Coverage Report
File AppJmolBinding.java
Coverage histogram
36% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| AppJmolBinding | 47 | 61 | 40 |
Contributing tests
This file is covered by 37 tests.
.
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 java.awt.Container; | |
| 24 | import java.io.File; | |
| 25 | import java.util.ArrayList; | |
| 26 | import java.util.List; | |
| 27 | import java.util.Map; | |
| 28 | ||
| 29 | import javax.swing.JComponent; | |
| 30 | ||
| 31 | import org.jmol.api.JmolAppConsoleInterface; | |
| 32 | import org.openscience.jmol.app.jmolpanel.console.AppConsole; | |
| 33 | ||
| 34 | import jalview.api.AlignmentViewPanel; | |
| 35 | import jalview.api.structures.JalviewStructureDisplayI; | |
| 36 | import jalview.bin.Console; | |
| 37 | import jalview.bin.Jalview; | |
| 38 | import jalview.datamodel.PDBEntry; | |
| 39 | import jalview.datamodel.SequenceI; | |
| 40 | import jalview.ext.jmol.JalviewJmolBinding; | |
| 41 | import jalview.io.DataSourceType; | |
| 42 | import jalview.structure.StructureSelectionManager; | |
| 43 | import jalview.util.MessageManager; | |
| 44 | import jalview.util.Platform; | |
| 45 | import javajs.util.BS; | |
| 46 | ||
| 47 | public class AppJmolBinding extends JalviewJmolBinding | |
| 48 | { | |
| 49 | 45 |  public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm, |
| 50 | PDBEntry[] pdbentry, SequenceI[][] sequenceIs, | |
| 51 | DataSourceType protocol) | |
| 52 | { | |
| 53 | 45 | super(sSm, pdbentry, sequenceIs, protocol); |
| 54 | 45 | setViewer(appJmol); |
| 55 | } | |
| 56 | ||
| 57 | 310 | @Override |
| 58 | public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment) | |
| 59 | { | |
| 60 | 310 | return new SequenceRenderer(((AlignmentPanel) alignment).av); |
| 61 | } | |
| 62 | ||
| 63 | 32 | @Override |
| 64 | public void sendConsoleEcho(String strEcho) | |
| 65 | { | |
| 66 | 32 | if (console != null) |
| 67 | { | |
| 68 | 18 | console.sendConsoleEcho(strEcho); |
| 69 | } | |
| 70 | } | |
| 71 | ||
| 72 | 0 | @Override |
| 73 | public void sendConsoleMessage(String strStatus) | |
| 74 | { | |
| 75 | 0 | if (console != null && strStatus != null) |
| 76 | // && !strStatus.equals("Script completed")) | |
| 77 | // should we squash the script completed string ? | |
| 78 | { | |
| 79 | 0 | console.sendConsoleMessage(strStatus); |
| 80 | } | |
| 81 | } | |
| 82 | ||
| 83 | 0 | @Override |
| 84 | public void showUrl(String url, String target) | |
| 85 | { | |
| 86 | 0 | try |
| 87 | { | |
| 88 | 0 | jalview.util.BrowserLauncher.openURL(url); |
| 89 | } catch (Exception e) | |
| 90 | { | |
| 91 | 0 | Console.error("Failed to launch Jmol-associated url " + url, e); |
| 92 | // TODO: 2.6 : warn user if browser was not configured. | |
| 93 | } | |
| 94 | } | |
| 95 | ||
| 96 | 102 | @Override |
| 97 | public void refreshGUI() | |
| 98 | { | |
| 99 | 102 | if (getMappedStructureCount() == 0) |
| 100 | { | |
| 101 | // too soon! | |
| 102 | 52 | return; |
| 103 | } | |
| 104 | // appJmolWindow.repaint(); | |
| 105 | 50 | javax.swing.SwingUtilities.invokeLater(new Runnable() |
| 106 | { | |
| 107 | 50 | @Override |
