X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=738c4dc831caf71090ddf09bd57ff458f468be44;hb=0ebcd487f08f9873987d9a32edce7df47aa27927;hp=bc1d610e47060e44ed3ed0bebbbcc071efdd9611;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git
diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index bc1d610..738c4dc 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -20,10 +20,13 @@
*/
package jalview.datamodel;
-public class DBRefEntry
+import jalview.api.DBRefEntryI;
+
+public class DBRefEntry implements DBRefEntryI
{
String source = "", version = "", accessionId = "";
+ private int startRes, endRes;
/**
* maps from associated sequence to the database sequence's coordinate system
*/
@@ -34,6 +37,7 @@ public class DBRefEntry
}
+
public DBRefEntry(String source, String version, String accessionId)
{
this(source, version, accessionId, null);
@@ -60,21 +64,30 @@ public class DBRefEntry
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))))
@@ -85,76 +98,153 @@ public class DBRefEntry
}
/**
+ * Answers true if this object is either equivalent to, or can be 'improved'
+ * by, the given entry. Specifically, answers true if
+ *
+ * - 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
+ * - mappings are not compared but if this entry has no mapping, replace
+ * with that for the other entry
+ *
+ *
+ * @param other
+ * @return
+ */
+ @Override
+ public boolean updateFrom(DBRefEntry 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.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;
@@ -183,4 +273,34 @@ public class DBRefEntry
return ((source != null) ? source : "") + ":"
+ ((accessionId != null) ? accessionId : "");
}
+
+ @Override
+ public String toString()
+ {
+ return getSrcAccString();
+ }
+
+ @Override
+ public int getStartRes()
+ {
+ return startRes;
+ }
+
+ @Override
+ public void setStartRes(int startRes)
+ {
+ this.startRes = startRes;
+ }
+
+ @Override
+ public int getEndRes()
+ {
+ return endRes;
+ }
+
+ @Override
+ public void setEndRes(int endRes)
+ {
+ this.endRes = endRes;
+ }
}