X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=98868ce64edbae6634dd50e80337b580a6ed6613;hb=77bcd1f60d9c26328d8859445f4225cd0ef571a9;hp=0b1fb6ddcac21154465755813c5e33d2fca895a9;hpb=9b6d2ddd33ba5e479953700040e1129847e47a06;p=jalview.git
diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 0b1fb6d..98868ce 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -22,11 +22,26 @@ package jalview.datamodel;
import jalview.api.DBRefEntryI;
+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 = "";
+
+ String accessionId = "";
- private int startRes, endRes;
/**
* maps from associated sequence to the database sequence's coordinate system
*/
@@ -63,13 +78,14 @@ public class DBRefEntry implements DBRefEntryI
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())));
}
@Override
@@ -86,9 +102,8 @@ public class DBRefEntry implements DBRefEntryI
{
return true;
}
- if (equalRef(entry)
- && ((map == null && entry.map == null) || (map != null
- && entry.map != null && map.equals(entry.map))))
+ if (equalRef(entry) && ((map == null && entry.map == null)
+ || (map != null && entry.map != null && map.equals(entry.map))))
{
return true;
}
@@ -96,6 +111,86 @@ public class DBRefEntry implements DBRefEntryI
}
/**
+ * 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(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
@@ -104,6 +199,7 @@ public class DBRefEntry implements DBRefEntryI
@Override
public boolean equalRef(DBRefEntryI entry)
{
+ // TODO is this method and equals() not needed?
if (entry == null)
{
return false;
@@ -113,12 +209,12 @@ 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())))
+ && (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;
}
@@ -143,28 +239,25 @@ public class DBRefEntry implements DBRefEntryI
return accessionId;
}
-
@Override
public void setAccessionId(String accessionId)
{
this.accessionId = accessionId;
}
-
@Override
public void setSource(String source)
{
this.source = source;
}
-
@Override
public void setVersion(String version)
{
this.version = version;
}
-
+ @Override
public Mapping getMap()
{
return map;
@@ -201,26 +294,64 @@ public class DBRefEntry implements DBRefEntryI
}
@Override
- public int getStartRes()
+ public boolean isPrimaryCandidate()
{
- return startRes;
- }
-
- @Override
- public void setStartRes(int startRes)
- {
- this.startRes = startRes;
- }
-
- @Override
- public int getEndRes()
- {
- return endRes;
+ /*
+ * 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;
+ }
+ // check map is between identical single contiguous ranges
+ List fromRanges = map.getMap().getFromRanges();
+ List toRanges = map.getMap().getToRanges();
+ if (fromRanges.size() != 1 || toRanges.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;
+ }
+ // 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;
}
- @Override
- public void setEndRes(int endRes)
+ /**
+ * Mappings to chromosome are held with accessionId as "chromosome:id"
+ *
+ * @return
+ */
+ public boolean isChromosome()
{
- this.endRes = endRes;
+ return accessionId != null && accessionId.startsWith(CHROMOSOME + ":");
}
}