X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=0004abe7068b971dece2c1e8b87224627fc909f8;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=19935160b43444fe53ff151eabd86167fa810e17;hpb=26b115b0a77d521da92a06572d9b7819c2d0d49a;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 1993516..0004abe 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -24,7 +24,6 @@ import jalview.api.DBRefEntryI;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 
-import java.util.Arrays;
 import java.util.List;
 
 public class DBRefEntry implements DBRefEntryI
@@ -38,13 +37,15 @@ public class DBRefEntry implements DBRefEntryI
    */
   public static final String CHROMOSOME = "chromosome";
 
-  String source = "";
+  private String source = "";
 
-  String version = "", ucversion;
+  private String version = "";
+  
+  private String ucversion = "";
 
-  String accessionId = "";
+  private String accessionId = "";
   
-  String sourceKey;
+  int sourceKey = Integer.MIN_VALUE;
 
   String canonicalSourceName;
 
@@ -58,7 +59,12 @@ public class DBRefEntry implements DBRefEntryI
   {
 
   }
-
+/**
+ * 
+ * @param source may not be null
+ * @param version may be null
+ * @param accessionId may be null
+ */
   public DBRefEntry(String source, String version, String accessionId)
   {
     this(source, version, accessionId, null);
@@ -67,36 +73,37 @@ public class DBRefEntry implements DBRefEntryI
   /**
    * 
    * @param source
-   *          canonical source (uppercase only)
+   *          canonical source (turned to uppercase; cannot be null)
    * @param version
-   *          (source dependent version string)
+   *          (source dependent version string or null)
    * @param accessionId
-   *          (source dependent accession number string)
+   *          (source dependent accession number string or null)
    * @param map
    *          (mapping from local sequence numbering to source accession
-   *          numbering)
+   *          numbering or null)
    */
   public DBRefEntry(String source, String version, String accessionId,
           Mapping map)
   {
-	  // BH 2019.01.25 made these always non-null. 
-	  // Is there a difference between "" and null for version? 
-	  // evidence is that source CANNOT be null. 
-    setSource(source);
+	
+    this.source = source.toUpperCase();
     setVersion(version);
-    setAccessionId(accessionId);
+    this.accessionId = accessionId;
     this.map = map;
   }
 
+  /**
+   * Clone an entry, this time not allowing any null fields except map.
+   * 
+   */
   public DBRefEntry(DBRefEntryI entry)
   {
-	  this(entry.getSource(), entry.getVersion(), entry.getAccessionId(), entry.getMap() == null ? null : new Mapping(entry.getMap()));
-//    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())));
+    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
@@ -227,20 +234,16 @@ public class DBRefEntry implements DBRefEntryI
       return true;
     }
     
-    // BH 2019.01.25  source, accessionId, and version cannot be null. 
+    // BH 2019.01.25/2019.02.04  source cannot/should not be null. 
     // for example, StructureChooser has dbRef.getSource().equalsIgnoreCase...
     
-    if (entry != null
+    return (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;
+                    && version.equalsIgnoreCase(entry.getVersion())));
   }
 
   @Override
@@ -249,17 +252,23 @@ public class DBRefEntry implements DBRefEntryI
     return source;
   }
 
-  public String getSourceKey() 
+  public int getSourceKey() 
   {
-	return sourceKey;
+	return (sourceKey == Integer.MIN_VALUE ? (sourceKey =  DBRefSource.getSourceKey(getCanonicalSourceName())) : sourceKey);
   }
 
+  /**
+   * can be null
+   */
   @Override
   public String getVersion()
   {
     return version;
   }
 
+  /**
+   * can be null
+   */
   @Override
   public String getAccessionId()
   {
@@ -269,22 +278,28 @@ public class DBRefEntry implements DBRefEntryI
   @Override
   public void setAccessionId(String accessionId)
   {
-    this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase();
+	  this.accessionId = accessionId;
+//    this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase();
   }
 
+  /**
+   * CAUTION! allows setting source null or not uppercase!
+   */
   @Override
   public void setSource(String source)
   {
-    this.source = (source == null ? "" : source).toUpperCase();
-    this.canonicalSourceName = 	DBRefUtils.getCanonicalName(this.source);
-    this.sourceKey = ";" + canonicalSourceName + ";";
+	  this.source = source;
+	  
+//    this.source = (source == null ? "" : source).toUpperCase();
+//    this.canonicalSourceName = 	DBRefUtils.getCanonicalName(this.source);
+//    this.sourceKey = DBRefSource.getSourceKey(this.canonicalSourceName);
   }
 
   @Override
   public void setVersion(String version)
   {
-    this.version = (version == null ? "" : version);
-    this.ucversion = this.version.toUpperCase();
+    this.version = version;
+    this.ucversion = (version == null ? null : version.toUpperCase());
   }
 
   @Override
@@ -354,26 +369,13 @@ public class DBRefEntry implements DBRefEntryI
         return false;
       }
     }
-    if (version == null || version == "")
+    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[] sources = DBRefSource.allSources();
-    for (int i = sources.length; --i >= 0;)
-    {
-      if (ucversion.startsWith(sources[i])) // BH 2019.01.25 .toUpperCase() unnecessary here for allSources
-      {
-        // 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;
+    
+    return DBRefSource.isPrimaryCandidate(ucversion);
   }
 
   /**
@@ -386,8 +388,16 @@ public class DBRefEntry implements DBRefEntryI
     return accessionId != null && accessionId.startsWith(CHROMOSOME + ":");
   }
 
-  public Object getCanonicalSourceName() {
-	return canonicalSourceName;
+  /**
+   * stores the upper-case canonical name of the source for use in
+   * Sequence.getPrimaryDBRefs().
+   * 
+   * @author Bob Hanson
+   * 
+   * @return
+   */
+  public String getCanonicalSourceName() {
+	return (canonicalSourceName == null ? (canonicalSourceName = DBRefUtils.getCanonicalName(this.source)) : canonicalSourceName);
   }