/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*/
package jalview.structure;
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
public class StructureMapping
{
return pdbid;
}
+ /**
+ *
+ * @param seqpos
+ * @return 0 or corresponding atom number for the sequence position
+ */
public int getAtomNum(int seqpos)
{
if (mapping.length > seqpos)
}
}
+ /**
+ *
+ * @param seqpos
+ * @return 0 or the corresponding residue number for the sequence position
+ */
public int getPDBResNum(int seqpos)
{
if (mapping.length > seqpos)
}
}
+ /**
+ *
+ * @param pdbResNum
+ * @return -1 or the corresponding sequence position for a pdb residue number
+ */
public int getSeqPos(int pdbResNum)
{
for (int i = 0; i < mapping.length; i++)
}
return -1;
}
+
+ /**
+ * transfer a copy of an alignment annotation row in the PDB chain coordinate
+ * system onto the mapped sequence
+ *
+ * @param ana
+ * @return the copy that was remapped to the mapped sequence
+ * @note this method will create a copy and add it to the dataset sequence for
+ * the mapped sequence as well as the mapped sequence (if it is not a
+ * dataset sequence).
+ */
+ public AlignmentAnnotation transfer(AlignmentAnnotation ana)
+ {
+ AlignmentAnnotation ala_copy = new AlignmentAnnotation(ana);
+ SequenceI ds = sequence;
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
+ // need to relocate annotation from pdb coordinates to local sequence
+ // -1,-1 doesn't look at pdbresnum but fails to remap sequence positions...
+
+ ala_copy.remap(ds, mapping, -1, -1, 0);
+ ds.addAlignmentAnnotation(ala_copy);
+ if (ds != sequence)
+ {
+ // mapping wasn't to an original dataset sequence, so we make a copy on
+ // the mapped sequence too
+ ala_copy = new AlignmentAnnotation(ala_copy);
+ sequence.addAlignmentAnnotation(ala_copy);
+ }
+ return ala_copy;
+ }
}