/*
- * 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.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
+
+import java.util.HashMap;
public class StructureMapping
{
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;
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;
}
}
+ /**
+ *
+ * @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;
+ }
+
+ /**
+ * 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;
}
}