X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=3104772f712b409efc20e9a6a8ad00cdc0915801;hb=c0501eaa85c0594f9275766f64de8ea44a59c368;hp=3202ac9f8b067fddcbf26f82e52811390f9fcdf9;hpb=04c8f7bff663aa469127e9eed4164e02933782f1;p=jalview.git diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java index 3202ac9..3104772 100755 --- a/src/jalview/io/AlignFile.java +++ b/src/jalview/io/AlignFile.java @@ -341,9 +341,9 @@ public abstract class AlignFile extends FileParse */ protected void initData() { - seqs = new Vector(); - annotations = new Vector(); - seqGroups = new ArrayList(); + seqs = new Vector<>(); + annotations = new Vector<>(); + seqGroups = new ArrayList<>(); parseCalled = false; } @@ -356,7 +356,7 @@ public abstract class AlignFile extends FileParse @Override public void setSeqs(SequenceI[] s) { - seqs = new Vector(); + seqs = new Vector<>(); for (int i = 0; i < s.length; i++) { @@ -427,7 +427,7 @@ public abstract class AlignFile extends FileParse { if (newickStrings == null) { - newickStrings = new Vector(); + newickStrings = new Vector<>(); } newickStrings.addElement(new String[] { treeName, newickString }); } @@ -451,4 +451,16 @@ public abstract class AlignFile extends FileParse { seqs.add(seq); } + + /** + * Used only for hmmer statistics, so should probably be removed at some + * point. TODO remove this + * + * @return + */ + public Vector getAnnotations() + { + return annotations; + } + }