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JAL-2110 ensuring mapped dbrefs between protein and cds
[jalview.git]
/
src
/
jalview
/
datamodel
/
Alignment.java
diff --git
a/src/jalview/datamodel/Alignment.java
b/src/jalview/datamodel/Alignment.java
index
2b194cc
..
f5665db
100755
(executable)
--- a/
src/jalview/datamodel/Alignment.java
+++ b/
src/jalview/datamodel/Alignment.java
@@
-30,7
+30,6
@@
import java.util.Collections;
import java.util.Enumeration;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.Enumeration;
import java.util.HashSet;
import java.util.Hashtable;
-import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.List;
import java.util.Map;
import java.util.Set;
@@
-1724,6
+1723,10
@@
public class Alignment implements AlignmentI
{
return AlignmentUtils.alignProteinAsDna(this, al);
}
{
return AlignmentUtils.alignProteinAsDna(this, al);
}
+ else if (thatIsProtein && thisIsNucleotide)
+ {
+ return AlignmentUtils.alignCdsAsProtein(this, al);
+ }
return AlignmentUtils.alignAs(this, al);
}
return AlignmentUtils.alignAs(this, al);
}