*/
package MCview;
-import java.awt.Color;
-import java.io.IOException;
-import java.lang.reflect.Constructor;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
import jalview.analysis.AlignSeq;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.io.AlignFile;
import jalview.io.FileParse;
+import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
-public class PDBfile extends jalview.io.AlignFile
+import java.awt.Color;
+import java.io.IOException;
+import java.lang.reflect.Constructor;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+public class PDBfile extends AlignFile
{
private static String CALC_ID_PREFIX = "JalviewPDB";
"getSeqsAsArray", new Class[]
{}).invoke(jmf));
cl.getMethod("addAnnotations", new Class[]
- { Alignment.class }).invoke(jmf, al);
+ { AlignmentI.class }).invoke(jmf, al);
for (SequenceI sq : al.getSequences())
{
if (sq.getDatasetSequence() != null)
}
}
- public void setColours(jalview.schemes.ColourSchemeI cs)
+ public void setColours(ColourSchemeI cs)
{
for (int i = 0; i < chains.size(); i++)
{