jalviewX
File AppJmolBinding.java
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28% of files have more coverage
Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| AppJmolBinding | 39 | 33 | 30 | 24 |
Contributing tests
This file is covered by 17 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 jalview.api.AlignmentViewPanel; | |
| 24 | import jalview.api.structures.JalviewStructureDisplayI; | |
| 25 | import jalview.bin.Cache; | |
| 26 | import jalview.datamodel.PDBEntry; | |
| 27 | import jalview.datamodel.SequenceI; | |
| 28 | import jalview.ext.jmol.JalviewJmolBinding; | |
| 29 | import jalview.io.DataSourceType; | |
| 30 | import jalview.structure.StructureSelectionManager; | |
| 31 | ||
| 32 | import java.awt.Container; | |
| 33 | import java.util.Map; | |
| 34 | ||
| 35 | import org.jmol.api.JmolAppConsoleInterface; | |
| 36 | import javajs.util.BS; | |
| 37 | import org.openscience.jmol.app.jmolpanel.console.AppConsole; | |
| 38 | ||
| 39 | public class AppJmolBinding extends JalviewJmolBinding | |
| 40 | { | |
| 41 | private AppJmol appJmolWindow; | |
| 42 | ||
| 43 | 10 |  public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm, |
| 44 | PDBEntry[] pdbentry, SequenceI[][] sequenceIs, | |
| 45 | DataSourceType protocol) | |
| 46 | { | |
| 47 | 10 | super(sSm, pdbentry, sequenceIs, protocol); |
| 48 | 10 | appJmolWindow = appJmol; |
| 49 | } | |
| 50 | ||
| 51 | 12 | @Override |
| 52 | protected IProgressIndicator getIProgressIndicator() | |
| 53 | { | |
| 54 | 12 | return appJmolWindow.progressBar; |
| 55 | } | |
| 56 | ||
| 57 | 9 | @Override |
| 58 | public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment) | |
| 59 | { | |
| 60 | 9 | return new SequenceRenderer(((AlignmentPanel) alignment).av); |
| 61 | } | |
| 62 | ||
| 63 | 22 | @Override |
| 64 | public void sendConsoleEcho(String strEcho) | |
| 65 | { | |
| 66 | 22 | if (console != null) |
| 67 | { | |
| 68 | 0 | 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 | Cache.log.error("Failed to launch Jmol-associated url " + url, e); |
| 92 | // TODO: 2.6 : warn user if browser was not configured. | |
| 93 | } | |
| 94 | } | |
| 95 | ||
| 96 | 11 | @Override |
| 97 | public void refreshGUI() | |
| 98 | { | |
| 99 | // appJmolWindow.repaint(); | |
| 100 | 11 | javax.swing.SwingUtilities.invokeLater(new Runnable() |
| 101 | { | |
| 102 | 11 | @Override |
| 103 | public void run() | |
| 104 | { | |
| 105 | 11 | appJmolWindow.updateTitleAndMenus(); |
| 106 | 10 | appJmolWindow.revalidate(); |
| 107 | } | |
| 108 | }); | |
| 109 | } | |
| 110 | ||
| 111 | 911 | @Override |
| 112 | public void updateColours(Object source) | |
| 113 | { | |
| 114 | 911 | AlignmentPanel ap = (AlignmentPanel) source; |
| 115 | // ignore events from panels not used to colour this view | |
| 116 | 911 | if (!appJmolWindow.isUsedforcolourby(ap)) |
| 117 | { | |
| 118 | 892 | return; |
| 119 | } | |
| 120 | 19 | if (!isLoadingFromArchive()) |
| 121 | { | |
| 122 | 19 | colourBySequence(ap); |
| 123 | } | |
| 124 | } | |
| 125 | ||
| 126 | 318 | @Override |
| 127 | public void notifyScriptTermination(String strStatus, int msWalltime) | |
| 128 | { | |
| 129 | // todo - script termination doesn't happen ? | |
| 130 | // if (console != null) | |
| 131 | // console.notifyScriptTermination(strStatus, | |
| 132 | // msWalltime); | |
| 133 | } | |
| 134 | ||
| 135 | 0 | @Override |
| 136 | public void showUrl(String url) | |
| 137 | { | |
| 138 | 0 | showUrl(url, "jmol"); |
| 139 | } | |
| 140 | ||
| 141 | 0 | public void newJmolPopup(String menuName) |
| 142 | { | |
| 143 | // jmolpopup = new JmolAwtPopup(); | |
| 144 | // jmolpopup.jpiInitialize((viewer), menuName); | |
| 145 | } | |
| 146 | ||
| 147 | 0 | @Override |
| 148 | public void selectionChanged(BS arg0) | |
| 149 | { | |
| 150 | // TODO Auto-generated method stub | |
| 151 | ||
| 152 | } | |
| 153 | ||
| 154 | 11 | @Override |
| 155 | public void refreshPdbEntries() | |
| 156 | { | |
| 157 | // TODO Auto-generated method stub | |
| 158 | ||
| 159 | } | |
| 160 | ||
| 161 | 0 | @Override |
| 162 | public void showConsole(boolean b) | |
| 163 | { | |
| 164 | 0 | appJmolWindow.showConsole(b); |
| 165 | } | |
| 166 | ||
| 167 | 10 | @Override |
| 168 | protected JmolAppConsoleInterface createJmolConsole( | |
| 169 | Container consolePanel, String buttonsToShow) | |
| 170 | { | |
| 171 | 10 | viewer.setJmolCallbackListener(this); |
| 172 | 10 | return null;//BH can't do this yet. new AppConsole(viewer, consolePanel, buttonsToShow); |
| 173 | } | |
| 174 | ||
| 175 | 10 | @Override |
| 176 | protected void releaseUIResources() | |
| 177 | { | |
| 178 | 10 | appJmolWindow = null; |
| 179 | 10 | closeConsole(); |
| 180 | } | |
| 181 | ||
| 182 | 82 | @Override |
| 183 | public void releaseReferences(Object svl) | |
| 184 | { | |
| 185 | 82 | if (svl instanceof SeqPanel) |
| 186 | { | |
| 187 | 82 | appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap); |
| 188 | } | |
| 189 | } | |
| 190 | ||
| 191 | 0 | @Override |
| 192 | public Map<String, Object> getJSpecViewProperty(String arg0) | |
| 193 | { | |
| 194 | // TODO Auto-generated method stub | |
| 195 | 0 | return null; |
| 196 | } | |
| 197 | ||
| 198 | 0 | @Override |
| 199 | public JalviewStructureDisplayI getViewer() | |
| 200 | { | |
| 201 | 0 | return appJmolWindow; |
| 202 | } | |
| 203 | ||
| 204 | 11 | @Override |
| 205 | public jalview.api.FeatureRenderer getFeatureRenderer( | |
| 206 | AlignmentViewPanel alignment) | |
| 207 | { | |
| 208 | 11 | AlignmentPanel ap = (alignment == null) |
| 209 | ? appJmolWindow.getAlignmentPanel() | |
| 210 | : (AlignmentPanel) alignment; | |
| 211 | 11 | if (ap.av.isShowSequenceFeatures()) |
| 212 | { | |
| 213 | 1 | return ap.av.getAlignPanel().getSeqPanel().seqCanvas.fr; |
| 214 | } | |
| 215 | ||
| 216 | 10 | return null; |
| 217 | } | |
| 218 | } |