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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()
{
*/
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;
}
/**
- * DOCUMENT ME!
+ * Create the seqs Vector from a set of parsed sequences in an AlignFile,
+ * FeaturesFile, RnamlFile, or StockholmFile.
*
* @param s
* DOCUMENT ME!
*
* @param s
* DOCUMENT ME!
@@
-338,7
+339,7
@@
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++)
{
@@
-409,7
+410,7
@@
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 });
}