Jalview.isJS() --> Platform.isJS(), DBRefEntry[] --> List<DBRefEntry>

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

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 98868ce..1993516 100755 (executable)
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -21,6 +21,8 @@
 package jalview.datamodel;
 
 import jalview.api.DBRefEntryI;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
 
 import java.util.Arrays;
 import java.util.List;
@@ -38,9 +40,14 @@ public class DBRefEntry implements DBRefEntryI
 
   String source = "";
 
-  String version = "";
+  String version = "", ucversion;
 
   String accessionId = "";
+  
+  String sourceKey;
+
+  String canonicalSourceName;
+
 
   /**
    * maps from associated sequence to the database sequence's coordinate system
@@ -72,20 +79,24 @@ public class DBRefEntry implements DBRefEntryI
   public DBRefEntry(String source, String version, String accessionId,
           Mapping map)
   {
-    this.source = source.toUpperCase();
-    this.version = version;
-    this.accessionId = accessionId;
+         // 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);
+    setVersion(version);
+    setAccessionId(accessionId);
     this.map = map;
   }
 
   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.getMap() == null ? null : new Mapping(entry.getMap())));
+         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())));
   }
 
   @Override
@@ -93,21 +104,28 @@ 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;
   }
 
   /**
@@ -208,6 +226,10 @@ public class DBRefEntry implements DBRefEntryI
     {
       return true;
     }
+    
+    // BH 2019.01.25  source, accessionId, and version cannot be null. 
+    // for example, StructureChooser has dbRef.getSource().equalsIgnoreCase...
+    
     if (entry != null
             && (source != null && entry.getSource() != null
                     && source.equalsIgnoreCase(entry.getSource()))
@@ -227,6 +249,11 @@ public class DBRefEntry implements DBRefEntryI
     return source;
   }
 
+  public String getSourceKey() 
+  {
+       return sourceKey;
+  }
+
   @Override
   public String getVersion()
   {
@@ -242,19 +269,22 @@ public class DBRefEntry implements DBRefEntryI
   @Override
   public void setAccessionId(String accessionId)
   {
-    this.accessionId = accessionId;
+    this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase();
   }
 
   @Override
   public void setSource(String source)
   {
-    this.source = source;
+    this.source = (source == null ? "" : source).toUpperCase();
+    this.canonicalSourceName =         DBRefUtils.getCanonicalName(this.source);
+    this.sourceKey = ";" + canonicalSourceName + ";";
   }
 
   @Override
   public void setVersion(String version)
   {
-    this.version = version;
+    this.version = (version == null ? "" : version);
+    this.ucversion = this.version.toUpperCase();
   }
 
   @Override
@@ -301,19 +331,20 @@ 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;
       }
@@ -323,17 +354,17 @@ public class DBRefEntry implements DBRefEntryI
         return false;
       }
     }
-    if (version == null)
+    if (version == null || version == "")
     {
       // 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()))
+    String[] sources = DBRefSource.allSources();
+    for (int i = sources.length; --i >= 0;)
     {
-      if (ucv.startsWith(primsrc.toUpperCase()))
+      if (ucversion.startsWith(sources[i])) // BH 2019.01.25 .toUpperCase() unnecessary here for allSources
       {
         // by convention, many secondary references inherit the primary
         // reference's
@@ -354,4 +385,10 @@ public class DBRefEntry implements DBRefEntryI
   {
     return accessionId != null && accessionId.startsWith(CHROMOSOME + ":");
   }
+
+  public Object getCanonicalSourceName() {
+       return canonicalSourceName;
+  }
+
+
 }