Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

[jalview.git] / src / jalview / datamodel / DBRefEntry.java

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index f557ff8..4a5c888 100755 (executable)
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -20,6 +20,8 @@
  */
 package jalview.datamodel;
 
+import java.util.Locale;
+
 import jalview.api.DBRefEntryI;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
@@ -39,6 +41,8 @@ public class DBRefEntry implements DBRefEntryI
   int sourceKey = Integer.MIN_VALUE;
 
   String canonicalSourceName;
+  
+  boolean isCanonicalAccession;
 
   /*
    * maps from associated sequence to the database sequence's coordinate system
@@ -61,12 +65,25 @@ public class DBRefEntry implements DBRefEntryI
    */
   public DBRefEntry(String source, String version, String accessionId)
   {
-    this(source, version, accessionId, null);
+    this(source, version, accessionId, null,false);
   }
 
   /**
    * 
    * @param source
+   *                      may not be null
+   * @param version
+   *                      may be null
+   * @param accessionId
+   *                      may be null
+   */
+  public DBRefEntry(String source, String version, String accessionId, Mapping map)
+  {
+    this(source, version, accessionId, map,false);
+  }
+  /**
+   * 
+   * @param source
    *          canonical source (turned to uppercase; cannot be null)
    * @param version
    *          (source dependent version string or null)
@@ -77,13 +94,14 @@ public class DBRefEntry implements DBRefEntryI
    *          numbering or null)
    */
   public DBRefEntry(String source, String version, String accessionId,
-          Mapping map)
+          Mapping map,boolean isCanonical)
   {
        
-    this.source = source.toUpperCase();
+    this.source = source.toUpperCase(Locale.ROOT);
     setVersion(version);
     this.accessionId = accessionId;
     this.map = map;
+    this.isCanonicalAccession=isCanonical;
   }
 
   /**
@@ -97,7 +115,7 @@ public class DBRefEntry implements DBRefEntryI
                     : new String(entry.getVersion())),
             (entry.getAccessionId() == null ? ""
                     : new String(entry.getAccessionId())),
-            (entry.getMap() == null ? null : new Mapping(entry.getMap())));
+            (entry.getMap() == null ? null : new Mapping(entry.getMap())),entry.isCanonical());
   }
 
   @Override
@@ -156,6 +174,7 @@ public class DBRefEntry implements DBRefEntryI
       return true;
     }
 
+    boolean improved=false;
     /*
      * source must either match or be both null
      */
@@ -179,6 +198,19 @@ public class DBRefEntry implements DBRefEntryI
       return false;
     }
 
+    if (!isCanonicalAccession && other.isCanonical())
+    {
+      isCanonicalAccession = true;
+      improved = true;
+    }
+    else
+    {
+      if (isCanonicalAccession && !other.isCanonical())
+      {
+        // other is not an authoritative source of canonical accessions
+        return false;
+      }
+    }
     /*
      * if my version is null, "0" or "source:0" then replace with other version,
      * otherwise the versions have to match
@@ -195,12 +227,15 @@ public class DBRefEntry implements DBRefEntryI
       if (version != null && (otherVersion == null
               || !version.equalsIgnoreCase(otherVersion)))
       {
-        return false;
+        // FIXME: there may be a problem with old version strings not allowing
+        // updating of dbrefentries
+        return improved;
       }
     }
 
     /*
-     * if I have no mapping, take that of the other dbref
+     * if I have no mapping, take that of the other dbref 
+     * - providing it had a version and so do I
      */
     if (map == null)
     {
@@ -273,7 +308,7 @@ public class DBRefEntry implements DBRefEntryI
   public void setAccessionId(String accessionId)
   {
          this.accessionId = accessionId;
-//    this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase();
+//    this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase(Locale.ROOT);
   }
 
   /**
@@ -284,7 +319,7 @@ public class DBRefEntry implements DBRefEntryI
   {
          this.source = source;
          
-//    this.source = (source == null ? "" : source).toUpperCase();
+//    this.source = (source == null ? "" : source).toUpperCase(Locale.ROOT);
 //    this.canonicalSourceName =       DBRefUtils.getCanonicalName(this.source);
 //    this.sourceKey = DBRefSource.getSourceKey(this.canonicalSourceName);
   }
@@ -293,7 +328,7 @@ public class DBRefEntry implements DBRefEntryI
   public void setVersion(String version)
   {
     this.version = version;
-    this.ucversion = (version == null ? null : version.toUpperCase());
+    this.ucversion = (version == null ? null : version.toUpperCase(Locale.ROOT));
   }
 
   @Override
@@ -383,4 +418,22 @@ public class DBRefEntry implements DBRefEntryI
   public String getCanonicalSourceName() {
        return (canonicalSourceName == null ? (canonicalSourceName = DBRefUtils.getCanonicalName(this.source)) : canonicalSourceName);
   }
+
+  /**
+   * 
+   * @param canonical
+   */
+  public void setCanonical(boolean canonical)
+  {
+    isCanonicalAccession = canonical;
+  }
+  /**
+   * 
+   * @return true if this is the primary canonical accession for the database source
+   */
+  public boolean isCanonical()
+  {
+    // TODO Auto-generated method stub
+    return isCanonicalAccession;
+  }
 }