2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.api.StructureSelectionManagerProvider;
24 import jalview.datamodel.PDBEntry;
25 import jalview.datamodel.SequenceI;
26 import jalview.io.DataSourceType;
27 import jalview.io.StructureFile;
28 import jalview.structure.StructureSelectionManager;
29 import jalview.util.MessageManager;
32 * GUI related routines for associating PDB files with sequences
37 public class AssociatePdbFileWithSeq
41 * Associates the given file as a PDB structure for the given sequence.
51 public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
52 SequenceI sequence, boolean prompt,
53 StructureSelectionManagerProvider ssmp, boolean forViewer)
55 PDBEntry entry = new PDBEntry();
56 StructureFile pdbfile = null;
57 pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
58 .setMapping(forViewer, new SequenceI[]
59 { sequence }, null, choice, file);
62 // stacktrace already thrown so just return
65 if (pdbfile.getId() == null)
71 reply = JvOptionPane.showInternalInputDialog(Desktop.desktop,
73 .getString("label.couldnt_find_pdb_id_in_file"),
74 MessageManager.getString("label.no_pdb_id_in_file"),
75 JvOptionPane.QUESTION_MESSAGE);
86 entry.setId(pdbfile.getId());
88 entry.setType(PDBEntry.Type.FILE);
92 entry.setFile(choice);
93 sequence.getDatasetSequence().addPDBId(entry);
94 StructureSelectionManager.getStructureSelectionManager(ssmp)
95 .registerPDBEntry(entry);