourceName);
+ }
+
+ @Override
+ public void setVersion(String version)
+ {
this.version = version;
-}
-/**
- * @return the map
- */
-public Mapping getMap() {
+ this.ucversion = (version == null ? null : version.toUpperCase());
+ }
+
+ @Override
+ public Mapping getMap()
+ {
return map;
-}
-/**
- * @param map the map to set
- */
-public void setMap(Mapping map) {
+ }
+
+ /**
+ * @param map
+ * the map to set
+ */
+ public void setMap(Mapping map)
+ {
this.map = map;
-}
-public boolean hasMap()
-{
- return map!=null;
-}
-/**
- *
- * @return source+":"+accessionId
- */
-public String getSrcAccString()
-{
- return ((source!=null) ? source : "")
- + ":" + ((accessionId!=null) ? accessionId : "");
-}
+ }
+
+ public boolean hasMap()
+ {
+ return map != null;
+ }
+
+ /**
+ *
+ * @return source+":"+accessionId
+ */
+ public String getSrcAccString()
+ {
+ return ((source != null) ? source : "") + ":"
+ + ((accessionId != null) ? accessionId : "");
+ }
+
+ @Override
+ public String toString()
+ {
+ return getSrcAccString();
+ }
+
+ @Override
+ 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)
+ {
+ 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)
+ {
+ // no version string implies the reference has not been verified at all.
+ return false;
+ }
+
+ 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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff