2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.structure;
20 import jalview.datamodel.*;
22 public class StructureMapping
24 String mappingDetails;
34 // Mapping index 0 is resNum, index 1 is atomNo
37 public StructureMapping(SequenceI seq, String pdbfile, String pdbid,
38 String chain, int[][] mapping, String mappingDetails)
41 this.pdbfile = pdbfile;
43 this.pdbchain = chain;
44 this.mapping = mapping;
45 this.mappingDetails = mappingDetails;
48 public SequenceI getSequence()
53 public String getChain()
58 public String getPdbId()
63 public int getAtomNum(int seqpos)
65 if (mapping.length > seqpos)
67 return mapping[seqpos][1];
75 public int getPDBResNum(int seqpos)
77 if (mapping.length > seqpos)
79 return mapping[seqpos][0];
87 public int getSeqPos(int pdbResNum)
89 for (int i = 0; i < mapping.length; i++)
91 if (mapping[i][0] == pdbResNum)