JAL-1645 source formatting and organise imports

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 322fd54..bb45b67 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -20,6 +20,10 @@
  */
 package jalview.datamodel;
 
+import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.analysis.WUSSParseException;
+
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -28,10 +32,6 @@ import java.util.Iterator;
 import java.util.Map;
 import java.util.Map.Entry;
 
-import jalview.analysis.Rna;
-import jalview.analysis.SecStrConsensus.SimpleBP;
-import jalview.analysis.WUSSParseException;
-
 /**
  * DOCUMENT ME!
  * 
@@ -164,6 +164,7 @@ public class AlignmentAnnotation
     }
     setScore(mxval);
   }
+
   /**
    * map of positions in the associated annotation
    */
@@ -692,10 +693,10 @@ public class AlignmentAnnotation
     this.scaleColLabel = annotation.scaleColLabel;
     this.showAllColLabels = annotation.showAllColLabels;
     this.calcId = annotation.calcId;
-    if (annotation.properties!=null)
+    if (annotation.properties != null)
     {
-      properties = new HashMap<String,String>();
-      for (Map.Entry<String, String> val:annotation.properties.entrySet())
+      properties = new HashMap<String, String>();
+      for (Map.Entry<String, String> val : annotation.properties.entrySet())
       {
         properties.put(val.getKey(), val.getValue());
       }
@@ -1042,7 +1043,8 @@ public class AlignmentAnnotation
     {
       if (sequenceRef != null)
       {
-        boolean rIsDs=sequenceRef.getDatasetSequence()==null,tIsDs=sequenceI.getDatasetSequence()==null;
+        boolean rIsDs = sequenceRef.getDatasetSequence() == null, tIsDs = sequenceI
+                .getDatasetSequence() == null;
         if (sequenceRef != sequenceI
                 && (rIsDs && !tIsDs && sequenceRef != sequenceI
                         .getDatasetSequence())
@@ -1238,8 +1240,10 @@ public class AlignmentAnnotation
   {
     if (sp2sq.getMappedWidth() != sp2sq.getWidth())
     {
-      // TODO: employ getWord/MappedWord to transfer annotation between cDNA and Protein reference frames
-      throw new Error("liftOver currently not implemented for transfer of annotation between different types of seqeunce");
+      // TODO: employ getWord/MappedWord to transfer annotation between cDNA and
+      // Protein reference frames
+      throw new Error(
+              "liftOver currently not implemented for transfer of annotation between different types of seqeunce");
     }
     boolean mapIsTo = (sp2sq != null) ? (sp2sq.getTo() == sq || sp2sq
             .getTo() == sq.getDatasetSequence()) : false;
@@ -1354,9 +1358,9 @@ public class AlignmentAnnotation
 
   public void setProperty(String property, String value)
   {
-    if (properties==null)
+    if (properties == null)
     {
-      properties = new HashMap<String,String>();
+      properties = new HashMap<String, String>();
     }
     properties.put(property, value);
   }