JAL-2189 source formatting

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 68c8c50..c8b94ce 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -233,8 +233,7 @@ public class Sequence extends ASequence implements SequenceI
     {
       char[] oseq = seq.getSequence();
       initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length),
-              seq.getStart(),
-            seq.getEnd());
+              seq.getStart(), seq.getEnd());
     }
     description = seq.getDescription();
     if (seq != datasetSequence)
@@ -293,7 +292,6 @@ public class Sequence extends ASequence implements SequenceI
     }
   }
 
-
   @Override
   public void setSequenceFeatures(SequenceFeature[] features)
   {
@@ -318,7 +316,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public synchronized void addSequenceFeature(SequenceFeature sf)
   {
-    if (sequenceFeatures==null && datasetSequence != null)
+    if (sequenceFeatures == null && datasetSequence != null)
     {
       datasetSequence.addSequenceFeature(sf);
       return;
@@ -348,8 +346,9 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (sequenceFeatures == null)
     {
-      if (datasetSequence!=null) {
-         datasetSequence.deleteFeature(sf);
+      if (datasetSequence != null)
+      {
+        datasetSequence.deleteFeature(sf);
       }
       return;
     }
@@ -1094,7 +1093,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public SequenceI deriveSequence()
   {
-    Sequence seq=null;
+    Sequence seq = null;
     if (datasetSequence == null)
     {
       if (isValidDatasetSequence())
@@ -1108,7 +1107,7 @@ public class Sequence extends ASequence implements SequenceI
       else
       {
         // Create a new, valid dataset sequence
-       createDatasetSequence();
+        createDatasetSequence();
       }
     }
     return new Sequence(this);
@@ -1156,9 +1155,9 @@ public class Sequence extends ASequence implements SequenceI
       dsseq.setDescription(description);
       // move features and database references onto dataset sequence
       dsseq.sequenceFeatures = sequenceFeatures;
-      sequenceFeatures=null;
+      sequenceFeatures = null;
       dsseq.dbrefs = dbrefs;
-      dbrefs=null;
+      dbrefs = null;
       // TODO: search and replace any references to this sequence with
       // references to the dataset sequence in Mappings on dbref
       dsseq.pdbIds = pdbIds;
@@ -1416,15 +1415,14 @@ public class Sequence extends ASequence implements SequenceI
     return null;
   }
 
-
   @Override
   public List<DBRefEntry> getPrimaryDBRefs()
   {
-    if (datasetSequence!=null)
+    if (datasetSequence != null)
     {
       return datasetSequence.getPrimaryDBRefs();
     }
-    if (dbrefs==null || dbrefs.length==0)
+    if (dbrefs == null || dbrefs.length == 0)
     {
       return Collections.emptyList();
     }