Merge branch 'develop' into features/mchmmer

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index f7bf4d8..d6bfd93 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -666,7 +666,7 @@ public class AlignmentAnnotation
     this.calcId = annotation.calcId;
     if (annotation.properties != null)
     {
-      properties = new HashMap<String, String>();
+      properties = new HashMap<>();
       for (Map.Entry<String, String> val : annotation.properties.entrySet())
       {
         properties.put(val.getKey(), val.getValue());
@@ -702,7 +702,7 @@ public class AlignmentAnnotation
       if (annotation.sequenceMapping != null)
       {
         Integer p = null;
-        sequenceMapping = new HashMap<Integer, Annotation>();
+        sequenceMapping = new HashMap<>();
         Iterator<Integer> pos = annotation.sequenceMapping.keySet()
                 .iterator();
         while (pos.hasNext())
@@ -782,7 +782,7 @@ public class AlignmentAnnotation
       int epos = sequenceRef.findPosition(endRes);
       if (sequenceMapping != null)
       {
-        Map<Integer, Annotation> newmapping = new HashMap<Integer, Annotation>();
+        Map<Integer, Annotation> newmapping = new HashMap<>();
         Iterator<Integer> e = sequenceMapping.keySet().iterator();
         while (e.hasNext())
         {
@@ -909,7 +909,7 @@ public class AlignmentAnnotation
     {
       return;
     }
-    sequenceMapping = new HashMap<Integer, Annotation>();
+    sequenceMapping = new HashMap<>();
 
     int seqPos;
 
@@ -1190,7 +1190,7 @@ public class AlignmentAnnotation
   /**
    * properties associated with the calcId
    */
-  protected Map<String, String> properties = new HashMap<String, String>();
+  protected Map<String, String> properties = new HashMap<>();
 
   /**
    * base colour for line graphs. If null, will be set automatically by
@@ -1236,7 +1236,7 @@ public class AlignmentAnnotation
             : false;
 
     // TODO build a better annotation element map and get rid of annotations[]
-    Map<Integer, Annotation> mapForsq = new HashMap<Integer, Annotation>();
+    Map<Integer, Annotation> mapForsq = new HashMap<>();
     if (sequenceMapping != null)
     {
       if (sp2sq != null)
@@ -1289,7 +1289,7 @@ public class AlignmentAnnotation
     if (mapping != null)
     {
       Map<Integer, Annotation> old = sequenceMapping;
-      Map<Integer, Annotation> remap = new HashMap<Integer, Annotation>();
+      Map<Integer, Annotation> remap = new HashMap<>();
       int index = -1;
       for (int mp[] : mapping.values())
       {
@@ -1347,7 +1347,7 @@ public class AlignmentAnnotation
   {
     if (properties == null)
     {
-      properties = new HashMap<String, String>();
+      properties = new HashMap<>();
     }
     properties.put(property, value);
   }
@@ -1477,8 +1477,7 @@ public class AlignmentAnnotation
           Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
           String label)
   {
-
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
+    List<AlignmentAnnotation> aa = new ArrayList<>();
     for (AlignmentAnnotation ann : list)
     {
       if ((calcId == null || (ann.getCalcId() != null
@@ -1522,7 +1521,6 @@ public class AlignmentAnnotation
   public static Iterable<AlignmentAnnotation> findAnnotation(
           List<AlignmentAnnotation> list, String calcId)
   {
-
     List<AlignmentAnnotation> aa = new ArrayList<>();
     if (calcId == null)
     {