/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * 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.Arrays;
+import java.util.List;
+
+public class DBRefEntry implements DBRefEntryI
{
- String source = "", version = "", accessionId = "";
+ /*
+ * the mapping to chromosome (genome) is held as an instance with
+ * source = speciesId
+ * version = assemblyId
+ * accessionId = "chromosome:" + chromosomeId
+ * map = mapping from sequence to reference assembly
+ */
+ public static final String CHROMOSOME = "chromosome";
+
+ String source = "";
+
+ String version = "", ucversion;
+
+ String accessionId = "";
+
+ String sourceKey;
+
+ String canonicalSourceName;
+
/**
* maps from associated sequence to the database sequence's coordinate system
public DBRefEntry(String source, String version, String accessionId,
Mapping map)
{
- this.source = source.toUpperCase();
- this.version = version;
- this.accessionId = accessionId;
+ // BH 2019.01.25 made these always non-null.
+ // Is there a difference between "" and null for version?
+ // evidence is that source CANNOT be null.
+ setSource(source);
+ setVersion(version);
+ setAccessionId(accessionId);
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(), entry.getVersion(), entry.getAccessionId(), entry.getMap() == null ? null : new Mapping(entry.getMap()));
+// 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())));
}
- public boolean equals(DBRefEntry entry)
+ @Override
+ public boolean equals(Object o)
{
- if (entry == this)
- return true;
- if (entry == null)
+ // 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;
+ }
+
+ /**
+ * 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 (equalRef(entry)
- && ((map == null && entry.map == null) || (map != null
- && entry.map != null && map.equals(entry.map))))
+ }
+ if (other == this)
{
return true;
}
- return false;
+
+ /*
+ * 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;
}
/**
* @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)
{
+ // 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
- .equalsIgnoreCase(entry.source))
- && (accessionId != null && entry.accessionId != null && accessionId
- .equalsIgnoreCase(entry.accessionId))
- && (version != null && entry.version != null && version
- .equalsIgnoreCase(entry.version)))
+ }
+
+ // BH 2019.01.25 source, accessionId, and version cannot be null.
+ // for example, StructureChooser has dbRef.getSource().equalsIgnoreCase...
+
+ 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;
}
+ @Override
public String getSource()
{
return source;
}
+ public String getSourceKey()
+ {
+ return sourceKey;
+ }
+
+ @Override
public String getVersion()
{
return version;
}
+ @Override
public String getAccessionId()
{
return accessionId;
}
- /**
- * @param accessionId
- * the accessionId to set
- */
+ @Override
public void setAccessionId(String accessionId)
{
- this.accessionId = accessionId;
+ this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase();
}
- /**
- * @param source
- * the source to set
- */
+ @Override
public void setSource(String source)
{
- this.source = source;
+ this.source = (source == null ? "" : source).toUpperCase();
+ this.canonicalSourceName = DBRefUtils.getCanonicalName(this.source);
+ this.sourceKey = ";" + canonicalSourceName + ";";
}
- /**
- * @param version
- * the version to set
- */
+ @Override
public void setVersion(String version)
{
- this.version = version;
+ this.version = (version == null ? "" : version);
+ this.ucversion = this.version.toUpperCase();
}
- /**
- * @return the map
- */
+ @Override
public Mapping getMap()
{
return map;
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 || version == "")
+ {
+ // 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[] sources = DBRefSource.allSources();
+ for (int i = sources.length; --i >= 0;)
+ {
+ if (ucversion.startsWith(sources[i])) // BH 2019.01.25 .toUpperCase() unnecessary here for allSources
+ {
+ // 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;
+ }
+
+ /**
+ * Mappings to chromosome are held with accessionId as "chromosome:id"
+ *
+ * @return
+ */
+ public boolean isChromosome()
+ {
+ return accessionId != null && accessionId.startsWith(CHROMOSOME + ":");
+ }
+
+ public Object getCanonicalSourceName() {
+ return canonicalSourceName;
+ }
+
+
}
git://source.jalview.org / jalview.git / blobdiff