2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 The Jalview Authors
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/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
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)