JAL-1780 JAL-653 organise imports

[jalview.git] / src / jalview / io / AlignFile.java

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index b2f8b2b..b66fb11 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -188,7 +188,7 @@ public abstract class AlignFile extends FileParse
 
     for (int i = 0; i < seqs.size(); i++)
     {
-      s[i] = (SequenceI) seqs.elementAt(i);
+      s[i] = seqs.elementAt(i);
     }
 
     return s;
@@ -212,7 +212,7 @@ public abstract class AlignFile extends FileParse
        * Rna.GetBasePairsFromAlignmentAnnotation(annotations.elementAt(i));
        * Rna.HelixMap(pairArray);
        */
-      AlignmentAnnotation an = (AlignmentAnnotation) annotations
+      AlignmentAnnotation an = annotations
               .elementAt(i);
       an.validateRangeAndDisplay();
       al.addAnnotation(an);
@@ -287,8 +287,8 @@ public abstract class AlignFile extends FileParse
    */
   protected void initData()
   {
-    seqs = new Vector();
-    annotations = new Vector();
+    seqs = new Vector<SequenceI>();
+    annotations = new Vector<AlignmentAnnotation>();
     seqGroups = new ArrayList<SequenceGroup>();
     parseCalled=false;
   }
@@ -301,7 +301,7 @@ public abstract class AlignFile extends FileParse
    */
   protected void setSeqs(SequenceI[] s)
   {
-    seqs = new Vector();
+    seqs = new Vector<SequenceI>();
 
     for (int i = 0; i < s.length; i++)
     {
@@ -361,13 +361,13 @@ public abstract class AlignFile extends FileParse
   /**
    * vector of String[] treeName, newickString pairs
    */
-  Vector newickStrings = null;
+  Vector<String[]> newickStrings = null;
 
   protected void addNewickTree(String treeName, String newickString)
   {
     if (newickStrings == null)
     {
-      newickStrings = new Vector();
+      newickStrings = new Vector<String[]>();
     }
     newickStrings.addElement(new String[]
     { treeName, newickString });
@@ -375,11 +375,7 @@ public abstract class AlignFile extends FileParse
 
   protected int getTreeCount()
   {
-    if (newickStrings == null)
-    {
-      return 0;
-    }
-    return newickStrings.size();
+    return newickStrings == null ? 0 : newickStrings.size();
   }
 
 }