X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=f7837f75c0b8fd7a563b8b6f9bef3755ab18bd82;hb=99830f5e58e49c6839c777b23aa6df200318064b;hp=66a075e8a53e1474e0d88642f5b1ae8f7cca5260;hpb=7308f8601e2037183869fd33509871e8c7a2b5e7;p=jalview.git
diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 66a075e..f7837f7 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -22,11 +22,13 @@ package jalview.datamodel;
import jalview.api.DBRefEntryI;
+import java.util.Arrays;
+import java.util.List;
+
public class DBRefEntry implements DBRefEntryI
{
String source = "", version = "", accessionId = "";
- private int startRes, endRes;
/**
* maps from associated sequence to the database sequence's coordinate system
*/
@@ -37,7 +39,6 @@ public class DBRefEntry implements DBRefEntryI
}
-
public DBRefEntry(String source, String version, String accessionId)
{
this(source, version, accessionId, null);
@@ -67,10 +68,10 @@ public class DBRefEntry implements DBRefEntryI
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.getVersion() == null ? ""
+ : new String(entry.getVersion())),
+ (entry.getAccessionId() == null ? ""
+ : new String(entry.getAccessionId())),
(entry.getMap() == null ? null : new Mapping(entry.getMap())));
}
@@ -88,9 +89,8 @@ 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;
}
@@ -103,7 +103,8 @@ public class DBRefEntry implements DBRefEntryI
*
* - 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
+ * "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
*
@@ -140,7 +141,8 @@ public class DBRefEntry implements DBRefEntryI
String otherAccession = other.getAccessionId();
if ((accessionId == null && otherAccession != null)
|| (accessionId != null && otherAccession == null)
- || (accessionId != null && !accessionId.equalsIgnoreCase(otherAccession)))
+ || (accessionId != null
+ && !accessionId.equalsIgnoreCase(otherAccession)))
{
return false;
}
@@ -150,6 +152,7 @@ public class DBRefEntry implements DBRefEntryI
* otherwise the versions have to match
*/
String otherVersion = other.getVersion();
+
if ((version == null || version.equals("0") || version.endsWith(":0"))
&& otherVersion != null)
{
@@ -157,7 +160,8 @@ public class DBRefEntry implements DBRefEntryI
}
else
{
- if (!version.equalsIgnoreCase(otherVersion))
+ if (version != null && (otherVersion == null
+ || !version.equalsIgnoreCase(otherVersion)))
{
return false;
}
@@ -192,12 +196,12 @@ 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;
}
@@ -222,28 +226,24 @@ 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()
{
@@ -281,26 +281,54 @@ public class DBRefEntry implements DBRefEntryI
}
@Override
- public int getStartRes()
- {
- return startRes;
- }
-
- @Override
- public void setStartRes(int startRes)
+ public boolean isPrimaryCandidate()
{
- this.startRes = startRes;
- }
-
- @Override
- public int getEndRes()
- {
- return endRes;
- }
-
- @Override
- public void setEndRes(int endRes)
- {
- this.endRes = 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;
}
}