/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+
public class StructureMapping
{
String mappingDetails;
String pdbchain;
- // Mapping index 0 is resNum, index 1 is atomNo
- int[][] mapping;
+ public static final int UNASSIGNED_VALUE = -1;
+
+ private static final int PDB_RES_NUM_INDEX = 0;
+
+ private static final int PDB_ATOM_NUM_INDEX = 1;
+
+ // Mapping key is residue index while value is an array containing PDB resNum,
+ // and atomNo
+ HashMap<Integer, int[]> mapping;
+ /**
+ * Constructor
+ *
+ * @param seq
+ * @param pdbfile
+ * @param pdbid
+ * @param chain
+ * @param mapping
+ * a map from sequence to two values, { resNo, atomNo } in the
+ * structure
+ * @param mappingDetails
+ */
public StructureMapping(SequenceI seq, String pdbfile, String pdbid,
- String chain, int[][] mapping, String mappingDetails)
+ String chain, HashMap<Integer, int[]> mapping,
+ String mappingDetails)
{
sequence = seq;
this.pdbfile = pdbfile;
return pdbid;
}
+ /**
+ *
+ * @param seqpos
+ * @return 0 or corresponding atom number for the sequence position
+ */
public int getAtomNum(int seqpos)
{
- if (mapping.length > seqpos)
+ int[] resNumAtomMap = mapping.get(seqpos);
+ if (resNumAtomMap != null)
{
- return mapping[seqpos][1];
+ return resNumAtomMap[PDB_ATOM_NUM_INDEX];
}
else
{
- return 0;
+ return UNASSIGNED_VALUE;
}
}
+ /**
+ *
+ * @param seqpos
+ * @return 0 or the corresponding residue number for the sequence position
+ */
public int getPDBResNum(int seqpos)
{
- if (mapping.length > seqpos)
+ int[] resNumAtomMap = mapping.get(seqpos);
+ if (resNumAtomMap != null)
{
- return mapping[seqpos][0];
+ return resNumAtomMap[PDB_RES_NUM_INDEX];
}
else
{
- return 0;
+ return UNASSIGNED_VALUE;
}
}
+ /**
+ * Returns a (possibly empty) list of [start, end] residue positions in the
+ * mapped structure, corresponding to the given range of sequence positions
+ *
+ * @param fromSeqPos
+ * @param toSeqPos
+ * @return
+ */
+ public List<int[]> getPDBResNumRanges(int fromSeqPos, int toSeqPos)
+ {
+ List<int[]> result = new ArrayList<int[]>();
+ int startRes = -1;
+ int endRes = -1;
+
+ for (int i = fromSeqPos; i <= toSeqPos; i++)
+ {
+ int resNo = getPDBResNum(i);
+ if (resNo == UNASSIGNED_VALUE)
+ {
+ continue; // no mapping from this sequence position
+ }
+ if (startRes == -1)
+ {
+ startRes = resNo;
+ endRes = resNo;
+ }
+ if (resNo >= startRes && resNo <= endRes)
+ {
+ // within the current range - no change
+ continue;
+ }
+ if (resNo == startRes - 1)
+ {
+ // extend beginning of current range
+ startRes--;
+ continue;
+ }
+ if (resNo == endRes + 1)
+ {
+ // extend end of current range
+ endRes++;
+ continue;
+ }
+
+ /*
+ * resNo is not within or contiguous with last range,
+ * so write out the last range
+ */
+ result.add(new int[] { startRes, endRes });
+ startRes = resNo;
+ endRes = resNo;
+ }
+
+ /*
+ * and add the last range
+ */
+ if (startRes != -1)
+ {
+ result.add(new int[] { startRes, endRes });
+ }
+
+ return result;
+ }
+
+ /**
+ *
+ * @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++)
+ for (Integer seqPos : mapping.keySet())
{
- if (mapping[i][0] == pdbResNum)
+ if (pdbResNum == getPDBResNum(seqPos))
{
- return i;
+ return seqPos;
}
}
- return -1;
+ return UNASSIGNED_VALUE;
}
/**
*
* @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);
- ala_copy.remap(sequence, mapping, 0, -1, 1);
+ 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;
}
+
+ public String getMappingDetailsOutput()
+ {
+ return mappingDetails;
+ }
+
+ public HashMap<Integer, int[]> getMapping()
+ {
+ return mapping;
+ }
}