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JAL-2110 JAL-2131 JAL-1765 remove reference to jalview.datamodel.Alignment from Align...
[jalview.git]
/
src
/
jalview
/
datamodel
/
Alignment.java
diff --git
a/src/jalview/datamodel/Alignment.java
b/src/jalview/datamodel/Alignment.java
index
ed1c92e
..
34f8f6e
100755
(executable)
--- a/
src/jalview/datamodel/Alignment.java
+++ b/
src/jalview/datamodel/Alignment.java
@@
-45,7
+45,7
@@
import java.util.Vector;
*/
public class Alignment implements AlignmentI
{
*/
public class Alignment implements AlignmentI
{
- protected Alignment dataset;
+ private Alignment dataset;
protected List<SequenceI> sequences;
protected List<SequenceI> sequences;
@@
-987,7
+987,7
@@
public class Alignment implements AlignmentI
}
@Override
}
@Override
- public void setDataset(Alignment data)
+ public void setDataset(AlignmentI data)
{
if (dataset == null && data == null)
{
{
if (dataset == null && data == null)
{
@@
-995,7
+995,12
@@
public class Alignment implements AlignmentI
}
else if (dataset == null && data != null)
{
}
else if (dataset == null && data != null)
{
- dataset = data;
+ if (!(data instanceof Alignment))
+ {
+ throw new Error(
+ "Implementation Error: jalview.datamodel.Alignment does not yet support other implementations of AlignmentI as its dataset reference");
+ }
+ dataset = (Alignment) data;
for (int i = 0; i < getHeight(); i++)
{
SequenceI currentSeq = getSequenceAt(i);
for (int i = 0; i < getHeight(); i++)
{
SequenceI currentSeq = getSequenceAt(i);