JAL-3253-applet JAL-3383

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

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index cea2870..c2cf667 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -323,14 +323,15 @@ public abstract class AlignFile extends FileParse
    */
   protected void initData()
   {
-    seqs = new Vector<SequenceI>();
-    annotations = new Vector<AlignmentAnnotation>();
-    seqGroups = new ArrayList<SequenceGroup>();
+    seqs = new Vector<>();
+    annotations = new Vector<>();
+    seqGroups = new ArrayList<>();
     parseCalled = false;
   }
 
   /**
-   * DOCUMENT ME!
+   * Create the seqs Vector from a set of parsed sequences in an AlignFile,
+   * FeaturesFile, RnamlFile, or StockholmFile.
    * 
    * @param s
    *          DOCUMENT ME!
@@ -338,7 +339,7 @@ public abstract class AlignFile extends FileParse
   @Override
   public void setSeqs(SequenceI[] s)
   {
-    seqs = new Vector<SequenceI>();
+    seqs = new Vector<>();
 
     for (int i = 0; i < s.length; i++)
     {
@@ -409,7 +410,7 @@ public abstract class AlignFile extends FileParse
   {
     if (newickStrings == null)
     {
-      newickStrings = new Vector<String[]>();
+      newickStrings = new Vector<>();
     }
     newickStrings.addElement(new String[] { treeName, newickString });
   }