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JAL-2909 Wire up coordinates dialog with bam file reader
[jalview.git]
/
src
/
jalview
/
io
/
AlignFile.java
diff --git
a/src/jalview/io/AlignFile.java
b/src/jalview/io/AlignFile.java
index
a603cca
..
c931cb8
100755
(executable)
--- a/
src/jalview/io/AlignFile.java
+++ b/
src/jalview/io/AlignFile.java
@@
-174,11
+174,6
@@
public abstract class AlignFile extends FileParse
}
parseCalled = true;
parse();
}
parseCalled = true;
parse();
- // sets the index of each sequence in the alignment
- for (int i = 0, c = seqs.size(); i < c; i++)
- {
- seqs.get(i).setIndex(i);
- }
}
/**
}
/**
@@
-309,9
+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;
}
@@
-324,7
+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++)
{
@@
-395,7
+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 });
}
@@
-419,4
+414,13
@@
public abstract class AlignFile extends FileParse
{
seqs.add(seq);
}
{
seqs.add(seq);
}
+
+ @Override
+ public Object[] preprocess()
+ {
+ // most AlignFiles will not need to return any preprocessing information
+ // those that do should override this method
+ return null;
+ }
+
}
}