/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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 java.util.Arrays;
+
+public class DBRefEntry implements DBRefEntryI
{
String source = "", version = "", 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() == 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)
{
+ // 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 (entry == null)
- return false;
+ }
if (equalRef(entry)
&& ((map == null && entry.map == null) || (map != null
&& entry.map != null && map.equals(entry.map))))
}
/**
+ * 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
* @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)))
+ }
+ 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;
}
+ @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;
}
- /**
- * @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 ((source != null) ? source : "") + ":"
+ ((accessionId != null) ? accessionId : "");
}
+
+ @Override
+ public String toString()
+ {
+ return getSrcAccString();
+ }
+
+ @Override
+ public boolean isPrimary()
+ {
+ /*
+ * 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)
+ {
+ return false;
+ }
+ if (map.getMap().getFromRatio() != map.getMap().getToRatio()
+ || map.getMap().getFromRatio() != 1)
+ {
+ return false;
+ }
+ }
+ if (version == null)
+ {
+ // 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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff