import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.StructureViewer.ViewerType;
try
{
AlignmentI[] als = new Alignment[_alignwith.size()];
- ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
+ HiddenColumns[] alc = new HiddenColumns[_alignwith.size()];
int[] alm = new int[_alignwith.size()];
int a = 0;
{
als[a] = ap.av.getAlignment();
alm[a] = -1;
- alc[a++] = ap.av.getColumnSelection();
+ alc[a++] = ap.av.getAlignment().getHiddenColumns();
}
reply = getBinding().superposeStructures(als, alm, alc);
if (reply != null)
{
// TODO: cope with multiple PDB files in view
in = new BufferedReader(
- new FileReader(getBinding().getPdbFile()[0]));
+ new FileReader(getBinding().getStructureFiles()[0]));
File outFile = chooser.getSelectedFile();
PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
* enable 'Superpose with' if more than one mapped structure
*/
viewSelectionMenu.setEnabled(false);
- if (getBinding().getPdbFile().length > 1
+ if (getBinding().getStructureFiles().length > 1
&& getBinding().getSequence().length > 1)
{
viewSelectionMenu.setEnabled(true);