X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;fp=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=f557ff865aeebf4faf93e5b77f3483c99cb449af;hp=bc8d0cf1d1723e423b1d1d62608ce1a62d2bb6fa;hb=17e4ea278bc9a5fb280db1252ce78b7a295215f5;hpb=fa2429b3c8cd5eb56c4a56572af6e9c4adc916c9

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index bc8d0cf..f557ff8 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -21,19 +21,26 @@
 package jalview.datamodel;
 
 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
 {
   String source = "";
 
-  String version = "";
+  private String version = "";
+  
+  private String ucversion;
 
-  String accessionId = "";
+  private String accessionId = "";
+  
+  int sourceKey = Integer.MIN_VALUE;
 
-  /**
+  String canonicalSourceName;
+
+  /*
    * maps from associated sequence to the database sequence's coordinate system
    */
   Mapping map = null;
@@ -43,6 +50,15 @@ 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);
@@ -51,24 +67,29 @@ 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)
   {
+	
     this.source = source.toUpperCase();
-    this.version = version;
+    setVersion(version);
     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() == null ? "" : new String(entry.getSource())),
@@ -84,21 +105,28 @@ public class DBRefEntry implements DBRefEntryI
   {
     // 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 (equalRef(entry) && ((map == null && entry.map == null)
-            || (map != null && entry.map != null && map.equals(entry.map))))
-    {
-      return true;
-    }
-    return false;
+	  
+	  
+//    if (o == null || !(o instanceof DBRefEntry))
+//    {
+//      return false;
+//    }
+//    DBRefEntry entry = (DBRefEntry) o;
+//    if (entry == this)
+//    {
+//      return true;
+//    }
+    Mapping em;
+    return (o != null && o instanceof DBRefEntry 
+    		&& (o == this 
+    		|| equalRef((DBRefEntry) o) 
+    		  && (map == null) == ((em = ((DBRefEntry) o).map) == null) 
+    		  && (map == null || map.equals(em))));
+//    	
+//    {
+//      return true;
+//    }
+//    return false;
   }
 
   /**
@@ -199,17 +227,17 @@ public class DBRefEntry implements DBRefEntryI
     {
       return true;
     }
-    if (entry != null
+    
+    // BH 2019.01.25/2019.02.04  source cannot/should not be null. 
+    // for example, StructureChooser has dbRef.getSource().equalsIgnoreCase...
+    
+    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
@@ -218,12 +246,23 @@ public class DBRefEntry implements DBRefEntryI
     return source;
   }
 
+  public int getSourceKey() 
+  {
+	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()
   {
@@ -233,19 +272,28 @@ public class DBRefEntry implements DBRefEntryI
   @Override
   public void setAccessionId(String accessionId)
   {
-    this.accessionId = accessionId;
+	  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;
+	  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;
+    this.ucversion = (version == null ? null : version.toUpperCase());
   }
 
   @Override
@@ -292,19 +340,20 @@ public class DBRefEntry implements DBRefEntryI
      */
     if (map != null)
     {
-      if (map.getTo() != null)
+      SequenceI mto = map.getTo();
+      if (mto != null)
       {
         return false;
       }
-      if (map.getMap().getFromRatio() != map.getMap().getToRatio()
-              || map.getMap().getFromRatio() != 1)
+      MapList ml = map.getMap();
+      if (ml.getFromRatio() != ml.getToRatio()
+              || ml.getFromRatio() != 1)
       {
         return false;
       }
       // check map is between identical single contiguous ranges
-      List<int[]> fromRanges = map.getMap().getFromRanges();
-      List<int[]> toRanges = map.getMap().getToRanges();
-      if (fromRanges.size() != 1 || toRanges.size() != 1)
+      List<int[]> fromRanges, toRanges;
+      if ((fromRanges = ml.getFromRanges()).size() != 1 || (toRanges = ml.getToRanges()).size() != 1)
       {
         return false;
       }
@@ -319,20 +368,19 @@ public class DBRefEntry implements DBRefEntryI
       // 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;
+    
+    return DBRefSource.isPrimaryCandidate(ucversion);
+  }
+
+  /**
+   * 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);
   }
 }