2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.structure;
21 import jalview.datamodel.*;
23 public class StructureMapping
25 String mappingDetails;
35 // Mapping index 0 is resNum, index 1 is atomNo
38 public StructureMapping(SequenceI seq, String pdbfile, String pdbid,
39 String chain, int[][] mapping, String mappingDetails)
42 this.pdbfile = pdbfile;
44 this.pdbchain = chain;
45 this.mapping = mapping;
46 this.mappingDetails = mappingDetails;
49 public SequenceI getSequence()
54 public String getChain()
59 public String getPdbId()
64 public int getAtomNum(int seqpos)
66 if (mapping.length > seqpos)
68 return mapping[seqpos][1];
76 public int getPDBResNum(int seqpos)
78 if (mapping.length > seqpos)
80 return mapping[seqpos][0];
88 public int getSeqPos(int pdbResNum)
90 for (int i = 0; i < mapping.length; i++)
92 if (mapping[i][0] == pdbResNum)