JAL-3210 Barebones gradle/buildship/eclipse. See README

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

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