import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map.Entry;
+
public class StructureMapping
{
+ public static final int UNASSIGNED = -1;
+
+ public static final int PDB_RES_NUM_INDEX = 0;
+
+ public static final int PDB_ATOM_NUM_INDEX = 1;
+
+ /**
+ * Space character constant, for consistent representation when no chain
+ * specified
+ */
+ public static String NO_CHAIN = " ";
+
String mappingDetails;
SequenceI sequence;
String pdbchain;
- // Mapping index 0 is resNum, index 1 is atomNo
- int[][] mapping;
+ // 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;
this.pdbchain = chain;
this.mapping = mapping;
this.mappingDetails = mappingDetails;
- new Exception("StructureMapping with " + pdbfile).printStackTrace();
}
public SequenceI getSequence()
}
/**
+ * Answers the structure atom number mapped to the given sequence position, or
+ * -1 if no mapping
*
* @param seqpos
- * @return 0 or corresponding atom number for the sequence position
+ * @return
*/
public int getAtomNum(int seqpos)
{
- if (mapping.length > seqpos)
- {
- return mapping[seqpos][1];
- }
- else
- {
- return 0;
- }
+ int[] resNumAtomMap = mapping.get(seqpos);
+ return (resNumAtomMap == null ? UNASSIGNED
+ : resNumAtomMap[PDB_ATOM_NUM_INDEX]);
}
/**
+ * Answers the structure residue number mapped to the given sequence position,
+ * or -1 if no mapping
*
* @param seqpos
- * @return 0 or the corresponding residue number for the sequence position
+ * @return
*/
public int getPDBResNum(int seqpos)
{
- if (mapping.length > seqpos)
+ int[] resNumAtomMap = mapping.get(seqpos);
+ return (resNumAtomMap == null ? UNASSIGNED
+ : resNumAtomMap[PDB_RES_NUM_INDEX]);
+ }
+
+ /**
+ * 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++)
{
- return mapping[seqpos][0];
+ int resNo = getPDBResNum(i);
+ if (resNo == UNASSIGNED)
+ {
+ 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;
}
- else
+
+ /*
+ * and add the last range
+ */
+ if (startRes != -1)
{
- return 0;
+ result.add(new int[] { startRes, endRes });
}
+
+ return result;
}
/**
+ * Answers the sequence position mapped to the given structure residue number,
+ * or -1 if no mapping is found
*
* @param pdbResNum
- * @return -1 or the corresponding sequence position for a pdb residue number
+ * @return
*/
public int getSeqPos(int pdbResNum)
{
- for (int i = 0; i < mapping.length; i++)
+ for (Entry<Integer, int[]> map : mapping.entrySet())
{
- if (mapping[i][0] == pdbResNum)
+ if (pdbResNum == map.getValue()[PDB_RES_NUM_INDEX])
{
- return i;
+ return map.getKey();
}
}
- return -1;
+ return UNASSIGNED;
}
/**
}
return ala_copy;
}
+
+ public String getMappingDetailsOutput()
+ {
+ return mappingDetails;
+ }
+
}