| 108 | public void run() | |
| 109 | { | |
| 110 | 50 | JalviewStructureDisplayI theViewer = getViewer(); |
| 111 | // invokes colourbySequence() via seqColour_ActionPerformed() | |
| 112 | 50 | theViewer.updateTitleAndMenus(); |
| 113 | 46 | ((JComponent) theViewer).revalidate(); |
| 114 | } | |
| 115 | }); | |
| 116 | } | |
| 117 | ||
| 118 | 8 | @Override |
| 119 | public void notifyScriptTermination(String strStatus, int msWalltime) | |
| 120 | { | |
| 121 | // todo - script termination doesn't happen ? | |
| 122 | // if (console != null) | |
| 123 | // console.notifyScriptTermination(strStatus, | |
| 124 | // msWalltime); | |
| 125 | } | |
| 126 | ||
| 127 | 0 | @Override |
| 128 | public void showUrl(String url) | |
| 129 | { | |
| 130 | 0 | showUrl(url, "jmol"); |
| 131 | } | |
| 132 | ||
| 133 | 0 | public void newJmolPopup(String menuName) |
| 134 | { | |
| 135 | // jmolpopup = new JmolAwtPopup(); | |
| 136 | // jmolpopup.jpiInitialize((viewer), menuName); | |
| 137 | } | |
| 138 | ||
| 139 | 0 | @Override |
| 140 | public void selectionChanged(BS arg0) | |
| 141 | { | |
| 142 | } | |
| 143 | ||
| 144 | 0 | @Override |
| 145 | public void showConsole(boolean b) | |
| 146 | { | |
| 147 | 0 | getViewer().showConsole(b); |
| 148 | } | |
| 149 | ||
| 150 | 45 | @Override |
| 151 | protected JmolAppConsoleInterface createJmolConsole( | |
| 152 | Container consolePanel, String buttonsToShow) | |
| 153 | { | |
| 154 | 45 | jmolViewer.setJmolCallbackListener(this); |
| 155 | // BH comment: can't do this yet [for JS only, or generally?] | |
| 156 | 45 | return Platform.isJS() || Jalview.isHeadlessMode() ? null |
| 157 | : new AppConsole(jmolViewer, consolePanel, buttonsToShow); | |
| 158 | } | |
| 159 | ||
| 160 | 23 | @Override |
| 161 | protected void releaseUIResources() | |
| 162 | { | |
| 163 | 23 | setViewer(null); |
| 164 | 23 | closeConsole(); |
| 165 | } | |
| 166 | ||
| 167 | 36 | @Override |
| 168 | public void releaseReferences(Object svl) | |
| 169 | { | |
| 170 | 36 | if (svl instanceof SeqPanel) |
| 171 | { | |
| 172 | 36 | getViewer().removeAlignmentPanel(((SeqPanel) svl).ap); |
| 173 | } | |
| 174 | } | |
| 175 | ||
| 176 | 0 | @Override |
| 177 | public Map<String, Object> getJSpecViewProperty(String arg0) | |
| 178 | { | |
| 179 | // TODO Auto-generated method stub | |
| 180 | 0 | return null; |
| 181 | } | |
| 182 | ||
| 183 | 0 | @SuppressWarnings("unused") |
| 184 | public void cacheFiles(List<File> files) | |
| 185 | { | |
| 186 | 0 | if (files == null) |
| 187 | { | |
| 188 | 0 | return; |
| 189 | } | |
| 190 | 0 | for (File f : files) |
| 191 | { | |
| 192 | 0 | Platform.cacheFileData(f); |
| 193 | } | |
| 194 | } | |
| 195 | ||
| 196 | /** | |
| 197 | * Retrieves and saves as file any modelled PDB entries for which we do not | |
| 198 | * already have a file saved. Returns a list of absolute paths to structure | |
| 199 | * files which were either retrieved, or already stored but not modelled in | |
| 200 | * the structure viewer (i.e. files to add to the viewer display). | |
| 201 | * | |
| 202 | * Currently only used by Jmol - similar but different code used for Chimera/X | |
