+ superposeStructures(alignment, -1, null);
+ }
+
+ /**
+ * superpose the structures associated with sequences in the alignment
+ * according to their corresponding positions. ded)
+ *
+ * @param refStructure
+ * - select which pdb file to use as reference (default is -1 - the
+ * first structure in the alignment)
+ */
+ public void superposeStructures(AlignmentI alignment, int refStructure)
+ {
+ superposeStructures(alignment, refStructure, null);
+ }
+
+ /**
+ * superpose the structures associated with sequences in the alignment
+ * according to their corresponding positions. ded)
+ *
+ * @param refStructure
+ * - select which pdb file to use as reference (default is -1 - the
+ * first structure in the alignment)
+ * @param hiddenCols
+ * TODO
+ */
+ public void superposeStructures(AlignmentI alignment, int refStructure,
+ ColumnSelection hiddenCols)
+ {
+ superposeStructures(new AlignmentI[] { alignment },
+ new int[] { refStructure },
+ new ColumnSelection[] { hiddenCols });
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public String superposeStructures(AlignmentI[] _alignment,
+ int[] _refStructure, ColumnSelection[] _hiddenCols)
+ {
+ while (viewer.isScriptExecuting())
+ {
+ try
+ {
+ Thread.sleep(10);
+ } catch (InterruptedException i)
+ {
+ }
+ }
+
+ /*
+ * get the distinct structure files modelled
+ * (a file with multiple chains may map to multiple sequences)
+ */