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JAL-2989 refactoring to reduce code duplication
[jalview.git]
/
src
/
jalview
/
io
/
AlignFile.java
diff --git
a/src/jalview/io/AlignFile.java
b/src/jalview/io/AlignFile.java
index
2340283
..
dcdf98e
100755
(executable)
--- a/
src/jalview/io/AlignFile.java
+++ b/
src/jalview/io/AlignFile.java
@@
-304,9
+304,9
@@
public abstract class AlignFile extends FileParse
*/
protected void initData()
{
*/
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;
}
parseCalled = false;
}
@@
-319,7
+319,7
@@
public abstract class AlignFile extends FileParse
@Override
public void setSeqs(SequenceI[] s)
{
@Override
public void setSeqs(SequenceI[] s)
{
- seqs = new Vector<SequenceI>();
+ seqs = new Vector<>();
for (int i = 0; i < s.length; i++)
{
for (int i = 0; i < s.length; i++)
{
@@
-390,7
+390,7
@@
public abstract class AlignFile extends FileParse
{
if (newickStrings == null)
{
{
if (newickStrings == null)
{
- newickStrings = new Vector<String[]>();
+ newickStrings = new Vector<>();
}
newickStrings.addElement(new String[] { treeName, newickString });
}
}
newickStrings.addElement(new String[] { treeName, newickString });
}
@@
-414,4
+414,16
@@
public abstract class AlignFile extends FileParse
{
seqs.add(seq);
}
{
seqs.add(seq);
}
+
+ /**
+ * Used only for hmmer statistics, so should probably be removed at some
+ * point. TODO remove this
+ *
+ * @return
+ */
+ public Vector<AlignmentAnnotation> getAnnotations()
+ {
+ return annotations;
+ }
+
}
}