Coverage Report
File AssociatePdbFileWithSeq.java
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43% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| AssociatePdbFileWithSeq | 43 | 31 | 18 |
Contributing tests
This file is covered by 33 tests.
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| 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 java.io.File; | |
| 24 | ||
| 25 | import jalview.api.StructureSelectionManagerProvider; | |
| 26 | import jalview.bin.Console; | |
| 27 | import jalview.datamodel.PDBEntry; | |
| 28 | import jalview.datamodel.SequenceI; | |
| 29 | import jalview.io.DataSourceType; | |
| 30 | import jalview.io.StructureFile; | |
| 31 | import jalview.structure.StructureImportSettings.TFType; | |
| 32 | import jalview.structure.StructureSelectionManager; | |
| 33 | import jalview.util.MessageManager; | |
| 34 | import jalview.util.Platform; | |
| 35 | ||
| 36 | /** | |
| 37 | * GUI related routines for associating PDB files with sequences. A single | |
| 38 | * static method. | |
| 39 | * | |
| 40 | * @author JimP | |
| 41 | * | |
| 42 | */ | |
| 43 | public class AssociatePdbFileWithSeq | |
| 44 | { | |
| 45 | ||
| 46 | 0 |  private AssociatePdbFileWithSeq() |
| 47 | { | |
| 48 | // inaccessible | |
| 49 | } | |
| 50 | ||
| 51 | /** | |
| 52 | * Associate the given PDB file name or URL with a sequence. Do not map | |
| 53 | * mouse-over events. | |
| 54 | * | |
| 55 | * @param fileName | |
| 56 | * or URL | |
| 57 | * @param type | |
| 58 | * will be DataType.FILE or DataType.URL | |
| 59 | * @param sequence | |
| 60 | * to associate | |
| 61 | * @param prompt | |
| 62 | * true if the user should be asked what to do if the specified file | |
| 63 | * does not seem to contain PDB information (StructureChooser only) | |
| 64 | * @return null if file is not found | |
| 65 | */ | |
| 66 | 3 | public static PDBEntry associatePdbWithSeq(String fileName, |
| 67 | DataSourceType type, SequenceI sequence, boolean prompt) | |
| 68 | { | |
| 69 | 3 | return associatePdbWithSeq(fileName, type, sequence, null, prompt, Desktop.getInstance(), |
| 70 | TFType.DEFAULT, null, false); | |
| 71 | } | |
| 72 | 67 | public static PDBEntry associatePdbWithSeq(String fileName, DataSourceType type, |
| 73 | SequenceI sequence,boolean prompt, | |
| 74 | StructureSelectionManagerProvider ssmp, TFType tft, | |
| 75 | String paeFilename, boolean doXferSettings) | |
| 76 | { | |
| 77 | 67 | return associatePdbWithSeq(fileName, type, sequence, null, prompt, ssmp, |
| 78 | tft, paeFilename, doXferSettings); | |
| 79 | } | |
| 80 | 72 | public static PDBEntry associatePdbWithSeq(String fileName, DataSourceType type, |
| 81 | SequenceI sequence, String[] chains, boolean prompt, | |
| 82 | StructureSelectionManagerProvider ssmp, TFType tft, | |
| 83 | String paeFilename, boolean doXferSettings) | |
| 84 | { | |
| 85 | 72 | PDBEntry entry = new PDBEntry(); |
| 86 | ||
| 87 | 70 | SequenceI[] seqs= new SequenceI[chains==null ? 1 : chains.length]; |
| 88 | 144 | for (int i=0;i<seqs.length;i++) { |
| 89 | 72 | seqs[i] = sequence; |
| 90 | } | |
| 91 | ||
| 92 | 72 | StructureFile pdbfile = StructureSelectionManager |
| 93 | .getStructureSelectionManager(ssmp) | |
| 94 | .setMapping(false, seqs, chains, fileName, type, tft, paeFilename, | |
| 95 | doXferSettings); | |
| 96 | 72 | if (pdbfile == null) |
| 97 | { | |
| 98 | // stacktrace already thrown so just return | |
| 99 | 0 | return null; |
| 100 | } | |
| 101 | 72 | String id = pdbfile.getId(); |
| 102 | ? | if (id == null && (id = (prompt |
| 103 | ? JvOptionPane.showInternalInputDialog(Desktop.getDesktopPane(), | |
| 104 | MessageManager | |
| 105 | .getString("label.couldnt_find_pdb_id_in_file"), | |
| 106 | MessageManager.getString("label.no_pdb_id_in_file"), | |
| 107 | JvOptionPane.QUESTION_MESSAGE) | |
| 108 | : null)) == null) | |
| 109 | { | |
| 110 | 0 | return null; |
| 111 | } | |
| 112 | ||
| 113 | // TODO move this to a method in SequenceI and the comparator to PDBEntry | |
| 114 | 72 | File sfile=new File(fileName); |
| 115 | 72 | if (sequence.getDatasetSequence()!=null && sequence.getDatasetSequence().hasPDBEntries()) { |
| 116 | 72 | for (PDBEntry pe: sequence.getDatasetSequence().getAllPDBEntries()) { |
| 117 | 109 | try { |
| 118 | // Normalise for local platform since we have just loaded this file. PASTED files will fail. | |
| 119 | 109 | if (new File(pe.getFile()).getCanonicalPath().equals(sfile.getCanonicalPath())) { |
| 120 | 72 | if (chains==null || chains[0].equals(pe.getChainCode())) { |
| 121 | 72 | return pe; |
| 122 | } | |
| 123 | } } catch (Exception ex) { | |
| 124 | 0 | Console.error("Unexpected exception when examining structure file paths",ex); |
| 125 | } | |
| 126 | } | |
| 127 | } | |
| 128 | 0 | entry.setId(id); |
| 129 | 0 | entry.setType(PDBEntry.Type.FILE); |
| 130 | 0 | entry.setFile(fileName); |
| 131 | 0 | sequence.getDatasetSequence().addPDBId(entry); |
| 132 | 0 | entry.setStructureFile(pdbfile); |
| 133 | 0 | StructureSelectionManager.getStructureSelectionManager(ssmp) |
| 134 | .registerPDBEntry(entry); | |
| 135 | 0 | if (tft != null) |
| 136 | 0 | entry.setTempFacType(tft); |
| 137 | 0 | if (paeFilename != null) |
| 138 | 0 | entry.setPAEFile(paeFilename); |
| 139 | 0 | return entry; |
| 140 | } | |
| 141 | } |