1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.appletgui

File AppletJmolBinding.java

 

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4
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Classes

Class
Line #
Actions
AppletJmolBinding 37 22 23
0.00%
 

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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.appletgui;
22   
23    import jalview.api.AlignmentViewPanel;
24    import jalview.datamodel.PDBEntry;
25    import jalview.datamodel.SequenceI;
26    import jalview.ext.jmol.JalviewJmolBinding;
27    import jalview.io.DataSourceType;
28    import jalview.structure.StructureSelectionManager;
29   
30    import java.awt.Container;
31    import java.util.Map;
32   
33    import org.jmol.api.JmolAppConsoleInterface;
34    import org.jmol.console.AppletConsole;
35    import javajs.util.BS;
36   
 
37    class AppletJmolBinding extends JalviewJmolBinding
38    {
39   
40    /**
41    * Window that contains the bound Jmol instance
42    */
43    private AppletJmol appletJmolBinding;
44   
 
45  0 toggle public AppletJmolBinding(AppletJmol appletJmol,
46    StructureSelectionManager sSm, PDBEntry[] pdbentry,
47    SequenceI[][] seq, DataSourceType protocol)
48    {
49  0 super(sSm, pdbentry, seq, protocol);
50  0 appletJmolBinding = appletJmol;
51    }
52   
 
53  0 toggle @Override
54    public jalview.api.SequenceRenderer getSequenceRenderer(
55    AlignmentViewPanel alignment)
56    {
57  0 return new SequenceRenderer(((AlignmentPanel) alignment).av);
58    }
59   
 
60  0 toggle @Override
61    public void sendConsoleEcho(String strEcho)
62    {
63  0 if (appletJmolBinding.scriptWindow == null)
64    {
65  0 appletJmolBinding.showConsole(true);
66    }
67   
68  0 appletJmolBinding.addToHistory(strEcho);
69    }
70   
 
71  0 toggle @Override
72    public void sendConsoleMessage(String strStatus)
73    {
74  0 if (appletJmolBinding.history != null && strStatus != null
75    && !strStatus.equals("Script completed"))
76    {
77  0 appletJmolBinding.addToHistory(strStatus);
78    }
79    }
80   
 
81  0 toggle @Override
82    public void showUrl(String url, String target)
83    {
84  0 appletJmolBinding.ap.alignFrame.showURL(url, target);
85   
86    }
87   
 
88  0 toggle @Override
89    public void refreshGUI()
90    {
91  0 appletJmolBinding.updateTitleAndMenus();
92    }
93   
 
94  0 toggle @Override
95    public void updateColours(Object source)
96    {
97  0 AlignmentPanel ap = (AlignmentPanel) source;
98  0 colourBySequence(ap);
99    }
100   
 
101  0 toggle @Override
102    public void showUrl(String url)
103    {
104  0 try
105    {
106  0 appletJmolBinding.ap.av.applet.getAppletContext()
107    .showDocument(new java.net.URL(url), "jmol");
108    } catch (java.net.MalformedURLException ex)
109    {
110    }
111    }
112   
 
113  0 toggle public void newJmolPopup(boolean translateLocale, String menuName,
114    boolean asPopup)
115    {
116    // jmolpopup = new JmolAwtPopup(); // is this used?
117    // jmolpopup.jpiInitialize((viewer), menuName);
118    }
119   
 
120  0 toggle @Override
121    public void notifyScriptTermination(String strStatus, int msWalltime)
122    {
123    // do nothing.
124    }
125   
 
126  0 toggle @Override
127    public void selectionChanged(BS arg0)
128    {
129    // TODO Auto-generated method stub
130   
131    }
132   
 
133  0 toggle @Override
134    public void refreshPdbEntries()
135    {
136    // noop
137    }
138   
 
139  0 toggle @Override
140    public void showConsole(boolean show)
141    {
142  0 appletJmolBinding.showConsole(show);
143    }
144   
 
145  0 toggle @Override
146    protected JmolAppConsoleInterface createJmolConsole(
147    Container consolePanel, String buttonsToShow)
148    {
149  0 JmolAppConsoleInterface appc = new AppletConsole();
150  0 appc.start(jmolViewer);
151  0 return appc;
152    }
153   
 
154  0 toggle @Override
155    protected void releaseUIResources()
156    {
157  0 appletJmolBinding = null;
158  0 closeConsole();
159    }
160   
 
161  0 toggle @Override
162    public void releaseReferences(Object svl)
163    {
164    }
165   
 
166  0 toggle @Override
167    public int[] resizeInnerPanel(String data)
168    {
169  0 return null;
170    }
171   
 
172  0 toggle @Override
173    public Map<String, Object> getJSpecViewProperty(String arg0)
174    {
175  0 return null;
176    }
177    }