Coverage Report
File AssociatePdbFileWithSeq.java
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21% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| AssociatePdbFileWithSeq | 38 | 24 | 9 |
Contributing tests
This file is covered by 7 tests.
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Source view
| 1 | /* | |
| 2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
| 3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
| 4 | * | |
| 5 | * This file is part of Jalview. | |
| 6 | * | |
| 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. | |
| 11 | * | |
| 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. | |
| 16 | * | |
| 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. | |
| 20 | */ | |
| 21 | package jalview.gui; | |
| 22 | ||
| 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.StructureImportSettings.TFType; | |
| 29 | import jalview.structure.StructureSelectionManager; | |
| 30 | import jalview.util.MessageManager; | |
| 31 | ||
| 32 | /** | |
| 33 | * GUI related routines for associating PDB files with sequences | |
| 34 | * | |
| 35 | * @author JimP | |
| 36 | * | |
| 37 | */ | |
| 38 | public class AssociatePdbFileWithSeq | |
| 39 | { | |
| 40 | ||
| 41 | /** | |
| 42 | * assocate the given PDB file with | |
| 43 | * | |
| 44 | * @param choice | |
| 45 | * @param sequence | |
| 46 | */ | |
| 47 | 3 |  public PDBEntry associatePdbWithSeq(String choice, DataSourceType file, |
| 48 | SequenceI sequence, boolean prompt, | |
| 49 | StructureSelectionManagerProvider ssmp) | |
| 50 | { | |
| 51 | 3 | return associatePdbWithSeq(choice, file, sequence, prompt, ssmp, |
| 52 | TFType.DEFAULT, null, false); | |
| 53 | } | |
| 54 | ||
| 55 | 9 | public PDBEntry associatePdbWithSeq(String choice, DataSourceType file, |
| 56 | SequenceI sequence, boolean prompt, | |
| 57 | StructureSelectionManagerProvider ssmp, TFType tft, | |
| 58 | String paeFilename, boolean doXferSettings) | |
| 59 | { | |
| 60 | 9 | PDBEntry entry = new PDBEntry(); |
| 61 | 9 | StructureFile pdbfile = StructureSelectionManager |
| 62 | .getStructureSelectionManager(ssmp) | |
| 63 | .setMapping(false, new SequenceI[] | |
| 64 | { sequence }, null, choice, file, tft, paeFilename, | |
| 65 | doXferSettings); | |
| 66 | 9 | if (pdbfile == null) |
| 67 | { | |
| 68 | // stacktrace already thrown so just return | |
| 69 | 0 | return null; |
| 70 | } | |
| 71 | 9 | if (pdbfile.getId() == null) |
| 72 | { | |
| 73 | 0 | String reply = null; |
| 74 | ||
| 75 | 0 | if (prompt) |
| 76 | { | |
| 77 | 0 | reply = JvOptionPane.showInternalInputDialog(Desktop.desktop, |
| 78 | MessageManager | |
| 79 | .getString("label.couldnt_find_pdb_id_in_file"), | |
| 80 | MessageManager.getString("label.no_pdb_id_in_file"), | |
| 81 | JvOptionPane.QUESTION_MESSAGE); | |
| 82 | } | |
| 83 | 0 | if (reply == null) |
| 84 | { | |
| 85 | 0 | return null; |
| 86 | } | |
| 87 | ||
| 88 | 0 | entry.setId(reply); |
| 89 | } | |
| 90 | else | |
| 91 | { | |
| 92 | 9 | entry.setId(pdbfile.getId()); |
| 93 | } | |
| 94 | 9 | entry.setType(PDBEntry.Type.FILE); |
| 95 | ||
| 96 | 9 | if (pdbfile != null) |
| 97 | { | |
| 98 | 9 | entry.setFile(choice); |
| 99 | 9 | sequence.getDatasetSequence().addPDBId(entry); |
| 100 | 9 | entry.setStructureFile(pdbfile); |
| 101 | 9 | StructureSelectionManager.getStructureSelectionManager(ssmp) |
| 102 | .registerPDBEntry(entry); | |
| 103 | } | |
| 104 | 9 | if (tft != null) |
| 105 | 9 | entry.setProperty("TFType", tft.name()); |
| 106 | 9 | if (paeFilename != null) |
| 107 | 6 | entry.setProperty("PAEFile", paeFilename); |
| 108 | 9 | return entry; |
| 109 | } | |
| 110 | } |