JAL-3438 spotless for 2.11.2.0

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

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 93a5460..aedfd3b 100755 (executable)
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -33,16 +33,16 @@ public class DBRefEntry implements DBRefEntryI
   String source = "";
 
   private String version = "";
-  
+
   private String ucversion;
 
   private String accessionId = "";
-  
+
   int sourceKey = Integer.MIN_VALUE;
 
   String canonicalSourceName;
-  
-  boolean isCanonicalAccession=false;
+
+  boolean isCanonicalAccession = false;
 
   /*
    * maps from associated sequence to the database sequence's coordinate system
@@ -57,30 +57,32 @@ public class DBRefEntry implements DBRefEntryI
   /**
    * 
    * @param source
-   *                      may not be null
+   *          may not be null
    * @param version
-   *                      may be null
+   *          may be null
    * @param accessionId
-   *                      may be null
+   *          may be null
    */
   public DBRefEntry(String source, String version, String accessionId)
   {
-    this(source, version, accessionId, null,false);
+    this(source, version, accessionId, null, false);
   }
 
   /**
    * 
    * @param source
-   *                      may not be null
+   *          may not be null
    * @param version
-   *                      may be null
+   *          may be null
    * @param accessionId
-   *                      may be null
+   *          may be null
    */
-  public DBRefEntry(String source, String version, String accessionId, Mapping map)
+  public DBRefEntry(String source, String version, String accessionId,
+          Mapping map)
   {
-    this(source, version, accessionId, map,false);
+    this(source, version, accessionId, map, false);
   }
+
   /**
    * 
    * @param source
@@ -94,14 +96,14 @@ public class DBRefEntry implements DBRefEntryI
    *          numbering or null)
    */
   public DBRefEntry(String source, String version, String accessionId,
-          Mapping map,boolean isCanonical)
+          Mapping map, boolean isCanonical)
   {
-       
+
     this.source = source.toUpperCase(Locale.ROOT);
     setVersion(version);
     this.accessionId = accessionId;
     this.map = map;
-    this.isCanonicalAccession=isCanonical;
+    this.isCanonicalAccession = isCanonical;
   }
 
   /**
@@ -115,7 +117,8 @@ 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.isCanonical());
+            (entry.getMap() == null ? null : new Mapping(entry.getMap())),
+            entry.isCanonical());
   }
 
   @Override
@@ -123,28 +126,26 @@ 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 (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;
+    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;
   }
 
   /**
@@ -174,7 +175,7 @@ public class DBRefEntry implements DBRefEntryI
       return true;
     }
 
-    boolean improved=false;
+    boolean improved = false;
     /*
      * source must either match or be both null
      */
@@ -262,10 +263,10 @@ public class DBRefEntry implements DBRefEntryI
     {
       return true;
     }
-    
-    // BH 2019.01.25/2019.02.04  source cannot/should not be 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()))
@@ -281,9 +282,12 @@ public class DBRefEntry implements DBRefEntryI
     return source;
   }
 
-  public int getSourceKey() 
+  public int getSourceKey()
   {
-       return (sourceKey == Integer.MIN_VALUE ? (sourceKey =  DBRefSource.getSourceKey(getCanonicalSourceName())) : sourceKey);
+    return (sourceKey == Integer.MIN_VALUE
+            ? (sourceKey = DBRefSource
+                    .getSourceKey(getCanonicalSourceName()))
+            : sourceKey);
   }
 
   /**
@@ -307,8 +311,9 @@ public class DBRefEntry implements DBRefEntryI
   @Override
   public void setAccessionId(String accessionId)
   {
-         this.accessionId = accessionId;
-//    this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase(Locale.ROOT);
+    this.accessionId = accessionId;
+    // this.accessionId = (accessionId == null ? "" :
+    // accessionId).toUpperCase(Locale.ROOT);
   }
 
   /**
@@ -317,18 +322,19 @@ public class DBRefEntry implements DBRefEntryI
   @Override
   public void setSource(String source)
   {
-         this.source = source;
-         
-//    this.source = (source == null ? "" : source).toUpperCase(Locale.ROOT);
-//    this.canonicalSourceName =       DBRefUtils.getCanonicalName(this.source);
-//    this.sourceKey = DBRefSource.getSourceKey(this.canonicalSourceName);
+    this.source = source;
+
+    // this.source = (source == null ? "" : source).toUpperCase(Locale.ROOT);
+    // 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(Locale.ROOT));
+    this.ucversion = (version == null ? null
+            : version.toUpperCase(Locale.ROOT));
   }
 
   @Override
@@ -381,14 +387,14 @@ public class DBRefEntry implements DBRefEntryI
         return false;
       }
       MapList ml = map.getMap();
-      if (ml.getFromRatio() != ml.getToRatio()
-              || ml.getFromRatio() != 1)
+      if (ml.getFromRatio() != ml.getToRatio() || ml.getFromRatio() != 1)
       {
         return false;
       }
       // check map is between identical single contiguous ranges
       List<int[]> fromRanges, toRanges;
-      if ((fromRanges = ml.getFromRanges()).size() != 1 || (toRanges = ml.getToRanges()).size() != 1)
+      if ((fromRanges = ml.getFromRanges()).size() != 1
+              || (toRanges = ml.getToRanges()).size() != 1)
       {
         return false;
       }
@@ -403,7 +409,7 @@ public class DBRefEntry implements DBRefEntryI
       // no version string implies the reference has not been verified at all.
       return false;
     }
-    
+
     return DBRefSource.isPrimaryCandidate(ucversion);
   }
 
@@ -415,8 +421,12 @@ public class DBRefEntry implements DBRefEntryI
    * 
    * @return
    */
-  public String getCanonicalSourceName() {
-       return (canonicalSourceName == null ? (canonicalSourceName = DBRefUtils.getCanonicalName(this.source)) : canonicalSourceName);
+  public String getCanonicalSourceName()
+  {
+    return (canonicalSourceName == null
+            ? (canonicalSourceName = DBRefUtils
+                    .getCanonicalName(this.source))
+            : canonicalSourceName);
   }
 
   /**
@@ -427,9 +437,11 @@ public class DBRefEntry implements DBRefEntryI
   {
     isCanonicalAccession = canonical;
   }
+
   /**
    * 
-   * @return true if this is the primary canonical accession for the database source
+   * @return true if this is the primary canonical accession for the database
+   *         source
    */
   public boolean isCanonical()
   {