| 203 | * and Pymol so still need to refactor | |
| 204 | * | |
| 205 | * @param structureViewer | |
| 206 | * UI proxy for the structure viewer | |
| 207 | * @return list of absolute paths to structures retrieved that need to be | |
| 208 | * added to the display | |
| 209 | */ | |
| 210 | 39 | public List<String> fetchPdbFiles(StructureViewerBase structureViewer) |
| 211 | { | |
| 212 | // todo - record which pdbids were successfully imported. | |
| 213 | 39 | StringBuilder errormsgs = new StringBuilder(); |
| 214 | ||
| 215 | 39 | List<String> files = new ArrayList<>(); |
| 216 | 39 | String pdbid = ""; |
| 217 | 39 | try |
| 218 | { | |
| 219 | 39 | String[] filesInViewer = getStructureFiles(); |
| 220 | // TODO: replace with reference fetching/transfer code (validate PDBentry | |
| 221 | // as a DBRef?) | |
| 222 | ||
| 223 | 79 | for (int pi = 0; pi < getPdbCount(); pi++) |
| 224 | { | |
| 225 | 40 | PDBEntry strucEntry = getPdbEntry(pi); |
| 226 | ||
| 227 | 40 | String file = strucEntry.getFile(); |
| 228 | 40 | if (file == null) |
| 229 | { | |
| 230 | 0 | pdbid = strucEntry.getId(); |
| 231 | 0 | try |
| 232 | { | |
| 233 | 0 | file = structureViewer.fetchPdbFile(strucEntry); |
| 234 | } catch (OutOfMemoryError oomerror) | |
| 235 | { | |
| 236 | 0 | new OOMWarning("Retrieving PDB id " + pdbid, oomerror); |
| 237 | } catch (Exception ex) | |
| 238 | { | |
| 239 | 0 | ex.printStackTrace(); |
| 240 | 0 | errormsgs.append("'").append(pdbid).append("'"); |
| 241 | } | |
| 242 | 0 | if (file != null) |
| 243 | { | |
| 244 | // success | |
| 245 | 0 | files.add(file); |
| 246 | } | |
| 247 | else | |
| 248 | { | |
| 249 | 0 | errormsgs.append("'").append(pdbid).append("' "); |
| 250 | } | |
| 251 | } | |
| 252 | else | |
| 253 | { | |
| 254 | 40 | if (filesInViewer != null && filesInViewer.length > 0) |
| 255 | { | |
| 256 | 2 | structureViewer.setAddingStructures(true); // already files loaded. |
| 257 | 3 | for (int c = 0; c < filesInViewer.length; c++) |
| 258 | { | |
| 259 | 2 | if (Platform.pathEquals(filesInViewer[c], file)) |
| 260 | { | |
| 261 | 1 | file = null; |
| 262 | 1 | break; |
| 263 | } | |
| 264 | } | |
| 265 | } | |
| 266 | 40 | if (file != null) |
| 267 | { | |
| 268 | 39 | files.add(file); |
| 269 | } | |
| 270 | } | |
| 271 | } | |
| 272 | } catch (OutOfMemoryError oomerror) | |
| 273 | { | |
| 274 | 0 | new OOMWarning("Retrieving PDB files: " + pdbid, oomerror); |
| 275 | } catch (Exception ex) | |
| 276 | { | |
| 277 | 0 | ex.printStackTrace(); |
| 278 | 0 | errormsgs.append("When retrieving pdbfiles : current was: '") |
| 279 | .append(pdbid).append("'"); | |
| 280 | } | |
| 281 | 39 | if (errormsgs.length() > 0) |
| 282 | { | |
| 283 | 0 | JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
| 284 | MessageManager.formatMessage( | |
| 285 | "label.pdb_entries_couldnt_be_retrieved", new String[] | |
| 286 | { errormsgs.toString() }), | |
| 287 | MessageManager.getString("label.couldnt_load_file"), | |
| 288 | JvOptionPane.ERROR_MESSAGE); | |
| 289 | } | |
| 290 | 39 | return files; |
| 291 | } | |
| 292 | ||
| 293 | } |